WHAT IF Check report

This file was created 2011-12-16 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 pdb1kee.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 C

All-atom RMS fit for the two chains : 0.365
CA-only RMS fit for the two chains : 0.168

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 E

All-atom RMS fit for the two chains : 0.357
CA-only RMS fit for the two chains : 0.206

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 G

All-atom RMS fit for the two chains : 0.383
CA-only RMS fit for the two chains : 0.239

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 G

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 D

All-atom RMS fit for the two chains : 0.299
CA-only RMS fit for the two chains : 0.140

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 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: B and F

All-atom RMS fit for the two chains : 0.289
CA-only RMS fit for the two chains : 0.128

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 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.

5768 ADP   (2001-)  A  -
5769 ADP   (2007-)  A  -
5770 ORN   (5011-)  A  -
5771 NET   (5012-)  A  -
5789 ADP   (2023-)  C  -
5791 ADP   (2029-)  C  -
5792 ORN   (5033-)  C  -
5793 NET   (5034-)  C  -
5810 ADP   (2045-)  E  -
5812 ADP   (2051-)  E  -
5813 ORN   (5055-)  E  -
5814 NET   (5056-)  E  -
5831 ADP   (2066-)  G  -
5836 NET   (5077-)  G  -
5837 ORN   (5076-)  G  -
5838 ADP   (2072-)  G  -

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

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

1326 143   ( 269-)  B
2763 143   ( 269-)  D
4200 143   ( 269-)  F
5637 143   ( 269-)  H

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'.

 716 PRO   ( 716-)  A      CG
 716 PRO   ( 716-)  A      CD
2153 PRO   ( 716-)  C      CG
2153 PRO   ( 716-)  C      CD
3590 PRO   ( 716-)  E      CG
3590 PRO   ( 716-)  E      CD
5027 PRO   ( 716-)  G      CG
5027 PRO   ( 716-)  G      CD

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) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 3.864 over 34631 bonds
Average difference in B over a bond : 10.65
RMS difference in B over a bond : 14.99

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

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

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

  42 TYR   (  42-)  A
  65 TYR   (  65-)  A
 330 TYR   ( 330-)  A
 354 TYR   ( 354-)  A
 438 TYR   ( 438-)  A
 526 TYR   ( 526-)  A
 544 TYR   ( 544-)  A
 547 TYR   ( 547-)  A
 730 TYR   ( 737-)  A
 784 TYR   ( 799-)  A
 823 TYR   ( 838-)  A
 872 TYR   ( 887-)  A
1021 TYR   (1036-)  A
1025 TYR   (1040-)  A
1307 TYR   ( 250-)  B
1434 TYR   ( 377-)  B
1767 TYR   ( 330-)  C
1791 TYR   ( 354-)  C
1875 TYR   ( 438-)  C
1981 TYR   ( 544-)  C
1984 TYR   ( 547-)  C
2054 TYR   ( 617-)  C
2167 TYR   ( 737-)  C
2221 TYR   ( 799-)  C
2260 TYR   ( 838-)  C
And so on for a total of 61 lines.

Warning: Phenylalanine convention problem

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

 111 PHE   ( 111-)  A
 164 PHE   ( 164-)  A
 172 PHE   ( 172-)  A
 188 PHE   ( 188-)  A
 237 PHE   ( 237-)  A
 286 PHE   ( 286-)  A
 348 PHE   ( 348-)  A
 409 PHE   ( 409-)  A
 453 PHE   ( 453-)  A
 536 PHE   ( 536-)  A
 837 PHE   ( 852-)  A
 909 PHE   ( 924-)  A
 913 PHE   ( 928-)  A
 954 PHE   ( 969-)  A
1072 PHE   (  15-)  B
1149 PHE   (  92-)  B
1207 PHE   ( 150-)  B
1249 PHE   ( 192-)  B
1405 PHE   ( 348-)  B
1601 PHE   ( 164-)  C
1625 PHE   ( 188-)  C
1723 PHE   ( 286-)  C
1785 PHE   ( 348-)  C
1846 PHE   ( 409-)  C
1890 PHE   ( 453-)  C
And so on for a total of 71 lines.

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.

   6 ASP   (   6-)  A
  27 ASP   (  27-)  A
  57 ASP   (  57-)  A
  62 ASP   (  62-)  A
  84 ASP   (  84-)  A
 121 ASP   ( 121-)  A
 124 ASP   ( 124-)  A
 133 ASP   ( 133-)  A
 161 ASP   ( 161-)  A
 207 ASP   ( 207-)  A
 226 ASP   ( 226-)  A
 246 ASP   ( 246-)  A
 338 ASP   ( 338-)  A
 353 ASP   ( 353-)  A
 416 ASP   ( 416-)  A
 417 ASP   ( 417-)  A
 430 ASP   ( 430-)  A
 441 ASP   ( 441-)  A
 450 ASP   ( 450-)  A
 459 ASP   ( 459-)  A
 499 ASP   ( 499-)  A
 521 ASP   ( 521-)  A
 539 ASP   ( 539-)  A
 558 ASP   ( 558-)  A
 579 ASP   ( 579-)  A
And so on for a total of 251 lines.

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.

  25 GLU   (  25-)  A
  39 GLU   (  39-)  A
  40 GLU   (  40-)  A
  59 GLU   (  59-)  A
  67 GLU   (  67-)  A
  81 GLU   (  81-)  A
 101 GLU   ( 101-)  A
 103 GLU   ( 103-)  A
 109 GLU   ( 109-)  A
 110 GLU   ( 110-)  A
 127 GLU   ( 127-)  A
 153 GLU   ( 153-)  A
 154 GLU   ( 154-)  A
 190 GLU   ( 190-)  A
 208 GLU   ( 208-)  A
 215 GLU   ( 215-)  A
 219 GLU   ( 219-)  A
 235 GLU   ( 235-)  A
 274 GLU   ( 274-)  A
 365 GLU   ( 365-)  A
 393 GLU   ( 393-)  A
 419 GLU   ( 419-)  A
 467 GLU   ( 467-)  A
 468 GLU   ( 468-)  A
 473 GLU   ( 473-)  A
And so on for a total of 280 lines.

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.

  72 GLU   (  72-)  A      CD   OE2   1.33    4.5
 153 GLU   ( 153-)  A      CD   OE1   1.33    4.1
 217 GLU   ( 217-)  A      CD   OE2   1.33    4.2
 430 ASP   ( 430-)  A      CG   OD1   1.33    4.0
 478 GLU   ( 478-)  A      CD   OE1   1.33    4.0
 512 GLU   ( 512-)  A      CD   OE2   1.33    4.2
 577 GLU   ( 577-)  A      CD   OE1   1.33    4.1
 683 GLU   ( 683-)  A      CD   OE1   1.33    4.3
 703 GLU   ( 703-)  A      CD   OE1   1.33    4.1
 726 ASP   ( 733-)  A      CG   OD1   1.33    4.1
 743 ASP   ( 758-)  A      CG   OD1   1.33    4.1
 750 ASP   ( 765-)  A      CG   OD1   1.33    4.2
 765 GLU   ( 780-)  A      CD   OE1   1.33    4.1
 821 GLU   ( 836-)  A      CD   OE2   1.33    4.1
 936 GLU   ( 951-)  A      CD   OE2   1.33    4.2
 940 GLU   ( 955-)  A      CD   OE1   1.33    4.1
1009 GLU   (1024-)  A      CD   OE1   1.33    4.1
1068 ASP   (  11-)  B      CG   OD1   1.33    4.4
1124 ASP   (  67-)  B      CG   OD1   1.33    4.2
1181 GLU   ( 124-)  B      CD   OE1   1.33    4.1
1240 GLU   ( 183-)  B      CD   OE2   1.34    4.7
1425 ASP   ( 368-)  B      CG   OD1   1.33    4.1
1429 GLU   ( 372-)  B      CD   OE1   1.33    4.5
1496 GLU   (  59-)  C      CD   OE1   1.34    4.7
1547 GLU   ( 110-)  C      CD   OE1   1.34    4.9
And so on for a total of 90 lines.

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

 |  1.000736  0.000172 -0.000046|
 |  0.000172  1.000714 -0.000208|
 | -0.000046 -0.000208  1.000355|
Proposed new scale matrix

 |  0.006557 -0.000001  0.000000|
 | -0.000001  0.006079  0.000001|
 |  0.000000  0.000000  0.003000|
With corresponding cell

    A    = 152.505  B   = 164.510  C    = 333.340
    Alpha=  90.014  Beta=  90.003  Gamma=  89.980

The CRYST1 cell dimensions

    A    = 152.400  B   = 164.400  C    = 333.200
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 72.133
(Under-)estimated Z-score: 6.259

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.

  39 GLU   (  39-)  A      C    CA   CB  100.76   -4.9
 111 PHE   ( 111-)  A      CA   CB   CG  108.34   -5.5
 170 PRO   ( 170-)  A      N    CA   CB  107.72    4.3
 172 PHE   ( 172-)  A      CA   CB   CG  108.74   -5.1
 188 PHE   ( 188-)  A      CA   CB   CG  109.03   -4.8
 200 PRO   ( 200-)  A      N    CA   CB  108.65    5.1
 238 ASP   ( 238-)  A      CA   CB   CG  108.16   -4.4
 266 ASN   ( 266-)  A      CA   CB   CG  117.91    5.3
 283 ASN   ( 283-)  A      CA   CB   CG  122.95   10.4
 294 ARG   ( 294-)  A      CG   CD   NE  117.76    4.3
 367 PHE   ( 367-)  A      CA   CB   CG  106.92   -6.9
 400 ARG   ( 400-)  A      CG   CD   NE  117.30    4.0
 416 ASP   ( 416-)  A      CA   CB   CG  105.52   -7.1
 417 ASP   ( 417-)  A      CA   CB   CG  118.59    6.0
 434 ASP   ( 434-)  A      CA   CB   CG  116.70    4.1
 450 ASP   ( 450-)  A      CA   CB   CG  116.67    4.1
 453 PHE   ( 453-)  A      CA   CB   CG  109.48   -4.3
 457 ASN   ( 457-)  A      CA   CB   CG  105.97   -6.6
 488 PHE   ( 488-)  A      CA   CB   CG  109.32   -4.5
 522 LEU   ( 522-)  A      C    CA   CB  120.11    5.3
 525 VAL   ( 525-)  A      N    CA   CB  117.72    4.2
 527 LYS   ( 527-)  A      N    CA   CB  117.79    4.3
 536 PHE   ( 536-)  A      CA   CB   CG  108.18   -5.6
 539 ASP   ( 539-)  A      CA   CB   CG  108.31   -4.3
 548 GLU   ( 548-)  A      C    CA   CB  119.62    5.0
And so on for a total of 302 lines.

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.

   6 ASP   (   6-)  A
  25 GLU   (  25-)  A
  27 ASP   (  27-)  A
  39 GLU   (  39-)  A
  40 GLU   (  40-)  A
  57 ASP   (  57-)  A
  59 GLU   (  59-)  A
  62 ASP   (  62-)  A
  67 GLU   (  67-)  A
  81 GLU   (  81-)  A
  84 ASP   (  84-)  A
 101 GLU   ( 101-)  A
 103 GLU   ( 103-)  A
 109 GLU   ( 109-)  A
 110 GLU   ( 110-)  A
 121 ASP   ( 121-)  A
 124 ASP   ( 124-)  A
 127 GLU   ( 127-)  A
 133 ASP   ( 133-)  A
 153 GLU   ( 153-)  A
 154 GLU   ( 154-)  A
 161 ASP   ( 161-)  A
 190 GLU   ( 190-)  A
 207 ASP   ( 207-)  A
 208 GLU   ( 208-)  A
And so on for a total of 531 lines.

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.

 548 GLU   ( 548-)  A      CA    -6.8    22.83    33.96
 719 GLU   ( 726-)  A      CA    -6.9    22.69    33.96
 984 PRO   ( 999-)  A      N     -9.4   -33.45    -2.48
1241 ALA   ( 184-)  B      CA    -6.2    26.27    34.09
1609 PHE   ( 172-)  C      CA    -7.1    22.67    33.98
1776 ILE   ( 339-)  C      CA    -8.2    20.87    33.24
1985 GLU   ( 548-)  C      CA    -6.1    23.89    33.96
2421 PRO   ( 999-)  C      N     -7.1   -25.87    -2.48
3213 ILE   ( 339-)  E      CA   -12.9    13.77    33.24
3309 ARG   ( 435-)  E      CA    -6.3    23.59    33.91
3858 PRO   ( 999-)  E      N     -7.8   -28.21    -2.48
4394 PRO   (  83-)  G      N      7.4    21.89    -2.48
4631 ALA   ( 320-)  G      CA    -6.2    26.16    34.09
4650 ILE   ( 339-)  G      CA    -9.7    18.56    33.24
5269 ALA   ( 973-)  G      CA    -6.1    26.30    34.09
5550 PRO   ( 182-)  H      N      6.2    17.88    -2.48
The average deviation= 1.451

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.

3213 ILE   ( 339-)  E    8.01
4650 ILE   ( 339-)  G    7.50
1776 ILE   ( 339-)  C    6.42
1591 GLU   ( 154-)  C    5.44
4147 LEU   ( 216-)  F    5.07
3486 THR   ( 612-)  E    4.99
 682 VAL   ( 682-)  A    4.86
2027 ARG   ( 590-)  C    4.70
3652 ALA   ( 793-)  E    4.69
5298 GLN   (1002-)  G    4.52
1872 ARG   ( 435-)  C    4.49
 543 MET   ( 543-)  A    4.43
2283 LEU   ( 861-)  C    4.41
3027 GLU   ( 153-)  E    4.39
4412 GLU   ( 101-)  G    4.38
1110 VAL   (  53-)  B    4.28
2583 ALA   (  89-)  D    4.24
 161 ASP   ( 161-)  A    4.24
2897 ALA   (  23-)  E    4.24
4338 ASP   (  27-)  G    4.24
 605 THR   ( 605-)  A    4.23
5189 VAL   ( 893-)  G    4.21
5089 ALA   ( 793-)  G    4.21
5153 THR   ( 857-)  G    4.18
1980 MET   ( 543-)  C    4.17
3935 SER   (   4-)  F    4.15
1146 ALA   (  89-)  B    4.15
4392 GLU   (  81-)  G    4.14
2547 VAL   (  53-)  D    4.14
3525 ALA   ( 651-)  E    4.10
3853 VAL   ( 994-)  E    4.10
5146 VAL   ( 850-)  G    4.09
2042 THR   ( 605-)  C    4.07
3083 SER   ( 209-)  E    4.07
5667 ASP   ( 299-)  H    4.04
 319 ILE   ( 319-)  A    4.04
3829 GLU   ( 970-)  E    4.03
5584 LEU   ( 216-)  H    4.00
3855 GLU   ( 996-)  E    4.00

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.

1525 PRO   (  88-)  C    -3.0
2962 PRO   (  88-)  E    -3.0
  88 PRO   (  88-)  A    -3.0
4399 PRO   (  88-)  G    -3.0
1639 LYS   ( 202-)  C    -2.8
4513 LYS   ( 202-)  G    -2.8
3445 ARG   ( 571-)  E    -2.8
4563 PRO   ( 252-)  G    -2.7
4393 ARG   (  82-)  G    -2.7
1689 PRO   ( 252-)  C    -2.7
4842 THR   ( 531-)  G    -2.7
 202 LYS   ( 202-)  A    -2.7
5141 ARG   ( 845-)  G    -2.7
5271 HIS   ( 975-)  G    -2.7
2544 ARG   (  50-)  D    -2.7
 375 THR   ( 375-)  A    -2.7
 646 THR   ( 646-)  A    -2.7
1414 SER   ( 357-)  B    -2.6
3249 THR   ( 375-)  E    -2.6
2373 GLU   ( 951-)  C    -2.6
1812 THR   ( 375-)  C    -2.6
 936 GLU   ( 951-)  A    -2.6
5725 SER   ( 357-)  H    -2.6
4882 ARG   ( 571-)  G    -2.6
4288 SER   ( 357-)  F    -2.6
And so on for a total of 215 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.

  23 ALA   (  23-)  A  Poor phi/psi
 164 PHE   ( 164-)  A  PRO omega poor
 172 PHE   ( 172-)  A  Poor phi/psi
 226 ASP   ( 226-)  A  Poor phi/psi
 251 ALA   ( 251-)  A  PRO omega poor
 276 GLY   ( 276-)  A  Poor phi/psi
 302 PRO   ( 302-)  A  Poor phi/psi
 375 THR   ( 375-)  A  Poor phi/psi
 403 GLU   ( 403-)  A  Poor phi/psi
 409 PHE   ( 409-)  A  Poor phi/psi
 457 ASN   ( 457-)  A  Poor phi/psi
 484 LEU   ( 484-)  A  Poor phi/psi
 521 ASP   ( 521-)  A  Poor phi/psi
 531 THR   ( 531-)  A  Poor phi/psi
 533 ALA   ( 533-)  A  Poor phi/psi
 534 ALA   ( 534-)  A  Poor phi/psi
 548 GLU   ( 548-)  A  Poor phi/psi
 558 ASP   ( 558-)  A  Poor phi/psi
 646 THR   ( 646-)  A  Poor phi/psi
 686 LYS   ( 686-)  A  Poor phi/psi
 710 TYR   ( 710-)  A  PRO omega poor
 755 GLY   ( 770-)  A  Poor phi/psi
 781 LEU   ( 796-)  A  PRO omega poor
 785 THR   ( 800-)  A  Poor phi/psi
 806 GLN   ( 821-)  A  Poor phi/psi
And so on for a total of 160 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 : -4.108

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.

2023 SER   ( 586-)  C    0.34
3713 SER   ( 854-)  E    0.35
4705 SER   ( 394-)  G    0.36
1341 VAL   ( 284-)  B    0.36
1831 SER   ( 394-)  C    0.36
  29 SER   (  29-)  A    0.36
 312 SER   ( 312-)  A    0.36
 394 SER   ( 394-)  A    0.36
 839 SER   ( 854-)  A    0.36
1157 SER   ( 100-)  B    0.36
2778 VAL   ( 284-)  D    0.36
 268 SER   ( 268-)  A    0.37
2276 SER   ( 854-)  C    0.37
3142 SER   ( 268-)  E    0.38
5150 SER   ( 854-)  G    0.38
5468 SER   ( 100-)  H    0.38
1156 SER   (  99-)  B    0.38
4340 SER   (  29-)  G    0.38
2593 SER   (  99-)  D    0.39

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 LYS   (   3-)  A      0
   7 ILE   (   7-)  A      0
   9 SER   (   9-)  A      0
  17 PRO   (  17-)  A      0
  20 ILE   (  20-)  A      0
  22 GLN   (  22-)  A      0
  23 ALA   (  23-)  A      0
  24 CYS   (  24-)  A      0
  40 GLU   (  40-)  A      0
  52 ALA   (  52-)  A      0
  60 MET   (  60-)  A      0
  69 ILE   (  69-)  A      0
  83 PRO   (  83-)  A      0
  89 THR   (  89-)  A      0
  90 MET   (  90-)  A      0
  93 GLN   (  93-)  A      0
 105 GLN   ( 105-)  A      0
 107 VAL   ( 107-)  A      0
 116 ILE   ( 116-)  A      0
 139 ILE   ( 139-)  A      0
 146 SER   ( 146-)  A      0
 149 ALA   ( 149-)  A      0
 150 HIS   ( 150-)  A      0
 151 THR   ( 151-)  A      0
 152 MET   ( 152-)  A      0
And so on for a total of 1999 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 : 1.949

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!

2004 GLY   ( 567-)  C   3.26   29
 567 GLY   ( 567-)  A   3.24   20
4878 GLY   ( 567-)  G   3.21   19
3441 GLY   ( 567-)  E   3.09   30
 709 GLY   ( 709-)  A   2.26   12
3583 GLY   ( 709-)  E   2.10   14
2146 GLY   ( 709-)  C   1.98   11

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

  23 ALA   (  23-)  A   1.75

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]

   2 PRO   (   2-)  A    0.04 LOW
  17 PRO   (  17-)  A    0.16 LOW
  58 PRO   (  58-)  A    0.13 LOW
  68 PRO   (  68-)  A    0.01 LOW
  83 PRO   (  83-)  A    0.16 LOW
 165 PRO   ( 165-)  A    0.16 LOW
 170 PRO   ( 170-)  A    0.11 LOW
 200 PRO   ( 200-)  A    0.10 LOW
 290 PRO   ( 290-)  A    0.10 LOW
 360 PRO   ( 360-)  A    0.11 LOW
 411 PRO   ( 411-)  A    0.09 LOW
 418 PRO   ( 418-)  A    0.17 LOW
 524 PRO   ( 524-)  A    0.18 LOW
 555 PRO   ( 555-)  A    0.07 LOW
 647 PRO   ( 647-)  A    0.12 LOW
 660 PRO   ( 660-)  A    0.16 LOW
 690 PRO   ( 690-)  A    0.20 LOW
 711 PRO   ( 711-)  A    0.11 LOW
 716 PRO   ( 716-)  A    0.00 LOW
 782 PRO   ( 797-)  A    0.02 LOW
 829 PRO   ( 844-)  A    0.10 LOW
 836 PRO   ( 851-)  A    0.11 LOW
 845 PRO   ( 860-)  A    0.17 LOW
 870 PRO   ( 885-)  A    0.12 LOW
 871 PRO   ( 886-)  A    0.17 LOW
And so on for a total of 161 lines.

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].

  88 PRO   (  88-)  A   -47.7 half-chair C-beta/C-alpha (-54 degrees)
 302 PRO   ( 302-)  A   -52.3 half-chair C-beta/C-alpha (-54 degrees)
 318 PRO   ( 318-)  A   -60.2 half-chair C-beta/C-alpha (-54 degrees)
 345 PRO   ( 345-)  A   -54.2 half-chair C-beta/C-alpha (-54 degrees)
 350 PRO   ( 350-)  A   101.4 envelop C-beta (108 degrees)
 603 PRO   ( 603-)  A   -53.4 half-chair C-beta/C-alpha (-54 degrees)
 635 PRO   ( 635-)  A   -40.9 envelop C-alpha (-36 degrees)
 666 PRO   ( 666-)  A   148.8 envelop C-alpha (144 degrees)
 890 PRO   ( 905-)  A    -7.4 envelop N (0 degrees)
1239 PRO   ( 182-)  B   -46.2 half-chair C-beta/C-alpha (-54 degrees)
1277 PRO   ( 220-)  B   130.7 half-chair C-beta/C-alpha (126 degrees)
1304 PRO   ( 247-)  B   -34.3 envelop C-alpha (-36 degrees)
1415 PRO   ( 358-)  B   -56.1 half-chair C-beta/C-alpha (-54 degrees)
1525 PRO   (  88-)  C   -62.7 half-chair C-beta/C-alpha (-54 degrees)
1755 PRO   ( 318-)  C   -59.1 half-chair C-beta/C-alpha (-54 degrees)
1782 PRO   ( 345-)  C   -51.8 half-chair C-beta/C-alpha (-54 degrees)
1787 PRO   ( 350-)  C   114.8 envelop C-beta (108 degrees)
1797 PRO   ( 360-)  C   -62.2 half-chair C-beta/C-alpha (-54 degrees)
2040 PRO   ( 603-)  C   -45.7 half-chair C-beta/C-alpha (-54 degrees)
2072 PRO   ( 635-)  C   -58.8 half-chair C-beta/C-alpha (-54 degrees)
2103 PRO   ( 666-)  C   133.8 half-chair C-beta/C-alpha (126 degrees)
2540 PRO   (  46-)  D   119.4 half-chair C-beta/C-alpha (126 degrees)
2714 PRO   ( 220-)  D   120.9 half-chair C-beta/C-alpha (126 degrees)
2741 PRO   ( 247-)  D  -121.4 half-chair C-delta/C-gamma (-126 degrees)
2840 PRO   ( 346-)  D   -46.3 half-chair C-beta/C-alpha (-54 degrees)
2852 PRO   ( 358-)  D   -43.2 envelop C-alpha (-36 degrees)
2891 PRO   (  17-)  E  -127.7 half-chair C-delta/C-gamma (-126 degrees)
2962 PRO   (  88-)  E   -44.6 envelop C-alpha (-36 degrees)
3176 PRO   ( 302-)  E    -0.6 envelop N (0 degrees)
3192 PRO   ( 318-)  E   -59.1 half-chair C-beta/C-alpha (-54 degrees)
3219 PRO   ( 345-)  E   -43.9 envelop C-alpha (-36 degrees)
3540 PRO   ( 666-)  E   107.1 envelop C-beta (108 degrees)
3703 PRO   ( 844-)  E    -4.2 envelop N (0 degrees)
3744 PRO   ( 885-)  E    46.6 half-chair C-delta/C-gamma (54 degrees)
3858 PRO   ( 999-)  E   165.8 half-chair C-alpha/N (162 degrees)
4151 PRO   ( 220-)  F   135.6 envelop C-alpha (144 degrees)
4289 PRO   ( 358-)  F   -30.9 envelop C-alpha (-36 degrees)
4328 PRO   (  17-)  G   -59.1 half-chair C-beta/C-alpha (-54 degrees)
4399 PRO   (  88-)  G   -46.9 half-chair C-beta/C-alpha (-54 degrees)
4476 PRO   ( 165-)  G   -18.1 half-chair C-alpha/N (-18 degrees)
4563 PRO   ( 252-)  G   -60.0 half-chair C-beta/C-alpha (-54 degrees)
4601 PRO   ( 290-)  G   -58.6 half-chair C-beta/C-alpha (-54 degrees)
4629 PRO   ( 318-)  G   -46.0 half-chair C-beta/C-alpha (-54 degrees)
4656 PRO   ( 345-)  G   -55.5 half-chair C-beta/C-alpha (-54 degrees)
4946 PRO   ( 635-)  G   -55.2 half-chair C-beta/C-alpha (-54 degrees)
4977 PRO   ( 666-)  G   140.2 envelop C-alpha (144 degrees)
5201 PRO   ( 905-)  G   -10.8 half-chair C-alpha/N (-18 degrees)
5550 PRO   ( 182-)  H   -63.5 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.

 960 HIS   ( 975-)  A      ND1 <-> 5271 HIS   ( 975-)  G      ND1    0.57    2.43  INTRA BF
2875 MET   (   1-)  E      N   <-> 3098 LYS   ( 224-)  E      NZ     0.55    2.30  INTRA BF
3603 ARG   ( 736-)  E      NH2 <-> 5843 HOH   (5947 )  E      O      0.48    2.22  INTRA BF
1395 GLN   ( 338-)  B      NE2 <-> 5840 HOH   (5234 )  B      O      0.46    2.24  INTRA
2716 GLN   ( 222-)  D      NE2 <-> 5842 HOH   (2212 )  D      O      0.44    2.26  INTRA BF
1519 ARG   (  82-)  C      NH1 <-> 5841 HOH   (5109 )  C      O      0.44    2.26  INTRA BF
1174 LYS   ( 117-)  B      NZ  <-> 5840 HOH   (5060 )  B      O      0.43    2.27  INTRA BL
2917 ARG   (  43-)  E      NH2 <-> 2955 GLU   (  81-)  E      OE1    0.42    2.28  INTRA BF
1996 ARG   ( 559-)  C      NH1 <-> 5841 HOH   (5704 )  C      O      0.41    2.29  INTRA BF
 675 ARG   ( 675-)  A      NH2 <-> 5839 HOH   (5504 )  A      O      0.41    2.29  INTRA BF
 797 GLN   ( 812-)  A      NE2 <-> 5839 HOH   (5766 )  A      O      0.41    2.29  INTRA BL
1946 ARG   ( 509-)  C      NH1 <-> 1949 GLU   ( 512-)  C      OE2    0.41    2.29  INTRA BF
4354 ARG   (  43-)  G      NH2 <-> 4392 GLU   (  81-)  G      OE1    0.41    2.29  INTRA BF
2722 VAL   ( 228-)  D      O   <-> 2725 MET   ( 231-)  D      N      0.41    2.29  INTRA BF
4068 ASN   ( 137-)  F      N   <-> 5844 HOH   (3285 )  F      O      0.41    2.29  INTRA BF
  43 ARG   (  43-)  A      NH2 <->   81 GLU   (  81-)  A      OE1    0.41    2.29  INTRA BF
3616 ASP   ( 757-)  E      O   <-> 3692 LYS   ( 833-)  E      NZ     0.41    2.29  INTRA BF
5176 THR   ( 880-)  G      N   <-> 5845 HOH   (3925 )  G      O      0.41    2.29  INTRA BF
2572 GLN   (  78-)  D      NE2 <-> 5842 HOH   (1782 )  D      O      0.41    2.29  INTRA BL
1442 THR   (   5-)  C      N   <-> 5841 HOH   (5597 )  C      O      0.41    2.29  INTRA BF
4412 GLU   ( 101-)  G      OE1 <-> 4415 ARG   ( 104-)  G      NH2    0.41    2.29  INTRA BF
1329 HIS   ( 272-)  B      ND1 <-> 1406 SER   ( 349-)  B      OG     0.40    2.30  INTRA BF
2324 GLY   ( 902-)  C      O   <-> 2449 ARG   (1027-)  C      NH2    0.40    2.30  INTRA BF
 989 ARG   (1004-)  A      NE  <-> 5839 HOH   (5858 )  A      O      0.40    2.30  INTRA BF
  40 GLU   (  40-)  A      OE2 <->  325 LYS   ( 325-)  A      NZ     0.40    2.30  INTRA BF
And so on for a total of 1442 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

5294 ARG   ( 998-)  G      -7.71
3217 ARG   ( 343-)  E      -7.37
2420 ARG   ( 998-)  C      -7.33
4654 ARG   ( 343-)  G      -7.33
1780 ARG   ( 343-)  C      -7.27
3857 ARG   ( 998-)  E      -7.27
 343 ARG   ( 343-)  A      -7.27
 983 ARG   ( 998-)  A      -6.94
 907 ARG   ( 922-)  A      -6.49
2344 ARG   ( 922-)  C      -6.47
3781 ARG   ( 922-)  E      -6.41
1620 TYR   ( 183-)  C      -6.36
3057 TYR   ( 183-)  E      -6.34
4494 TYR   ( 183-)  G      -6.32
3854 HIS   ( 995-)  E      -6.30
 183 TYR   ( 183-)  A      -6.27
4485 MET   ( 174-)  G      -6.27
 174 MET   ( 174-)  A      -6.10
3048 MET   ( 174-)  E      -6.07
1093 MET   (  36-)  B      -5.95
2306 ILE   ( 884-)  C      -5.92
5180 ILE   ( 884-)  G      -5.90
 869 ILE   ( 884-)  A      -5.88
1611 MET   ( 174-)  C      -5.86
3743 ILE   ( 884-)  E      -5.83
And so on for a total of 72 lines.

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

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: G

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: H

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.

2934 MET   (  60-)  E   -2.90
4550 ALA   ( 239-)  G   -2.87
2897 ALA   (  23-)  E   -2.86
4334 ALA   (  23-)  G   -2.86
3113 ALA   ( 239-)  E   -2.85
1676 ALA   ( 239-)  C   -2.85
1460 ALA   (  23-)  C   -2.83
3279 GLY   ( 405-)  E   -2.82
  23 ALA   (  23-)  A   -2.79
2315 VAL   ( 893-)  C   -2.75
1842 GLY   ( 405-)  C   -2.70
4716 GLY   ( 405-)  G   -2.70
 878 VAL   ( 893-)  A   -2.70
3752 VAL   ( 893-)  E   -2.70
 405 GLY   ( 405-)  A   -2.69
 884 LYS   ( 899-)  A   -2.65
3177 ARG   ( 303-)  E   -2.64
3758 LYS   ( 899-)  E   -2.64
 819 ASN   ( 834-)  A   -2.62
5189 VAL   ( 893-)  G   -2.61
2646 GLY   ( 152-)  D   -2.60
4083 GLY   ( 152-)  F   -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.

 403 GLU   ( 403-)  A     -  406 ALA   ( 406-)  A        -1.64
 575 GLY   ( 575-)  A     -  578 PHE   ( 578-)  A        -1.78
2012 GLY   ( 575-)  C     - 2015 PHE   ( 578-)  C        -1.82
2314 GLU   ( 892-)  C     - 2317 LEU   ( 895-)  C        -1.86
3449 GLY   ( 575-)  E     - 3452 PHE   ( 578-)  E        -1.77
3751 GLU   ( 892-)  E     - 3754 LEU   ( 895-)  E        -1.84
4016 LEU   (  85-)  F     - 4019 ILE   (  88-)  F        -1.84
4886 GLY   ( 575-)  G     - 4889 PHE   ( 578-)  G        -1.77
5453 LEU   (  85-)  H     - 5456 ILE   (  88-)  H        -1.78

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

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

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.

5839 HOH   (5602 )  A      O     -7.91   96.67   90.05
5839 HOH   (5612 )  A      O      1.21  105.39   88.17
5839 HOH   (5613 )  A      O     -6.72  102.09   76.78
5839 HOH   (5616 )  A      O     -4.86   95.97   89.87
5839 HOH   (5618 )  A      O      2.96  107.81   89.12
5841 HOH   (5750 )  C      O     63.17   40.71   49.46
5841 HOH   (5754 )  C      O     63.42   52.29   62.22
5842 HOH   (2221 )  D      O      8.10  -56.74  -60.28

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.

5839 HOH   (5120 )  A      O
5839 HOH   (5487 )  A      O
5839 HOH   (5557 )  A      O
5839 HOH   (5575 )  A      O
5839 HOH   (5665 )  A      O
5839 HOH   (5691 )  A      O
5839 HOH   (5707 )  A      O
5839 HOH   (5722 )  A      O
5839 HOH   (5779 )  A      O
5839 HOH   (5789 )  A      O
5839 HOH   (5790 )  A      O
5839 HOH   (5795 )  A      O
5839 HOH   (5807 )  A      O
5839 HOH   (5833 )  A      O
5839 HOH   (5845 )  A      O
5839 HOH   (5862 )  A      O
5840 HOH   (5024 )  B      O
5840 HOH   (5164 )  B      O
5840 HOH   (5227 )  B      O
5840 HOH   (5250 )  B      O
5841 HOH   (5053 )  C      O
5841 HOH   (5360 )  C      O
5841 HOH   (5442 )  C      O
5841 HOH   (5492 )  C      O
5841 HOH   (5545 )  C      O
And so on for a total of 74 lines.

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.

 105 GLN   ( 105-)  A
 266 ASN   ( 266-)  A
 491 GLN   ( 491-)  A
 523 HIS   ( 523-)  A
 769 GLN   ( 784-)  A
 773 HIS   ( 788-)  A
 797 GLN   ( 812-)  A
 820 ASN   ( 835-)  A
 921 ASN   ( 936-)  A
 972 ASN   ( 987-)  A
 985 HIS   (1000-)  A
1279 GLN   ( 222-)  B
1369 HIS   ( 312-)  B
1408 GLN   ( 351-)  B
1542 GLN   ( 105-)  C
1680 HIS   ( 243-)  C
1703 ASN   ( 266-)  C
2206 GLN   ( 784-)  C
2358 ASN   ( 936-)  C
2409 ASN   ( 987-)  C
2414 ASN   ( 992-)  C
2417 HIS   ( 995-)  C
2457 GLN   (1035-)  C
2545 GLN   (  51-)  D
2845 GLN   ( 351-)  D
And so on for a total of 53 lines.

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.

   7 ILE   (   7-)  A      N
  61 ALA   (  61-)  A      N
 169 ARG   ( 169-)  A      NH1
 173 THR   ( 173-)  A      N
 176 GLY   ( 176-)  A      N
 184 ASN   ( 184-)  A      N
 210 LEU   ( 210-)  A      N
 224 LYS   ( 224-)  A      N
 225 ASN   ( 225-)  A      ND2
 236 ASN   ( 236-)  A      ND2
 241 GLY   ( 241-)  A      N
 244 THR   ( 244-)  A      N
 279 THR   ( 279-)  A      N
 285 GLN   ( 285-)  A      NE2
 340 THR   ( 340-)  A      OG1
 344 THR   ( 344-)  A      N
 377 GLN   ( 377-)  A      N
 383 GLU   ( 383-)  A      N
 389 ARG   ( 389-)  A      NE
 390 THR   ( 390-)  A      N
 396 GLN   ( 396-)  A      NE2
 484 LEU   ( 484-)  A      N
 534 ALA   ( 534-)  A      N
 556 SER   ( 556-)  A      OG
 570 ASN   ( 570-)  A      N
And so on for a total of 276 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.

 215 GLU   ( 215-)  A      OE1
 236 ASN   ( 236-)  A      OD1
 391 GLN   ( 391-)  A      OE1
 746 GLU   ( 761-)  A      OE2
1054 HIS   (1069-)  A      ND1
1330 GLN   ( 273-)  B      OE1
1410 HIS   ( 353-)  B      NE2
1652 GLU   ( 215-)  C      OE2
1673 ASN   ( 236-)  C      OD1
1828 GLN   ( 391-)  C      OE1
2183 GLU   ( 761-)  C      OE2
2265 ASN   ( 843-)  C      OD1
2422 HIS   (1000-)  C      NE2
2767 GLN   ( 273-)  D      OE1
2847 HIS   ( 353-)  D      NE2
3089 GLU   ( 215-)  E      OE2
3110 ASN   ( 236-)  E      OD1
3208 GLU   ( 334-)  E      OE2
3265 GLN   ( 391-)  E      OE1
3547 GLU   ( 673-)  E      OE2
3612 ASP   ( 753-)  E      OD1
3620 GLU   ( 761-)  E      OE1
3620 GLU   ( 761-)  E      OE2
3671 GLN   ( 812-)  E      OE1
4204 GLN   ( 273-)  F      OE1
4284 HIS   ( 353-)  F      NE2
4526 GLU   ( 215-)  G      OE2
4547 ASN   ( 236-)  G      OD1
4702 GLN   ( 391-)  G      OE1
4984 GLU   ( 673-)  G      OE2
5049 ASP   ( 753-)  G      OD1
5057 GLU   ( 761-)  G      OE2
5139 ASN   ( 843-)  G      OD1
5212 GLU   ( 916-)  G      OE2
5641 GLN   ( 273-)  H      OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

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

5756   K   (5005-)  A   -.-  -.-  Part of ionic cluster
5758   K   (5009-)  A   -.-  -.-  Part of ionic cluster
5761   K   (5014-)  A    0.29  -.-   Poor packing (Few ligands (4) )
5777   K   (5027-)  C   -.-  -.-  Part of ionic cluster
5779   K   (5031-)  C   -.-  -.-  Part of ionic cluster
5781   K   (5035-)  C    0.52  -.-   Poor packing
5782   K   (5036-)  C   -.-  -.-  Too few ligands (3)
5783   K   (5037-)  C    1.81  -.-   Poor packing
5799   K   (5049-)  E   -.-  -.-  Part of ionic cluster
5801   K   (5053-)  E   -.-  -.-  Part of ionic cluster
5801   K   (5053-)  E     6.64   1.10 Should be NA
5803   K   (5057-)  E    0.60  -.-   Poor packing
5819   K   (2069-)  G     1.95   0.73 Scores about as good as NA
5820   K   (5070-)  G   -.-  -.-  Part of ionic cluster
5822   K   (5074-)  G   -.-  -.-  Part of ionic cluster
5822   K   (5074-)  G     3.01   0.82 Is perhaps NA
5825   K   (5079-)  G    0.48  -.-   Poor packing (Few ligands (4) )
5826   K   (5080-)  G    0.46  -.-   Poor packing
5833   K   (5081-)  H    0.56  -.-   Poor packing

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.

5839 HOH   (5049 )  A      O  0.90  K  4 *1 and *2
5839 HOH   (5060 )  A      O  0.92  K  4 *1 and *2
5839 HOH   (5236 )  A      O  0.92  K  5 *1 and *2 NCS 1/1
5839 HOH   (5258 )  A      O  1.15  K  4 *1 and *2
5839 HOH   (5341 )  A      O  0.83  K  4 *1 and *2
5839 HOH   (5351 )  A      O  1.02  K  4 *1 and *2
5839 HOH   (5369 )  A      O  1.10  K  5 *1 and *2 Ion-B
5839 HOH   (5405 )  A      O  1.05  K  4 *1 and *2
5839 HOH   (5467 )  A      O  0.97  K  5 *1 and *2 H2O-B
5839 HOH   (5584 )  A      O  0.97  K  4 *1 and *2
5839 HOH   (5712 )  A      O  0.84  K  4 *1 and *2 H2O-B
5840 HOH   (5027 )  B      O  1.19  K  4 *1 and *2
5840 HOH   (5055 )  B      O  1.04  K  4 *1 and *2
5840 HOH   (5124 )  B      O  1.02  K  5 *1 and *2
5840 HOH   (5249 )  B      O  1.09  K  4 *1 and *2 ION-B
5841 HOH   (5261 )  C      O  0.78  K  4 *1 and *2 NCS 2/2
5841 HOH   (5275 )  C      O  0.79  K  4 *1 and *2 NCS 2/2
5841 HOH   (5355 )  C      O  0.91  K  5 *1 and *2 NCS 1/1
5841 HOH   (5364 )  C      O  1.18  K  4 *1 and *2 NCS 2/2
5841 HOH   (5612 )  C      O  1.12  K  4 *1 and *2
5841 HOH   (5613 )  C      O  0.79  K  4 *1 and *2
5841 HOH   (5619 )  C      O  0.85  K  5 *1 and *2 NCS 1/1
5842 HOH   (1498 )  D      O  1.03  K  4 *1 and *2 NCS 1/1
5843 HOH   (5213 )  E      O  0.99  K  5 *1 and *2 NCS 2/2
5843 HOH   (5281 )  E      O  0.82  K  5 *1 and *2 NCS 2/2
And so on for a total of 51 lines.

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.

  25 GLU   (  25-)  A   H-bonding suggests Gln; but Alt-Rotamer
 334 GLU   ( 334-)  A   H-bonding suggests Gln; but Alt-Rotamer
 410 ASP   ( 410-)  A   H-bonding suggests Asn
 518 ASP   ( 518-)  A   H-bonding suggests Asn
 683 GLU   ( 683-)  A   H-bonding suggests Gln
 738 ASP   ( 753-)  A   H-bonding suggests Asn
 754 ASP   ( 769-)  A   H-bonding suggests Asn; but Alt-Rotamer
 776 ASP   ( 791-)  A   H-bonding suggests Asn; but Alt-Rotamer
 792 ASP   ( 807-)  A   H-bonding suggests Asn
1009 GLU   (1024-)  A   H-bonding suggests Gln
1010 ASP   (1025-)  A   H-bonding suggests Asn
1026 ASP   (1041-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1098 GLU   (  41-)  B   H-bonding suggests Gln; but Alt-Rotamer
1268 ASP   ( 211-)  B   H-bonding suggests Asn; but Alt-Rotamer
1771 GLU   ( 334-)  C   H-bonding suggests Gln; but Alt-Rotamer
1847 ASP   ( 410-)  C   H-bonding suggests Asn
1867 ASP   ( 430-)  C   H-bonding suggests Asn; but Alt-Rotamer
2175 ASP   ( 753-)  C   H-bonding suggests Asn
2213 ASP   ( 791-)  C   H-bonding suggests Asn; but Alt-Rotamer
2606 ASP   ( 112-)  D   H-bonding suggests Asn
3208 GLU   ( 334-)  E   H-bonding suggests Gln
3392 ASP   ( 518-)  E   H-bonding suggests Asn
3628 ASP   ( 769-)  E   H-bonding suggests Asn; but Alt-Rotamer
3650 ASP   ( 791-)  E   H-bonding suggests Asn; but Alt-Rotamer
3666 ASP   ( 807-)  E   H-bonding suggests Asn; but Alt-Rotamer
3884 ASP   (1025-)  E   H-bonding suggests Asn
3900 ASP   (1041-)  E   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
4043 ASP   ( 112-)  F   H-bonding suggests Asn
4373 ASP   (  62-)  G   H-bonding suggests Asn
4645 GLU   ( 334-)  G   H-bonding suggests Gln; but Alt-Rotamer
4994 GLU   ( 683-)  G   H-bonding suggests Gln
5049 ASP   ( 753-)  G   H-bonding suggests Asn
5065 ASP   ( 769-)  G   H-bonding suggests Asn
5087 ASP   ( 791-)  G   H-bonding suggests Asn
5103 ASP   ( 807-)  G   H-bonding suggests Asn; but Alt-Rotamer
5321 ASP   (1025-)  G   H-bonding suggests Asn
5337 ASP   (1041-)  G   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
5480 ASP   ( 112-)  H   H-bonding suggests Asn
5579 ASP   ( 211-)  H   H-bonding suggests Asn; but Alt-Rotamer
5630 ASP   ( 262-)  H   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 :   0.159
  2nd generation packing quality :  -1.226
  Ramachandran plot appearance   :  -1.452
  chi-1/chi-2 rotamer normality  :  -4.108 (bad)
  Backbone conformation          :   0.334

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.800
  Bond angles                    :   1.199
  Omega angle restraints         :   0.354 (tight)
  Side chain planarity           :   0.690
  Improper dihedral distribution :   1.261
  B-factor distribution          :   3.864 (loose)
  Inside/Outside distribution    :   1.013

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.800
  Bond angles                    :   1.199
  Omega angle restraints         :   0.354 (tight)
  Side chain planarity           :   0.690
  Improper dihedral distribution :   1.261
  B-factor distribution          :   3.864 (loose)
  Inside/Outside distribution    :   1.013
==============

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.