WHAT IF Check report

This file was created 2011-12-15 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 pdb3fz7.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.478
CA-only RMS fit for the two chains : 0.320

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.440
CA-only RMS fit for the two chains : 0.175

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.503
CA-only RMS fit for the two chains : 0.266

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.466
CA-only RMS fit for the two chains : 0.252

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.528
CA-only RMS fit for the two chains : 0.311

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2752 PO4   ( 467-)  A  -
2753 PO4   ( 467-)  F  -
2754 PO4   ( 467-)  D  -
2755 PO4   ( 467-)  B  -
2756 PO4   ( 467-)  E  -
2757 PO4   ( 467-)  C  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 6

Crystal temperature (K) :100.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 8.31

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

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.

 358 ARG   ( 370-)  A
1050 ARG   ( 144-)  C
1276 ARG   ( 370-)  C
1328 ARG   ( 422-)  C
1846 ARG   (  31-)  E
1998 ARG   ( 183-)  E
2185 ARG   ( 370-)  E

Warning: Tyrosine convention problem

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

 327 TYR   ( 339-)  A
 996 TYR   (  90-)  C
1665 TYR   ( 305-)  D
1807 TYR   ( 447-)  D
2669 TYR   ( 390-)  F

Warning: Phenylalanine convention problem

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

 421 PHE   ( 433-)  A
 475 PHE   (  32-)  B
 631 PHE   ( 188-)  B
 720 PHE   ( 277-)  B
 852 PHE   ( 409-)  B
1183 PHE   ( 277-)  C
1339 PHE   ( 433-)  C
2248 PHE   ( 433-)  E
2712 PHE   ( 433-)  F

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.

1059 ASP   ( 153-)  C
1323 ASP   ( 417-)  C
2287 ASP   (   8-)  F

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.

 344 GLU   ( 356-)  A
 423 GLU   ( 435-)  A
 471 GLU   (  28-)  B
 479 GLU   (  36-)  B
 799 GLU   ( 356-)  B
 878 GLU   ( 435-)  B
 942 GLU   (  36-)  C
 955 GLU   (  49-)  C
1262 GLU   ( 356-)  C
1341 GLU   ( 435-)  C
1388 GLU   (  28-)  D
1396 GLU   (  36-)  D
1448 GLU   (  88-)  D
1716 GLU   ( 356-)  D
1864 GLU   (  49-)  E
2015 GLU   ( 200-)  E
2171 GLU   ( 356-)  E
2315 GLU   (  36-)  F
2328 GLU   (  49-)  F
2635 GLU   ( 356-)  F
2714 GLU   ( 435-)  F

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.

2125 ILE   ( 310-)  E      CA   CB    1.61    4.2
2589 ILE   ( 310-)  F      CA   CB    1.61    4.1

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.997746  0.000142  0.000066|
 |  0.000142  0.998185  0.000213|
 |  0.000066  0.000213  0.997245|
Proposed new scale matrix

 |  0.008672  0.005004 -0.000002|
 | -0.000001  0.010010 -0.000002|
 |  0.000000 -0.000001  0.004854|
With corresponding cell

    A    = 115.306  B   = 115.327  C    = 206.000
    Alpha=  89.980  Beta=  89.997  Gamma= 119.978

The CRYST1 cell dimensions

    A    = 115.564  B   = 115.564  C    = 206.561
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 479.657
(Under-)estimated Z-score: 16.141

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.

  37 GLU   (  49-)  A      N    CA   CB  117.43    4.1
  37 GLU   (  49-)  A      CA   CB   CG  122.32    4.1
 414 ARG   ( 426-)  A      CG   CD   NE  103.02   -4.4
 512 ASP   (  69-)  B      N    CA   C    97.85   -4.8
 600 LEU   ( 157-)  B      CA   CB   CG  131.24    4.3
 684 HIS   ( 241-)  B      CG   ND1  CE1 109.71    4.1
 709 ARG   ( 266-)  B      CG   CD   NE  103.01   -4.4
 829 GLU   ( 386-)  B      N    CA   C   123.17    4.3
 894 HIS   ( 451-)  B      CG   ND1  CE1 109.73    4.1
 955 GLU   (  49-)  C      N    CA   CB  117.84    4.3
1394 LEU   (  34-)  D      CB   CG   CD1  97.66   -4.3
1395 HIS   (  35-)  D      CG   ND1  CE1 109.60    4.0
1543 ARG   ( 183-)  D      CB   CG   CD  104.64   -4.7
1635 HIS   ( 275-)  D      CG   ND1  CE1 109.70    4.1
2241 ARG   ( 426-)  E      CG   CD   NE  102.11   -4.9
2328 GLU   (  49-)  F      N    CA   CB  119.64    5.4
2328 GLU   (  49-)  F      CA   CB   CG  122.32    4.1
2536 ASP   ( 257-)  F      C    CA   CB  102.01   -4.3
2615 ARG   ( 336-)  F      CB   CG   CD  105.12   -4.5
2705 ARG   ( 426-)  F      CG   CD   NE  103.32   -4.2

Error: Nomenclature error(s)

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

 344 GLU   ( 356-)  A
 358 ARG   ( 370-)  A
 423 GLU   ( 435-)  A
 471 GLU   (  28-)  B
 479 GLU   (  36-)  B
 799 GLU   ( 356-)  B
 878 GLU   ( 435-)  B
 942 GLU   (  36-)  C
 955 GLU   (  49-)  C
1050 ARG   ( 144-)  C
1059 ASP   ( 153-)  C
1262 GLU   ( 356-)  C
1276 ARG   ( 370-)  C
1323 ASP   ( 417-)  C
1328 ARG   ( 422-)  C
1341 GLU   ( 435-)  C
1388 GLU   (  28-)  D
1396 GLU   (  36-)  D
1448 GLU   (  88-)  D
1716 GLU   ( 356-)  D
1846 ARG   (  31-)  E
1864 GLU   (  49-)  E
1998 ARG   ( 183-)  E
2015 GLU   ( 200-)  E
2171 GLU   ( 356-)  E
2185 ARG   ( 370-)  E
2287 ASP   (   8-)  F
2315 GLU   (  36-)  F
2328 GLU   (  49-)  F
2635 GLU   ( 356-)  F
2714 GLU   ( 435-)  F

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.

  37 GLU   (  49-)  A      CA    -6.4    23.45    33.96
 168 ILE   ( 180-)  A      CB     6.3    40.54    32.31
 492 GLU   (  49-)  B      CA    -7.0    22.51    33.96
The average deviation= 1.114

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.

1157 ALA   ( 251-)  C    4.59
 512 ASP   (  69-)  B    4.54
2619 THR   ( 340-)  F    4.16
 765 GLY   ( 322-)  B    4.05

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.

2641 PRO   ( 362-)  F    -2.9
1722 PRO   ( 362-)  D    -2.7
  19 ARG   (  31-)  A    -2.6
 376 PRO   ( 388-)  A    -2.6
1294 PRO   ( 388-)  C    -2.5
2364 ILE   (  85-)  F    -2.5
2667 PRO   ( 388-)  F    -2.5
1445 ILE   (  85-)  D    -2.5
 748 TYR   ( 305-)  B    -2.5
1343 LEU   ( 437-)  C    -2.5
1900 ILE   (  85-)  E    -2.4
 991 ILE   (  85-)  C    -2.4
1365 GLN   ( 459-)  C    -2.4
 528 ILE   (  85-)  B    -2.4
  73 ILE   (  85-)  A    -2.4
 631 PHE   ( 188-)  B    -2.4
 109 THR   ( 121-)  A    -2.4
 447 GLN   ( 459-)  A    -2.4
 986 ILE   (  80-)  C    -2.4
 902 GLN   ( 459-)  B    -2.4
2274 GLN   ( 459-)  E    -2.4
1569 PHE   ( 209-)  D    -2.3
2302 ILE   (  23-)  F    -2.3
1391 ARG   (  31-)  D    -2.3
2001 GLN   ( 186-)  E    -2.3
And so on for a total of 82 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.

  44 ALA   (  56-)  A  Poor phi/psi
  66 LEU   (  78-)  A  omega poor
  97 HIS   ( 109-)  A  Poor phi/psi
 109 THR   ( 121-)  A  omega poor
 149 PRO   ( 161-)  A  Poor phi/psi
 175 LEU   ( 187-)  A  omega poor
 205 TYR   ( 217-)  A  omega poor
 222 THR   ( 234-)  A  Poor phi/psi
 248 TRP   ( 260-)  A  omega poor
 249 ASP   ( 261-)  A  Poor phi/psi
 264 LYS   ( 276-)  A  Poor phi/psi
 267 LEU   ( 279-)  A  Poor phi/psi
 274 TRP   ( 286-)  A  omega poor
 292 ASP   ( 304-)  A  omega poor
 305 PHE   ( 317-)  A  Poor phi/psi
 307 ARG   ( 319-)  A  Poor phi/psi
 449 ASN   ( 461-)  A  omega poor
 460 ARG   (  17-)  B  omega poor
 469 ILE   (  26-)  B  omega poor
 470 ALA   (  27-)  B  omega poor
 471 GLU   (  28-)  B  Poor phi/psi
 472 SER   (  29-)  B  Poor phi/psi
 473 LYS   (  30-)  B  omega poor
 478 HIS   (  35-)  B  omega poor
 499 ALA   (  56-)  B  Poor phi/psi
And so on for a total of 143 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

1355 SER   ( 449-)  C    0.36
2572 GLU   ( 293-)  F    0.36
 999 SER   (  93-)  C    0.38

Warning: Unusual backbone conformations

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

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

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

   8 ALA   (  20-)  A      0
  14 ILE   (  26-)  A      0
  15 ALA   (  27-)  A      0
  16 GLU   (  28-)  A      0
  17 SER   (  29-)  A      0
  19 ARG   (  31-)  A      0
  22 LEU   (  34-)  A      0
  46 GLN   (  58-)  A      0
  48 LEU   (  60-)  A      0
  50 THR   (  62-)  A      0
  51 PHE   (  63-)  A      0
  53 GLN   (  65-)  A      0
  54 THR   (  66-)  A      0
  72 TRP   (  84-)  A      0
  73 ILE   (  85-)  A      0
  78 TYR   (  90-)  A      0
  96 TRP   ( 108-)  A      0
 107 VAL   ( 119-)  A      0
 112 ILE   ( 124-)  A      0
 114 SER   ( 126-)  A      0
 140 THR   ( 152-)  A      0
 141 ASP   ( 153-)  A      0
 142 LYS   ( 154-)  A      0
 143 PRO   ( 155-)  A      0
 149 PRO   ( 161-)  A      0
And so on for a total of 1031 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

2123 GLY   ( 308-)  E   2.30   11
 296 GLY   ( 308-)  A   2.16   14
 828 GLY   ( 385-)  B   1.88   78
2470 PRO   ( 191-)  F   1.77   12
 634 PRO   ( 191-)  B   1.66   14
 179 PRO   ( 191-)  A   1.61   15
1551 PRO   ( 191-)  D   1.51   11
1097 PRO   ( 191-)  C   1.50   11

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]

 149 PRO   ( 161-)  A    0.14 LOW
 179 PRO   ( 191-)  A    0.14 LOW
 359 PRO   ( 371-)  A    0.17 LOW
 476 PRO   (  33-)  B    0.17 LOW
 556 PRO   ( 113-)  B    0.18 LOW
 699 PRO   ( 256-)  B    0.17 LOW
 724 PRO   ( 281-)  B    0.12 LOW
 997 PRO   (  91-)  C    0.15 LOW
1019 PRO   ( 113-)  C    0.13 LOW
1113 PRO   ( 207-)  C    0.19 LOW
1162 PRO   ( 256-)  C    0.17 LOW
1171 PRO   ( 265-)  C    0.17 LOW
1277 PRO   ( 371-)  C    0.18 LOW
1521 PRO   ( 161-)  D    0.17 LOW
1731 PRO   ( 371-)  D    0.16 LOW
1976 PRO   ( 161-)  E    0.05 LOW
2071 PRO   ( 256-)  E    0.18 LOW
2440 PRO   ( 161-)  F    0.16 LOW
2544 PRO   ( 265-)  F    0.12 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  79 PRO   (  91-)  A   -65.1 envelop C-beta (-72 degrees)
 101 PRO   ( 113-)  A    46.7 half-chair C-delta/C-gamma (54 degrees)
 253 PRO   ( 265-)  A  -115.8 envelop C-gamma (-108 degrees)
 284 PRO   ( 296-)  A   111.9 envelop C-beta (108 degrees)
 350 PRO   ( 362-)  A   -58.8 half-chair C-beta/C-alpha (-54 degrees)
 376 PRO   ( 388-)  A   -54.9 half-chair C-beta/C-alpha (-54 degrees)
 708 PRO   ( 265-)  B  -158.9 half-chair N/C-delta (-162 degrees)
 814 PRO   ( 371-)  B  -120.9 half-chair C-delta/C-gamma (-126 degrees)
 831 PRO   ( 388-)  B   -62.9 half-chair C-beta/C-alpha (-54 degrees)
1017 PRO   ( 111-)  C   108.8 envelop C-beta (108 degrees)
1187 PRO   ( 281-)  C    16.7 half-chair N/C-delta (18 degrees)
1202 PRO   ( 296-)  C   100.0 envelop C-beta (108 degrees)
1471 PRO   ( 111-)  D   107.0 envelop C-beta (108 degrees)
1473 PRO   ( 113-)  D    49.3 half-chair C-delta/C-gamma (54 degrees)
1580 PRO   ( 220-)  D   101.4 envelop C-beta (108 degrees)
1641 PRO   ( 281-)  D   -50.6 half-chair C-beta/C-alpha (-54 degrees)
1722 PRO   ( 362-)  D   -53.8 half-chair C-beta/C-alpha (-54 degrees)
1812 PRO   ( 452-)  D    46.4 half-chair C-delta/C-gamma (54 degrees)
2096 PRO   ( 281-)  E   -36.5 envelop C-alpha (-36 degrees)
2186 PRO   ( 371-)  E  -112.6 envelop C-gamma (-108 degrees)
2203 PRO   ( 388-)  E   -52.2 half-chair C-beta/C-alpha (-54 degrees)
2430 PRO   ( 151-)  F    51.4 half-chair C-delta/C-gamma (54 degrees)
2470 PRO   ( 191-)  F   111.7 envelop C-beta (108 degrees)
2641 PRO   ( 362-)  F   -65.3 envelop C-beta (-72 degrees)
2650 PRO   ( 371-)  F  -113.6 envelop C-gamma (-108 degrees)
2731 PRO   ( 452-)  F    14.4 half-chair N/C-delta (18 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.

2120 TYR   ( 305-)  E      OH  <-> 2758 HOH   ( 725 )  D      O      0.89    1.51  INTRA
 471 GLU   (  28-)  B      O   <->  473 LYS   (  30-)  B      N      0.67    2.03  INTRA BF
1945 CYS   ( 130-)  E      SG  <-> 1980 CYS   ( 165-)  E      SG     0.66    2.79  INTRA
 118 CYS   ( 130-)  A      SG  <->  153 CYS   ( 165-)  A      SG     0.59    2.86  INTRA
 965 ASN   (  59-)  C      O   <-> 1332 ARG   ( 426-)  C      NH2    0.54    2.16  INTRA
2120 TYR   ( 305-)  E      CZ  <-> 2758 HOH   ( 725 )  D      O      0.52    2.28  INTRA
1795 GLU   ( 435-)  D      CG  <-> 2758 HOH   (1171 )  D      O      0.51    2.29  INTRA BF
 502 ASN   (  59-)  B      O   <->  869 ARG   ( 426-)  B      NH2    0.51    2.19  INTRA
 605 VAL   ( 162-)  B      CG2 <->  609 TRP   ( 166-)  B      CD1    0.49    2.71  INTRA
 132 ARG   ( 144-)  A      NH1 <->  225 ASP   ( 237-)  A      O      0.48    2.22  INTRA BF
1531 ARG   ( 171-)  D      NH2 <-> 2758 HOH   ( 498 )  D      O      0.46    2.24  INTRA BF
 573 CYS   ( 130-)  B      SG  <->  608 CYS   ( 165-)  B      SG     0.45    3.00  INTRA
1258 TYR   ( 352-)  C      OH  <-> 1341 GLU   ( 435-)  C      OE2    0.44    1.96  INTRA
2460 PRO   ( 181-)  F      O   <-> 2472 ARG   ( 193-)  F      NH2    0.44    2.26  INTRA BL
2744 HIS   ( 465-)  F      ND1 <-> 2758 HOH   ( 756 )  D      O      0.44    2.26  INTRA
 624 PRO   ( 181-)  B      O   <->  636 ARG   ( 193-)  B      NH2    0.40    2.30  INTRA
2706 ARG   ( 427-)  F      NH1 <-> 2758 HOH   ( 596 )  D      O      0.39    2.31  INTRA BL
1419 ASN   (  59-)  D      O   <-> 1786 ARG   ( 426-)  D      NH2    0.38    2.32  INTRA
1665 TYR   ( 305-)  D      CE1 <-> 2758 HOH   ( 731 )  D      O      0.38    2.42  INTRA BF
 171 ARG   ( 183-)  A      NH2 <->  174 GLN   ( 186-)  A      OE1    0.37    2.33  INTRA BF
1036 CYS   ( 130-)  C      SG  <-> 1071 CYS   ( 165-)  C      SG     0.35    3.10  INTRA
 841 ARG   ( 398-)  B      CD  <-> 2758 HOH   (1211 )  D      O      0.34    2.46  INTRA BL
 795 TYR   ( 352-)  B      OH  <->  878 GLU   ( 435-)  B      OE2    0.34    2.06  INTRA
 188 GLU   ( 200-)  A      CG  <-> 2758 HOH   (1221 )  D      O      0.33    2.47  INTRA
1541 PRO   ( 181-)  D      O   <-> 1553 ARG   ( 193-)  D      NH2    0.33    2.37  INTRA BL
And so on for a total of 362 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

1929 LYS   ( 114-)  E      -6.58
 557 LYS   ( 114-)  B      -6.53
2393 LYS   ( 114-)  F      -6.51
1474 LYS   ( 114-)  D      -6.43
 102 LYS   ( 114-)  A      -6.41
1020 LYS   ( 114-)  C      -6.39
 911 GLN   (   5-)  C      -6.10
1666 LEU   ( 306-)  D      -5.50
 749 LEU   ( 306-)  B      -5.50
2585 LEU   ( 306-)  F      -5.46
2028 TYR   ( 213-)  E      -5.27
2121 LEU   ( 306-)  E      -5.24
1846 ARG   (  31-)  E      -5.21
 201 TYR   ( 213-)  A      -5.20
1212 LEU   ( 306-)  C      -5.19
1119 TYR   ( 213-)  C      -5.15
 294 LEU   ( 306-)  A      -5.10
 278 ARG   ( 290-)  A      -5.06
1650 ARG   ( 290-)  D      -5.04
 656 TYR   ( 213-)  B      -5.01

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

1440 ILE   (  80-)  D   -2.81
2359 ILE   (  80-)  F   -2.75
1895 ILE   (  80-)  E   -2.73
 986 ILE   (  80-)  C   -2.71
 523 ILE   (  80-)  B   -2.65
  68 ILE   (  80-)  A   -2.62
1995 ILE   ( 180-)  E   -2.61
1540 ILE   ( 180-)  D   -2.58
 168 ILE   ( 180-)  A   -2.58
 900 ILE   ( 457-)  B   -2.55
2459 ILE   ( 180-)  F   -2.55
1086 ILE   ( 180-)  C   -2.54
 623 ILE   ( 180-)  B   -2.53
 445 ILE   ( 457-)  A   -2.51

Warning: Abnormal packing Z-score for sequential residues

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

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

 899 GLY   ( 456-)  B     -  902 GLN   ( 459-)  B        -1.76

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

2758 HOH   ( 556 )  D      O     14.35   52.35    4.42
2758 HOH   ( 649 )  D      O     62.11    9.67    1.73
2758 HOH   (1032 )  D      O     23.30  -48.85  -14.15
2758 HOH   (1116 )  D      O    -31.82   17.93  -29.92
2758 HOH   (1127 )  D      O    -42.39   48.53  -14.19

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.

2758 HOH   ( 492 )  D      O
2758 HOH   ( 506 )  D      O
2758 HOH   ( 531 )  D      O
2758 HOH   ( 538 )  D      O
2758 HOH   ( 632 )  D      O
2758 HOH   ( 653 )  D      O
2758 HOH   ( 654 )  D      O
2758 HOH   ( 655 )  D      O
2758 HOH   ( 664 )  D      O
2758 HOH   ( 699 )  D      O
2758 HOH   ( 718 )  D      O
2758 HOH   ( 725 )  D      O
2758 HOH   ( 759 )  D      O
2758 HOH   ( 795 )  D      O
2758 HOH   ( 847 )  D      O
2758 HOH   ( 961 )  D      O
2758 HOH   ( 965 )  D      O
2758 HOH   ( 980 )  D      O
2758 HOH   (1009 )  D      O
2758 HOH   (1053 )  D      O
2758 HOH   (1069 )  D      O
2758 HOH   (1083 )  D      O
2758 HOH   (1099 )  D      O
2758 HOH   (1104 )  D      O
2758 HOH   (1137 )  D      O
2758 HOH   (1144 )  D      O
2758 HOH   (1171 )  D      O
2758 HOH   (1383 )  D      O
2758 HOH   (1416 )  D      O
2758 HOH   (1434 )  D      O
2758 HOH   (1460 )  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.

 209 GLN   ( 221-)  A
 514 ASN   (  71-)  B
 535 GLN   (  92-)  B
1250 ASN   ( 344-)  C
1581 GLN   ( 221-)  D
1704 ASN   ( 344-)  D
1819 GLN   ( 459-)  D
1982 HIS   ( 167-)  E

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.

  18 LYS   (  30-)  A      N
  19 ARG   (  31-)  A      N
  71 ASN   (  83-)  A      N
  72 TRP   (  84-)  A      NE1
 110 ASN   ( 122-)  A      ND2
 114 SER   ( 126-)  A      N
 114 SER   ( 126-)  A      OG
 115 SER   ( 127-)  A      N
 152 ILE   ( 164-)  A      N
 176 PHE   ( 188-)  A      N
 192 GLY   ( 204-)  A      N
 201 TYR   ( 213-)  A      N
 211 LEU   ( 223-)  A      N
 234 SER   ( 246-)  A      OG
 245 ASP   ( 257-)  A      N
 249 ASP   ( 261-)  A      N
 263 HIS   ( 275-)  A      NE2
 266 GLY   ( 278-)  A      N
 306 SER   ( 318-)  A      N
 307 ARG   ( 319-)  A      NH2
 310 GLY   ( 322-)  A      N
 358 ARG   ( 370-)  A      N
 378 TYR   ( 390-)  A      N
 404 THR   ( 416-)  A      N
 405 ASP   ( 417-)  A      N
And so on for a total of 170 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.

  85 ASP   (  97-)  A      OD1
 540 ASP   (  97-)  B      OD1
1003 ASP   (  97-)  C      OD1
1122 ASN   ( 216-)  C      OD1
1341 GLU   ( 435-)  C      OE2
1457 ASP   (  97-)  D      OD1
1513 ASP   ( 153-)  D      OD2
1912 ASP   (  97-)  E      OD1
2284 GLN   (   5-)  F      OE1
2376 ASP   (  97-)  F      OD1
2577 GLU   ( 298-)  F      OE1

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.

2758 HOH   ( 496 )  D      O  1.06  K  4
2758 HOH   ( 635 )  D      O  0.94  K  4
2758 HOH   ( 752 )  D      O  0.94  K  4
2758 HOH   ( 872 )  D      O  0.98  K  4
2758 HOH   (1179 )  D      O  1.04  K  4
2758 HOH   (1232 )  D      O  1.09  K  4
2758 HOH   (1298 )  D      O  0.89  K  4
2758 HOH   (1340 )  D      O  0.90  K  5
2758 HOH   (1465 )  D      O  1.05  K  4

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.

1210 ASP   ( 304-)  C   H-bonding suggests Asn
1261 ASP   ( 355-)  C   H-bonding suggests Asn
1593 ASP   ( 233-)  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 :  -0.239
  2nd generation packing quality :  -1.128
  Ramachandran plot appearance   :  -1.474
  chi-1/chi-2 rotamer normality  :  -2.044
  Backbone conformation          :  -0.033

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.741
  Bond angles                    :   0.834
  Omega angle restraints         :   1.195
  Side chain planarity           :   0.710
  Improper dihedral distribution :   0.922
  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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.741
  Bond angles                    :   0.834
  Omega angle restraints         :   1.195
  Side chain planarity           :   0.710
  Improper dihedral distribution :   0.922
  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.