WHAT IF Check report

This file was created 2012-01-31 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 pdb5rub.ent

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   1 ASP   (   2-)  A  -   CB
  53 ARG   (  65-)  A  -   CG
  53 ARG   (  65-)  A  -   CD
  53 ARG   (  65-)  A  -   NE
  53 ARG   (  65-)  A  -   CZ
  53 ARG   (  65-)  A  -   NH1
  53 ARG   (  65-)  A  -   NH2
 313 SER   ( 334-)  A  -   CB
 313 SER   ( 334-)  A  -   OG
 314 SER   ( 335-)  A  -   CB
 314 SER   ( 335-)  A  -   OG
 722 GLN   ( 298-)  B  -   CD
 722 GLN   ( 298-)  B  -   OE1
 722 GLN   ( 298-)  B  -   NE2

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

   1 ASP   (   2-)  A  -   N
  50 THR   (  51-)  A  -   CA
  52 THR   (  53-)  A  -   CA
 435 GLY   ( 456-)  A  -   C
 435 GLY   ( 456-)  A  -   O
 436 VAL   ( 457-)  A  -   C
 436 VAL   ( 457-)  A  -   O
 437 ASP   (   2-)  B  -   N
 437 ASP   (   2-)  B  -   CA
 437 ASP   (   2-)  B  -   C
 437 ASP   (   2-)  B  -   O
 487 GLY   (  52-)  B  -   O
 488 THR   (  64-)  B  -   N

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

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. 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:

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

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

  27 TYR   (  28-)  A
  35 TYR   (  36-)  A
  37 TYR   (  38-)  A
 115 TYR   ( 127-)  A
 120 TYR   ( 132-)  A
 320 TYR   ( 341-)  A
 332 TYR   ( 353-)  A
 405 TYR   ( 426-)  A
 427 TYR   ( 448-)  A
 556 TYR   ( 132-)  B
 670 TYR   ( 246-)  B
 753 TYR   ( 341-)  B
 838 TYR   ( 426-)  B
 860 TYR   ( 448-)  B

Warning: Phenylalanine convention problem

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

  44 PHE   (  45-)  A
 124 PHE   ( 136-)  A
 171 PHE   ( 183-)  A
 189 PHE   ( 201-)  A
 267 PHE   ( 279-)  A
 271 PHE   ( 283-)  A
 376 PHE   ( 397-)  A
 416 PHE   ( 437-)  A
 419 PHE   ( 440-)  A
 514 PHE   (  90-)  B
 600 PHE   ( 176-)  B
 625 PHE   ( 201-)  B
 662 PHE   ( 238-)  B
 707 PHE   ( 283-)  B
 730 PHE   ( 306-)  B
 852 PHE   ( 440-)  B

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.

  15 ASP   (  16-)  A
  56 ASP   (  68-)  A
  63 ASP   (  75-)  A
  79 ASP   (  91-)  A
 113 ASP   ( 125-)  A
 144 ASP   ( 156-)  A
 176 ASP   ( 188-)  A
 181 ASP   ( 193-)  A
 201 ASP   ( 213-)  A
 208 ASP   ( 220-)  A
 223 ASP   ( 235-)  A
 224 ASP   ( 236-)  A
 251 ASP   ( 263-)  A
 269 ASP   ( 281-)  A
 315 ASP   ( 336-)  A
 404 ASP   ( 425-)  A
 424 ASP   ( 445-)  A
 437 ASP   (   2-)  B
 451 ASP   (  16-)  B
 499 ASP   (  75-)  B
 515 ASP   (  91-)  B
 541 ASP   ( 117-)  B
 561 ASP   ( 137-)  B
 612 ASP   ( 188-)  B
 637 ASP   ( 213-)  B
 644 ASP   ( 220-)  B
 660 ASP   ( 236-)  B
 758 ASP   ( 346-)  B
 813 ASP   ( 401-)  B
 831 ASP   ( 419-)  B
 855 ASP   ( 443-)  B
 857 ASP   ( 445-)  B

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.

  21 GLU   (  22-)  A
  61 GLU   (  73-)  A
  67 GLU   (  79-)  A
 212 GLU   ( 224-)  A
 233 GLU   ( 245-)  A
 241 GLU   ( 253-)  A
 326 GLU   ( 347-)  A
 360 GLU   ( 381-)  A
 449 GLU   (  14-)  B
 483 GLU   (  48-)  B
 497 GLU   (  73-)  B
 500 GLU   (  76-)  B
 503 GLU   (  79-)  B
 554 GLU   ( 130-)  B
 578 GLU   ( 154-)  B
 602 GLU   ( 178-)  B
 645 GLU   ( 221-)  B
 663 GLU   ( 239-)  B
 669 GLU   ( 245-)  B
 673 GLU   ( 249-)  B
 793 GLU   ( 381-)  B
 844 GLU   ( 432-)  B

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.

 210 THR   ( 222-)  A      CA   CB    1.61    4.1
 261 THR   ( 273-)  A      CA   CB    1.62    4.3
 267 PHE   ( 279-)  A      N    CA    1.54    4.1
 305 ALA   ( 317-)  A      CA   C     1.61    4.0
 490 GLY   (  66-)  B      N    CA    1.52    4.2
 526 ALA   ( 102-)  B      N    CA    1.54    4.1
 587 THR   ( 163-)  B      CA   CB    1.61    4.1
 646 THR   ( 222-)  B      CA   CB    1.62    4.7

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

 |  0.996657  0.000279  0.009088|
 |  0.000279  0.996376 -0.000431|
 |  0.009088 -0.000431  0.992190|
Proposed new scale matrix

 |  0.015314 -0.000004  0.000424|
 | -0.000004  0.014216  0.000006|
 | -0.000088  0.000004  0.009689|
With corresponding cell

    A    =  65.285  B   =  70.346  C    = 103.218
    Alpha=  90.051  Beta=  91.064  Gamma=  89.968

The CRYST1 cell dimensions

    A    =  65.500  B   =  70.600  C    = 104.100
    Alpha=  90.000  Beta=  92.100  Gamma=  90.000

Variance: 1202.697
(Under-)estimated Z-score: 25.559

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   1 ASP   (   2-)  A      CA   C    O   110.43   -6.1
   1 ASP   (   2-)  A      CA   CB   CG  126.90   14.3
   1 ASP   (   2-)  A      CB   CG   OD1 127.76    4.1
   2 GLN   (   3-)  A      CA   C    O   131.79    6.5
   2 GLN   (   3-)  A      CB   CG   CD  120.21    4.5
   3 SER   (   4-)  A     -C    N    CA  131.64    5.5
   6 TYR   (   7-)  A      CA   C    O   112.63   -4.8
   7 VAL   (   8-)  A      CA   CB   CG2 120.01    5.6
   8 ASN   (   9-)  A      CB   CG   ND2 122.80    4.3
  13 GLU   (  14-)  A      CG   CD   OE2 105.37   -5.7
  13 GLU   (  14-)  A      CG   CD   OE1 134.04    6.8
  15 ASP   (  16-)  A      CB   CG   OD1 107.30   -4.8
  18 ALA   (  19-)  A      N    CA   CB  103.59   -4.5
  21 GLU   (  22-)  A      CB   CG   CD  123.30    6.3
  24 LEU   (  25-)  A     -CA  -C    N   126.69    5.2
  28 ILE   (  29-)  A      N    CA   C    99.42   -4.2
  29 MET   (  30-)  A      CA   CB   CG  123.03    4.5
  33 ALA   (  34-)  A      N    CA   CB  101.01   -6.3
  40 THR   (  41-)  A      CA   CB   OG1 100.78   -5.9
  41 ALA   (  42-)  A     -O   -C    N   129.63    4.1
  43 HIS   (  44-)  A      CA   CB   CG  106.40   -7.4
  44 PHE   (  45-)  A      C    CA   CB  118.63    4.5
  44 PHE   (  45-)  A      CA   CB   CG  119.60    5.8
  50 THR   (  51-)  A     -C    N    CA  129.33    4.2
  50 THR   (  51-)  A      C    CA   CB  118.27    4.3
And so on for a total of 489 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.022
RMS-deviation in bond angles: 3.701

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.

  15 ASP   (  16-)  A
  21 GLU   (  22-)  A
  56 ASP   (  68-)  A
  61 GLU   (  73-)  A
  63 ASP   (  75-)  A
  67 GLU   (  79-)  A
  79 ASP   (  91-)  A
 113 ASP   ( 125-)  A
 144 ASP   ( 156-)  A
 176 ASP   ( 188-)  A
 181 ASP   ( 193-)  A
 201 ASP   ( 213-)  A
 208 ASP   ( 220-)  A
 212 GLU   ( 224-)  A
 223 ASP   ( 235-)  A
 224 ASP   ( 236-)  A
 233 GLU   ( 245-)  A
 241 GLU   ( 253-)  A
 251 ASP   ( 263-)  A
 269 ASP   ( 281-)  A
 315 ASP   ( 336-)  A
 326 GLU   ( 347-)  A
 360 GLU   ( 381-)  A
 404 ASP   ( 425-)  A
 424 ASP   ( 445-)  A
And so on for a total of 54 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.

 129 VAL   ( 141-)  A      CB     7.1   -23.71   -32.96
 533 MET   ( 109-)  B      CA     6.4    45.63    34.17
The average deviation= 1.652

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.

 490 GLY   (  66-)  B    6.88
 749 ARG   ( 337-)  B    6.36
 807 GLY   ( 395-)  B    6.08
 209 GLU   ( 221-)  A    6.06
 227 GLU   ( 239-)  A    5.76
 775 CYS   ( 363-)  B    5.43
 803 THR   ( 391-)  B    5.33
 276 ARG   ( 288-)  A    4.92
 426 ILE   ( 447-)  A    4.76
 756 THR   ( 344-)  B    4.73
 206 ALA   ( 218-)  A    4.72
 645 GLU   ( 221-)  B    4.66
 323 THR   ( 344-)  A    4.57
 371 ALA   ( 392-)  A    4.55
 183 PRO   ( 195-)  A    4.54
 603 ALA   ( 179-)  B    4.39
 554 GLU   ( 130-)  B    4.35
 423 ALA   ( 444-)  A    4.31
 314 SER   ( 335-)  A    4.23
 817 ALA   ( 405-)  B    4.23
 315 ASP   ( 336-)  A    4.19
 372 GLY   ( 393-)  A    4.18
 570 LEU   ( 146-)  B    4.16
 322 LEU   ( 343-)  A    4.11
 750 ALA   ( 338-)  B    4.10
 181 ASP   ( 193-)  A    4.05
 383 VAL   ( 404-)  A    4.05
 866 ALA   ( 454-)  B    4.04
 147 LEU   ( 159-)  A    4.00

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.879

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.

 587 THR   ( 163-)  B    -3.1
 151 THR   ( 163-)  A    -2.8
 182 GLU   ( 194-)  A    -2.5
 516 ARG   (  92-)  B    -2.4
 129 VAL   ( 141-)  A    -2.4
 438 GLN   (   3-)  B    -2.4
 489 ARG   (  65-)  B    -2.3
 536 ASN   ( 112-)  B    -2.3
 868 GLY   ( 456-)  B    -2.3
 725 ARG   ( 301-)  B    -2.3
 240 GLY   ( 252-)  A    -2.2
 565 VAL   ( 141-)  B    -2.2
  62 VAL   (  74-)  A    -2.2
 154 LYS   ( 166-)  A    -2.2
 788 MET   ( 376-)  B    -2.2
 432 LYS   ( 453-)  A    -2.2
  97 MET   ( 109-)  A    -2.1
  54 GLY   (  66-)  A    -2.1
 502 ARG   (  78-)  B    -2.1
 288 LYS   ( 300-)  A    -2.1
 337 GLY   ( 358-)  A    -2.1
 435 GLY   ( 456-)  A    -2.1
 185 GLY   ( 197-)  A    -2.1
 721 PRO   ( 297-)  B    -2.1
 621 GLY   ( 197-)  B    -2.1
 535 ASN   ( 111-)  B    -2.1
 326 GLU   ( 347-)  A    -2.1
 448 LYS   (  13-)  B    -2.1
 744 ILE   ( 320-)  B    -2.1
 676 GLY   ( 252-)  B    -2.1
 419 PHE   ( 440-)  A    -2.1
 867 LEU   ( 455-)  B    -2.0
 274 TYR   ( 286-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   2 GLN   (   3-)  A  Poor phi/psi
   4 SER   (   5-)  A  Poor phi/psi
  49 SER   (  50-)  A  Poor phi/psi
  54 GLY   (  66-)  A  Poor phi/psi
  67 GLU   (  79-)  A  Poor phi/psi
  85 GLY   (  97-)  A  Poor phi/psi
 104 GLY   ( 116-)  A  Poor phi/psi
 130 ASN   ( 142-)  A  Poor phi/psi
 154 LYS   ( 166-)  A  PRO omega poor
 174 GLY   ( 186-)  A  Poor phi/psi
 304 GLY   ( 316-)  A  Poor phi/psi
 314 SER   ( 335-)  A  Poor phi/psi
 331 PHE   ( 352-)  A  Poor phi/psi
 337 GLY   ( 358-)  A  Poor phi/psi
 485 SER   (  50-)  B  Poor phi/psi
 503 GLU   (  79-)  B  Poor phi/psi
 533 MET   ( 109-)  B  Poor phi/psi
 536 ASN   ( 112-)  B  Poor phi/psi
 539 MET   ( 115-)  B  Poor phi/psi
 566 ASN   ( 142-)  B  Poor phi/psi
 580 ASP   ( 156-)  B  Poor phi/psi
 590 LYS   ( 166-)  B  PRO omega poor
 610 GLY   ( 186-)  B  Poor phi/psi
 714 GLY   ( 290-)  B  Poor phi/psi
 716 GLY   ( 292-)  B  Poor phi/psi
 740 GLY   ( 316-)  B  Poor phi/psi
 764 PHE   ( 352-)  B  Poor phi/psi
 799 ASN   ( 387-)  B  Poor phi/psi
 807 GLY   ( 395-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.019

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.019

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.

 387 ARG   ( 408-)  A    0.38
  91 SER   ( 103-)  A    0.39

Warning: Unusual backbone conformations

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

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

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

   3 SER   (   4-)  A      0
   6 TYR   (   7-)  A      0
   7 VAL   (   8-)  A      0
   8 ASN   (   9-)  A      0
  21 GLU   (  22-)  A      0
  22 HIS   (  23-)  A      0
  32 LYS   (  33-)  A      0
  33 ALA   (  34-)  A      0
  35 TYR   (  36-)  A      0
  48 SER   (  49-)  A      0
  49 SER   (  50-)  A      0
  51 GLY   (  52-)  A      0
  52 THR   (  53-)  A      0
  53 ARG   (  65-)  A      0
  54 GLY   (  66-)  A      0
  55 VAL   (  67-)  A      0
  60 TYR   (  72-)  A      0
  61 GLU   (  73-)  A      0
  68 LEU   (  80-)  A      0
  81 ASN   (  93-)  A      0
  83 THR   (  95-)  A      0
  88 MET   ( 100-)  A      0
  96 THR   ( 108-)  A      0
  97 MET   ( 109-)  A      0
  99 ASN   ( 111-)  A      0
And so on for a total of 300 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 : 2.177

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!

 597 PRO   ( 173-)  B   1.99   10
 538 GLY   ( 114-)  B   1.68   17

Warning: Unusual peptide bond conformations

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

 209 GLU   ( 221-)  A   1.54

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]

 117 PRO   ( 129-)  A    0.47 HIGH
 141 PRO   ( 153-)  A    0.18 LOW
 183 PRO   ( 195-)  A    0.19 LOW
 330 PRO   ( 351-)  A    0.08 LOW
 356 PRO   ( 377-)  A    0.49 HIGH
 420 PRO   ( 441-)  A    0.47 HIGH
 627 PRO   ( 203-)  B    0.10 LOW
 834 PRO   ( 422-)  B    0.10 LOW
 853 PRO   ( 441-)  B    0.19 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].

  31 PRO   (  32-)  A    32.2 envelop C-delta (36 degrees)
 285 PRO   ( 297-)  A    49.3 half-chair C-delta/C-gamma (54 degrees)
 467 PRO   (  32-)  B   -22.9 half-chair C-alpha/N (-18 degrees)
 563 PRO   ( 139-)  B    46.0 half-chair C-delta/C-gamma (54 degrees)
 619 PRO   ( 195-)  B    10.2 half-chair N/C-delta (18 degrees)
 721 PRO   ( 297-)  B   -56.4 half-chair C-beta/C-alpha (-54 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.

 489 ARG   (  65-)  B      NH2 <->  871 HOH   ( 647 )  B      O      0.98    1.72  INTRA BF
 535 ASN   ( 111-)  B      O   <->  537 GLN   ( 113-)  B      N      0.70    2.00  INTRA BF
 823 ARG   ( 411-)  B      NH1 <->  871 HOH   ( 815 )  B      O      0.65    2.05  INTRA
 121 ARG   ( 133-)  A      NH2 <->  870 HOH   ( 510 )  A      O      0.64    2.06  INTRA
   1 ASP   (   2-)  A      O   <->    2 GLN   (   3-)  A      CG     0.59    2.11  INTRA BF
  53 ARG   (  65-)  A      N   <->  870 HOH   ( 506 )  A      O      0.59    2.11  INTRA
 864 ARG   ( 452-)  B      NH1 <->  871 HOH   ( 860 )  B      O      0.55    2.15  INTRA BF
 557 ARG   ( 133-)  B      NH1 <->  871 HOH   ( 717 )  B      O      0.53    2.17  INTRA
 437 ASP   (   2-)  B      O   <->  871 HOH   ( 745 )  B      O      0.53    1.87  INTRA
 749 ARG   ( 337-)  B      CD  <->  753 TYR   ( 341-)  B      CZ     0.52    2.68  INTRA BF
 712 ARG   ( 288-)  B      NH2 <->  715 HIS   ( 291-)  B      NE2    0.52    2.48  INTRA BF
 488 THR   (  64-)  B      N   <->  494 LEU   (  70-)  B      CD1    0.51    2.59  INTRA BL
 107 GLU   ( 119-)  A      O   <->  289 ARG   ( 301-)  A      NH2    0.50    2.20  INTRA BF
 618 GLU   ( 194-)  B      OE1 <->  619 PRO   ( 195-)  B      CG     0.49    2.31  INTRA
 487 GLY   (  52-)  B      CA  <->  871 HOH   ( 845 )  B      O      0.48    2.32  INTRA BF
 723 SER   ( 299-)  B      CA  <->  725 ARG   ( 301-)  B      NH1    0.48    2.62  INTRA BF
 655 ASN   ( 231-)  B      ND2 <->  871 HOH   ( 537 )  B      O      0.47    2.23  INTRA
 487 GLY   (  52-)  B      C   <->  871 HOH   ( 845 )  B      O      0.47    2.33  INTRA BF
 328 GLN   ( 349-)  A      OE1 <->  333 ARG   ( 354-)  A      NE     0.47    2.23  INTRA
 787 ARG   ( 375-)  B      NH1 <->  855 ASP   ( 443-)  B      OD2    0.47    2.23  INTRA BF
 437 ASP   (   2-)  B      N   <->  479 HIS   (  44-)  B      CB     0.44    2.66  INTRA
 488 THR   (  64-)  B      CG2 <->  489 ARG   (  65-)  B      N      0.44    2.56  INTRA BF
 350 MET   ( 371-)  A      SD  <->  354 ARG   ( 375-)  A      CB     0.44    2.96  INTRA BF
 121 ARG   ( 133-)  A      NE  <->  870 HOH   ( 510 )  A      O      0.43    2.27  INTRA
  36 GLY   (  37-)  A      N   <->  870 HOH   ( 666 )  A      O      0.43    2.27  INTRA BF
And so on for a total of 340 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

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.

 489 ARG   (  65-)  B      -6.37
 809 PHE   ( 397-)  B      -5.83
 154 LYS   ( 166-)  A      -5.58
 397 ARG   ( 418-)  A      -5.53
 830 ARG   ( 418-)  B      -5.53
 681 HIS   ( 257-)  B      -5.46
 245 HIS   ( 257-)  A      -5.34
 590 LYS   ( 166-)  B      -5.26
 266 ARG   ( 278-)  A      -5.25
 702 ARG   ( 278-)  B      -5.24
 794 ASN   ( 382-)  B      -5.23
 361 ASN   ( 382-)  A      -5.22
 579 VAL   ( 155-)  B      -5.10
 425 GLN   ( 446-)  A      -5.07
 812 ILE   ( 400-)  B      -5.06
 143 VAL   ( 155-)  A      -5.03

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

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.

 869 VAL   ( 457-)  B   -2.79

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

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.

 870 HOH   ( 516 )  A      O     23.51    0.98   60.92
 870 HOH   ( 534 )  A      O     31.32  -10.73   44.58
 870 HOH   ( 584 )  A      O     18.77   23.11   57.00
 870 HOH   ( 671 )  A      O     37.06   -5.98   45.65
 870 HOH   ( 737 )  A      O     26.13   27.41   45.61
 871 HOH   ( 482 )  B      O     59.55   24.23    3.50
 871 HOH   ( 534 )  B      O     42.44  -30.40   18.54
 871 HOH   ( 586 )  B      O     64.02  -11.78  -14.84
 871 HOH   ( 640 )  B      O     58.14   28.95   10.09
 871 HOH   ( 652 )  B      O     64.88   16.58    2.11
 871 HOH   ( 683 )  B      O     60.24   28.23   17.64
 871 HOH   ( 685 )  B      O     58.58   30.37   17.92
 871 HOH   ( 696 )  B      O     38.65   -2.38   -0.39
 871 HOH   ( 719 )  B      O     57.50  -14.43   -0.34
 871 HOH   ( 748 )  B      O     44.23   -1.03  -17.09
 871 HOH   ( 772 )  B      O     67.92   -3.53  -26.08

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.

 870 HOH   ( 538 )  A      O
 870 HOH   ( 570 )  A      O
 870 HOH   ( 577 )  A      O
 870 HOH   ( 586 )  A      O
 870 HOH   ( 621 )  A      O
 870 HOH   ( 622 )  A      O
 870 HOH   ( 629 )  A      O
 870 HOH   ( 631 )  A      O
 870 HOH   ( 641 )  A      O
 870 HOH   ( 698 )  A      O
 870 HOH   ( 743 )  A      O
 870 HOH   ( 759 )  A      O
 870 HOH   ( 771 )  A      O
 870 HOH   ( 779 )  A      O
 870 HOH   ( 780 )  A      O
 870 HOH   ( 792 )  A      O
 870 HOH   ( 793 )  A      O
 870 HOH   ( 799 )  A      O
 870 HOH   ( 800 )  A      O
 871 HOH   ( 528 )  B      O
 871 HOH   ( 569 )  B      O
 871 HOH   ( 597 )  B      O
 871 HOH   ( 602 )  B      O
 871 HOH   ( 621 )  B      O
 871 HOH   ( 624 )  B      O
 871 HOH   ( 687 )  B      O
 871 HOH   ( 692 )  B      O
 871 HOH   ( 696 )  B      O
 871 HOH   ( 701 )  B      O
 871 HOH   ( 722 )  B      O
 871 HOH   ( 759 )  B      O
 871 HOH   ( 761 )  B      O
 871 HOH   ( 772 )  B      O
 871 HOH   ( 785 )  B      O
 871 HOH   ( 798 )  B      O
 871 HOH   ( 805 )  B      O
 871 HOH   ( 809 )  B      O
 871 HOH   ( 813 )  B      O
 871 HOH   ( 830 )  B      O
 871 HOH   ( 834 )  B      O
 871 HOH   ( 836 )  B      O
 871 HOH   ( 849 )  B      O
 871 HOH   ( 850 )  B      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.

   8 ASN   (   9-)  A
  22 HIS   (  23-)  A
  81 ASN   (  93-)  A
 275 HIS   ( 287-)  A
 296 HIS   ( 308-)  A
 458 HIS   (  23-)  B
 537 GLN   ( 113-)  B
 655 ASN   ( 231-)  B

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.

   4 SER   (   5-)  A      N
   7 VAL   (   8-)  A      N
   9 LEU   (  10-)  A      N
  14 GLU   (  15-)  A      N
  51 GLY   (  52-)  A      N
  52 THR   (  53-)  A      N
  64 GLU   (  76-)  A      N
  66 ARG   (  78-)  A      NE
  91 SER   ( 103-)  A      N
 106 VAL   ( 118-)  A      N
 121 ARG   ( 133-)  A      NE
 145 GLY   ( 157-)  A      N
 147 LEU   ( 159-)  A      N
 157 LEU   ( 169-)  A      N
 181 ASP   ( 193-)  A      N
 189 PHE   ( 201-)  A      N
 212 GLU   ( 224-)  A      N
 222 ALA   ( 234-)  A      N
 256 GLY   ( 268-)  A      N
 277 ALA   ( 289-)  A      N
 280 GLY   ( 292-)  A      N
 288 LYS   ( 300-)  A      N
 291 TYR   ( 303-)  A      N
 326 GLU   ( 347-)  A      N
 347 SER   ( 368-)  A      N
And so on for a total of 62 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.

 182 GLU   ( 194-)  A      OE2
 251 ASP   ( 263-)  A      OD2
 458 HIS   (  23-)  B      NE2
 687 ASP   ( 263-)  B      OD2
 732 HIS   ( 308-)  B      NE2

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 870 HOH   ( 469 )  A      O  0.87  K  5
 870 HOH   ( 487 )  A      O  0.99  K  4
 871 HOH   ( 532 )  B      O  1.03 NA  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.

 209 GLU   ( 221-)  A   H-bonding suggests Gln; but Alt-Rotamer
 251 ASP   ( 263-)  A   H-bonding suggests Asn; but Alt-Rotamer
 437 ASP   (   2-)  B   H-bonding suggests Asn
 687 ASP   ( 263-)  B   H-bonding suggests Asn; but Alt-Rotamer
 857 ASP   ( 445-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.502
  2nd generation packing quality :  -1.503
  Ramachandran plot appearance   :  -1.986
  chi-1/chi-2 rotamer normality  :  -3.019 (poor)
  Backbone conformation          :  -0.161

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.001
  Bond angles                    :   2.022 (loose)
  Omega angle restraints         :   0.396 (tight)
  Side chain planarity           :   1.040
  Improper dihedral distribution :   1.421
  B-factor distribution          :   0.788
  Inside/Outside distribution    :   0.989

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 : 1.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -2.4
  chi-1/chi-2 rotamer normality  :  -3.3 (poor)
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.001
  Bond angles                    :   2.022 (loose)
  Omega angle restraints         :   0.396 (tight)
  Side chain planarity           :   1.040
  Improper dihedral distribution :   1.421
  B-factor distribution          :   0.788
  Inside/Outside distribution    :   0.989
==============

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.