WHAT IF Check report

This file was created 2011-12-18 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 pdb3s5l.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.519
CA-only RMS fit for the two chains : 0.248

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and E

All-atom RMS fit for the two chains : 0.837
CA-only RMS fit for the two chains : 0.494

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: B 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 : 1.009
CA-only RMS fit for the two chains : 0.182

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: G and H

All-atom RMS fit for the two chains : 1.149
CA-only RMS fit for the two chains : 0.812

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: G and H

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

1125 GOL   ( 962-)  H  E

Warning: Ligands for which a topology was generated automatically

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

1120 GOL   ( 968-)  A  -
1121 GOL   ( 961-)  D  -
1122 GOL   ( 966-)  B  -
1123 GOL   ( 969-)  B  -
1124 GOL   ( 960-)  E  -
1125 GOL   ( 962-)  H  E
1126 GOL   ( 963-)  E  -
1127 GOL   ( 965-)  G  -
1128 GOL   ( 967-)  G  -
1129 GOL   ( 964-)  H  -

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: D

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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

Warning: 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'.

 179 GLU   (   3-)  D      CB
 179 GLU   (   3-)  D      CG
 179 GLU   (   3-)  D      CD
 179 GLU   (   3-)  D      OE1
 179 GLU   (   3-)  D      OE2
 463 LYS   ( 105-)  B      CB
 463 LYS   ( 105-)  B      CG
 463 LYS   ( 105-)  B      CD
 463 LYS   ( 105-)  B      CE
 463 LYS   ( 105-)  B      NZ
 464 THR   ( 106-)  B      CB
 464 THR   ( 106-)  B      OG1
 464 THR   ( 106-)  B      CG2
 465 GLN   ( 107-)  B      CB
 465 GLN   ( 107-)  B      CG
 465 GLN   ( 107-)  B      CD
 465 GLN   ( 107-)  B      OE1
 465 GLN   ( 107-)  B      NE2
 466 PRO   ( 108-)  B      CB
 466 PRO   ( 108-)  B      CG
 466 PRO   ( 108-)  B      CD
 467 LEU   ( 109-)  B      CB
 467 LEU   ( 109-)  B      CG
 467 LEU   ( 109-)  B      CD1
 467 LEU   ( 109-)  B      CD2
And so on for a total of 99 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

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: D

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  48 ARG   (  50-)  A
 252 ARG   (  76-)  D
 299 ARG   ( 123-)  D
 406 ARG   (  48-)  B
 429 ARG   (  71-)  B
 438 ARG   (  80-)  B
 452 ARG   (  94-)  B
 488 ARG   ( 130-)  B
 547 ARG   ( 189-)  B
 588 ARG   (  39-)  E
 597 ARG   (  48-)  E
 604 ARG   (  55-)  E
 620 ARG   (  71-)  E
 621 ARG   (  72-)  E
 629 ARG   (  80-)  E
 679 ARG   ( 130-)  E
 682 ARG   ( 133-)  E
 715 ARG   ( 166-)  E
 738 ARG   ( 189-)  E
 824 ARG   (  60-)  G
 896 ARG   ( 134-)  G
1001 ARG   (  60-)  H
1004 ARG   (  63-)  H
1073 ARG   ( 134-)  H

Warning: Tyrosine convention problem

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

 148 TYR   ( 150-)  A
 255 TYR   (  79-)  D
 326 TYR   ( 150-)  D
 390 TYR   (  32-)  B
 460 TYR   ( 102-)  B
 581 TYR   (  32-)  E
 651 TYR   ( 102-)  E
 720 TYR   ( 171-)  E
 981 TYR   (  40-)  H

Warning: Phenylalanine convention problem

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

  49 PHE   (  51-)  A
 110 PHE   ( 112-)  A
 208 PHE   (  32-)  D
 227 PHE   (  51-)  D
 371 PHE   (  13-)  B
 375 PHE   (  17-)  B
 513 PHE   ( 155-)  B
 671 PHE   ( 122-)  E
 831 PHE   (  67-)  G
 932 PHE   ( 170-)  G
1109 PHE   ( 170-)  H

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.

  23 ASP   (  25-)  A
 108 ASP   ( 110-)  A
 201 ASP   (  25-)  D
 211 ASP   (  35-)  D
 286 ASP   ( 110-)  D
 424 ASP   (  66-)  B
 434 ASP   (  76-)  B
 606 ASP   (  57-)  E
 625 ASP   (  76-)  E
 820 ASP   (  56-)  G
 915 ASP   ( 153-)  G
 951 ASP   (  10-)  H
1092 ASP   ( 153-)  H

Warning: Glutamic acid convention problem

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

   1 GLU   (   3-)  A
   2 GLU   (   4-)  A
  28 GLU   (  30-)  A
  44 GLU   (  46-)  A
  45 GLU   (  47-)  A
  96 GLU   (  98-)  A
 132 GLU   ( 134-)  A
 156 GLU   ( 158-)  A
 164 GLU   ( 166-)  A
 170 GLU   ( 172-)  A
 177 GLU   ( 179-)  A
 206 GLU   (  30-)  D
 223 GLU   (  47-)  D
 231 GLU   (  55-)  D
 247 GLU   (  71-)  D
 310 GLU   ( 134-)  D
 317 GLU   ( 141-)  D
 342 GLU   ( 166-)  D
 372 GLU   (  14-)  B
 394 GLU   (  36-)  B
 404 GLU   (  46-)  B
 410 GLU   (  52-)  B
 417 GLU   (  59-)  B
 445 GLU   (  87-)  B
 486 GLU   ( 128-)  B
 520 GLU   ( 162-)  B
 527 GLU   ( 169-)  B
 563 GLU   (  14-)  E
 585 GLU   (  36-)  E
 595 GLU   (  46-)  E
 601 GLU   (  52-)  E
 618 GLU   (  69-)  E
 636 GLU   (  87-)  E
 686 GLU   ( 137-)  E
 687 GLU   ( 138-)  E
 718 GLU   ( 169-)  E
 777 GLU   (  13-)  G
 841 GLU   (  77-)  G
 851 GLU   (  87-)  G
 931 GLU   ( 169-)  G
 954 GLU   (  13-)  H
1018 GLU   (  77-)  H
1032 GLU   (  91-)  H
1058 GLU   ( 119-)  H
1089 GLU   ( 150-)  H

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

 |  0.998111  0.000050 -0.000164|
 |  0.000050  0.998461  0.000143|
 | -0.000164  0.000143  0.998929|
Proposed new scale matrix

 |  0.010636  0.000000  0.000002|
 |  0.000000  0.008367 -0.000001|
 |  0.000001 -0.000001  0.007286|
With corresponding cell

    A    =  94.019  B   = 119.519  C    = 137.253
    Alpha=  89.984  Beta=  90.019  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  94.200  B   = 119.700  C    = 137.400
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 87.691
(Under-)estimated Z-score: 6.901

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.

   7 GLN   (   9-)  A      N    CA   C    99.88   -4.0
  86 GLU   (  88-)  A      N    CA   C    96.90   -5.1
 161 CYS   ( 163-)  A      N    CA   C    97.43   -4.9
 264 GLU   (  88-)  D      N    CA   C    98.34   -4.6
 339 CYS   ( 163-)  D      N    CA   C    96.37   -5.3
 456 LYS   (  98-)  B      N    CA   C    98.72   -4.5
 647 LYS   (  98-)  E      N    CA   C    99.80   -4.1
 805 GLY   (  41-)  G      N    CA   C    98.99   -4.7
 824 ARG   (  60-)  G      CB   CG   CD  105.59   -4.3
 982 GLY   (  41-)  H      N    CA   C   100.69   -4.1

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.

   1 GLU   (   3-)  A
   2 GLU   (   4-)  A
  23 ASP   (  25-)  A
  28 GLU   (  30-)  A
  44 GLU   (  46-)  A
  45 GLU   (  47-)  A
  48 ARG   (  50-)  A
  96 GLU   (  98-)  A
 108 ASP   ( 110-)  A
 132 GLU   ( 134-)  A
 156 GLU   ( 158-)  A
 164 GLU   ( 166-)  A
 170 GLU   ( 172-)  A
 177 GLU   ( 179-)  A
 201 ASP   (  25-)  D
 206 GLU   (  30-)  D
 211 ASP   (  35-)  D
 223 GLU   (  47-)  D
 231 GLU   (  55-)  D
 247 GLU   (  71-)  D
 252 ARG   (  76-)  D
 286 ASP   ( 110-)  D
 299 ARG   ( 123-)  D
 310 GLU   ( 134-)  D
 317 GLU   ( 141-)  D
And so on for a total of 82 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 339 CYS   ( 163-)  D    5.59
  86 GLU   (  88-)  A    5.41
 805 GLY   (  41-)  G    5.23
 161 CYS   ( 163-)  A    5.13
 456 LYS   (  98-)  B    4.91
 264 GLU   (  88-)  D    4.78
 982 GLY   (  41-)  H    4.62
 671 PHE   ( 122-)  E    4.53
 320 LEU   ( 144-)  D    4.47
 604 ARG   (  55-)  E    4.43
 647 LYS   (  98-)  E    4.42

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.

 869 HIS   ( 107-)  G    -3.2
 111 THR   ( 113-)  A    -2.7
1077 ILE   ( 138-)  H    -2.7
 289 THR   ( 113-)  D    -2.6
 910 GLN   ( 148-)  G    -2.5
 299 ARG   ( 123-)  D    -2.5
 978 LEU   (  37-)  H    -2.4
 329 PHE   ( 153-)  D    -2.4
 943 LYS   (   2-)  H    -2.4
1116 LEU   ( 177-)  H    -2.3
 275 LEU   (  99-)  D    -2.3
 151 PHE   ( 153-)  A    -2.3
 662 ASN   ( 113-)  E    -2.3
  98 ARG   ( 100-)  A    -2.3
 512 THR   ( 154-)  B    -2.3
 115 VAL   ( 117-)  A    -2.2
 255 TYR   (  79-)  D    -2.2
 293 VAL   ( 117-)  D    -2.2
 587 VAL   (  38-)  E    -2.2
1104 GLN   ( 165-)  H    -2.2
 521 THR   ( 163-)  B    -2.2
 643 ARG   (  94-)  E    -2.2
1095 THR   ( 156-)  H    -2.2
 864 LEU   ( 100-)  G    -2.2
 918 THR   ( 156-)  G    -2.2
 706 THR   ( 157-)  E    -2.2
 174 LYS   ( 176-)  A    -2.1
1080 GLY   ( 141-)  H    -2.1
1055 LEU   ( 116-)  H    -2.1
 396 VAL   (  38-)  B    -2.1
 965 ILE   (  24-)  H    -2.1
 516 LEU   ( 158-)  B    -2.1
 903 GLY   ( 141-)  G    -2.1
 515 THR   ( 157-)  B    -2.1
 471 ASN   ( 113-)  B    -2.1
 539 THR   ( 181-)  B    -2.0
 741 LYS   (   4-)  C    -2.0
 852 ASP   (  88-)  G    -2.0
 333 THR   ( 157-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  13 ASN   (  15-)  A  PRO omega poor
  16 GLN   (  18-)  A  Poor phi/psi
  76 ASN   (  78-)  A  Poor phi/psi
 111 THR   ( 113-)  A  PRO omega poor
 127 THR   ( 129-)  A  Poor phi/psi
 141 HIS   ( 143-)  A  Poor phi/psi
 191 ASN   (  15-)  D  PRO omega poor
 194 GLN   (  18-)  D  Poor phi/psi
 254 ASN   (  78-)  D  Poor phi/psi
 289 THR   ( 113-)  D  PRO omega poor
 305 THR   ( 129-)  D  Poor phi/psi
 307 GLY   ( 131-)  D  Poor phi/psi
 319 HIS   ( 143-)  D  Poor phi/psi
 360 ASP   (   2-)  B  Poor phi/psi
 391 ASN   (  33-)  B  Poor phi/psi
 448 THR   (  90-)  B  Poor phi/psi
 469 HIS   ( 111-)  B  Poor phi/psi
 470 HIS   ( 112-)  B  Poor phi/psi
 471 ASN   ( 113-)  B  Poor phi/psi
 481 TYR   ( 123-)  B  PRO omega poor
 492 ASN   ( 134-)  B  Poor phi/psi
 511 TRP   ( 153-)  B  Poor phi/psi
 551 ASP   (   2-)  E  Poor phi/psi
 582 ASN   (  33-)  E  Poor phi/psi
 639 THR   (  90-)  E  Poor phi/psi
 660 HIS   ( 111-)  E  Poor phi/psi
 662 ASN   ( 113-)  E  Poor phi/psi
 672 TYR   ( 123-)  E  PRO omega poor
 702 TRP   ( 153-)  E  Poor phi/psi
 773 GLY   (   9-)  G  Poor phi/psi
 797 GLN   (  33-)  G  Poor phi/psi
 816 ASN   (  52-)  G  Poor phi/psi
 844 ASP   (  80-)  G  Poor phi/psi
 852 ASP   (  88-)  G  Poor phi/psi
 927 GLN   ( 165-)  G  Poor phi/psi
 939 LEU   ( 177-)  G  Poor phi/psi
 950 GLY   (   9-)  H  Poor phi/psi
 974 GLN   (  33-)  H  Poor phi/psi
 993 ASN   (  52-)  H  Poor phi/psi
1021 ASP   (  80-)  H  Poor phi/psi
1044 ASN   ( 103-)  H  Poor phi/psi
1045 SER   ( 104-)  H  Poor phi/psi
1052 SER   ( 113-)  H  Poor phi/psi
1055 LEU   ( 116-)  H  Poor phi/psi
1071 SER   ( 132-)  H  Poor phi/psi
1081 LYS   ( 142-)  H  Poor phi/psi
1082 THR   ( 143-)  H  Poor phi/psi
1083 LEU   ( 144-)  H  Poor phi/psi
1104 GLN   ( 165-)  H  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.103

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.

 930 VAL   ( 168-)  G    0.36

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!

   9 GLU   (  11-)  A      0
  13 ASN   (  15-)  A      0
  15 ASP   (  17-)  A      0
  24 PHE   (  26-)  A      0
  29 ILE   (  31-)  A      0
  30 PHE   (  32-)  A      0
  49 PHE   (  51-)  A      0
  75 SER   (  77-)  A      0
  76 ASN   (  78-)  A      0
  77 TYR   (  79-)  A      0
  97 LEU   (  99-)  A      0
  98 ARG   ( 100-)  A      0
 108 ASP   ( 110-)  A      0
 109 LYS   ( 111-)  A      0
 110 PHE   ( 112-)  A      0
 111 THR   ( 113-)  A      0
 112 PRO   ( 114-)  A      0
 113 PRO   ( 115-)  A      0
 114 VAL   ( 116-)  A      0
 116 ASN   ( 118-)  A      0
 121 ARG   ( 123-)  A      0
 127 THR   ( 129-)  A      0
 128 THR   ( 130-)  A      0
 131 SER   ( 133-)  A      0
 135 PHE   ( 137-)  A      0
And so on for a total of 471 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.747

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!

1050 GLY   ( 111-)  H   1.81   80
 483 GLY   ( 125-)  B   1.65   53
 674 GLY   ( 125-)  E   1.54   53

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]

 466 PRO   ( 108-)  B    0.00 LOW
1065 PRO   ( 126-)  H    0.46 HIGH

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].

 732 PRO   ( 183-)  E  -117.6 half-chair C-delta/C-gamma (-126 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.

 508 ASN   ( 150-)  B      ND2 <->  512 THR   ( 154-)  B      CG2    0.33    2.77  INTRA BL
 491 ARG   ( 133-)  B      NH2 <->  527 GLU   ( 169-)  B      OE2    0.30    2.40  INTRA BF
 783 SER   (  19-)  G      N   <->  851 GLU   (  87-)  G      OE2    0.30    2.40  INTRA BF
 679 ARG   ( 130-)  E      NH2 <->  725 GLU   ( 176-)  E      OE1    0.28    2.42  INTRA
 878 LEU   ( 116-)  G      CD1 <->  892 CYS   ( 130-)  G      SG     0.28    3.12  INTRA BF
 900 ILE   ( 138-)  G      CG2 <->  901 GLN   ( 139-)  G      N      0.27    2.73  INTRA BF
1053 LEU   ( 114-)  H      N   <-> 1085 VAL   ( 146-)  H      O      0.27    2.43  INTRA BF
1071 SER   ( 132-)  H      CA  <-> 1096 TRP   ( 157-)  H      NE1    0.26    2.84  INTRA BF
 252 ARG   (  76-)  D      NH2 <->  606 ASP   (  57-)  E      OD2    0.26    2.44  INTRA BL
 968 HIS   (  27-)  H      NE2 <->  970 LYS   (  29-)  H      CE     0.25    2.85  INTRA
 322 ARG   ( 146-)  D      NH1 <-> 1131 HOH   ( 202 )  D      O      0.25    2.45  INTRA BL
1054 THR   ( 115-)  H      CG2 <-> 1055 LEU   ( 116-)  H      N      0.24    2.76  INTRA BF
 372 GLU   (  14-)  B      OE2 <->  387 ARG   (  29-)  B      NH1    0.24    2.46  INTRA
  53 GLU   (  55-)  A      N   <->  741 LYS   (   4-)  C      CE     0.24    2.86  INTRA
 395 SER   (  37-)  B      O   <->  408 VAL   (  50-)  B      N      0.24    2.46  INTRA BL
 682 ARG   ( 133-)  E      NH2 <->  718 GLU   ( 169-)  E      OE2    0.23    2.47  INTRA BF
1093 SER   ( 154-)  H      OG  <-> 1115 VAL   ( 176-)  H      N      0.23    2.47  INTRA BF
 410 GLU   (  52-)  B      OE1 <->  413 ARG   (  55-)  B      NH2    0.22    2.48  INTRA BF
 645 GLU   (  96-)  E      O   <->  647 LYS   (  98-)  E      NZ     0.22    2.48  INTRA
1097 THR   ( 158-)  H      CG2 <-> 1110 LYS   ( 171-)  H      NZ     0.22    2.88  INTRA BF
 806 SER   (  42-)  G      O   <->  823 ARG   (  59-)  G      NH2    0.21    2.49  INTRA
 404 GLU   (  46-)  B      OE2 <->  406 ARG   (  48-)  B      NH2    0.19    2.51  INTRA BF
 824 ARG   (  60-)  G      NH1 <-> 1127 GOL   ( 965-)  G      C2     0.19    2.91  INTRA BF
  52 PHE   (  54-)  A      CA  <->  741 LYS   (   4-)  C      CE     0.19    3.01  INTRA
 342 GLU   ( 166-)  D      OE1 <->  549 MET   (   0-)  E      N      0.18    2.52  INTRA
And so on for a total of 151 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: 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Warning: Abnormal packing environment for some residues

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

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

 869 HIS   ( 107-)  G      -7.21
 276 ARG   ( 100-)  D      -6.99
  98 ARG   ( 100-)  A      -6.92
1073 ARG   ( 134-)  H      -6.81
 896 ARG   ( 134-)  G      -6.37
1051 GLN   ( 112-)  H      -6.10
 658 LEU   ( 109-)  E      -5.98
 497 LYS   ( 139-)  B      -5.64
 470 HIS   ( 112-)  B      -5.62
 715 ARG   ( 166-)  E      -5.51
 688 LYS   ( 139-)  E      -5.34
 524 ARG   ( 166-)  B      -5.32
 942 LYS   (   1-)  H      -5.29
1078 GLN   ( 139-)  H      -5.25
1116 LEU   ( 177-)  H      -5.25
 547 ARG   ( 189-)  B      -5.19
 661 HIS   ( 112-)  E      -5.18
  16 GLN   (  18-)  A      -5.14
 784 GLN   (  20-)  G      -5.06
  48 ARG   (  50-)  A      -5.01

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: 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: 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: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Warning: Low packing Z-score for some residues

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

 467 LEU   ( 109-)  B   -3.28
1075 LYS   ( 136-)  H   -3.05
1081 LYS   ( 142-)  H   -3.04
 465 GLN   ( 107-)  B   -3.03
1048 LEU   ( 109-)  H   -2.97
 659 GLN   ( 110-)  E   -2.96
 468 GLN   ( 110-)  B   -2.96
1047 THR   ( 106-)  H   -2.93
1083 LEU   ( 144-)  H   -2.77
 870 LEU   ( 108-)  G   -2.69
1090 LEU   ( 151-)  H   -2.61
 815 LEU   (  51-)  G   -2.61
1042 THR   ( 101-)  H   -2.55
 992 LEU   (  51-)  H   -2.54
 913 LEU   ( 151-)  G   -2.54
 469 HIS   ( 111-)  B   -2.53
 463 LYS   ( 105-)  B   -2.52
 654 LYS   ( 105-)  E   -2.52

Warning: Abnormal packing Z-score for sequential residues

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

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

 462 SER   ( 104-)  B     -  465 GLN   ( 107-)  B        -2.15
 466 PRO   ( 108-)  B     -  469 HIS   ( 111-)  B        -2.60

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: 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: C

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Water, ion, and hydrogenbond related checks

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.

1130 HOH   ( 217 )  A      O    -69.19  -79.26  -95.25
1130 HOH   ( 248 )  A      O    -31.77  -18.90  -83.27
1130 HOH   ( 257 )  A      O    -64.37  -80.74  -95.56
1131 HOH   ( 214 )  D      O    -78.90  -33.95  -36.16

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.

 141 HIS   ( 143-)  A
 147 HIS   ( 149-)  A
 319 HIS   ( 143-)  D
 428 GLN   (  70-)  B
 440 ASN   (  82-)  B
 492 ASN   ( 134-)  B
 494 GLN   ( 136-)  B
 611 ASN   (  62-)  E
 619 GLN   (  70-)  E
 631 ASN   (  82-)  E
 662 ASN   ( 113-)  E
 683 ASN   ( 134-)  E
 685 GLN   ( 136-)  E
 837 ASN   (  73-)  G
 874 GLN   ( 112-)  G
1035 GLN   (  94-)  H
1049 GLN   ( 110-)  H
1078 GLN   ( 139-)  H
1104 GLN   ( 165-)  H

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.

  43 LEU   (  45-)  A      N
  53 GLU   (  55-)  A      N
 116 ASN   ( 118-)  A      ND2
 119 TRP   ( 121-)  A      NE1
 175 GLN   ( 177-)  A      N
 221 LEU   (  45-)  D      N
 294 ASN   ( 118-)  D      ND2
 404 GLU   (  46-)  B      N
 429 ARG   (  71-)  B      NH2
 458 THR   ( 100-)  B      OG1
 502 SER   ( 144-)  B      OG
 532 GLN   ( 174-)  B      NE2
 550 GLY   (   1-)  E      N
 578 ARG   (  29-)  E      NE
 586 SER   (  37-)  E      OG
 595 GLU   (  46-)  E      N
 624 VAL   (  75-)  E      N
 631 ASN   (  82-)  E      ND2
 649 THR   ( 100-)  E      OG1
 658 LEU   ( 109-)  E      N
 661 HIS   ( 112-)  E      N
 691 VAL   ( 142-)  E      N
 693 SER   ( 144-)  E      OG
 723 GLN   ( 174-)  E      NE2
 738 ARG   ( 189-)  E      NE
 745 GLN   (   8-)  C      NE2
 758 GLN   (   8-)  F      NE2
 788 ILE   (  24-)  G      N
 818 ARG   (  54-)  G      NH2
 822 ARG   (  58-)  G      NE
 824 ARG   (  60-)  G      N
 869 HIS   ( 107-)  G      N
 872 GLN   ( 110-)  G      N
 892 CYS   ( 130-)  G      N
 894 SER   ( 132-)  G      OG
 905 THR   ( 143-)  G      N
 927 GLN   ( 165-)  G      N
 944 VAL   (   3-)  H      N
 965 ILE   (  24-)  H      N
 968 HIS   (  27-)  H      NE2
 996 ALA   (  55-)  H      N
1001 ARG   (  60-)  H      NH1
1004 ARG   (  63-)  H      N
1070 ARG   ( 131-)  H      N
1073 ARG   ( 134-)  H      N
1081 LYS   ( 142-)  H      N
1092 ASP   ( 153-)  H      N
1093 SER   ( 154-)  H      OG
1116 LEU   ( 177-)  H      N

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.

   1 GLU   (   3-)  A      OE1
  64 ASP   (  66-)  A      OD1
 187 GLU   (  11-)  D      OE1
 242 ASP   (  66-)  D      OD2
 325 HIS   ( 149-)  D      ND1
 855 GLU   (  91-)  G      OE2
 915 ASP   ( 153-)  G      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1130 HOH   ( 200 )  A      O  1.01  K  4

Warning: Possible wrong residue type

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

  19 GLU   (  21-)  A   H-bonding suggests Gln
  64 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
  69 GLU   (  71-)  A   H-bonding suggests Gln
 197 GLU   (  21-)  D   H-bonding suggests Gln
 242 ASP   (  66-)  D   H-bonding suggests Asn; but Alt-Rotamer
 334 GLU   ( 158-)  D   H-bonding suggests Gln
 357 ASP   ( 181-)  D   H-bonding suggests Asn
 510 ASP   ( 152-)  B   H-bonding suggests Asn; Ligand-contact
 701 ASP   ( 152-)  E   H-bonding suggests Asn; Ligand-contact
 852 ASP   (  88-)  G   H-bonding suggests Asn
 855 GLU   (  91-)  G   H-bonding suggests Gln
1032 GLU   (  91-)  H   H-bonding suggests Gln

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 :   0.258
  2nd generation packing quality :  -1.215
  Ramachandran plot appearance   :  -0.676
  chi-1/chi-2 rotamer normality  :  -2.103
  Backbone conformation          :   0.051

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.404 (tight)
  Bond angles                    :   0.701
  Omega angle restraints         :   0.318 (tight)
  Side chain planarity           :   0.286 (tight)
  Improper dihedral distribution :   0.693
  B-factor distribution          :   0.508
  Inside/Outside distribution    :   1.009

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.404 (tight)
  Bond angles                    :   0.701
  Omega angle restraints         :   0.318 (tight)
  Side chain planarity           :   0.286 (tight)
  Improper dihedral distribution :   0.693
  B-factor distribution          :   0.508
  Inside/Outside distribution    :   1.009
==============

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.