WHAT IF Check report

This file was created 2014-07-17 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 pdb3rg6.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: C and D

All-atom RMS fit for the two chains : 1.162
CA-only RMS fit for the two chains : 0.899

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: C and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: C and E

All-atom RMS fit for the two chains : 0.612
CA-only RMS fit for the two chains : 0.406

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: C and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: C and F

All-atom RMS fit for the two chains : 1.312
CA-only RMS fit for the two chains : 1.053

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: C and F

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: D and E

All-atom RMS fit for the two chains : 0.871
CA-only RMS fit for the two chains : 0.574

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: D and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: D and F

All-atom RMS fit for the two chains : 0.579
CA-only RMS fit for the two chains : 0.378

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: D and F

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 148705.172
Volume of the Unit Cell V= 5969974.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.018
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.240

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: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

Warning: Missing atoms

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

   1 LYS   (  18-)  A      CG
   1 LYS   (  18-)  A      CD
   1 LYS   (  18-)  A      CE
   1 LYS   (  18-)  A      NZ
  45 THR   (  62-)  A      OG1
  45 THR   (  62-)  A      CG2
  47 LEU   (  71-)  A      CG
  47 LEU   (  71-)  A      CD1
  47 LEU   (  71-)  A      CD2
  48 THR   (  72-)  A      OG1
  48 THR   (  72-)  A      CG2
  49 ASP   (  73-)  A      CG
  49 ASP   (  73-)  A      OD1
  49 ASP   (  73-)  A      OD2
  64 GLN   (  88-)  A      CG
  64 GLN   (  88-)  A      CD
  64 GLN   (  88-)  A      OE1
  64 GLN   (  88-)  A      NE2
 101 LYS   ( 125-)  A      CG
 101 LYS   ( 125-)  A      CD
 101 LYS   ( 125-)  A      CE
 101 LYS   ( 125-)  A      NZ
 148 LYS   ( 172-)  A      CG
 148 LYS   ( 172-)  A      CD
 148 LYS   ( 172-)  A      CE
And so on for a total of 395 lines.

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 LYS   (  18-)  A    High
   8 ASP   (  25-)  A    High
  26 PRO   (  43-)  A    High
  27 GLY   (  44-)  A    High
  47 LEU   (  71-)  A    High
  65 GLY   (  89-)  A    High
  67 GLU   (  91-)  A    High
 104 ARG   ( 128-)  A    High
 413 ASP   ( 440-)  A    High
 416 ARG   ( 443-)  A    High
 420 LYS   ( 447-)  A    High
 430 ASP   ( 457-)  A    High
 432 TRP   ( 459-)  A    High
 433 LYS   ( 460-)  A    High
 434 GLU   ( 461-)  A    High
 437 PHE   ( 464-)  A    High
 439 PHE   ( 466-)  A    High
 440 GLU   ( 467-)  A    High
 441 THR   ( 468-)  A    High
 442 MET   ( 469-)  A    High
 443 MET   (   1-)  C    High
 444 ASN   (   2-)  C    High
 445 LEU   (   3-)  C    High
 446 LYS   (   4-)  C    High
 447 GLN   (   5-)  C    High
And so on for a total of 423 lines.

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 450 LYS   (   8-)  C    0.50
 458 SER   (  16-)  C    0.50
 471 GLN   (  29-)  C    0.60
 569 LYS   (  12-)  D    0.50
 586 GLN   (  29-)  D    0.50
 644 GLU   (  87-)  D    0.60
 646 VAL   (  89-)  D    0.70
1109 LYS   (   8-)  E    0.50
1117 SER   (  16-)  E    0.50
1130 GLN   (  29-)  E    0.60
1228 LYS   (  12-)  F    0.50
1245 GLN   (  29-)  F    0.50
1303 GLU   (  87-)  F    0.60
1305 VAL   (  89-)  F    0.70

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 8

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: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 107 ARG   ( 131-)  A
 132 ARG   ( 156-)  A
 511 ARG   (  69-)  C
 769 ARG   ( 131-)  B
 794 ARG   ( 156-)  B
1051 ARG   ( 418-)  B
1170 ARG   (  69-)  E

Warning: Tyrosine convention problem

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

   4 TYR   (  21-)  A
 158 TYR   ( 182-)  A
 732 TYR   (  94-)  B
 800 TYR   ( 162-)  B
 820 TYR   ( 182-)  B
1233 TYR   (  17-)  F

Warning: Phenylalanine convention problem

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

  20 PHE   (  37-)  A
  22 PHE   (  39-)  A
 184 PHE   ( 208-)  A
 367 PHE   ( 391-)  A
 375 PHE   ( 399-)  A
 502 PHE   (  60-)  C
 526 PHE   (  84-)  C
 617 PHE   (  60-)  D
 684 PHE   (  37-)  B
 686 PHE   (  39-)  B
 743 PHE   ( 105-)  B
 846 PHE   ( 208-)  B
 996 PHE   ( 360-)  B
 997 PHE   ( 361-)  B
1027 PHE   ( 391-)  B
1161 PHE   (  60-)  E
1276 PHE   (  60-)  F
1300 PHE   (  84-)  F

Warning: Aspartic acid convention problem

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

  51 ASP   (  75-)  A
 176 ASP   ( 200-)  A
 413 ASP   ( 440-)  A
 430 ASP   ( 457-)  A
 608 ASP   (  51-)  D
 622 ASP   (  65-)  D
 713 ASP   (  75-)  B
 772 ASP   ( 134-)  B
1073 ASP   ( 440-)  B
1267 ASP   (  51-)  F
1281 ASP   (  65-)  F

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  67 GLU   (  91-)  A
 410 GLU   ( 437-)  A
 495 GLU   (  53-)  C
 521 GLU   (  79-)  C
 632 GLU   (  75-)  D
 636 GLU   (  79-)  D
 729 GLU   (  91-)  B
1070 GLU   ( 437-)  B
1094 GLU   ( 461-)  B
1154 GLU   (  53-)  E
1180 GLU   (  79-)  E
1291 GLU   (  75-)  F
1295 GLU   (  79-)  F

Geometric checks

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

 |  0.998382  0.000037  0.000054|
 |  0.000037  0.998487  0.000101|
 |  0.000054  0.000101  0.997984|
Proposed new scale matrix

 |  0.004093  0.000000  0.000000|
 |  0.000000  0.004092  0.000000|
 |  0.000000 -0.000001  0.010053|
With corresponding cell

    A    = 244.342  B   = 244.368  C    =  99.470
    Alpha=  89.996  Beta=  90.002  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 244.750  B   = 244.750  C    =  99.669
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 127.198
(Under-)estimated Z-score: 8.312

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.

 873 HIS   ( 235-)  B      CG   ND1  CE1 109.75    4.2

Error: Nomenclature error(s)

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

  51 ASP   (  75-)  A
  67 GLU   (  91-)  A
 107 ARG   ( 131-)  A
 132 ARG   ( 156-)  A
 176 ASP   ( 200-)  A
 410 GLU   ( 437-)  A
 413 ASP   ( 440-)  A
 430 ASP   ( 457-)  A
 495 GLU   (  53-)  C
 511 ARG   (  69-)  C
 521 GLU   (  79-)  C
 608 ASP   (  51-)  D
 622 ASP   (  65-)  D
 632 GLU   (  75-)  D
 636 GLU   (  79-)  D
 713 ASP   (  75-)  B
 729 GLU   (  91-)  B
 769 ARG   ( 131-)  B
 772 ASP   ( 134-)  B
 794 ARG   ( 156-)  B
1051 ARG   ( 418-)  B
1070 GLU   ( 437-)  B
1073 ASP   ( 440-)  B
1094 GLU   ( 461-)  B
1154 GLU   (  53-)  E
1170 ARG   (  69-)  E
1180 GLU   (  79-)  E
1267 ASP   (  51-)  F
1281 ASP   (  65-)  F
1291 GLU   (  75-)  F
1295 GLU   (  79-)  F

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.

 606 VAL   (  49-)  D    5.28
 311 ASP   ( 335-)  A    4.96
 971 ASP   ( 335-)  B    4.52
 275 ASP   ( 299-)  A    4.20
  51 ASP   (  75-)  A    4.16

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.

 149 PRO   ( 173-)  A    -2.8
 811 PRO   ( 173-)  B    -2.7
 268 ARG   ( 292-)  A    -2.7
 930 ARG   ( 292-)  B    -2.6
 854 LEU   ( 216-)  B    -2.6
 847 GLN   ( 209-)  B    -2.5
 140 ARG   ( 164-)  A    -2.5
1297 ILE   (  81-)  F    -2.5
 802 ARG   ( 164-)  B    -2.4
 874 TYR   ( 236-)  B    -2.4
 185 GLN   ( 209-)  A    -2.3
  91 THR   ( 115-)  A    -2.3
 667 THR   (  20-)  B    -2.3
 923 GLY   ( 285-)  B    -2.3
 757 GLY   ( 119-)  B    -2.3
 769 ARG   ( 131-)  B    -2.3
   3 THR   (  20-)  A    -2.3
 592 PRO   (  35-)  D    -2.3
 724 PRO   (  86-)  B    -2.2
 690 PRO   (  43-)  B    -2.2
 606 VAL   (  49-)  D    -2.2
   2 LEU   (  19-)  A    -2.2
 236 PRO   ( 260-)  A    -2.2
 422 SER   ( 449-)  A    -2.2
 261 GLY   ( 285-)  A    -2.2
 491 VAL   (  49-)  C    -2.1
 900 ILE   ( 262-)  B    -2.1
1082 SER   ( 449-)  B    -2.1
 899 ILE   ( 261-)  B    -2.1
 685 ARG   (  38-)  B    -2.1
 238 ILE   ( 262-)  A    -2.1
 181 SER   ( 205-)  A    -2.1
 107 ARG   ( 131-)  A    -2.1
 967 VAL   ( 329-)  B    -2.1
 753 THR   ( 115-)  B    -2.1
 932 MET   ( 294-)  B    -2.0
 151 LEU   ( 175-)  A    -2.0
 174 LYS   ( 198-)  A    -2.0
 957 GLY   ( 319-)  B    -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.

  20 PHE   (  37-)  A  omega poor
  42 SER   (  59-)  A  Poor phi/psi
  51 ASP   (  75-)  A  Poor phi/psi
  57 CYS   (  81-)  A  omega poor
  68 ASN   (  92-)  A  Poor phi/psi
  80 LEU   ( 104-)  A  omega poor
 136 ASN   ( 160-)  A  Poor phi/psi
 148 LYS   ( 172-)  A  PRO omega poor
 150 LYS   ( 174-)  A  Poor phi/psi
 169 GLY   ( 193-)  A  Poor phi/psi
 184 PHE   ( 208-)  A  omega poor
 185 GLN   ( 209-)  A  Poor phi/psi
 270 MET   ( 294-)  A  Poor phi/psi
 274 ILE   ( 298-)  A  omega poor
 309 GLU   ( 333-)  A  Poor phi/psi
 310 GLY   ( 334-)  A  Poor phi/psi, omega poor
 343 SER   ( 367-)  A  Poor phi/psi
 352 SER   ( 376-)  A  omega poor
 411 GLY   ( 438-)  A  Poor phi/psi
 433 LYS   ( 460-)  A  omega poor
 559 ASN   (   2-)  D  Poor phi/psi
 706 SER   (  59-)  B  Poor phi/psi
 710 THR   (  72-)  B  omega poor
 719 CYS   (  81-)  B  omega poor
 730 ASN   (  92-)  B  Poor phi/psi
 757 GLY   ( 119-)  B  Poor phi/psi
 758 ASN   ( 120-)  B  Poor phi/psi
 790 ILE   ( 152-)  B  Poor phi/psi
 798 ASN   ( 160-)  B  Poor phi/psi
 810 LYS   ( 172-)  B  PRO omega poor
 811 PRO   ( 173-)  B  Poor phi/psi
 812 LYS   ( 174-)  B  Poor phi/psi
 831 GLY   ( 193-)  B  Poor phi/psi
 838 ASP   ( 200-)  B  omega poor
 842 ASN   ( 204-)  B  Poor phi/psi
 847 GLN   ( 209-)  B  Poor phi/psi
 848 ARG   ( 210-)  B  omega poor
 890 GLU   ( 252-)  B  omega poor
 923 GLY   ( 285-)  B  Poor phi/psi
 932 MET   ( 294-)  B  Poor phi/psi
 966 VAL   ( 328-)  B  omega poor
1003 SER   ( 367-)  B  Poor phi/psi, omega poor
1013 GLY   ( 377-)  B  Poor phi/psi
1014 GLY   ( 378-)  B  Poor phi/psi
1071 GLY   ( 438-)  B  Poor phi/psi
1278 GLU   (  62-)  F  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.017

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.017

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.

 314 SER   ( 338-)  A    0.36
 974 SER   ( 338-)  B    0.36
 780 VAL   ( 142-)  B    0.38
 332 SER   ( 356-)  A    0.38
 201 SER   ( 225-)  A    0.39
 863 SER   ( 225-)  B    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!

  26 PRO   (  43-)  A      0
  42 SER   (  59-)  A      0
  43 THR   (  60-)  A      0
  45 THR   (  62-)  A      0
  46 TRP   (  63-)  A      0
  47 LEU   (  71-)  A      0
  48 THR   (  72-)  A      0
  49 ASP   (  73-)  A      0
  50 MET   (  74-)  A      0
  58 TYR   (  82-)  A      0
  61 GLU   (  85-)  A      0
  64 GLN   (  88-)  A      0
  67 GLU   (  91-)  A      0
  68 ASN   (  92-)  A      0
  69 SER   (  93-)  A      0
  80 LEU   ( 104-)  A      0
  83 GLU   ( 107-)  A      0
  85 SER   ( 109-)  A      0
  96 ASN   ( 120-)  A      0
  97 VAL   ( 121-)  A      0
 100 PHE   ( 124-)  A      0
 102 ALA   ( 126-)  A      0
 104 ARG   ( 128-)  A      0
 109 GLU   ( 133-)  A      0
 110 ASP   ( 134-)  A      0
And so on for a total of 377 lines.

Warning: Backbone oxygen evaluation

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

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

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

 727 GLY   (  89-)  B   2.21   40
  65 GLY   (  89-)  A   2.20   41
 845 PRO   ( 207-)  B   1.89   10
 644 GLU   (  87-)  D   1.77   10

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].

  26 PRO   (  43-)  A  -124.3 half-chair C-delta/C-gamma (-126 degrees)
  62 PRO   (  86-)  A   -60.4 half-chair C-beta/C-alpha (-54 degrees)
 149 PRO   ( 173-)  A   -37.2 envelop C-alpha (-36 degrees)
 183 PRO   ( 207-)  A    99.0 envelop C-beta (108 degrees)
 218 PRO   ( 242-)  A  -123.8 half-chair C-delta/C-gamma (-126 degrees)
 236 PRO   ( 260-)  A     4.6 envelop N (0 degrees)
 385 PRO   ( 412-)  A  -117.8 half-chair C-delta/C-gamma (-126 degrees)
 592 PRO   (  35-)  D   101.5 envelop C-beta (108 degrees)
 690 PRO   (  43-)  B  -129.8 half-chair C-delta/C-gamma (-126 degrees)
 724 PRO   (  86-)  B   -19.4 half-chair C-alpha/N (-18 degrees)
 811 PRO   ( 173-)  B   -45.1 half-chair C-beta/C-alpha (-54 degrees)
 845 PRO   ( 207-)  B  -125.9 half-chair C-delta/C-gamma (-126 degrees)
 898 PRO   ( 260-)  B    33.8 envelop C-delta (36 degrees)
1005 PRO   ( 369-)  B    46.4 half-chair C-delta/C-gamma (54 degrees)
1040 PRO   ( 407-)  B  -119.9 half-chair C-delta/C-gamma (-126 degrees)
1280 PRO   (  64-)  F   101.5 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

   2 LEU   (  19-)  A      CD1  <->    46 TRP   (  63-)  A      CH2  0.44    2.76  INTRA BF
 226 ARG   ( 250-)  A      NH2  <->   744 GLU   ( 106-)  B      OE2  0.44    2.26  INTRA BL
  82 GLU   ( 106-)  A      OE2  <->   888 ARG   ( 250-)  B      NH2  0.34    2.36  INTRA BL
1236 TYR   (  20-)  F      OH   <->  1240 ARG   (  24-)  F      NH1  0.30    2.40  INTRA BF
   2 LEU   (  19-)  A      CD1  <->    46 TRP   (  63-)  A      CZ3  0.29    2.91  INTRA BF
 132 ARG   ( 156-)  A      NH2  <->   140 ARG   ( 164-)  A      O    0.28    2.42  INTRA BL
 980 ASP   ( 344-)  B      OD2  <->   993 ARG   ( 357-)  B      NH2  0.26    2.44  INTRA BL
 292 ARG   ( 316-)  A      NH1  <->   345 PRO   ( 369-)  A      O    0.26    2.44  INTRA BL
 918 TRP   ( 280-)  B      O    <->   922 ASN   ( 284-)  B      ND2  0.23    2.47  INTRA BL
 769 ARG   ( 131-)  B      NH1  <->   939 GLN   ( 301-)  B      O    0.23    2.47  INTRA BL
 539 ASN   (  97-)  C      ND2  <->   628 MET   (  71-)  D      O    0.23    2.47  INTRA BF
 794 ARG   ( 156-)  B      NH2  <->   802 ARG   ( 164-)  B      O    0.21    2.49  INTRA BL
 174 LYS   ( 198-)  A      CB   <->   212 TYR   ( 236-)  A      CD2  0.20    3.00  INTRA BL
 763 LYS   ( 125-)  B      N    <->  1248 GLU   (  32-)  F      OE2  0.20    2.50  INTRA BF
 150 LYS   ( 174-)  A      CG   <->   151 LEU   ( 175-)  A      N    0.20    2.80  INTRA BL
 320 ASP   ( 344-)  A      OD2  <->   333 ARG   ( 357-)  A      NH2  0.20    2.50  INTRA BL
 356 HIS   ( 380-)  A      N    <->   359 HIS   ( 383-)  A      CD2  0.20    2.90  INTRA BL
 816 SER   ( 178-)  B      O    <->   819 ASN   ( 181-)  B      N    0.19    2.51  INTRA BL
 271 HIS   ( 295-)  A      ND1  <->   275 ASP   ( 299-)  A      OD2  0.19    2.51  INTRA BL
 793 GLU   ( 155-)  B      OE2  <->   960 HIS   ( 322-)  B      NE2  0.19    2.51  INTRA BL
 292 ARG   ( 316-)  A      NH2  <->   324 GLU   ( 348-)  A      O    0.19    2.51  INTRA BL
 202 GLN   ( 226-)  A      NE2  <->   209 LYS   ( 233-)  A      N    0.19    2.66  INTRA BL
1066 ASP   ( 433-)  B      N    <->  1070 GLU   ( 437-)  B      OE1  0.19    2.51  INTRA BF
  15 ASP   (  32-)  A      O    <->   112 ARG   ( 136-)  A      NH2  0.19    2.51  INTRA BL
 145 CYS   ( 169-)  A      SG   <->   165 CYS   ( 189-)  A      SG   0.18    3.27  INTRA BL
And so on for a total of 141 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Warning: Abnormal packing environment for some residues

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

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

 766 ARG   ( 128-)  B      -6.71
 726 GLN   (  88-)  B      -6.65
 104 ARG   ( 128-)  A      -6.51
 184 PHE   ( 208-)  A      -6.49
1320 HIS   ( 104-)  F      -6.24
 661 HIS   ( 104-)  D      -6.17
 846 PHE   ( 208-)  B      -6.13
 122 GLN   ( 146-)  A      -6.10
 784 GLN   ( 146-)  B      -5.98
 276 ARG   ( 300-)  A      -5.93
 938 ARG   ( 300-)  B      -5.93
 607 GLN   (  50-)  D      -5.53
 829 ARG   ( 191-)  B      -5.48
 800 TYR   ( 162-)  B      -5.47
 555 LEU   ( 113-)  C      -5.47
 167 ARG   ( 191-)  A      -5.46
 138 TYR   ( 162-)  A      -5.44
1151 GLN   (  50-)  E      -5.40
 434 GLU   ( 461-)  A      -5.36
1266 GLN   (  50-)  F      -5.32
 983 ARG   ( 347-)  B      -5.25
 323 ARG   ( 347-)  A      -5.24
1062 ASN   ( 429-)  B      -5.22
 402 ASN   ( 429-)  A      -5.21
 260 ASN   ( 284-)  A      -5.19
1130 GLN   (  29-)  E      -5.12
1063 GLU   ( 430-)  B      -5.10
1094 GLU   ( 461-)  B      -5.09
 403 GLU   ( 430-)  A      -5.09

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: 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: 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: E

Note: Quality value plot

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

Chain identifier: F

Warning: Low packing Z-score for some residues

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

 812 LYS   ( 174-)  B   -3.58
 307 LYS   ( 331-)  A   -3.46
 742 LEU   ( 104-)  B   -3.12
1093 LYS   ( 460-)  B   -2.95
1164 LYS   (  63-)  E   -2.75
 619 GLU   (  62-)  D   -2.69
 272 ALA   ( 296-)  A   -2.68
 763 LYS   ( 125-)  B   -2.68
1068 TYR   ( 435-)  B   -2.65
 934 ALA   ( 296-)  B   -2.65
1278 GLU   (  62-)  F   -2.65
 101 LYS   ( 125-)  A   -2.61
1149 LYS   (  48-)  E   -2.57
1162 LEU   (  61-)  E   -2.54
 810 LYS   ( 172-)  B   -2.51
1098 GLU   ( 465-)  B   -2.51
  50 MET   (  74-)  A   -2.51

Warning: Abnormal packing Z-score for sequential residues

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

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

 661 HIS   ( 104-)  D     -  664 ARG   ( 107-)  D        -1.56
1276 PHE   (  60-)  F     - 1279 LYS   (  63-)  F        -1.91

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: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

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.

  68 ASN   (  92-)  A
 211 HIS   ( 235-)  A
 214 ASN   ( 238-)  A
 326 HIS   ( 350-)  A
 578 GLN   (  21-)  D
 726 GLN   (  88-)  B
 730 ASN   (  92-)  B
 847 GLN   ( 209-)  B
 873 HIS   ( 235-)  B
 876 ASN   ( 238-)  B
 986 HIS   ( 350-)  B
1106 GLN   (   5-)  E
1266 GLN   (  50-)  F

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 TYR   (  21-)  A      N
  21 ARG   (  38-)  A      NE
  69 SER   (  93-)  A      N
  79 ASP   ( 103-)  A      N
  97 VAL   ( 121-)  A      N
  98 PHE   ( 122-)  A      N
 102 ALA   ( 126-)  A      N
 107 ARG   ( 131-)  A      NH1
 132 ARG   ( 156-)  A      NH2
 140 ARG   ( 164-)  A      N
 146 THR   ( 170-)  A      N
 147 ILE   ( 171-)  A      N
 151 LEU   ( 175-)  A      N
 156 LYS   ( 180-)  A      N
 167 ARG   ( 191-)  A      NE
 176 ASP   ( 200-)  A      N
 184 PHE   ( 208-)  A      N
 185 GLN   ( 209-)  A      NE2
 188 ARG   ( 212-)  A      N
 190 ARG   ( 214-)  A      NE
 209 LYS   ( 233-)  A      N
 209 LYS   ( 233-)  A      NZ
 211 HIS   ( 235-)  A      N
 212 TYR   ( 236-)  A      OH
 226 ARG   ( 250-)  A      NH1
And so on for a total of 121 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.

  25 GLN   (  42-)  A      OE1
 131 GLU   ( 155-)  A      OE1
 241 ASP   ( 265-)  A      OD2
 283 HIS   ( 307-)  A      ND1
 356 HIS   ( 380-)  A      ND1
 599 HIS   (  42-)  D      ND1
 744 GLU   ( 106-)  B      OE1
 793 GLU   ( 155-)  B      OE1
 902 HIS   ( 264-)  B      NE2
 903 ASP   ( 265-)  B      OD1

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.

 241 ASP   ( 265-)  A   H-bonding suggests Asn; but Alt-Rotamer
 311 ASP   ( 335-)  A   H-bonding suggests Asn
 430 ASP   ( 457-)  A   H-bonding suggests Asn
 451 ASP   (   9-)  C   H-bonding suggests Asn
 521 GLU   (  79-)  C   H-bonding suggests Gln
 566 ASP   (   9-)  D   H-bonding suggests Asn
 679 ASP   (  32-)  B   H-bonding suggests Asn
 903 ASP   ( 265-)  B   H-bonding suggests Asn
 921 ASP   ( 283-)  B   H-bonding suggests Asn
 937 ASP   ( 299-)  B   H-bonding suggests Asn
1063 GLU   ( 430-)  B   H-bonding suggests Gln
1090 ASP   ( 457-)  B   H-bonding suggests Asn
1110 ASP   (   9-)  E   H-bonding suggests Asn
1133 GLU   (  32-)  E   H-bonding suggests Gln
1163 GLU   (  62-)  E   H-bonding suggests Gln
1225 ASP   (   9-)  F   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 :  -0.909
  2nd generation packing quality :  -1.250
  Ramachandran plot appearance   :  -2.992
  chi-1/chi-2 rotamer normality  :  -4.017 (bad)
  Backbone conformation          :   0.078

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.366 (tight)
  Bond angles                    :   0.590 (tight)
  Omega angle restraints         :   0.928
  Side chain planarity           :   0.294 (tight)
  Improper dihedral distribution :   0.514
  B-factor distribution          :   0.401
  Inside/Outside distribution    :   1.041

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 : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.366 (tight)
  Bond angles                    :   0.590 (tight)
  Omega angle restraints         :   0.928
  Side chain planarity           :   0.294 (tight)
  Improper dihedral distribution :   0.514
  B-factor distribution          :   0.401
  Inside/Outside distribution    :   1.041
==============

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.