WHAT IF Check report

This file was created 2012-01-19 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 pdb1xhu.ent

Checks that need to be done early-on in validation

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected.

1085 HOH   ( 397 )  B      O       6

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 309 LEU   ( 258-)  A  -
 565 ILE   ( 257-)  B  -
 665 ILE   ( 101-)  C  -
 819 LEU   ( 258-)  C  -
1075 ILE   ( 257-)  D  -

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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  73 ARG   (  22-)  A      CG
  73 ARG   (  22-)  A      CD
  73 ARG   (  22-)  A      NE
  73 ARG   (  22-)  A      CZ
  73 ARG   (  22-)  A      NH1
  73 ARG   (  22-)  A      NH2
  75 LYS   (  24-)  A      CG
  75 LYS   (  24-)  A      CD
  75 LYS   (  24-)  A      CE
  75 LYS   (  24-)  A      NZ
 101 SER   (  50-)  A      OG
 210 LYS   ( 159-)  A      CG
 210 LYS   ( 159-)  A      CD
 210 LYS   ( 159-)  A      CE
 210 LYS   ( 159-)  A      NZ
 279 LYS   ( 228-)  A      CG
 279 LYS   ( 228-)  A      CD
 279 LYS   ( 228-)  A      CE
 279 LYS   ( 228-)  A      NZ
 302 LYS   ( 251-)  A      CD
 302 LYS   ( 251-)  A      CE
 302 LYS   ( 251-)  A      NZ
 309 LEU   ( 258-)  A      O
 309 LEU   ( 258-)  A      CG
 309 LEU   ( 258-)  A      CD1
And so on for a total of 244 lines.

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.

   1 DGUA  (   1-)  E    High
   2 DCYT  (   2-)  E    High
   3 DCYT  (   3-)  E    High
  13 DGUA  (  13-)  F    High
  26 DGUA  (  13-)  H    High
  27 DGUA  (   1-)  I    High
  28 DCYT  (   2-)  I    High
  29 DCYT  (   3-)  I    High
  34 DGUA  (   8-)  J    High
  38 DGUA  (  12-)  J    High
  39 DGUA  (  13-)  J    High
  40 DGUA  (   1-)  K    High
  41 DCYT  (   2-)  K    High
  42 DCYT  (   3-)  K    High
  47 DGUA  (   8-)  L    High
  52 DGUA  (  13-)  L    High
  72 LYS   (  21-)  A    High
  73 ARG   (  22-)  A    High
  74 PRO   (  23-)  A    High
  75 LYS   (  24-)  A    High
  76 SER   (  25-)  A    High
  77 GLY   (  26-)  A    High
  78 THR   (  27-)  A    High
  79 LEU   (  28-)  A    High
  81 GLY   (  30-)  A    High
And so on for a total of 326 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. 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 : 1.589 over 5592 bonds
Average difference in B over a bond : 5.24
RMS difference in B over a bond : 6.85

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

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 142 ARG   (  91-)  A

Warning: Tyrosine convention problem

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

  93 TYR   (  42-)  A
 316 TYR   (   8-)  B
 760 TYR   ( 199-)  C
1017 TYR   ( 199-)  D
1074 TYR   ( 256-)  D

Warning: Phenylalanine convention problem

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

  88 PHE   (  37-)  A
 156 PHE   ( 105-)  A
 215 PHE   ( 164-)  A
 242 PHE   ( 191-)  A
 304 PHE   ( 253-)  A
 345 PHE   (  37-)  B
 388 PHE   (  80-)  B
 413 PHE   ( 105-)  B
 472 PHE   ( 164-)  B
 499 PHE   ( 191-)  B
 542 PHE   ( 234-)  B
 561 PHE   ( 253-)  B
 567 PHE   (   3-)  C
 601 PHE   (  37-)  C
 725 PHE   ( 164-)  C
 752 PHE   ( 191-)  C
 855 PHE   (  37-)  D
 898 PHE   (  80-)  D
 923 PHE   ( 105-)  D
1009 PHE   ( 191-)  D

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.

  61 ASP   (  10-)  A
 102 ASP   (  51-)  A
 165 ASP   ( 114-)  A
 171 ASP   ( 120-)  A
 208 ASP   ( 157-)  A
 216 ASP   ( 165-)  A
 265 ASP   ( 214-)  A
 267 ASP   ( 216-)  A
 298 ASP   ( 247-)  A
 422 ASP   ( 114-)  B
 435 ASP   ( 127-)  B
 470 ASP   ( 162-)  B
 473 ASP   ( 165-)  B
 480 ASP   ( 172-)  B
 681 ASP   ( 120-)  C
 718 ASP   ( 157-)  C
 726 ASP   ( 165-)  C
 733 ASP   ( 172-)  C
 869 ASP   (  51-)  D
 932 ASP   ( 114-)  D
 945 ASP   ( 127-)  D
1065 ASP   ( 247-)  D

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.

  86 GLU   (  35-)  A
  89 GLU   (  38-)  A
 148 GLU   (  97-)  A
 153 GLU   ( 102-)  A
 157 GLU   ( 106-)  A
 158 GLU   ( 107-)  A
 175 GLU   ( 124-)  A
 225 GLU   ( 174-)  A
 240 GLU   ( 189-)  A
 275 GLU   ( 224-)  A
 355 GLU   (  47-)  B
 366 GLU   (  58-)  B
 410 GLU   ( 102-)  B
 432 GLU   ( 124-)  B
 468 GLU   ( 160-)  B
 478 GLU   ( 170-)  B
 482 GLU   ( 174-)  B
 505 GLU   ( 197-)  B
 602 GLU   (  38-)  C
 685 GLU   ( 124-)  C
 735 GLU   ( 174-)  C
 750 GLU   ( 189-)  C
 800 GLU   ( 239-)  C
 853 GLU   (  35-)  D
 856 GLU   (  38-)  D
 865 GLU   (  47-)  D
 915 GLU   (  97-)  D
 925 GLU   ( 107-)  D
 992 GLU   ( 174-)  D
1007 GLU   ( 189-)  D
1012 GLU   ( 194-)  D
1057 GLU   ( 239-)  D

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.

   8 DGUA  (   8-)  F      P    O5'   1.64    4.9
  17 DGUA  (   4-)  G      C2   N3    1.36    4.1
  21 DGUA  (   8-)  H      P    O5'   1.65    5.3
  34 DGUA  (   8-)  J      P    O5'   1.64    4.4
  47 DGUA  (   8-)  L      P    O5'   1.64    4.2

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.

   1 DGUA  (   1-)  E      N9   C8   N7  113.13    4.1
   4 DGUA  (   4-)  E      N9   C8   N7  113.36    4.5
   5 DGUA  (   5-)  E      N9   C8   N7  113.10    4.0
   8 DGUA  (   8-)  F      C2'  C1'  N9  105.51   -5.4
   8 DGUA  (   8-)  F      N9   C8   N7  113.19    4.2
   9 DADE  (   9-)  F      O4'  C1'  N9  111.54    4.7
  10 DCYT  (  10-)  F      C2'  C1'  N1  104.46   -6.1
  13 DGUA  (  13-)  F      N9   C8   N7  113.23    4.3
  14 DGUA  (   1-)  G      C2'  C1'  N9  106.78   -4.6
  14 DGUA  (   1-)  G      N9   C8   N7  113.33    4.5
  17 DGUA  (   4-)  G      N9   C8   N7  113.63    5.1
  18 DGUA  (   5-)  G      C3'  C4'  C5' 108.60   -4.1
  18 DGUA  (   5-)  G      N9   C8   N7  113.34    4.5
  21 DGUA  (   8-)  H      OP1  P    OP2 111.31   -5.5
  21 DGUA  (   8-)  H      C2'  C1'  N9  104.94   -5.8
  22 DADE  (   9-)  H      O4'  C1'  N9  111.05    4.1
  23 DCYT  (  10-)  H      C2'  C1'  N1  105.87   -5.2
  26 DGUA  (  13-)  H      N9   C8   N7  113.12    4.0
  33 DCYT  (   7-)  I      O3'  C3'  C2' 125.68    5.6
  34 DGUA  (   8-)  J      OP1  P    OP2 112.88   -4.5
  34 DGUA  (   8-)  J      N9   C8   N7  113.30    4.4
  38 DGUA  (  12-)  J      N9   C8   N7  113.34    4.5
  40 DGUA  (   1-)  K      N9   C8   N7  113.24    4.3
  43 DGUA  (   4-)  K      N9   C8   N7  113.34    4.5
  44 DGUA  (   5-)  K      N9   C8   N7  113.14    4.1
  47 DGUA  (   8-)  L      OP1  P    OP2 112.47   -4.8
  47 DGUA  (   8-)  L      N9   C8   N7  113.15    4.1
  49 DCYT  (  10-)  L      C2'  C1'  N1  107.06   -4.5
  51 DGUA  (  12-)  L      N9   C8   N7  113.15    4.1
  52 DGUA  (  13-)  L      N9   C8   N7  113.11    4.0

Error: Nomenclature error(s)

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

  61 ASP   (  10-)  A
  86 GLU   (  35-)  A
  89 GLU   (  38-)  A
 102 ASP   (  51-)  A
 142 ARG   (  91-)  A
 148 GLU   (  97-)  A
 153 GLU   ( 102-)  A
 157 GLU   ( 106-)  A
 158 GLU   ( 107-)  A
 165 ASP   ( 114-)  A
 171 ASP   ( 120-)  A
 175 GLU   ( 124-)  A
 208 ASP   ( 157-)  A
 216 ASP   ( 165-)  A
 225 GLU   ( 174-)  A
 240 GLU   ( 189-)  A
 265 ASP   ( 214-)  A
 267 ASP   ( 216-)  A
 275 GLU   ( 224-)  A
 298 ASP   ( 247-)  A
 355 GLU   (  47-)  B
 366 GLU   (  58-)  B
 410 GLU   ( 102-)  B
 422 ASP   ( 114-)  B
 432 GLU   ( 124-)  B
And so on for a total of 55 lines.

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.

 907 LEU   (  89-)  D    5.42
 139 LEU   (  88-)  A    5.03
 627 LEU   (  63-)  C    4.71
 421 ALA   ( 113-)  B    4.06
 299 LYS   ( 248-)  A    4.01

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

  22 DADE  (   9-)  H    0.13
   9 DADE  (   9-)  F    0.11
 Ramachandran Z-score : -4.970

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 : -4.970

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.

 704 ILE   ( 143-)  C    -3.0
 961 ILE   ( 143-)  D    -2.7
 725 PHE   ( 164-)  C    -2.7
 184 ILE   ( 133-)  A    -2.5
 236 THR   ( 185-)  A    -2.5
 951 ILE   ( 133-)  D    -2.4
 909 ARG   (  91-)  D    -2.4
 825 ILE   (   7-)  D    -2.4
 744 VAL   ( 183-)  C    -2.4
 414 GLU   ( 106-)  B    -2.4
 838 VAL   (  20-)  D    -2.4
 399 ARG   (  91-)  B    -2.4
 313 LYS   (   5-)  B    -2.4
 673 THR   ( 112-)  C    -2.4
 634 ILE   (  70-)  C    -2.3
 584 VAL   (  20-)  C    -2.3
 409 ILE   ( 101-)  B    -2.3
 888 ILE   (  70-)  D    -2.3
 420 THR   ( 112-)  B    -2.3
 841 PRO   (  23-)  D    -2.3
 628 PHE   (  64-)  C    -2.3
 133 SER   (  82-)  A    -2.3
1028 PHE   ( 210-)  D    -2.2
 934 LEU   ( 116-)  D    -2.2
 648 THR   (  84-)  C    -2.2
 635 ILE   (  71-)  C    -2.2
 840 ARG   (  22-)  D    -2.1
 723 ASP   ( 162-)  C    -2.1
 568 ILE   (   4-)  C    -2.1
 333 SER   (  25-)  B    -2.1
 472 PHE   ( 164-)  B    -2.1
 679 VAL   ( 118-)  C    -2.1
 217 ILE   ( 166-)  A    -2.1
 492 SER   ( 184-)  B    -2.1
 122 ILE   (  71-)  A    -2.1
 139 LEU   (  88-)  A    -2.0
 441 ILE   ( 133-)  B    -2.0
 631 ASN   (  67-)  C    -2.0
 775 ASP   ( 214-)  C    -2.0
  87 PRO   (  36-)  A    -2.0
 172 GLN   ( 121-)  A    -2.0
 942 GLU   ( 124-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  75 LYS   (  24-)  A  Poor phi/psi
  79 LEU   (  28-)  A  Poor phi/psi
  84 ALA   (  33-)  A  Poor phi/psi
 100 LEU   (  49-)  A  Poor phi/psi
 107 GLN   (  56-)  A  Poor phi/psi
 132 ASN   (  81-)  A  Poor phi/psi
 172 GLN   ( 121-)  A  Poor phi/psi
 185 SER   ( 134-)  A  Poor phi/psi
 186 LYS   ( 135-)  A  Poor phi/psi
 208 ASP   ( 157-)  A  Poor phi/psi
 255 ALA   ( 204-)  A  Poor phi/psi
 256 ALA   ( 205-)  A  Poor phi/psi
 261 PHE   ( 210-)  A  Poor phi/psi
 308 ILE   ( 257-)  A  Poor phi/psi
 332 LYS   (  24-)  B  Poor phi/psi
 333 SER   (  25-)  B  Poor phi/psi
 342 GLY   (  34-)  B  Poor phi/psi
 389 ASN   (  81-)  B  Poor phi/psi
 429 GLN   ( 121-)  B  Poor phi/psi
 451 ILE   ( 143-)  B  Poor phi/psi
 464 ILE   ( 156-)  B  Poor phi/psi
 467 LYS   ( 159-)  B  Poor phi/psi
 470 ASP   ( 162-)  B  Poor phi/psi
 514 MET   ( 206-)  B  Poor phi/psi
 518 PHE   ( 210-)  B  Poor phi/psi
And so on for a total of 62 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 : -4.466

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.

 280 SER   ( 229-)  A    0.36
  64 SER   (  13-)  A    0.40

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 DCYT  (   3-)  E      0
   4 DGUA  (   4-)  E      0
   5 DGUA  (   5-)  E      0
   6 DTHY  (   6-)  E      0
   7 DCYT  (   7-)  E      0
   8 DGUA  (   8-)  F      0
   9 DADE  (   9-)  F      0
  10 DCYT  (  10-)  F      0
  11 DCYT  (  11-)  F      0
  12 DGUA  (  12-)  F      0
  13 DGUA  (  13-)  F      0
  14 DGUA  (   1-)  G      0
  15 DCYT  (   2-)  G      0
  16 DCYT  (   3-)  G      0
  17 DGUA  (   4-)  G      0
  18 DGUA  (   5-)  G      0
  19 DTHY  (   6-)  G      0
  20 DCYT  (   7-)  G      0
  21 DGUA  (   8-)  H      0
  22 DADE  (   9-)  H      0
  23 DCYT  (  10-)  H      0
  24 DCYT  (  11-)  H      0
  25 DGUA  (  12-)  H      0
  26 DGUA  (  13-)  H      0
  27 DGUA  (   1-)  I      0
And so on for a total of 458 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 : 1.108

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]

 314 PRO   (   6-)  B    0.47 HIGH
 448 PRO   ( 140-)  B    0.48 HIGH
 886 PRO   (  68-)  D    0.47 HIGH
 958 PRO   ( 140-)  D    0.47 HIGH

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.

 910 GLY   (  92-)  D      N   <-> 1087 HOH   ( 268 )  D      O      0.54    2.16  INTRA BL
 172 GLN   ( 121-)  A      N   <-> 1084 HOH   ( 327 )  A      O      0.53    2.17  INTRA BL
1017 TYR   ( 199-)  D      N   <-> 1087 HOH   ( 306 )  D      O      0.47    2.23  INTRA BF
  43 DGUA  (   4-)  K      N3  <-> 1082 HOH   (   9 )  K      O      0.46    2.24  INTRA BL
  37 DCYT  (  11-)  J      N3  <->   43 DGUA  (   4-)  K      N1     0.46    2.54  INTRA BL
 432 GLU   ( 124-)  B      OE2 <->  475 ASN   ( 167-)  B      ND2    0.45    2.25  INTRA BL
 521 ARG   ( 213-)  B      NE  <-> 1085 HOH   ( 417 )  B      O      0.44    2.26  INTRA BL
   8 DGUA  (   8-)  F      N1  <->   20 DCYT  (   7-)  G      N3     0.43    2.57  INTRA BL
 673 THR   ( 112-)  C      OG1 <->  708 LYS   ( 147-)  C      NZ     0.41    2.29  INTRA BL
  44 DGUA  (   5-)  K      N7  <-> 1019 ASN   ( 201-)  D      ND2    0.40    2.60  INTRA BL
 175 GLU   ( 124-)  A      OE2 <->  218 ASN   ( 167-)  A      ND2    0.38    2.32  INTRA BL
 399 ARG   (  91-)  B      NH2 <->  414 GLU   ( 106-)  B      O      0.38    2.32  INTRA BL
  37 DCYT  (  11-)  J      N4  <->   43 DGUA  (   4-)  K      O6     0.37    2.33  INTRA BL
  11 DCYT  (  11-)  F      N3  <->   17 DGUA  (   4-)  G      N1     0.36    2.64  INTRA BL
 470 ASP   ( 162-)  B      N   <-> 1085 HOH   ( 285 )  B      O      0.34    2.36  INTRA BL
  40 DGUA  (   1-)  K      N2  <-> 1082 HOH   (  13 )  K      O      0.34    2.36  INTRA BL
1041 ARG   ( 223-)  D      N   <-> 1087 HOH   ( 314 )  D      O      0.33    2.37  INTRA BF
 343 GLU   (  35-)  B      N   <->  344 PRO   (  36-)  B      CD     0.33    2.67  INTRA BF
  44 DGUA  (   5-)  K      N2  <->   45 DTHY  (   6-)  K      C2     0.33    2.77  INTRA BL
  11 DCYT  (  11-)  F      N3  <->   17 DGUA  (   4-)  G      N2     0.33    2.67  INTRA BL
 252 ASN   ( 201-)  A      ND2 <-> 1076 HOH   (  11 )  E      O      0.31    2.39  INTRA BL
 973 MET   ( 155-)  D      SD  <-> 1087 HOH   ( 304 )  D      O      0.31    2.69  INTRA BF
 260 GLN   ( 209-)  A      NE2 <-> 1076 HOH   (  11 )  E      O      0.30    2.40  INTRA BL
 242 PHE   ( 191-)  A      CD2 <->  274 ARG   ( 223-)  A      NH1    0.30    2.80  INTRA BL
 182 ARG   ( 131-)  A      NE  <-> 1084 HOH   ( 273 )  A      O      0.30    2.40  INTRA BL
And so on for a total of 532 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

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.

 189 GLN   ( 138-)  A      -6.97
 586 ARG   (  22-)  C      -6.85
 446 GLN   ( 138-)  B      -6.69
 699 GLN   ( 138-)  C      -6.68
 840 ARG   (  22-)  D      -6.61
 956 GLN   ( 138-)  D      -6.60
 722 PHE   ( 161-)  C      -6.25
 330 ARG   (  22-)  B      -6.11
 399 ARG   (  91-)  B      -5.87
  82 HIS   (  31-)  A      -5.61
 979 PHE   ( 161-)  D      -5.58
 389 ASN   (  81-)  B      -5.52
 122 ILE   (  71-)  A      -5.49
 271 ASN   ( 220-)  A      -5.39
 866 ASN   (  48-)  D      -5.38
 781 ASN   ( 220-)  C      -5.34
 976 ASN   ( 158-)  D      -5.33
  99 ASN   (  48-)  A      -5.32
 379 ILE   (  71-)  B      -5.31
 466 ASN   ( 158-)  B      -5.30
 209 ASN   ( 158-)  A      -5.29
 142 ARG   (  91-)  A      -5.28
 563 LYS   ( 255-)  B      -5.26
 587 PRO   (  23-)  C      -5.22
 149 ASN   (  98-)  A      -5.20
1037 PHE   ( 219-)  D      -5.19
  72 LYS   (  21-)  A      -5.18
 662 ASN   (  98-)  C      -5.16
 774 ARG   ( 213-)  C      -5.15
 889 ILE   (  71-)  D      -5.13
 927 GLN   ( 109-)  D      -5.12
 719 ASN   ( 158-)  C      -5.09

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

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.

 418 ASN   ( 110-)  B   -4.01
  73 ARG   (  22-)  A   -3.41
 657 LYS   (  93-)  C   -3.18
 928 ASN   ( 110-)  D   -3.15
 927 GLN   ( 109-)  D   -3.15
 661 GLU   (  97-)  C   -3.14
 161 ASN   ( 110-)  A   -3.04
 619 LYS   (  55-)  C   -2.88
 417 GLN   ( 109-)  B   -2.81
 670 GLN   ( 109-)  C   -2.76
  75 LYS   (  24-)  A   -2.73
 699 GLN   ( 138-)  C   -2.73
 332 LYS   (  24-)  B   -2.72
 642 LYS   (  78-)  C   -2.69
 956 GLN   ( 138-)  D   -2.69
 837 LYS   (  19-)  D   -2.67
 309 LEU   ( 258-)  A   -2.67
 189 GLN   ( 138-)  A   -2.65
 446 GLN   ( 138-)  B   -2.60
 596 ALA   (  32-)  C   -2.59
 597 ALA   (  33-)  C   -2.57
 823 LYS   (   5-)  D   -2.57
  84 ALA   (  33-)  A   -2.55
 210 LYS   ( 159-)  A   -2.53
 588 LYS   (  24-)  C   -2.52
 842 LYS   (  24-)  D   -2.52

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.

 609 LEU   (  45-)  C     -  612 ASN   (  48-)  C        -1.43
 639 ALA   (  75-)  C     -  642 LYS   (  78-)  C        -2.01

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

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.

1084 HOH   ( 298 )  A      O     15.32    0.77  188.56
1084 HOH   ( 315 )  A      O      8.60   54.66  203.03
1084 HOH   ( 319 )  A      O     45.03   45.30  214.80
1084 HOH   ( 322 )  A      O     56.37   37.70  209.83
1084 HOH   ( 367 )  A      O     50.29   34.44  187.37
1084 HOH   ( 371 )  A      O     53.85   37.53  210.80
1084 HOH   ( 387 )  A      O     59.71   12.86  218.41
1084 HOH   ( 389 )  A      O     60.37   20.91  210.54
1084 HOH   ( 400 )  A      O     48.57   34.59  190.92
1085 HOH   ( 268 )  B      O     -5.33   23.53  201.89
1085 HOH   ( 302 )  B      O     35.68  -20.65  209.25
1085 HOH   ( 306 )  B      O     -5.02   20.53  200.95
1085 HOH   ( 310 )  B      O     -6.16   26.51  195.73
1085 HOH   ( 351 )  B      O     26.53   45.35  228.07
1085 HOH   ( 352 )  B      O     21.45   48.00  228.03
1085 HOH   ( 365 )  B      O     28.57   44.21  226.72
1085 HOH   ( 366 )  B      O     24.32   47.33  227.63
1085 HOH   ( 368 )  B      O     21.49   43.22  230.72
1085 HOH   ( 388 )  B      O     37.94  -14.13  202.81
1085 HOH   ( 428 )  B      O     35.06   41.45  240.58
1085 HOH   ( 441 )  B      O     18.97   46.40  245.11
1085 HOH   ( 442 )  B      O     22.77   44.84  240.37
1085 HOH   ( 443 )  B      O     24.23   46.66  230.81
1086 HOH   ( 271 )  C      O      7.09  -20.84  250.85
1086 HOH   ( 289 )  C      O     -8.71    3.15  240.08
1086 HOH   ( 304 )  C      O     25.13   14.65  177.97
1086 HOH   ( 318 )  C      O    -15.26  -13.97  220.64
1087 HOH   ( 285 )  D      O     22.00  -25.33  256.60
1087 HOH   ( 291 )  D      O      2.67    9.92  252.43
1087 HOH   ( 292 )  D      O     -2.65    7.41  250.38
1087 HOH   ( 318 )  D      O     -3.62    2.08  250.43

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.

1084 HOH   ( 309 )  A      O
1084 HOH   ( 314 )  A      O
1084 HOH   ( 336 )  A      O
1084 HOH   ( 337 )  A      O
1084 HOH   ( 354 )  A      O
1084 HOH   ( 355 )  A      O
1084 HOH   ( 356 )  A      O
1084 HOH   ( 357 )  A      O
1084 HOH   ( 394 )  A      O
1084 HOH   ( 397 )  A      O
1085 HOH   ( 340 )  B      O
1085 HOH   ( 348 )  B      O
1085 HOH   ( 362 )  B      O
1085 HOH   ( 363 )  B      O
1085 HOH   ( 364 )  B      O
1085 HOH   ( 369 )  B      O
1085 HOH   ( 370 )  B      O
1085 HOH   ( 371 )  B      O
1085 HOH   ( 372 )  B      O
1085 HOH   ( 379 )  B      O
1085 HOH   ( 383 )  B      O
1085 HOH   ( 397 )  B      O
1085 HOH   ( 422 )  B      O
1085 HOH   ( 424 )  B      O
1085 HOH   ( 441 )  B      O
1086 HOH   ( 265 )  C      O
1086 HOH   ( 280 )  C      O
1086 HOH   ( 283 )  C      O
1086 HOH   ( 285 )  C      O
1086 HOH   ( 287 )  C      O
1086 HOH   ( 290 )  C      O
1086 HOH   ( 300 )  C      O
1086 HOH   ( 304 )  C      O
1086 HOH   ( 305 )  C      O
1087 HOH   ( 265 )  D      O
1087 HOH   ( 281 )  D      O
1087 HOH   ( 282 )  D      O
1087 HOH   ( 285 )  D      O
1087 HOH   ( 289 )  D      O
1087 HOH   ( 290 )  D      O
1087 HOH   ( 291 )  D      O
1087 HOH   ( 292 )  D      O
1087 HOH   ( 318 )  D      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.

  63 ASN   (  12-)  A
 149 ASN   (  98-)  A
 160 GLN   ( 109-)  A
 161 ASN   ( 110-)  A
 218 ASN   ( 167-)  A
 262 HIS   ( 211-)  A
 356 ASN   (  48-)  B
 519 HIS   ( 211-)  B
 582 GLN   (  18-)  C
 595 HIS   (  31-)  C
 631 ASN   (  67-)  C
 778 GLN   ( 217-)  C
 836 GLN   (  18-)  D
 874 GLN   (  56-)  D
 916 ASN   (  98-)  D
 956 GLN   ( 138-)  D

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 DCYT  (   7-)  E      N4
  21 DGUA  (   8-)  H      N2
  34 DGUA  (   8-)  J      N2
  70 LYS   (  19-)  A      N
  76 SER   (  25-)  A      N
  80 SER   (  29-)  A      N
  81 GLY   (  30-)  A      N
 106 LYS   (  55-)  A      N
 107 GLN   (  56-)  A      N
 108 TYR   (  57-)  A      N
 131 PHE   (  80-)  A      N
 136 LEU   (  85-)  A      N
 143 GLY   (  92-)  A      N
 163 THR   ( 112-)  A      N
 182 ARG   ( 131-)  A      NE
 189 GLN   ( 138-)  A      N
 215 PHE   ( 164-)  A      N
 217 ILE   ( 166-)  A      N
 224 TRP   ( 173-)  A      NE1
 240 GLU   ( 189-)  A      N
 258 GLN   ( 207-)  A      NE2
 268 GLN   ( 217-)  A      NE2
 340 ALA   (  32-)  B      N
 342 GLY   (  34-)  B      N
 343 GLU   (  35-)  B      N
And so on for a total of 105 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.

 218 ASN   ( 167-)  A      OD1
 339 HIS   (  31-)  B      NE2
 480 ASP   ( 172-)  B      OD1
 685 GLU   ( 124-)  C      OE1
 719 ASN   ( 158-)  C      OD1
 927 GLN   ( 109-)  D      OE1
 990 ASP   ( 172-)  D      OD1

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.

1076 HOH   (   8 )  E      O  0.80 NA  5 *2 Ion-B
1084 HOH   ( 272 )  A      O  0.86  K  7
1085 HOH   ( 387 )  B      O  0.96  K  4 H2O-B

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.

 153 GLU   ( 102-)  A   H-bonding suggests Gln
 208 ASP   ( 157-)  A   H-bonding suggests Asn
 230 ASP   ( 179-)  A   H-bonding suggests Asn
 298 ASP   ( 247-)  A   H-bonding suggests Asn; but Alt-Rotamer
 343 GLU   (  35-)  B   H-bonding suggests Gln
 435 ASP   ( 127-)  B   H-bonding suggests Asn
 465 ASP   ( 157-)  B   H-bonding suggests Asn; but Alt-Rotamer
 675 ASP   ( 114-)  C   H-bonding suggests Asn
 718 ASP   ( 157-)  C   H-bonding suggests Asn
 853 GLU   (  35-)  D   H-bonding suggests Gln
 856 GLU   (  38-)  D   H-bonding suggests Gln
 869 ASP   (  51-)  D   H-bonding suggests Asn
 932 ASP   ( 114-)  D   H-bonding suggests Asn
 975 ASP   ( 157-)  D   H-bonding suggests Asn; but Alt-Rotamer
 996 GLU   ( 178-)  D   H-bonding suggests Gln
1012 GLU   ( 194-)  D   H-bonding suggests Gln; but Alt-Rotamer
1065 ASP   ( 247-)  D   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.033
  2nd generation packing quality :  -3.434 (poor)
  Ramachandran plot appearance   :  -4.970 (bad)
  chi-1/chi-2 rotamer normality  :  -4.466 (bad)
  Backbone conformation          :  -1.454

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.489 (tight)
  Bond angles                    :   0.674
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.267 (tight)
  Improper dihedral distribution :   0.651
  B-factor distribution          :   1.589 (loose)
  Inside/Outside distribution    :   0.994

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 : 2.95


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -2.1
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.489 (tight)
  Bond angles                    :   0.674
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.267 (tight)
  Improper dihedral distribution :   0.651
  B-factor distribution          :   1.589 (loose)
  Inside/Outside distribution    :   0.994
==============

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.