WHAT IF Check report

This file was created 2011-12-16 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 pdb3kdo.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.553
CA-only RMS fit for the two chains : 0.373

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 : 0.455
CA-only RMS fit for the two chains : 0.257

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 : 0.426
CA-only RMS fit for the two chains : 0.256

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: A and E

All-atom RMS fit for the two chains : 0.509
CA-only RMS fit for the two chains : 0.326

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 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: A and F

All-atom RMS fit for the two chains : 0.400
CA-only RMS fit for the two chains : 0.216

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 F

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.

4380 CAP   ( 600-)  A  -
4382 CAP   ( 600-)  B  -
4384 CAP   ( 600-)  C  -
4386 CAP   ( 600-)  D  -
4388 CAP   ( 600-)  E  -
4390 CAP   ( 600-)  F  -
4392 CAP   ( 600-)  G  -
4394 CAP   ( 600-)  H  -
4396 CAP   ( 600-)  I  -
4399 CAP   ( 600-)  J  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

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

Warning: Missing atoms

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

   1 TYR   (   9-)  A      CG
   1 TYR   (   9-)  A      CD1
   1 TYR   (   9-)  A      CD2
   1 TYR   (   9-)  A      CE1
   1 TYR   (   9-)  A      CE2
   1 TYR   (   9-)  A      CZ
   1 TYR   (   9-)  A      OH
   2 ASP   (  10-)  A      CG
   2 ASP   (  10-)  A      OD1
   2 ASP   (  10-)  A      OD2
  10 GLU   (  18-)  A      CG
  10 GLU   (  18-)  A      CD
  10 GLU   (  18-)  A      OE1
  10 GLU   (  18-)  A      OE2
  27 GLU   (  35-)  A      CG
  27 GLU   (  35-)  A      CD
  27 GLU   (  35-)  A      OE1
  27 GLU   (  35-)  A      OE2
  30 THR   (  38-)  A      OG1
  30 THR   (  38-)  A      CG2
  31 ILE   (  39-)  A      CG1
  31 ILE   (  39-)  A      CG2
  31 ILE   (  39-)  A      CD1
  33 GLN   (  41-)  A      CG
  33 GLN   (  41-)  A      CD
And so on for a total of 598 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

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.

 114 ARG   ( 122-)  A
 319 ARG   ( 327-)  A
 398 ARG   ( 406-)  A
 496 ARG   (  66-)  B
 547 ARG   ( 117-)  B
 552 ARG   ( 122-)  B
 695 ARG   ( 265-)  B
 839 ARG   ( 409-)  B
 987 ARG   ( 117-)  C
 992 ARG   ( 122-)  C
1197 ARG   ( 327-)  C
1279 ARG   ( 409-)  C
1429 ARG   ( 122-)  D
1716 ARG   ( 409-)  D
1740 ARG   ( 433-)  D
1813 ARG   (  66-)  E
1864 ARG   ( 117-)  E
1869 ARG   ( 122-)  E
2012 ARG   ( 265-)  E
2085 ARG   ( 338-)  E
2156 ARG   ( 409-)  E
2593 ARG   ( 409-)  F
2687 ARG   (  66-)  G
2743 ARG   ( 122-)  G
3176 ARG   ( 117-)  H
3468 ARG   ( 409-)  H
3619 ARG   ( 122-)  I
3906 ARG   ( 409-)  I
3930 ARG   ( 433-)  I
4052 ARG   ( 117-)  J
4057 ARG   ( 122-)  J
4200 ARG   ( 265-)  J
4273 ARG   ( 338-)  J
4344 ARG   ( 409-)  J

Warning: Tyrosine convention problem

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

   9 TYR   (  17-)  A
  54 TYR   (  62-)  A
  67 TYR   (  75-)  A
  83 TYR   (  91-)  A
 160 TYR   ( 168-)  A
 441 TYR   (  11-)  B
 442 TYR   (  12-)  B
 489 TYR   (  59-)  B
 492 TYR   (  62-)  B
 505 TYR   (  75-)  B
 521 TYR   (  91-)  B
 629 TYR   ( 199-)  B
 787 TYR   ( 357-)  B
 881 TYR   (  11-)  C
 882 TYR   (  12-)  C
 932 TYR   (  62-)  C
 945 TYR   (  75-)  C
 961 TYR   (  91-)  C
1382 TYR   (  75-)  D
1398 TYR   (  91-)  D
1506 TYR   ( 199-)  D
1649 TYR   ( 342-)  D
1664 TYR   ( 357-)  D
1731 TYR   ( 424-)  D
1758 TYR   (  11-)  E
And so on for a total of 58 lines.

Warning: Phenylalanine convention problem

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

  69 PHE   (  77-)  A
 133 PHE   ( 141-)  A
 348 PHE   ( 356-)  A
 507 PHE   (  77-)  B
 571 PHE   ( 141-)  B
 632 PHE   ( 202-)  B
 786 PHE   ( 356-)  B
 947 PHE   (  77-)  C
1011 PHE   ( 141-)  C
1226 PHE   ( 356-)  C
1384 PHE   (  77-)  D
1443 PHE   ( 136-)  D
1448 PHE   ( 141-)  D
1509 PHE   ( 202-)  D
1663 PHE   ( 356-)  D
1824 PHE   (  77-)  E
1883 PHE   ( 136-)  E
1888 PHE   ( 141-)  E
1949 PHE   ( 202-)  E
2046 PHE   ( 299-)  E
2103 PHE   ( 356-)  E
2261 PHE   (  77-)  F
2320 PHE   ( 136-)  F
2325 PHE   ( 141-)  F
2386 PHE   ( 202-)  F
2698 PHE   (  77-)  G
2762 PHE   ( 141-)  G
2823 PHE   ( 202-)  G
2977 PHE   ( 356-)  G
3136 PHE   (  77-)  H
3200 PHE   ( 141-)  H
3261 PHE   ( 202-)  H
3415 PHE   ( 356-)  H
3574 PHE   (  77-)  I
3638 PHE   ( 141-)  I
3853 PHE   ( 356-)  I
4012 PHE   (  77-)  J
4076 PHE   ( 141-)  J
4137 PHE   ( 202-)  J
4234 PHE   ( 299-)  J

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.

 340 ASP   ( 348-)  A
 946 ASP   (  76-)  C
1061 ASP   ( 191-)  C
1317 ASP   (  10-)  D
1383 ASP   (  76-)  D
1580 ASP   ( 273-)  D
1757 ASP   (  10-)  E
2260 ASP   (  76-)  F
2512 ASP   ( 328-)  F
2631 ASP   (  10-)  G
2697 ASP   (  76-)  G
3043 ASP   ( 422-)  G
3273 ASP   ( 214-)  H
3332 ASP   ( 273-)  H
3507 ASP   (  10-)  I
3770 ASP   ( 273-)  I
4126 ASP   ( 191-)  J

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.

1014 GLU   ( 144-)  C
1074 GLU   ( 204-)  C
1306 GLU   ( 436-)  C
1405 GLU   (  98-)  D
1511 GLU   ( 204-)  D
1810 GLU   (  63-)  E
1951 GLU   ( 204-)  E
1954 GLU   ( 207-)  E
2249 GLU   (  65-)  F
2388 GLU   ( 204-)  F
2391 GLU   ( 207-)  F
2719 GLU   (  98-)  G
2825 GLU   ( 204-)  G
2828 GLU   ( 207-)  G
3266 GLU   ( 207-)  H
3595 GLU   (  98-)  I
3700 GLU   ( 203-)  I
3701 GLU   ( 204-)  I
3739 GLU   ( 242-)  I
3927 GLU   ( 430-)  I
3970 GLU   (  35-)  J
4109 GLU   ( 174-)  J
4139 GLU   ( 204-)  J

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 181 KCX   ( 189-)  A      CH     CX
 181 KCX   ( 189-)  A      OX1    OQ1
 181 KCX   ( 189-)  A      OX2    OQ2
 619 KCX   ( 189-)  B      CH     CX
 619 KCX   ( 189-)  B      OX1    OQ1
 619 KCX   ( 189-)  B      OX2    OQ2
1059 KCX   ( 189-)  C      CH     CX
1059 KCX   ( 189-)  C      OX1    OQ1
1059 KCX   ( 189-)  C      OX2    OQ2
1496 KCX   ( 189-)  D      CH     CX
1496 KCX   ( 189-)  D      OX1    OQ1
1496 KCX   ( 189-)  D      OX2    OQ2
1936 KCX   ( 189-)  E      CH     CX
1936 KCX   ( 189-)  E      OX1    OQ1
1936 KCX   ( 189-)  E      OX2    OQ2
2373 KCX   ( 189-)  F      CH     CX
2373 KCX   ( 189-)  F      OX1    OQ1
2373 KCX   ( 189-)  F      OX2    OQ2
2810 KCX   ( 189-)  G      CH     CX
2810 KCX   ( 189-)  G      OX1    OQ1
2810 KCX   ( 189-)  G      OX2    OQ2
3248 KCX   ( 189-)  H      CH     CX
3248 KCX   ( 189-)  H      OX1    OQ1
3248 KCX   ( 189-)  H      OX2    OQ2
3686 KCX   ( 189-)  I      CH     CX
3686 KCX   ( 189-)  I      OX1    OQ1
3686 KCX   ( 189-)  I      OX2    OQ2
4124 KCX   ( 189-)  J      CH     CX
4124 KCX   ( 189-)  J      OX1    OQ1
4124 KCX   ( 189-)  J      OX2    OQ2

Geometric checks

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.

 114 ARG   ( 122-)  A
 319 ARG   ( 327-)  A
 340 ASP   ( 348-)  A
 398 ARG   ( 406-)  A
 496 ARG   (  66-)  B
 547 ARG   ( 117-)  B
 552 ARG   ( 122-)  B
 695 ARG   ( 265-)  B
 839 ARG   ( 409-)  B
 946 ASP   (  76-)  C
 987 ARG   ( 117-)  C
 992 ARG   ( 122-)  C
1014 GLU   ( 144-)  C
1061 ASP   ( 191-)  C
1074 GLU   ( 204-)  C
1197 ARG   ( 327-)  C
1279 ARG   ( 409-)  C
1306 GLU   ( 436-)  C
1317 ASP   (  10-)  D
1383 ASP   (  76-)  D
1405 GLU   (  98-)  D
1429 ARG   ( 122-)  D
1511 GLU   ( 204-)  D
1580 ASP   ( 273-)  D
1716 ARG   ( 409-)  D
And so on for a total of 74 lines.

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.

  46 THR   (  54-)  A    -3.1
3460 PRO   ( 401-)  H    -2.9
3486 THR   ( 427-)  H    -2.9
3989 THR   (  54-)  J    -2.8
 924 THR   (  54-)  C    -2.8
1972 THR   ( 225-)  E    -2.8
4160 THR   ( 225-)  J    -2.7
2547 PHE   ( 363-)  F    -2.7
 393 PRO   ( 401-)  A    -2.7
3860 PHE   ( 363-)  I    -2.7
 355 PHE   ( 363-)  A    -2.7
1532 THR   ( 225-)  D    -2.6
4298 PHE   ( 363-)  J    -2.6
2409 THR   ( 225-)  F    -2.6
1233 PHE   ( 363-)  C    -2.6
2984 PHE   ( 363-)  G    -2.6
 793 PHE   ( 363-)  B    -2.6
2846 THR   ( 225-)  G    -2.6
1095 THR   ( 225-)  C    -2.6
1855 ILE   ( 108-)  E    -2.6
 655 THR   ( 225-)  B    -2.6
3722 THR   ( 225-)  I    -2.6
1670 PHE   ( 363-)  D    -2.5
3557 PRO   (  60-)  I    -2.5
 217 THR   ( 225-)  A    -2.5
And so on for a total of 83 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

  26 ALA   (  34-)  A  Poor phi/psi
  43 SER   (  51-)  A  Poor phi/psi
  74 ASP   (  82-)  A  Poor phi/psi
 143 GLU   ( 151-)  A  Poor phi/psi
 155 LYS   ( 163-)  A  PRO omega poor
 187 THR   ( 195-)  A  Poor phi/psi
 224 ALA   ( 232-)  A  Poor phi/psi
 276 MET   ( 284-)  A  Poor phi/psi
 301 GLY   ( 309-)  A  Poor phi/psi
 349 TYR   ( 357-)  A  Poor phi/psi
 481 SER   (  51-)  B  Poor phi/psi
 593 LYS   ( 163-)  B  PRO omega poor
 625 THR   ( 195-)  B  Poor phi/psi
 662 ALA   ( 232-)  B  Poor phi/psi
 714 MET   ( 284-)  B  Poor phi/psi
 739 GLY   ( 309-)  B  Poor phi/psi
 787 TYR   ( 357-)  B  Poor phi/psi
 859 LYS   ( 429-)  B  Poor phi/psi
 921 SER   (  51-)  C  Poor phi/psi
1033 LYS   ( 163-)  C  PRO omega poor
1065 THR   ( 195-)  C  Poor phi/psi
1102 ALA   ( 232-)  C  Poor phi/psi
1154 MET   ( 284-)  C  Poor phi/psi
1179 GLY   ( 309-)  C  Poor phi/psi
1227 TYR   ( 357-)  C  Poor phi/psi
And so on for a total of 98 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 590 VAL   ( 160-)  B    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!

   7 LYS   (  15-)  A      0
  15 ARG   (  23-)  A      0
  42 SER   (  50-)  A      0
  43 SER   (  51-)  A      0
  44 THR   (  52-)  A      0
  47 TRP   (  55-)  A      0
  49 THR   (  57-)  A      0
  51 TYR   (  59-)  A      0
  52 PRO   (  60-)  A      0
  53 TRP   (  61-)  A      0
  54 TYR   (  62-)  A      0
  67 TYR   (  75-)  A      0
  68 ASP   (  76-)  A      0
  72 MET   (  80-)  A      0
  74 ASP   (  82-)  A      0
  76 SER   (  84-)  A      0
  86 HIS   (  94-)  A      0
  90 GLU   (  98-)  A      0
  91 ALA   (  99-)  A      0
 100 ILE   ( 108-)  A      0
 101 ALA   ( 109-)  A      0
 103 ASN   ( 111-)  A      0
 110 VAL   ( 118-)  A      0
 117 ASP   ( 125-)  A      0
 127 GLU   ( 135-)  A      0
And so on for a total of 1500 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 : 3.955

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!

2509 GLY   ( 325-)  F   2.42   12
3822 GLY   ( 325-)  I   2.37   16
 755 GLY   ( 325-)  B   2.36   17
4260 GLY   ( 325-)  J   2.34   19
2072 GLY   ( 325-)  E   2.29   17
1632 GLY   ( 325-)  D   2.26   17
2946 GLY   ( 325-)  G   2.20   14
1195 GLY   ( 325-)  C   2.08   13
 803 GLY   ( 373-)  B   1.89   80
3485 LYS   ( 426-)  H   1.81   49
1040 PRO   ( 170-)  C   1.74   12
2120 GLY   ( 373-)  E   1.70   80
4308 GLY   ( 373-)  J   1.63   80
  28 GLY   (  36-)  A   1.60   80
 365 GLY   ( 373-)  A   1.57   80
3890 GLY   ( 393-)  I   1.56   80
4328 GLY   ( 393-)  J   1.53   80

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].

 284 PRO   ( 292-)  A    52.8 half-chair C-delta/C-gamma (54 degrees)
 393 PRO   ( 401-)  A   103.9 envelop C-beta (108 degrees)
 532 PRO   ( 102-)  B   100.3 envelop C-beta (108 degrees)
 831 PRO   ( 401-)  B    99.9 envelop C-beta (108 degrees)
 850 PRO   ( 420-)  B   109.9 envelop C-beta (108 degrees)
1705 PRO   ( 398-)  D  -123.3 half-chair C-delta/C-gamma (-126 degrees)
2167 PRO   ( 420-)  E   129.3 half-chair C-beta/C-alpha (126 degrees)
2476 PRO   ( 292-)  F    51.7 half-chair C-delta/C-gamma (54 degrees)
3223 PRO   ( 164-)  H  -113.7 envelop C-gamma (-108 degrees)
3460 PRO   ( 401-)  H   118.0 half-chair C-beta/C-alpha (126 degrees)
3479 PRO   ( 420-)  H   121.9 half-chair C-beta/C-alpha (126 degrees)
3502 PRO   ( 443-)  H   109.7 envelop C-beta (108 degrees)
3557 PRO   (  60-)  I   -62.2 half-chair C-beta/C-alpha (-54 degrees)
3898 PRO   ( 401-)  I   101.5 envelop C-beta (108 degrees)
3917 PRO   ( 420-)  I   110.6 envelop C-beta (108 degrees)
4355 PRO   ( 420-)  J   108.2 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

3456 HIS   ( 397-)  H      ND1 <-> 3457 PRO   ( 398-)  H      CD     1.04    2.06  INTRA BF
3393 VAL   ( 334-)  H      CG1 <-> 3397 ARG   ( 338-)  H      NH2    0.77    2.33  INTRA
3456 HIS   ( 397-)  H      CG  <-> 3457 PRO   ( 398-)  H      CD     0.73    2.47  INTRA BF
  78 ILE   (  86-)  A      CD1 <->  341 VAL   ( 349-)  A      CG2    0.70    2.50  INTRA BF
 141 MET   ( 149-)  A      CE  <->  242 LYS   ( 250-)  A      CB     0.68    2.52  INTRA
 801 HIS   ( 371-)  B      CE1 <->  803 GLY   ( 373-)  B      C      0.68    2.52  INTRA BF
 801 HIS   ( 371-)  B      ND1 <->  803 GLY   ( 373-)  B      N      0.67    2.33  INTRA BF
1838 TYR   (  91-)  E      CZ  <-> 1855 ILE   ( 108-)  E      CD1    0.67    2.53  INTRA BL
 100 ILE   ( 108-)  A      CD1 <->  118 LEU   ( 126-)  A      CD1    0.65    2.55  INTRA
3456 HIS   ( 397-)  H      CE1 <-> 3457 PRO   ( 398-)  H      CD     0.64    2.56  INTRA BF
 326 VAL   ( 334-)  A      CG1 <->  330 ARG   ( 338-)  A      NH2    0.62    2.48  INTRA BF
2118 HIS   ( 371-)  E      ND1 <-> 2120 GLY   ( 373-)  E      N      0.58    2.42  INTRA BF
   6 ASP   (  14-)  A      CG  <-> 4400 HOH   (2019 )  A      O      0.56    2.24  INTRA BF
   6 ASP   (  14-)  A      CB  <-> 4400 HOH   (2019 )  A      O      0.55    2.25  INTRA BF
3341 ARG   ( 282-)  H      NH1 <-> 3344 HIS   ( 285-)  H      CE1    0.54    2.56  INTRA
 436 VAL   ( 444-)  A      O   <-> 3176 ARG   ( 117-)  H      CD     0.53    2.27  INTRA BF
  68 ASP   (  76-)  A      C   <->   69 PHE   (  77-)  A      CD1    0.52    2.58  INTRA BF
4088 LYS   ( 153-)  J      CE  <-> 4089 ASP   ( 154-)  J      OD1    0.51    2.29  INTRA
  72 MET   (  80-)  A      SD  <->   78 ILE   (  86-)  A      CD1    0.50    2.90  INTRA BF
 801 HIS   ( 371-)  B      CE1 <->  803 GLY   ( 373-)  B      CA     0.50    2.70  INTRA BF
  68 ASP   (  76-)  A      OD1 <->   69 PHE   (  77-)  A      N      0.50    2.10  INTRA BF
1035 LYS   ( 165-)  C      NZ  <-> 1061 ASP   ( 191-)  C      OD2    0.50    2.20  INTRA BL
2552 GLY   ( 368-)  F      N   <-> 4405 HOH   (1780 )  F      O      0.49    2.21  INTRA
2118 HIS   ( 371-)  E      CE1 <-> 2120 GLY   ( 373-)  E      C      0.48    2.72  INTRA BF
 859 LYS   ( 429-)  B      O   <->  862 ALA   ( 432-)  B      N      0.48    2.22  INTRA BF
And so on for a total of 1298 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

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.

  29 TYR   (  37-)  A      -8.94
2680 TYR   (  59-)  G      -6.95
 489 TYR   (  59-)  B      -6.54
3118 TYR   (  59-)  H      -6.53
2243 TYR   (  59-)  F      -6.16
3349 ARG   ( 290-)  H      -6.00
3787 ARG   ( 290-)  I      -5.95
2911 ARG   ( 290-)  G      -5.93
1597 ARG   ( 290-)  D      -5.86
2474 ARG   ( 290-)  F      -5.84
 282 ARG   ( 290-)  A      -5.79
 720 ARG   ( 290-)  B      -5.68
4225 ARG   ( 290-)  J      -5.65
   3 TYR   (  11-)  A      -5.64
2037 ARG   ( 290-)  E      -5.64
 929 TYR   (  59-)  C      -5.63
3914 GLN   ( 417-)  I      -5.59
3038 GLN   ( 417-)  G      -5.58
 409 GLN   ( 417-)  A      -5.56
2601 GLN   ( 417-)  F      -5.54
2187 HIS   ( 440-)  E      -5.53
4098 LYS   ( 163-)  J      -5.52
3994 TYR   (  59-)  J      -5.49
1160 ARG   ( 290-)  C      -5.47
3222 LYS   ( 163-)  H      -5.42
And so on for a total of 58 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

1306 GLU   ( 436-)  C      1308 - TRP    438- ( C)         -4.23
1743 GLU   ( 436-)  D      1745 - TRP    438- ( D)         -4.18
3057 GLU   ( 436-)  G      3059 - TRP    438- ( G)         -4.23
3499 HIS   ( 440-)  H      3501 - THR    442- ( H)         -4.83
3552 TRP   (  55-)  I      3554 - THR     57- ( I)         -4.67
3933 GLU   ( 436-)  I      3935 - TRP    438- ( I)         -4.22

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

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: I

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: J

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.

3556 TYR   (  59-)  I   -3.37
1366 TYR   (  59-)  D   -3.36
  51 TYR   (  59-)  A   -3.24
 109 ARG   ( 117-)  A   -3.20
 387 LEU   ( 395-)  A   -3.20
1365 LEU   (  58-)  D   -3.01
3555 LEU   (  58-)  I   -2.98
3381 LYS   ( 322-)  H   -2.87
1593 ALA   ( 286-)  D   -2.83
1156 ALA   ( 286-)  C   -2.79
 278 ALA   ( 286-)  A   -2.78
 716 ALA   ( 286-)  B   -2.76
2907 ALA   ( 286-)  G   -2.74
  50 LEU   (  58-)  A   -2.72
 488 LEU   (  58-)  B   -2.71
  31 ILE   (  39-)  A   -2.63
2242 LEU   (  58-)  F   -2.53

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.

 277 HIS   ( 285-)  A     -  280 PHE   ( 288-)  A        -1.79
2628 VAL   ( 444-)  F     - 2631 ASP   (  10-)  G        -1.60

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: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

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

4402 HOH   (1690 )  C      O
4408 HOH   (2070 )  I      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.

 346 GLN   ( 354-)  A
 784 GLN   ( 354-)  B
1224 GLN   ( 354-)  C
1280 GLN   ( 410-)  C
1310 HIS   ( 440-)  C
1621 HIS   ( 314-)  D
1661 GLN   ( 354-)  D
1747 HIS   ( 440-)  D
1940 ASN   ( 193-)  E
1965 ASN   ( 218-)  E
2101 GLN   ( 354-)  E
2498 HIS   ( 314-)  F
2531 ASN   ( 347-)  F
2538 GLN   ( 354-)  F
2968 ASN   ( 347-)  G
2975 GLN   ( 354-)  G
3061 HIS   ( 440-)  G
3413 GLN   ( 354-)  H
3469 GLN   ( 410-)  H
3851 GLN   ( 354-)  I
3873 GLN   ( 376-)  I
3907 GLN   ( 410-)  I
4174 GLN   ( 239-)  J
4289 GLN   ( 354-)  J

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.

  46 THR   (  54-)  A      OG1
  47 TRP   (  55-)  A      NE1
  53 TRP   (  61-)  A      N
  86 HIS   (  94-)  A      N
 103 ASN   ( 111-)  A      ND2
 114 ARG   ( 122-)  A      NH1
 155 LYS   ( 163-)  A      N
 158 VAL   ( 166-)  A      N
 163 GLU   ( 171-)  A      N
 181 KCX   ( 189-)  A      OX1
 183 ASP   ( 191-)  A      N
 191 TYR   ( 199-)  A      N
 196 GLU   ( 204-)  A      N
 197 ARG   ( 205-)  A      NE
 212 THR   ( 220-)  A      OG1
 217 THR   ( 225-)  A      OG1
 255 ALA   ( 263-)  A      N
 274 ARG   ( 282-)  A      NE
 314 LYS   ( 322-)  A      NZ
 321 ILE   ( 329-)  A      N
 341 VAL   ( 349-)  A      N
 359 SER   ( 367-)  A      N
 359 SER   ( 367-)  A      OG
 360 GLY   ( 368-)  A      N
 361 GLY   ( 369-)  A      N
And so on for a total of 252 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.

  70 HIS   (  78-)  A      ND1
 247 ASP   ( 255-)  A      OD1
 306 HIS   ( 314-)  A      ND1
 685 ASP   ( 255-)  B      OD1
 744 HIS   ( 314-)  B      ND1
1125 ASP   ( 255-)  C      OD1
1184 HIS   ( 314-)  C      ND1
1562 ASP   ( 255-)  D      OD1
1562 ASP   ( 255-)  D      OD2
1586 HIS   ( 279-)  D      NE2
2002 ASP   ( 255-)  E      OD1
2002 ASP   ( 255-)  E      OD2
2026 HIS   ( 279-)  E      NE2
2439 ASP   ( 255-)  F      OD1
2439 ASP   ( 255-)  F      OD2
2463 HIS   ( 279-)  F      NE2
2876 ASP   ( 255-)  G      OD1
2876 ASP   ( 255-)  G      OD2
2902 HIS   ( 281-)  G      NE2
2935 HIS   ( 314-)  G      ND1
3314 ASP   ( 255-)  H      OD1
3373 HIS   ( 314-)  H      ND1
3752 ASP   ( 255-)  I      OD1
3752 ASP   ( 255-)  I      OD2
3778 HIS   ( 281-)  I      NE2
3811 HIS   ( 314-)  I      ND1
4190 ASP   ( 255-)  J      OD1
4190 ASP   ( 255-)  J      OD2

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+.

4395  MG   ( 500-)  H     0.64   1.11 Is perhaps CA *2

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.

4400 HOH   (2106 )  A      O  0.90  K  4 ION-B
4401 HOH   (2076 )  B      O  1.14  K  5 Ion-B NCS 1/1
4402 HOH   (2079 )  C      O  1.00  K  6 Ion-B NCS 1/1
4402 HOH   (2081 )  C      O  0.92  K  5
4403 HOH   ( 892 )  D      O  0.88  K  4 ION-B
4403 HOH   (1425 )  D      O  1.00 NA  4 NCS 1/1
4404 HOH   (1270 )  E      O  0.98  K  4 NCS 3/3
4404 HOH   (1435 )  E      O  1.15  K  4 NCS 3/3
4406 HOH   ( 790 )  G      O  1.04  K  4 NCS 5/5
4409 HOH   (1850 )  J      O  1.12  K  5 Ion-B NCS 1/1

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.

  68 ASP   (  76-)  A   H-bonding suggests Asn
 225 ASP   ( 233-)  A   H-bonding suggests Asn
 247 ASP   ( 255-)  A   H-bonding suggests Asn
 327 ASP   ( 335-)  A   H-bonding suggests Asn
 337 ASP   ( 345-)  A   H-bonding suggests Asn; but Alt-Rotamer
 405 ASP   ( 413-)  A   H-bonding suggests Asn
 644 ASP   ( 214-)  B   H-bonding suggests Asn
 663 ASP   ( 233-)  B   H-bonding suggests Asn
 685 ASP   ( 255-)  B   H-bonding suggests Asn; but Alt-Rotamer
 843 ASP   ( 413-)  B   H-bonding suggests Asn
 852 ASP   ( 422-)  B   H-bonding suggests Asn; but Alt-Rotamer
1049 ASP   ( 179-)  C   H-bonding suggests Asn
1116 ASP   ( 246-)  C   H-bonding suggests Asn; but Alt-Rotamer
1125 ASP   ( 255-)  C   H-bonding suggests Asn; but Alt-Rotamer
1143 ASP   ( 273-)  C   H-bonding suggests Asn
1461 ASP   ( 154-)  D   H-bonding suggests Asn; but Alt-Rotamer
1562 ASP   ( 255-)  D   H-bonding suggests Asn; but Alt-Rotamer
1980 ASP   ( 233-)  E   H-bonding suggests Asn
2002 ASP   ( 255-)  E   H-bonding suggests Asn; but Alt-Rotamer
2160 ASP   ( 413-)  E   H-bonding suggests Asn
2439 ASP   ( 255-)  F   H-bonding suggests Asn; but Alt-Rotamer
2775 ASP   ( 154-)  G   H-bonding suggests Asn; but Alt-Rotamer
2854 ASP   ( 233-)  G   H-bonding suggests Asn
2876 ASP   ( 255-)  G   H-bonding suggests Asn; but Alt-Rotamer
3034 ASP   ( 413-)  G   H-bonding suggests Asn
3292 ASP   ( 233-)  H   H-bonding suggests Asn
3314 ASP   ( 255-)  H   H-bonding suggests Asn; but Alt-Rotamer
3332 ASP   ( 273-)  H   H-bonding suggests Asn
3394 ASP   ( 335-)  H   H-bonding suggests Asn
3730 ASP   ( 233-)  I   H-bonding suggests Asn
3752 ASP   ( 255-)  I   H-bonding suggests Asn; but Alt-Rotamer
3770 ASP   ( 273-)  I   H-bonding suggests Asn; but Alt-Rotamer
4149 ASP   ( 214-)  J   H-bonding suggests Asn
4168 ASP   ( 233-)  J   H-bonding suggests Asn
4190 ASP   ( 255-)  J   H-bonding suggests Asn; but Alt-Rotamer
4348 ASP   ( 413-)  J   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.465
  2nd generation packing quality :  -1.212
  Ramachandran plot appearance   :  -1.786
  chi-1/chi-2 rotamer normality  :  -0.720
  Backbone conformation          :  -0.132

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.171 (tight)
  Bond angles                    :   0.417 (tight)
  Omega angle restraints         :   0.719 (tight)
  Side chain planarity           :   0.137 (tight)
  Improper dihedral distribution :   0.347
  B-factor distribution          :   0.335
  Inside/Outside distribution    :   1.036

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 : 2.36


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :   0.8
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.171 (tight)
  Bond angles                    :   0.417 (tight)
  Omega angle restraints         :   0.719 (tight)
  Side chain planarity           :   0.137 (tight)
  Improper dihedral distribution :   0.347
  B-factor distribution          :   0.335
  Inside/Outside distribution    :   1.036
==============

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.