WHAT IF Check report

This file was created 2012-06-08 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 pdb1tw8.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.017
CA-only RMS fit for the two chains : 0.686

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 1.200
CA-only RMS fit for the two chains : 0.789

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 1.008
CA-only RMS fit for the two chains : 0.616

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 C

All-atom RMS fit for the two chains : 1.178
CA-only RMS fit for the two chains : 0.738

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 C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.979
CA-only RMS fit for the two chains : 0.657

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 D

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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'.

  72 LYS   (  21-)  A      CG
  72 LYS   (  21-)  A      CD
  72 LYS   (  21-)  A      CE
  72 LYS   (  21-)  A      NZ
  75 LYS   (  24-)  A      CG
  75 LYS   (  24-)  A      CD
  75 LYS   (  24-)  A      CE
  75 LYS   (  24-)  A      NZ
  86 GLU   (  35-)  A      CG
  86 GLU   (  35-)  A      CD
  86 GLU   (  35-)  A      OE1
  86 GLU   (  35-)  A      OE2
  90 LYS   (  39-)  A      CG
  90 LYS   (  39-)  A      CD
  90 LYS   (  39-)  A      CE
  90 LYS   (  39-)  A      NZ
 101 SER   (  50-)  A      OG
 153 GLU   ( 102-)  A      CG
 153 GLU   ( 102-)  A      CD
 153 GLU   ( 102-)  A      OE1
 153 GLU   ( 102-)  A      OE2
 210 LYS   ( 159-)  A      CG
 210 LYS   ( 159-)  A      CD
 210 LYS   ( 159-)  A      CE
 210 LYS   ( 159-)  A      NZ
And so on for a total of 156 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.

  13 DGUA  (  13-)  E    High
  26 DGUA  (  13-)  F    High
  27 DGUA  (   1-)  G    High
  28 DCYT  (   2-)  G    High
  29 DCYT  (   3-)  G    High
  39 DGUA  (  13-)  G    High
  40 DGUA  (   1-)  H    High
  41 DCYT  (   2-)  H    High
  42 DCYT  (   3-)  H    High
  52 DGUA  (  13-)  H    High
  73 ARG   (  22-)  A    High
  74 PRO   (  23-)  A    High
  78 THR   (  27-)  A    High
  86 GLU   (  35-)  A    High
 229 GLU   ( 178-)  A    High
 332 LYS   (  24-)  B    High
 333 SER   (  25-)  B    High
 334 GLY   (  26-)  B    High
 336 LEU   (  28-)  B    High
 567 PHE   (   3-)  C    High
 568 ILE   (   4-)  C    High
 569 LYS   (   5-)  C    High
 570 PRO   (   6-)  C    High
 571 ILE   (   7-)  C    High
 572 TYR   (   8-)  C    High
And so on for a total of 164 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

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.617 over 6597 bonds
Average difference in B over a bond : 4.91
RMS difference in B over a bond : 6.43

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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.

 142 ARG   (  91-)  A

Warning: Tyrosine convention problem

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

  93 TYR   (  42-)  A
 367 TYR   (  59-)  B
 476 TYR   ( 168-)  B
 763 TYR   ( 199-)  C
 820 TYR   ( 256-)  C

Warning: Phenylalanine convention problem

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

  88 PHE   (  37-)  A
 156 PHE   ( 105-)  A
 215 PHE   ( 164-)  A
 242 PHE   ( 191-)  A
 345 PHE   (  37-)  B
 388 PHE   (  80-)  B
 413 PHE   ( 105-)  B
 472 PHE   ( 164-)  B
 499 PHE   ( 191-)  B
 561 PHE   ( 253-)  B
 728 PHE   ( 164-)  C
 755 PHE   ( 191-)  C
 858 PHE   (  37-)  D
 865 PHE   (  44-)  D
 926 PHE   ( 105-)  D
 985 PHE   ( 164-)  D
1012 PHE   ( 191-)  D

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.

 165 ASP   ( 114-)  A
 171 ASP   ( 120-)  A
 208 ASP   ( 157-)  A
 230 ASP   ( 179-)  A
 265 ASP   ( 214-)  A
 370 ASP   (  62-)  B
 422 ASP   ( 114-)  B
 428 ASP   ( 120-)  B
 435 ASP   ( 127-)  B
 470 ASP   ( 162-)  B
 473 ASP   ( 165-)  B
 480 ASP   ( 172-)  B
 524 ASP   ( 216-)  B
 721 ASP   ( 157-)  C
 736 ASP   ( 172-)  C
 883 ASP   (  62-)  D
 948 ASP   ( 127-)  D
1000 ASP   ( 179-)  D

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.

  89 GLU   (  38-)  A
 125 GLU   (  74-)  A
 148 GLU   (  97-)  A
 157 GLU   ( 106-)  A
 158 GLU   ( 107-)  A
 175 GLU   ( 124-)  A
 225 GLU   ( 174-)  A
 240 GLU   ( 189-)  A
 275 GLU   ( 224-)  A
 355 GLU   (  47-)  B
 366 GLU   (  58-)  B
 410 GLU   ( 102-)  B
 432 GLU   ( 124-)  B
 478 GLU   ( 170-)  B
 482 GLU   ( 174-)  B
 505 GLU   ( 197-)  B
 532 GLU   ( 224-)  B
 599 GLU   (  35-)  C
 602 GLU   (  38-)  C
 622 GLU   (  58-)  C
 688 GLU   ( 124-)  C
 738 GLU   ( 174-)  C
 753 GLU   ( 189-)  C
 803 GLU   ( 239-)  C
 856 GLU   (  35-)  D
 859 GLU   (  38-)  D
 918 GLU   (  97-)  D
 981 GLU   ( 160-)  D
 995 GLU   ( 174-)  D
1010 GLU   ( 189-)  D
1015 GLU   ( 194-)  D
1045 GLU   ( 224-)  D
1060 GLU   ( 239-)  D

Geometric checks

Warning: Unusual bond angles

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

   1 DGUA  (   1-)  E      N9   C8   N7  113.13    4.1
   4 DGUA  (   4-)  E      N9   C8   N7  113.12    4.0
  10 DCYT  (  10-)  E      C2'  C1'  N1  105.79   -5.3
  13 DGUA  (  13-)  E      N9   C8   N7  113.18    4.2
  14 DGUA  (   1-)  F      N9   C8   N7  113.11    4.0
  18 DGUA  (   5-)  F      C3'  C4'  C5' 108.28   -4.3
  18 DGUA  (   5-)  F      N9   C8   N7  113.16    4.1
  23 DCYT  (  10-)  F      C2'  C1'  N1  107.27   -4.3
  26 DGUA  (  13-)  F      N9   C8   N7  113.27    4.3
  31 DGUA  (   5-)  G      N9   C8   N7  113.19    4.2
  38 DGUA  (  12-)  G      N9   C8   N7  113.21    4.2
  43 DGUA  (   4-)  H      N9   C8   N7  113.26    4.3
  44 DGUA  (   5-)  H      N9   C8   N7  113.13    4.1
  51 DGUA  (  12-)  H      N9   C8   N7  113.13    4.1
  52 DGUA  (  13-)  H      N9   C8   N7  113.21    4.2
 363 LYS   (  55-)  B      N    CA   C    99.56   -4.2
1054 HIS   ( 233-)  D      CG   ND1  CE1 109.75    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.

  89 GLU   (  38-)  A
 125 GLU   (  74-)  A
 142 ARG   (  91-)  A
 148 GLU   (  97-)  A
 157 GLU   ( 106-)  A
 158 GLU   ( 107-)  A
 165 ASP   ( 114-)  A
 171 ASP   ( 120-)  A
 175 GLU   ( 124-)  A
 208 ASP   ( 157-)  A
 225 GLU   ( 174-)  A
 230 ASP   ( 179-)  A
 240 GLU   ( 189-)  A
 265 ASP   ( 214-)  A
 275 GLU   ( 224-)  A
 355 GLU   (  47-)  B
 366 GLU   (  58-)  B
 370 ASP   (  62-)  B
 410 GLU   ( 102-)  B
 422 ASP   ( 114-)  B
 428 ASP   ( 120-)  B
 432 GLU   ( 124-)  B
 435 ASP   ( 127-)  B
 470 ASP   ( 162-)  B
 473 ASP   ( 165-)  B
And so on for a total of 52 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.

 140 LEU   (  89-)  A    4.75
 363 LYS   (  55-)  B    4.52

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

  20 DCYT  (   7-)  F    0.12
   7 DCYT  (   7-)  E    0.11
 Ramachandran Z-score : -4.684

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.684

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.

 122 ILE   (  71-)  A    -2.7
  79 LEU   (  28-)  A    -2.6
 575 ILE   (  11-)  C    -2.5
 638 GLU   (  74-)  C    -2.3
 631 ASN   (  67-)  C    -2.3
 964 ILE   ( 143-)  D    -2.3
 399 ARG   (  91-)  B    -2.3
 578 ILE   (  14-)  C    -2.3
 382 GLU   (  74-)  B    -2.3
 774 PHE   ( 210-)  C    -2.3
 229 GLU   ( 178-)  A    -2.2
 172 GLN   ( 121-)  A    -2.2
 336 LEU   (  28-)  B    -2.2
 493 THR   ( 185-)  B    -2.2
 903 SER   (  82-)  D    -2.2
 484 ASN   ( 176-)  B    -2.2
 441 ILE   ( 133-)  B    -2.2
 846 SER   (  25-)  D    -2.2
 758 GLU   ( 194-)  C    -2.2
 998 GLY   ( 177-)  D    -2.2
 912 ARG   (  91-)  D    -2.1
 828 ILE   (   7-)  D    -2.1
 922 ILE   ( 101-)  D    -2.1
 637 HIS   (  73-)  C    -2.1
 892 ILE   (  71-)  D    -2.1
 439 ARG   ( 131-)  B    -2.1
 152 ILE   ( 101-)  A    -2.1
 824 PHE   (   3-)  D    -2.1
1020 TYR   ( 199-)  D    -2.1
1039 GLY   ( 218-)  D    -2.0
 518 PHE   ( 210-)  B    -2.0
1031 PHE   ( 210-)  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.

  84 ALA   (  33-)  A  Poor phi/psi
 142 ARG   (  91-)  A  Poor phi/psi
 144 LYS   (  93-)  A  Poor phi/psi
 170 LYS   ( 119-)  A  Poor phi/psi
 171 ASP   ( 120-)  A  Poor phi/psi
 172 GLN   ( 121-)  A  Poor phi/psi
 210 LYS   ( 159-)  A  Poor phi/psi
 235 SER   ( 184-)  A  Poor phi/psi
 255 ALA   ( 204-)  A  Poor phi/psi
 256 ALA   ( 205-)  A  Poor phi/psi
 308 ILE   ( 257-)  A  Poor phi/psi
 331 PRO   (  23-)  B  Poor phi/psi
 333 SER   (  25-)  B  Poor phi/psi
 335 THR   (  27-)  B  Poor phi/psi
 341 ALA   (  33-)  B  Poor phi/psi
 382 GLU   (  74-)  B  Poor phi/psi
 389 ASN   (  81-)  B  Poor phi/psi
 390 SER   (  82-)  B  Poor phi/psi
 428 ASP   ( 120-)  B  Poor phi/psi
 429 GLN   ( 121-)  B  Poor phi/psi
 467 LYS   ( 159-)  B  Poor phi/psi
 471 LEU   ( 163-)  B  Poor phi/psi
 513 ALA   ( 205-)  B  Poor phi/psi
 556 LYS   ( 248-)  B  Poor phi/psi
 589 SER   (  25-)  C  Poor phi/psi
 620 GLN   (  56-)  C  Poor phi/psi
 631 ASN   (  67-)  C  Poor phi/psi
 637 HIS   (  73-)  C  Poor phi/psi
 638 GLU   (  74-)  C  Poor phi/psi
 646 SER   (  82-)  C  Poor phi/psi
 655 ARG   (  91-)  C  Poor phi/psi
 668 LEU   ( 104-)  C  Poor phi/psi
 684 ASP   ( 120-)  C  Poor phi/psi
 727 LEU   ( 163-)  C  Poor phi/psi
 747 VAL   ( 183-)  C  Poor phi/psi
 774 PHE   ( 210-)  C  Poor phi/psi
 844 PRO   (  23-)  D  Poor phi/psi
 845 LYS   (  24-)  D  Poor phi/psi
 846 SER   (  25-)  D  Poor phi/psi
 902 ASN   (  81-)  D  Poor phi/psi
 903 SER   (  82-)  D  Poor phi/psi
 941 ASP   ( 120-)  D  Poor phi/psi
 942 GLN   ( 121-)  D  Poor phi/psi
1016 PRO   ( 195-)  D  Poor phi/psi
1020 TYR   ( 199-)  D  Poor phi/psi
1026 ALA   ( 205-)  D  Poor phi/psi
1031 PHE   ( 210-)  D  Poor phi/psi
1035 ASP   ( 214-)  D  Poor phi/psi
1071 VAL   ( 250-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.214

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

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

chi-1/chi-2 correlation Z-score : -3.214

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.

  64 SER   (  13-)  A    0.39

Warning: Unusual backbone conformations

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

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

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

   3 DCYT  (   3-)  E      0
   4 DGUA  (   4-)  E      0
   5 DGUA  (   5-)  E      0
   6 DTHY  (   6-)  E      0
   7 DCYT  (   7-)  E      0
   8 DGUA  (   8-)  E      0
   9 DADE  (   9-)  E      0
  10 DCYT  (  10-)  E      0
  11 DCYT  (  11-)  E      0
  12 DGUA  (  12-)  E      0
  13 DGUA  (  13-)  E      0
  14 DGUA  (   1-)  F      0
  15 DCYT  (   2-)  F      0
  16 DCYT  (   3-)  F      0
  17 DGUA  (   4-)  F      0
  18 DGUA  (   5-)  F      0
  19 DTHY  (   6-)  F      0
  20 DCYT  (   7-)  F      0
  21 DGUA  (   8-)  F      0
  22 DADE  (   9-)  F      0
  23 DCYT  (  10-)  F      0
  24 DCYT  (  11-)  F      0
  25 DGUA  (  12-)  F      0
  26 DGUA  (  13-)  F      0
  27 DGUA  (   1-)  G      0
And so on for a total of 456 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 : 0.908

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!

  77 GLY   (  26-)  A   1.76   11

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 119 PRO   (  68-)  A    0.46 HIGH

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 931 ASN   ( 110-)  D      N   <-> 1096 HOH   ( 916 )  D      O      0.49    2.21  INTRA BL
 116 MET   (  65-)  A      SD  <-> 1093 HOH   ( 962 )  A      O      0.48    2.52  INTRA BF
 922 ILE   ( 101-)  D      N   <-> 1096 HOH   ( 931 )  D      O      0.38    2.32  INTRA BF
  37 DCYT  (  11-)  G      N3  <->   43 DGUA  (   4-)  H      N1     0.36    2.64  INTRA BL
 637 HIS   (  73-)  C      O   <->  639 ALA   (  75-)  C      N      0.32    2.38  INTRA BF
 418 ASN   ( 110-)  B      N   <-> 1094 HOH   ( 997 )  B      O      0.32    2.38  INTRA BL
 805 ARG   ( 241-)  C      NH2 <-> 1095 HOH   (1003 )  C      O      0.32    2.38  INTRA BF
 257 MET   ( 206-)  A      SD  <-> 1090 HOH   ( 833 )  F      O      0.30    2.70  INTRA BF
 499 PHE   ( 191-)  B      CD2 <->  531 ARG   ( 223-)  B      NH1    0.29    2.81  INTRA BL
  69 GLN   (  18-)  A      C   <-> 1093 HOH   ( 923 )  A      O      0.29    2.51  INTRA BF
1019 LEU   ( 198-)  D      CB  <-> 1096 HOH   ( 943 )  D      O      0.28    2.52  INTRA BL
  47 DGUA  (   8-)  H      N7  <->  705 ASN   ( 141-)  C      ND2    0.27    2.73  INTRA BL
 912 ARG   (  91-)  D      NH2 <->  929 LYS   ( 108-)  D      CB     0.27    2.83  INTRA BF
 914 LYS   (  93-)  D      NZ  <-> 1096 HOH   (1032 )  D      O      0.25    2.45  INTRA BF
 736 ASP   ( 172-)  C      OD2 <->  777 ARG   ( 213-)  C      NH2    0.25    2.45  INTRA BF
 658 ALA   (  94-)  C      N   <-> 1095 HOH   ( 928 )  C      O      0.24    2.46  INTRA BF
 693 LYS   ( 129-)  C      NZ  <->  705 ASN   ( 141-)  C      O      0.24    2.46  INTRA BL
 414 GLU   ( 106-)  B      CD  <-> 1094 HOH   (1081 )  B      O      0.23    2.57  INTRA BF
 399 ARG   (  91-)  B      NH2 <->  414 GLU   ( 106-)  B      O      0.23    2.47  INTRA BL
 921 SER   ( 100-)  D      C   <-> 1096 HOH   ( 931 )  D      O      0.23    2.57  INTRA BF
 183 ASN   ( 132-)  A      ND2 <->  224 TRP   ( 173-)  A      CH2    0.23    2.87  INTRA BL
  36 DCYT  (  10-)  G      N3  <->   44 DGUA  (   5-)  H      N1     0.23    2.77  INTRA BL
 242 PHE   ( 191-)  A      N   <-> 1093 HOH   (1003 )  A      O      0.23    2.47  INTRA BL
  34 DGUA  (   8-)  G      N7  <->  962 ASN   ( 141-)  D      ND2    0.23    2.77  INTRA BL
 399 ARG   (  91-)  B      NH1 <->  419 ASP   ( 111-)  B      OD1    0.22    2.48  INTRA BL
And so on for a total of 333 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 446 GLN   ( 138-)  B      -7.37
 959 GLN   ( 138-)  D      -7.24
 189 GLN   ( 138-)  A      -7.02
 843 ARG   (  22-)  D      -6.80
 702 GLN   ( 138-)  C      -6.77
 332 LYS   (  24-)  B      -6.72
 586 ARG   (  22-)  C      -6.61
  73 ARG   (  22-)  A      -6.56
 142 ARG   (  91-)  A      -5.53
 389 ASN   (  81-)  B      -5.51
 869 ASN   (  48-)  D      -5.44
 528 ASN   ( 220-)  B      -5.38
 892 ILE   (  71-)  D      -5.35
  99 ASN   (  48-)  A      -5.31
 209 ASN   ( 158-)  A      -5.30
 122 ILE   (  71-)  A      -5.30
1034 ARG   ( 213-)  D      -5.29
 379 ILE   (  71-)  B      -5.29
 573 GLN   (   9-)  C      -5.28
 330 ARG   (  22-)  B      -5.27
 673 GLN   ( 109-)  C      -5.22
 784 ASN   ( 220-)  C      -5.17
 149 ASN   (  98-)  A      -5.14
 635 ILE   (  71-)  C      -5.13
 560 PRO   ( 252-)  B      -5.08
  57 PRO   (   6-)  A      -5.04

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

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.

 931 ASN   ( 110-)  D   -4.13
 161 ASN   ( 110-)  A   -4.13
 674 ASN   ( 110-)  C   -4.06
 418 ASN   ( 110-)  B   -3.93
 940 LYS   ( 119-)  D   -3.81
 657 LYS   (  93-)  C   -3.32
 930 GLN   ( 109-)  D   -3.10
 718 LYS   ( 154-)  C   -3.00
 341 ALA   (  33-)  B   -2.87
 673 GLN   ( 109-)  C   -2.78
 588 LYS   (  24-)  C   -2.76
 959 GLN   ( 138-)  D   -2.72
 845 LYS   (  24-)  D   -2.71
 840 LYS   (  19-)  D   -2.71
 702 GLN   ( 138-)  C   -2.66
 189 GLN   ( 138-)  A   -2.65
 417 GLN   ( 109-)  B   -2.64
 445 ALA   ( 137-)  B   -2.60
 446 GLN   ( 138-)  B   -2.60
 429 GLN   ( 121-)  B   -2.59
  84 ALA   (  33-)  A   -2.57
 186 LYS   ( 135-)  A   -2.54
 227 ASN   ( 176-)  A   -2.53
 724 GLU   ( 160-)  C   -2.52
 701 ALA   ( 137-)  C   -2.52
  75 LYS   (  24-)  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.

 415 GLU   ( 107-)  B     -  418 ASN   ( 110-)  B        -2.37
 442 SER   ( 134-)  B     -  446 GLN   ( 138-)  B        -2.09
 700 SER   ( 136-)  C     -  703 ALA   ( 139-)  C        -2.16
 928 GLU   ( 107-)  D     -  931 ASN   ( 110-)  D        -2.21
 979 ASN   ( 158-)  D     -  982 PHE   ( 161-)  D        -2.01

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

1089 HOH   ( 116 )  E      O     51.72   40.07  214.43
1090 HOH   ( 821 )  F      O     20.39   44.33  207.61
1090 HOH   ( 838 )  F      O     38.88   46.39  210.51
1090 HOH   ( 839 )  F      O     36.70   46.22  212.04
1090 HOH   ( 843 )  F      O     20.85   46.77  207.31
1093 HOH   (1076 )  A      O      3.15   52.91  186.79
1093 HOH   (1090 )  A      O     65.87    5.61  199.94
1093 HOH   (1098 )  A      O     58.75   22.85  200.03
1094 HOH   ( 931 )  B      O     42.77   -1.12  191.55
1094 HOH   (1038 )  B      O     10.60   56.15  195.64
1094 HOH   (1100 )  B      O     40.06   44.17  219.69
1095 HOH   ( 958 )  C      O     34.76   21.16  175.46
1095 HOH   ( 991 )  C      O     35.47   21.95  177.82
1095 HOH   ( 994 )  C      O     -9.63  -29.99  227.61
1096 HOH   ( 924 )  D      O     56.36  -24.93  222.80

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1089 HOH   ( 397 )  E      O
1092 HOH   ( 398 )  H      O
1093 HOH   ( 916 )  A      O
1093 HOH   ( 938 )  A      O
1093 HOH   (1053 )  A      O
1093 HOH   (1089 )  A      O
1093 HOH   (1105 )  A      O
1094 HOH   ( 912 )  B      O
1094 HOH   ( 916 )  B      O
1094 HOH   ( 918 )  B      O
1094 HOH   ( 920 )  B      O
1094 HOH   ( 937 )  B      O
1094 HOH   (1001 )  B      O
1094 HOH   (1009 )  B      O
1094 HOH   (1094 )  B      O
1095 HOH   ( 966 )  C      O
1095 HOH   ( 993 )  C      O
1095 HOH   ( 996 )  C      O
1095 HOH   ( 998 )  C      O
1095 HOH   (1002 )  C      O
1096 HOH   ( 910 )  D      O
1096 HOH   ( 931 )  D      O
1096 HOH   ( 988 )  D      O
1096 HOH   (1010 )  D      O
1096 HOH   (1028 )  D      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  60 GLN   (   9-)  A
  69 GLN   (  18-)  A
  99 ASN   (  48-)  A
 149 ASN   (  98-)  A
 160 GLN   ( 109-)  A
 189 GLN   ( 138-)  A
 339 HIS   (  31-)  B
 356 ASN   (  48-)  B
 484 ASN   ( 176-)  B
 582 GLN   (  18-)  C
 781 GLN   ( 217-)  C
 833 ASN   (  12-)  D
 839 GLN   (  18-)  D
 877 GLN   (  56-)  D

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.

  47 DGUA  (   8-)  H      N2
  48 DADE  (   9-)  H      N6
  80 SER   (  29-)  A      N
  81 GLY   (  30-)  A      N
  83 ALA   (  32-)  A      N
  85 GLY   (  34-)  A      N
 108 TYR   (  57-)  A      N
 126 ALA   (  75-)  A      N
 130 LEU   (  79-)  A      N
 141 SER   (  90-)  A      OG
 143 GLY   (  92-)  A      N
 144 LYS   (  93-)  A      N
 152 ILE   ( 101-)  A      N
 163 THR   ( 112-)  A      N
 217 ILE   ( 166-)  A      N
 240 GLU   ( 189-)  A      N
 267 ASP   ( 216-)  A      N
 268 GLN   ( 217-)  A      NE2
 273 THR   ( 222-)  A      N
 274 ARG   ( 223-)  A      NE
 276 GLU   ( 225-)  A      N
 292 ARG   ( 241-)  A      NE
 330 ARG   (  22-)  B      N
 333 SER   (  25-)  B      N
 335 THR   (  27-)  B      OG1
And so on for a total of 116 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.

  98 GLU   (  47-)  A      OE2
 161 ASN   ( 110-)  A      OD1
 446 GLN   ( 138-)  B      OE1
 631 ASN   (  67-)  C      OD1
 722 ASN   ( 158-)  C      OD1
 736 ASP   ( 172-)  C      OD1
 771 GLN   ( 207-)  C      OE1
 781 GLN   ( 217-)  C      OE1
 852 HIS   (  31-)  D      ND1
 930 GLN   ( 109-)  D      OE1
 945 GLU   ( 124-)  D      OE1
 988 ASN   ( 167-)  D      OD1
 993 ASP   ( 172-)  D      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1079  CA   ( 805-)  F   -.-  -.-  Part of ionic cluster
1079  CA   ( 805-)  F     0.73   0.94 Scores about as good as NA *1 and *2
1080  CA   ( 806-)  H   -.-  -.-  Low probability ion. Occ=0.50
1084  NA   ( 902-)  B     1.18   0.96 Scores about as good as CA *1
1085  CA   ( 803-)  C     0.94   1.13 Scores about as good as NA *1 and *2
1087  CA   ( 804-)  D   -.-  -.-  Part of ionic cluster
1087  CA   ( 804-)  D     0.77   0.98 Scores about as good as NA *1 and *2
1088  NA   ( 904-)  D   -.-  -.-  Part of ionic cluster

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.

1093 HOH   (1103 )  A      O  0.99  K  4
1094 HOH   ( 904 )  B      O  0.93  K  5
1094 HOH   ( 990 )  B      O  1.14  K  4 Ion-B
1094 HOH   ( 992 )  B      O  1.03  K  5
1094 HOH   (1020 )  B      O  0.91  K  7
1094 HOH   (1056 )  B      O  1.01  K  6 Ion-B
1094 HOH   (1065 )  B      O  0.89  K  4 ION-B H2O-B

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.

 230 ASP   ( 179-)  A   H-bonding suggests Asn; but Alt-Rotamer
 555 ASP   ( 247-)  B   H-bonding suggests Asn
 626 ASP   (  62-)  C   H-bonding suggests Asn; but Alt-Rotamer
 721 ASP   ( 157-)  C   H-bonding suggests Asn
 978 ASP   ( 157-)  D   H-bonding suggests Asn
 983 ASP   ( 162-)  D   H-bonding suggests Asn
1035 ASP   ( 214-)  D   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 :  -0.805
  2nd generation packing quality :  -3.214 (poor)
  Ramachandran plot appearance   :  -4.684 (bad)
  chi-1/chi-2 rotamer normality  :  -3.214 (poor)
  Backbone conformation          :  -1.381

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.569 (tight)
  Omega angle restraints         :   0.165 (tight)
  Side chain planarity           :   0.227 (tight)
  Improper dihedral distribution :   0.563
  B-factor distribution          :   1.617 (loose)
  Inside/Outside distribution    :   1.005

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -2.2
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.569 (tight)
  Omega angle restraints         :   0.165 (tight)
  Side chain planarity           :   0.227 (tight)
  Improper dihedral distribution :   0.563
  B-factor distribution          :   1.617 (loose)
  Inside/Outside distribution    :   1.005
==============

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.