WHAT IF Check report

This file was created 2014-11-14 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 pdb2onn.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 : 0.224
CA-only RMS fit for the two chains : 0.081

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 : 0.217
CA-only RMS fit for the two chains : 0.092

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 : 0.218
CA-only RMS fit for the two chains : 0.083

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 : 0.206
CA-only RMS fit for the two chains : 0.096

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 : 0.226
CA-only RMS fit for the two chains : 0.100

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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

Warning: Artificial side chains detected

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

 352 ASN   ( 358-)  A
1791 TYR   ( 315-)  D
2496 VAL   (  32-)  F

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

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  80 ARG   (  86-)  A
  91 ARG   (  97-)  A
  93 ARG   (  99-)  A
 124 ARG   ( 130-)  A
 413 ARG   ( 419-)  A
 574 ARG   (  86-)  B
 578 ARG   (  90-)  B
 585 ARG   (  97-)  B
 587 ARG   (  99-)  B
 618 ARG   ( 130-)  B
 907 ARG   ( 419-)  B
1016 ARG   (  34-)  C
1068 ARG   (  86-)  C
1072 ARG   (  90-)  C
1079 ARG   (  97-)  C
1081 ARG   (  99-)  C
1112 ARG   ( 130-)  C
1233 ARG   ( 251-)  C
1359 ARG   ( 377-)  C
1401 ARG   ( 419-)  C
1510 ARG   (  34-)  D
1562 ARG   (  86-)  D
1566 ARG   (  90-)  D
1573 ARG   (  97-)  D
1575 ARG   (  99-)  D
And so on for a total of 53 lines.

Warning: Tyrosine convention problem

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

 112 TYR   ( 118-)  A
 126 TYR   ( 132-)  A
 350 TYR   ( 356-)  A
 373 TYR   ( 379-)  A
 419 TYR   ( 425-)  A
 450 TYR   ( 456-)  A
 479 TYR   ( 485-)  A
 606 TYR   ( 118-)  B
 620 TYR   ( 132-)  B
 641 TYR   ( 153-)  B
 844 TYR   ( 356-)  B
 867 TYR   ( 379-)  B
 913 TYR   ( 425-)  B
 944 TYR   ( 456-)  B
 973 TYR   ( 485-)  B
1100 TYR   ( 118-)  C
1114 TYR   ( 132-)  C
1135 TYR   ( 153-)  C
1297 TYR   ( 315-)  C
1338 TYR   ( 356-)  C
1361 TYR   ( 379-)  C
1407 TYR   ( 425-)  C
1438 TYR   ( 456-)  C
1462 TYR   ( 480-)  C
1467 TYR   ( 485-)  C
And so on for a total of 68 lines.

Warning: Phenylalanine convention problem

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

  31 PHE   (  37-)  A
 144 PHE   ( 150-)  A
 164 PHE   ( 170-)  A
 218 PHE   ( 224-)  A
 286 PHE   ( 292-)  A
 289 PHE   ( 295-)  A
 290 PHE   ( 296-)  A
 329 PHE   ( 335-)  A
 380 PHE   ( 386-)  A
 404 PHE   ( 410-)  A
 453 PHE   ( 459-)  A
 506 PHE   (  18-)  B
 525 PHE   (  37-)  B
 638 PHE   ( 150-)  B
 658 PHE   ( 170-)  B
 712 PHE   ( 224-)  B
 780 PHE   ( 292-)  B
 783 PHE   ( 295-)  B
 784 PHE   ( 296-)  B
 823 PHE   ( 335-)  B
 874 PHE   ( 386-)  B
 898 PHE   ( 410-)  B
 947 PHE   ( 459-)  B
1000 PHE   (  18-)  C
1019 PHE   (  37-)  C
And so on for a total of 99 lines.

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  24 ASP   (  30-)  A
 115 ASP   ( 121-)  A
 131 ASP   ( 137-)  A
 370 ASP   ( 376-)  A
 429 ASP   ( 435-)  A
 431 ASP   ( 437-)  A
 518 ASP   (  30-)  B
 609 ASP   ( 121-)  B
 625 ASP   ( 137-)  B
 923 ASP   ( 435-)  B
 925 ASP   ( 437-)  B
1012 ASP   (  30-)  C
1103 ASP   ( 121-)  C
1119 ASP   ( 137-)  C
1417 ASP   ( 435-)  C
1419 ASP   ( 437-)  C
1506 ASP   (  30-)  D
1597 ASP   ( 121-)  D
1613 ASP   ( 137-)  D
1852 ASP   ( 376-)  D
1911 ASP   ( 435-)  D
1913 ASP   ( 437-)  D
2000 ASP   (  30-)  E
2091 ASP   ( 121-)  E
2107 ASP   ( 137-)  E
2346 ASP   ( 376-)  E
2405 ASP   ( 435-)  E
2407 ASP   ( 437-)  E
2494 ASP   (  30-)  F
2585 ASP   ( 121-)  F
2601 ASP   ( 137-)  F
2899 ASP   ( 435-)  F
2901 ASP   ( 437-)  F
2988 ASP   (  30-)  G
3079 ASP   ( 121-)  G
3095 ASP   ( 137-)  G
3393 ASP   ( 435-)  G
3395 ASP   ( 437-)  G
3482 ASP   (  30-)  H
3573 ASP   ( 121-)  H
3589 ASP   ( 137-)  H
3828 ASP   ( 376-)  H
3887 ASP   ( 435-)  H
3889 ASP   ( 437-)  H

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.

  10 GLU   (  16-)  A
  90 GLU   (  96-)  A
 100 GLU   ( 106-)  A
 189 GLU   ( 195-)  A
 204 GLU   ( 210-)  A
 282 GLU   ( 288-)  A
 306 GLU   ( 312-)  A
 311 GLU   ( 317-)  A
 341 GLU   ( 347-)  A
 357 GLU   ( 363-)  A
 392 GLU   ( 398-)  A
 393 GLU   ( 399-)  A
 470 GLU   ( 476-)  A
 473 GLU   ( 479-)  A
 481 GLU   ( 487-)  A
 504 GLU   (  16-)  B
 545 GLU   (  57-)  B
 584 GLU   (  96-)  B
 594 GLU   ( 106-)  B
 683 GLU   ( 195-)  B
 698 GLU   ( 210-)  B
 776 GLU   ( 288-)  B
 800 GLU   ( 312-)  B
 805 GLU   ( 317-)  B
 808 GLU   ( 320-)  B
And so on for a total of 123 lines.

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

1458 GLU   ( 476-)  C      CD   OE2   1.06   -9.8
1817 GLN   ( 341-)  D      CD   OE1   1.34    5.2

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

 |  0.998821  0.000082 -0.000016|
 |  0.000082  0.999254  0.000020|
 | -0.000016  0.000020  0.999447|
Proposed new scale matrix

 |  0.007111  0.000000  0.000000|
 |  0.000000  0.006634  0.000000|
 |  0.000000  0.000000  0.005645|
With corresponding cell

    A    = 140.620  B   = 150.740  C    = 177.144
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 140.780  B   = 150.860  C    = 177.230
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 89.779
(Under-)estimated Z-score: 6.983

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.

   6 ASN   (  12-)  A      N    CA   C    99.54   -4.2
  77 HIS   (  83-)  A      CG   ND1  CE1 109.62    4.0
 134 HIS   ( 140-)  A      CG   ND1  CE1 109.61    4.0
 150 HIS   ( 156-)  A      CG   ND1  CE1 109.74    4.1
 184 VAL   ( 190-)  A      N    CA   C    99.34   -4.2
 524 THR   (  36-)  B      CA   CB   OG1 116.00    4.3
 779 HIS   ( 291-)  B      CG   ND1  CE1 109.94    4.3
1065 HIS   (  83-)  C      CG   ND1  CE1 109.71    4.1
1172 VAL   ( 190-)  C      N    CA   C    98.43   -4.6
1217 HIS   ( 235-)  C      CG   ND1  CE1 109.69    4.1
1458 GLU   ( 476-)  C      CG   CD   OE2 137.20    8.2
1458 GLU   ( 476-)  C      OE2  CD   OE1 104.54   -7.6
1767 HIS   ( 291-)  D      CG   ND1  CE1 109.68    4.1
2160 VAL   ( 190-)  E      N    CA   C    99.33   -4.2
2654 VAL   ( 190-)  F      N    CA   C    99.70   -4.1
3148 VAL   ( 190-)  G      N    CA   C    99.14   -4.3
3464 ASN   (  12-)  H      N    CA   C    99.61   -4.1
3535 HIS   (  83-)  H      CG   ND1  CE1 109.66    4.1
3743 HIS   ( 291-)  H      CG   ND1  CE1 109.61    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.

  10 GLU   (  16-)  A
  24 ASP   (  30-)  A
  80 ARG   (  86-)  A
  90 GLU   (  96-)  A
  91 ARG   (  97-)  A
  93 ARG   (  99-)  A
 100 GLU   ( 106-)  A
 115 ASP   ( 121-)  A
 124 ARG   ( 130-)  A
 131 ASP   ( 137-)  A
 189 GLU   ( 195-)  A
 204 GLU   ( 210-)  A
 282 GLU   ( 288-)  A
 306 GLU   ( 312-)  A
 311 GLU   ( 317-)  A
 341 GLU   ( 347-)  A
 357 GLU   ( 363-)  A
 370 ASP   ( 376-)  A
 392 GLU   ( 398-)  A
 393 GLU   ( 399-)  A
 413 ARG   ( 419-)  A
 429 ASP   ( 435-)  A
 431 ASP   ( 437-)  A
 470 GLU   ( 476-)  A
 473 GLU   ( 479-)  A
And so on for a total of 220 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 524 THR   (  36-)  B      C      6.2     9.56     0.30
The average deviation= 0.838

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.

 193 LEU   ( 199-)  A    5.93
3157 LEU   ( 199-)  G    5.71
 677 VAL   ( 189-)  B    5.05
2663 LEU   ( 199-)  F    4.84
2169 LEU   ( 199-)  E    4.77
 800 GLU   ( 312-)  B    4.77
1181 LEU   ( 199-)  C    4.76
2159 VAL   ( 189-)  E    4.75
1172 VAL   ( 190-)  C    4.69
2608 ILE   ( 144-)  F    4.67
1665 VAL   ( 189-)  D    4.60
3651 LEU   ( 199-)  H    4.57
 138 ILE   ( 144-)  A    4.56
3641 VAL   ( 189-)  H    4.53
3593 GLY   ( 141-)  H    4.42
3147 VAL   ( 189-)  G    4.42
1675 LEU   ( 199-)  D    4.42
3148 VAL   ( 190-)  G    4.37
3764 GLU   ( 312-)  H    4.36
3270 GLU   ( 312-)  G    4.33
1294 GLU   ( 312-)  C    4.32
 687 LEU   ( 199-)  B    4.31
2160 VAL   ( 190-)  E    4.28
 184 VAL   ( 190-)  A    4.28
 183 VAL   ( 189-)  A    4.27
3596 ILE   ( 144-)  H    4.26
 963 GLN   ( 475-)  B    4.18
2282 GLU   ( 312-)  E    4.15
1951 GLN   ( 475-)  D    4.12
2654 VAL   ( 190-)  F    4.12
1133 PHE   ( 151-)  C    4.10
1617 GLY   ( 141-)  D    4.07
2615 PHE   ( 151-)  F    4.05
2265 PHE   ( 295-)  E    4.01

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

1250 GLU   ( 268-)  C    7.93

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.

2371 PHE   ( 401-)  E    -3.5
1877 PHE   ( 401-)  D    -3.5
3853 PHE   ( 401-)  H    -3.5
2865 PHE   ( 401-)  F    -3.4
 395 PHE   ( 401-)  A    -3.3
3359 PHE   ( 401-)  G    -3.3
 889 PHE   ( 401-)  B    -3.2
1383 PHE   ( 401-)  C    -3.2
2603 TYR   ( 139-)  F    -2.5
3885 THR   ( 433-)  H    -2.5
2109 TYR   ( 139-)  E    -2.5
1674 PRO   ( 198-)  D    -2.4
1909 THR   ( 433-)  D    -2.4
1121 TYR   ( 139-)  C    -2.4
3650 PRO   ( 198-)  H    -2.4
3391 THR   ( 433-)  G    -2.4
 192 PRO   ( 198-)  A    -2.4
 686 PRO   ( 198-)  B    -2.4
3156 PRO   ( 198-)  G    -2.4
3760 THR   ( 308-)  H    -2.4
3097 TYR   ( 139-)  G    -2.4
3591 TYR   ( 139-)  H    -2.3
1180 PRO   ( 198-)  C    -2.3
 427 THR   ( 433-)  A    -2.3
2313 PRO   ( 343-)  E    -2.3
And so on for a total of 80 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.

  20 ASN   (  26-)  A  Poor phi/psi
  28 ARG   (  34-)  A  Poor phi/psi
 139 PRO   ( 145-)  A  Poor phi/psi
 174 GLY   ( 180-)  A  Poor phi/psi
 221 THR   ( 227-)  A  Poor phi/psi
 256 LEU   ( 262-)  A  Poor phi/psi
 292 GLN   ( 298-)  A  Poor phi/psi
 391 LYS   ( 397-)  A  Poor phi/psi
 395 PHE   ( 401-)  A  Poor phi/psi
 397 PRO   ( 403-)  A  Poor phi/psi
 448 ASN   ( 454-)  A  Poor phi/psi
 463 LYS   ( 469-)  A  Poor phi/psi
 471 LEU   ( 477-)  A  Poor phi/psi
 514 ASN   (  26-)  B  Poor phi/psi
 522 ARG   (  34-)  B  Poor phi/psi
 537 CYS   (  49-)  B  Poor phi/psi
 608 VAL   ( 120-)  B  Poor phi/psi
 633 PRO   ( 145-)  B  Poor phi/psi
 668 GLY   ( 180-)  B  Poor phi/psi
 715 THR   ( 227-)  B  Poor phi/psi
 750 LEU   ( 262-)  B  Poor phi/psi
 786 GLN   ( 298-)  B  Poor phi/psi
 889 PHE   ( 401-)  B  Poor phi/psi
 891 PRO   ( 403-)  B  Poor phi/psi
 942 ASN   ( 454-)  B  Poor phi/psi
And so on for a total of 110 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.

2087 SER   ( 117-)  E    0.35
 605 SER   ( 117-)  B    0.35
2581 SER   ( 117-)  F    0.35
2053 HIS   (  83-)  E    0.38
3075 SER   ( 117-)  G    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!

   7 GLN   (  13-)  A      0
   8 GLN   (  14-)  A      0
  12 PHE   (  18-)  A      0
  13 CYS   (  19-)  A      0
  14 ASN   (  20-)  A      0
  18 ILE   (  24-)  A      0
  20 ASN   (  26-)  A      0
  27 SER   (  33-)  A      0
  29 LYS   (  35-)  A      0
  31 PHE   (  37-)  A      0
  37 SER   (  43-)  A      0
  42 ILE   (  48-)  A      0
  43 CYS   (  49-)  A      0
  66 LEU   (  72-)  A      0
  73 MET   (  79-)  A      0
  92 ASP   (  98-)  A      0
 103 ASP   ( 109-)  A      0
 104 ASN   ( 110-)  A      0
 129 TRP   ( 135-)  A      0
 131 ASP   ( 137-)  A      0
 132 LYS   ( 138-)  A      0
 133 TYR   ( 139-)  A      0
 141 ASP   ( 147-)  A      0
 143 ASP   ( 149-)  A      0
 144 PHE   ( 150-)  A      0
And so on for a total of 1315 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 : 1.225

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]

1365 PRO   ( 383-)  C    0.45 HIGH
1810 PRO   ( 334-)  D    0.46 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.

2394 THR   ( 424-)  E      CG2 <-> 2440 MET   ( 470-)  E      CE     0.62    2.58  INTRA BF
2888 THR   ( 424-)  F      CG2 <-> 2934 MET   ( 470-)  F      CE     0.54    2.66  INTRA BF
1900 THR   ( 424-)  D      CG2 <-> 1946 MET   ( 470-)  D      CE     0.47    2.73  INTRA BF
 912 THR   ( 424-)  B      CG2 <->  958 MET   ( 470-)  B      CE     0.44    2.76  INTRA BF
1406 THR   ( 424-)  C      CG2 <-> 1452 MET   ( 470-)  C      CE     0.43    2.77  INTRA BF
3876 THR   ( 424-)  H      CG2 <-> 3922 MET   ( 470-)  H      CE     0.38    2.82  INTRA BF
 418 THR   ( 424-)  A      CG2 <->  464 MET   ( 470-)  A      CE     0.36    2.84  INTRA BF
1635 VAL   ( 159-)  D      CG1 <-> 1638 CYS   ( 162-)  D      SG     0.33    3.07  INTRA BL
3382 THR   ( 424-)  G      CG2 <-> 3428 MET   ( 470-)  G      CE     0.32    2.88  INTRA BF
2623 VAL   ( 159-)  F      CG1 <-> 2626 CYS   ( 162-)  F      SG     0.29    3.11  INTRA BL
1465 GLN   ( 483-)  C      NE2 <-> 1959 GLN   ( 483-)  D      NE2    0.28    2.57  INTRA BF
3763 GLN   ( 311-)  H      NE2 <-> 3863 LYS   ( 411-)  H      O      0.28    2.42  INTRA BF
2129 VAL   ( 159-)  E      CG1 <-> 2132 CYS   ( 162-)  E      SG     0.27    3.13  INTRA BL
2755 HIS   ( 291-)  F      NE2 <-> 2793 ARG   ( 329-)  F      NH1    0.23    2.77  INTRA BL
2563 ARG   (  99-)  F      NH2 <-> 2582 TYR   ( 118-)  F      O      0.23    2.47  INTRA BL
 371 ARG   ( 377-)  A      NH2 <-> 3961 HOH   ( 551 )  A      O      0.22    2.48  INTRA BF
2888 THR   ( 424-)  F      CG2 <-> 2934 MET   ( 470-)  F      SD     0.21    3.19  INTRA BF
 647 VAL   ( 159-)  B      CG1 <->  650 CYS   ( 162-)  B      SG     0.21    3.19  INTRA BL
 153 VAL   ( 159-)  A      CG1 <->  156 CYS   ( 162-)  A      SG     0.19    3.21  INTRA BL
2311 GLN   ( 341-)  E      NE2 <-> 3965 HOH   ( 572 )  E      O      0.19    2.51  INTRA
2544 ASP   (  80-)  F      OD1 <-> 3456 LYS   ( 498-)  G      NZ     0.18    2.52  INTRA BL
1141 VAL   ( 159-)  C      CG1 <-> 1144 CYS   ( 162-)  C      SG     0.18    3.22  INTRA BL
3551 ARG   (  99-)  H      NH2 <-> 3570 TYR   ( 118-)  H      O      0.17    2.53  INTRA BL
 791 CYS   ( 303-)  B      SG  <->  947 PHE   ( 459-)  B      CZ     0.17    3.23  INTRA
2534 PHE   (  70-)  F      O   <-> 2541 ARG   (  77-)  F      NH1    0.16    2.54  INTRA BL
And so on for a total of 239 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Warning: Abnormal packing environment for some residues

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

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

 865 ARG   ( 377-)  B      -6.05
 371 ARG   ( 377-)  A      -6.03
3335 ARG   ( 377-)  G      -6.00
1429 GLN   ( 447-)  C      -5.96
1923 GLN   ( 447-)  D      -5.95
3829 ARG   ( 377-)  H      -5.87
2347 ARG   ( 377-)  E      -5.86
2911 GLN   ( 447-)  F      -5.82
1853 ARG   ( 377-)  D      -5.81
 935 GLN   ( 447-)  B      -5.78
2417 GLN   ( 447-)  E      -5.76
2841 ARG   ( 377-)  F      -5.74
3405 GLN   ( 447-)  G      -5.74
2477 GLN   (  13-)  F      -5.70
1838 GLN   ( 362-)  D      -5.65
2332 GLN   ( 362-)  E      -5.65
2826 GLN   ( 362-)  F      -5.65
3320 GLN   ( 362-)  G      -5.64
 356 GLN   ( 362-)  A      -5.64
1344 GLN   ( 362-)  C      -5.64
3814 GLN   ( 362-)  H      -5.64
 850 GLN   ( 362-)  B      -5.62
 995 GLN   (  13-)  C      -5.62
 441 GLN   ( 447-)  A      -5.52
  28 ARG   (  34-)  A      -5.50
And so on for a total of 73 lines.

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Warning: Low packing Z-score for some residues

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

3909 ASP   ( 457-)  H   -2.57
 945 ASP   ( 457-)  B   -2.54
3415 ASP   ( 457-)  G   -2.52
 451 ASP   ( 457-)  A   -2.52
2427 ASP   ( 457-)  E   -2.51
1276 LEU   ( 294-)  C   -2.51
1439 ASP   ( 457-)  C   -2.51
1612 ALA   ( 136-)  D   -2.50

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Water, ion, and hydrogenbond related checks

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.

3963 HOH   ( 541 )  C      O
3963 HOH   ( 542 )  C      O
3964 HOH   ( 556 )  D      O
3964 HOH   ( 569 )  D      O
3966 HOH   ( 591 )  F      O
3967 HOH   ( 541 )  G      O
3968 HOH   ( 564 )  H      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.

   7 GLN   (  13-)  A
  20 ASN   (  26-)  A
 169 GLN   ( 175-)  A
 190 GLN   ( 196-)  A
 294 GLN   ( 300-)  A
 352 ASN   ( 358-)  A
 456 GLN   ( 462-)  A
 501 GLN   (  13-)  B
 514 ASN   (  26-)  B
 529 ASN   (  41-)  B
 663 GLN   ( 175-)  B
 684 GLN   ( 196-)  B
 788 GLN   ( 300-)  B
 950 GLN   ( 462-)  B
 995 GLN   (  13-)  C
1008 ASN   (  26-)  C
1023 ASN   (  41-)  C
1157 GLN   ( 175-)  C
1178 GLN   ( 196-)  C
1257 ASN   ( 275-)  C
1271 GLN   ( 289-)  C
1282 GLN   ( 300-)  C
1444 GLN   ( 462-)  C
1502 ASN   (  26-)  D
1517 ASN   (  41-)  D
And so on for a total of 58 lines.

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  15 GLN   (  21-)  A      N
  20 ASN   (  26-)  A      N
  37 SER   (  43-)  A      N
  70 TRP   (  76-)  A      N
 104 ASN   ( 110-)  A      ND2
 146 SER   ( 152-)  A      N
 146 SER   ( 152-)  A      OG
 162 TRP   ( 168-)  A      N
 167 LEU   ( 173-)  A      N
 169 GLN   ( 175-)  A      NE2
 172 LYS   ( 178-)  A      NZ
 187 VAL   ( 193-)  A      N
 210 GLY   ( 216-)  A      N
 238 THR   ( 244-)  A      OG1
 245 ARG   ( 251-)  A      N
 266 LYS   ( 272-)  A      NZ
 267 SER   ( 273-)  A      OG
 269 ASN   ( 275-)  A      ND2
 292 GLN   ( 298-)  A      NE2
 294 GLN   ( 300-)  A      NE2
 310 ASP   ( 316-)  A      N
 338 GLN   ( 344-)  A      NE2
 374 PHE   ( 380-)  A      N
 384 GLN   ( 390-)  A      N
 396 GLY   ( 402-)  A      N
And so on for a total of 298 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.

 150 HIS   ( 156-)  A      ND1
 158 GLN   ( 164-)  A      OE1
 400 GLN   ( 406-)  A      OE1
 451 ASP   ( 457-)  A      OD1
 451 ASP   ( 457-)  A      OD2
 470 GLU   ( 476-)  A      OE1
 597 ASP   ( 109-)  B      OD1
 644 HIS   ( 156-)  B      ND1
 652 GLN   ( 164-)  B      OE1
 832 GLN   ( 344-)  B      OE1
 894 GLN   ( 406-)  B      OE1
 945 ASP   ( 457-)  B      OD1
 964 GLU   ( 476-)  B      OE1
1091 ASP   ( 109-)  C      OD1
1138 HIS   ( 156-)  C      ND1
1146 GLN   ( 164-)  C      OE1
1257 ASN   ( 275-)  C      OD1
1326 GLN   ( 344-)  C      OE1
1388 GLN   ( 406-)  C      OE1
1439 ASP   ( 457-)  C      OD1
1439 ASP   ( 457-)  C      OD2
1632 HIS   ( 156-)  D      ND1
1640 GLN   ( 164-)  D      OE1
1751 ASN   ( 275-)  D      OD1
1820 GLN   ( 344-)  D      OE1
And so on for a total of 61 lines.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  54 ASP   (  60-)  A   H-bonding suggests Asn
 103 ASP   ( 109-)  A   H-bonding suggests Asn; but Alt-Rotamer
 230 GLU   ( 236-)  A   H-bonding suggests Gln; but Alt-Rotamer
 548 ASP   (  60-)  B   H-bonding suggests Asn
 597 ASP   ( 109-)  B   H-bonding suggests Asn; but Alt-Rotamer
 724 GLU   ( 236-)  B   H-bonding suggests Gln; but Alt-Rotamer
1042 ASP   (  60-)  C   H-bonding suggests Asn
1091 ASP   ( 109-)  C   H-bonding suggests Asn; but Alt-Rotamer
1218 GLU   ( 236-)  C   H-bonding suggests Gln; but Alt-Rotamer
1536 ASP   (  60-)  D   H-bonding suggests Asn; but Alt-Rotamer
1585 ASP   ( 109-)  D   H-bonding suggests Asn; but Alt-Rotamer
1712 GLU   ( 236-)  D   H-bonding suggests Gln; but Alt-Rotamer
2023 GLU   (  53-)  E   H-bonding suggests Gln
2030 ASP   (  60-)  E   H-bonding suggests Asn
2079 ASP   ( 109-)  E   H-bonding suggests Asn; but Alt-Rotamer
2206 GLU   ( 236-)  E   H-bonding suggests Gln; but Alt-Rotamer
2524 ASP   (  60-)  F   H-bonding suggests Asn
2573 ASP   ( 109-)  F   H-bonding suggests Asn; but Alt-Rotamer
2700 GLU   ( 236-)  F   H-bonding suggests Gln; but Alt-Rotamer
3018 ASP   (  60-)  G   H-bonding suggests Asn
3067 ASP   ( 109-)  G   H-bonding suggests Asn; but Alt-Rotamer
3194 GLU   ( 236-)  G   H-bonding suggests Gln; but Alt-Rotamer
3505 GLU   (  53-)  H   H-bonding suggests Gln
3512 ASP   (  60-)  H   H-bonding suggests Asn
3561 ASP   ( 109-)  H   H-bonding suggests Asn; but Alt-Rotamer
3688 GLU   ( 236-)  H   H-bonding suggests Gln; 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 :  -0.073
  2nd generation packing quality :  -1.109
  Ramachandran plot appearance   :  -1.301
  chi-1/chi-2 rotamer normality  :  -1.200
  Backbone conformation          :   0.274

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.358 (tight)
  Bond angles                    :   0.586 (tight)
  Omega angle restraints         :   0.223 (tight)
  Side chain planarity           :   0.438 (tight)
  Improper dihedral distribution :   0.704
  B-factor distribution          :   0.540
  Inside/Outside distribution    :   1.052

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 : 2.75


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.8
  2nd generation packing quality :   0.9
  Ramachandran plot appearance   :   1.1
  chi-1/chi-2 rotamer normality  :   1.1
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.358 (tight)
  Bond angles                    :   0.586 (tight)
  Omega angle restraints         :   0.223 (tight)
  Side chain planarity           :   0.438 (tight)
  Improper dihedral distribution :   0.704
  B-factor distribution          :   0.540
  Inside/Outside distribution    :   1.052
==============

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.