WHAT IF Check report

This file was created 2011-12-13 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 pdb3alq.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 : 0.441
CA-only RMS fit for the two chains : 0.227

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 : 0.684
CA-only RMS fit for the two chains : 0.440

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 : 0.496
CA-only RMS fit for the two chains : 0.239

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 : 0.538
CA-only RMS fit for the two chains : 0.290

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 : 0.728
CA-only RMS fit for the two chains : 0.474

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

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: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

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

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.

  63 SER   (  71-)  A    High
  64 THR   (  72-)  A    High
  65 HIS   (  73-)  A    High
 204 SER   (  71-)  B    High
 205 THR   (  72-)  B    High
 206 HIS   (  73-)  B    High
 345 SER   (  71-)  C    High
 346 THR   (  72-)  C    High
 347 HIS   (  73-)  C    High
 519 ASN   ( 112-)  D    High
 579 GLU   (  23-)  E    High
 627 SER   (  71-)  E    High
 628 THR   (  72-)  E    High
 629 HIS   (  73-)  E    High
 769 THR   (  72-)  F    High
 847 THR   (  17-)  R    High
 952 ARG   ( 122-)  R    High
 957 VAL   ( 127-)  R    High
 958 ALA   ( 128-)  R    High
 959 ARG   ( 129-)  R    High
 960 PRO   ( 130-)  R    High
 961 GLY   ( 131-)  R    High
 962 THR   ( 132-)  R    High
 963 GLU   ( 133-)  R    High
 969 CYS   ( 139-)  R    High
And so on for a total of 136 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) : 95.000

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: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Nomenclature related problems

Warning: Tyrosine convention problem

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

  51 TYR   (  59-)  A
  79 TYR   (  87-)  A
 103 TYR   ( 119-)  A
 125 TYR   ( 141-)  A
 135 TYR   ( 151-)  A
 192 TYR   (  59-)  B
 266 TYR   ( 141-)  B
 361 TYR   (  87-)  C
 385 TYR   ( 119-)  C
 407 TYR   ( 141-)  C
 417 TYR   ( 151-)  C
 474 TYR   (  59-)  D
 526 TYR   ( 119-)  D
 548 TYR   ( 141-)  D
 643 TYR   (  87-)  E
 667 TYR   ( 119-)  E
 689 TYR   ( 141-)  E
 699 TYR   ( 151-)  E
 756 TYR   (  59-)  F
 784 TYR   (  87-)  F
 808 TYR   ( 119-)  F
 830 TYR   ( 141-)  F
 854 TYR   (  24-)  R
 891 TYR   (  61-)  R
1018 TYR   (  24-)  S
1055 TYR   (  61-)  S
1180 TYR   (  24-)  T
1217 TYR   (  61-)  T
1341 TYR   (  24-)  U
1378 TYR   (  61-)  U
1502 TYR   (  24-)  V
1539 TYR   (  61-)  V
1664 TYR   (  24-)  W
1701 TYR   (  61-)  W

Warning: Phenylalanine convention problem

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

 128 PHE   ( 144-)  A
 269 PHE   ( 144-)  B
 390 PHE   ( 124-)  C
 410 PHE   ( 144-)  C
 479 PHE   (  64-)  D
 551 PHE   ( 144-)  D
 672 PHE   ( 124-)  E
 692 PHE   ( 144-)  E
 833 PHE   ( 144-)  F
 874 PHE   (  44-)  R
 955 PHE   ( 125-)  R
1038 PHE   (  44-)  S
1119 PHE   ( 125-)  S
1200 PHE   (  44-)  T
1281 PHE   ( 125-)  T
1361 PHE   (  44-)  U
1442 PHE   ( 125-)  U
1522 PHE   (  44-)  V
1603 PHE   ( 125-)  V
1765 PHE   ( 125-)  W

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.

 268 ASP   ( 143-)  B
 691 ASP   ( 143-)  E
 832 ASP   ( 143-)  F
 880 ASP   (  50-)  R
 884 ASP   (  54-)  R
 888 ASP   (  58-)  R
 911 ASP   (  81-)  R
 966 ASP   ( 136-)  R
1044 ASP   (  50-)  S
1048 ASP   (  54-)  S
1052 ASP   (  58-)  S
1075 ASP   (  81-)  S
1130 ASP   ( 136-)  S
1206 ASP   (  50-)  T
1210 ASP   (  54-)  T
1214 ASP   (  58-)  T
1237 ASP   (  81-)  T
1292 ASP   ( 136-)  T
1367 ASP   (  50-)  U
1371 ASP   (  54-)  U
1375 ASP   (  58-)  U
1398 ASP   (  81-)  U
1453 ASP   ( 136-)  U
1528 ASP   (  50-)  V
1532 ASP   (  54-)  V
1536 ASP   (  58-)  V
1559 ASP   (  81-)  V
1614 ASP   ( 136-)  V
1690 ASP   (  50-)  W
1694 ASP   (  54-)  W
1698 ASP   (  58-)  W
1721 ASP   (  81-)  W
1776 ASP   ( 136-)  W
1815 ASP   ( 175-)  W

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.

  15 GLU   (  23-)  A
  34 GLU   (  42-)  A
 130 GLU   ( 146-)  A
 175 GLU   (  42-)  B
 297 GLU   (  23-)  C
 316 GLU   (  42-)  C
 457 GLU   (  42-)  D
 598 GLU   (  42-)  E
 739 GLU   (  42-)  F
 852 GLU   (  22-)  R
 914 GLU   (  84-)  R
 921 GLU   (  91-)  R
1016 GLU   (  22-)  S
1078 GLU   (  84-)  S
1085 GLU   (  91-)  S
1178 GLU   (  22-)  T
1240 GLU   (  84-)  T
1247 GLU   (  91-)  T
1289 GLU   ( 133-)  T
1339 GLU   (  22-)  U
1401 GLU   (  84-)  U
1408 GLU   (  91-)  U
1450 GLU   ( 133-)  U
1500 GLU   (  22-)  V
1562 GLU   (  84-)  V
1569 GLU   (  91-)  V
1662 GLU   (  22-)  W
1724 GLU   (  84-)  W
1731 GLU   (  91-)  W

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.

 352 HIS   (  78-)  C      CG   ND1  CE1 109.62    4.0

Error: Nomenclature error(s)

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

  15 GLU   (  23-)  A
  34 GLU   (  42-)  A
 130 GLU   ( 146-)  A
 175 GLU   (  42-)  B
 268 ASP   ( 143-)  B
 297 GLU   (  23-)  C
 316 GLU   (  42-)  C
 457 GLU   (  42-)  D
 598 GLU   (  42-)  E
 691 ASP   ( 143-)  E
 739 GLU   (  42-)  F
 832 ASP   ( 143-)  F
 852 GLU   (  22-)  R
 880 ASP   (  50-)  R
 884 ASP   (  54-)  R
 888 ASP   (  58-)  R
 911 ASP   (  81-)  R
 914 GLU   (  84-)  R
 921 GLU   (  91-)  R
 966 ASP   ( 136-)  R
1016 GLU   (  22-)  S
1044 ASP   (  50-)  S
1048 ASP   (  54-)  S
1052 ASP   (  58-)  S
1075 ASP   (  81-)  S
And so on for a total of 63 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.

1540 THR   (  62-)  V    -3.0
  81 THR   (  89-)  A    -2.7
1584 LEU   ( 106-)  V    -2.7
 645 THR   (  89-)  E    -2.7
 347 HIS   (  73-)  C    -2.7
1610 THR   ( 132-)  V    -2.7
 786 THR   (  89-)  F    -2.7
1467 THR   ( 150-)  U    -2.6
1699 SER   (  59-)  W    -2.6
 504 THR   (  89-)  D    -2.5
 770 HIS   (  73-)  F    -2.5
 977 PHE   ( 147-)  R    -2.4
1537 SER   (  59-)  V    -2.4
 363 THR   (  89-)  C    -2.4
1138 PRO   ( 144-)  S    -2.3
 974 PRO   ( 144-)  R    -2.3
1772 THR   ( 132-)  W    -2.3
1056 THR   (  62-)  S    -2.3
1306 THR   ( 150-)  T    -2.3
 222 THR   (  89-)  B    -2.3
 890 THR   (  60-)  R    -2.3
1449 THR   ( 132-)  U    -2.2
1220 LEU   (  64-)  T    -2.2
 421 ILE   ( 155-)  C    -2.2
1222 ASN   (  66-)  T    -2.2
1376 SER   (  59-)  U    -2.2
 961 GLY   ( 131-)  R    -2.2
 410 PHE   ( 144-)  C    -2.2
 428 VAL   (  13-)  D    -2.2
1381 LEU   (  64-)  U    -2.2
1423 LEU   ( 106-)  U    -2.2
1262 LEU   ( 106-)  T    -2.2
1451 THR   ( 134-)  U    -2.2
1186 MET   (  30-)  T    -2.1
 960 PRO   ( 130-)  R    -2.1
 361 TYR   (  87-)  C    -2.1
  65 HIS   (  73-)  A    -2.1
1216 THR   (  60-)  T    -2.1
 325 PRO   (  51-)  C    -2.1
 569 VAL   (  13-)  E    -2.1
 170 LEU   (  37-)  B    -2.0
 841 PHE   ( 152-)  F    -2.0
1729 THR   (  89-)  W    -2.0
 402 ILE   ( 136-)  C    -2.0
1389 LEU   (  72-)  U    -2.0
1802 ILE   ( 162-)  W    -2.0
 833 PHE   ( 144-)  F    -2.0
 734 LEU   (  37-)  F    -2.0
 287 VAL   (  13-)  C    -2.0
  79 TYR   (  87-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  14 ALA   (  22-)  A  Poor phi/psi
  26 ASN   (  34-)  A  Poor phi/psi
  37 ASP   (  45-)  A  Poor phi/psi
  38 ASN   (  46-)  A  Poor phi/psi
  48 TYR   (  56-)  A  omega poor
 164 ARG   (  31-)  B  Poor phi/psi
 167 ASN   (  34-)  B  Poor phi/psi
 172 ASN   (  39-)  B  Poor phi/psi
 179 ASN   (  46-)  B  Poor phi/psi
 221 GLN   (  88-)  B  omega poor
 296 ALA   (  22-)  C  Poor phi/psi
 304 ASN   (  30-)  C  Poor phi/psi
 305 ARG   (  31-)  C  Poor phi/psi
 308 ASN   (  34-)  C  Poor phi/psi
 313 ASN   (  39-)  C  Poor phi/psi
 320 ASN   (  46-)  C  Poor phi/psi
 344 PRO   (  70-)  C  Poor phi/psi
 362 GLN   (  88-)  C  Poor phi/psi, omega poor
 446 ARG   (  31-)  D  Poor phi/psi
 449 ASN   (  34-)  D  Poor phi/psi
 461 ASN   (  46-)  D  Poor phi/psi
 590 ASN   (  34-)  E  Poor phi/psi
 595 ASN   (  39-)  E  Poor phi/psi
 719 ALA   (  22-)  F  Poor phi/psi
 727 ASN   (  30-)  F  Poor phi/psi
And so on for a total of 81 lines.

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 : -3.134

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!

  14 ALA   (  22-)  A      0
  15 GLU   (  23-)  A      0
  22 ASN   (  30-)  A      0
  23 ARG   (  31-)  A      0
  25 ALA   (  33-)  A      0
  26 ASN   (  34-)  A      0
  27 ALA   (  35-)  A      0
  28 LEU   (  36-)  A      0
  29 LEU   (  37-)  A      0
  30 ALA   (  38-)  A      0
  31 ASN   (  39-)  A      0
  36 ARG   (  44-)  A      0
  37 ASP   (  45-)  A      0
  38 ASN   (  46-)  A      0
  43 PRO   (  51-)  A      0
  45 GLU   (  53-)  A      0
  57 SER   (  65-)  A      0
  59 GLN   (  67-)  A      0
  79 TYR   (  87-)  A      0
  80 GLN   (  88-)  A      0
  81 THR   (  89-)  A      0
  86 LEU   (  94-)  A      0
  93 CYS   ( 101-)  A      0
  94 GLN   ( 102-)  A      0
  95 ALA   ( 111-)  A      0
And so on for a total of 1024 lines.

Warning: Backbone oxygen evaluation

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

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

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

1648 GLY   ( 170-)  V   1.64   13
1287 GLY   ( 131-)  T   1.50   11

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].

  43 PRO   (  51-)  A    49.3 half-chair C-delta/C-gamma (54 degrees)
  92 PRO   ( 100-)  A    41.3 envelop C-delta (36 degrees)
 101 PRO   ( 117-)  A    50.0 half-chair C-delta/C-gamma (54 degrees)
 184 PRO   (  51-)  B    41.5 envelop C-delta (36 degrees)
 233 PRO   ( 100-)  B    40.2 envelop C-delta (36 degrees)
 242 PRO   ( 117-)  B    50.5 half-chair C-delta/C-gamma (54 degrees)
 325 PRO   (  51-)  C    33.1 envelop C-delta (36 degrees)
 383 PRO   ( 117-)  C    39.4 envelop C-delta (36 degrees)
 515 PRO   ( 100-)  D    47.2 half-chair C-delta/C-gamma (54 degrees)
 524 PRO   ( 117-)  D    40.5 envelop C-delta (36 degrees)
 607 PRO   (  51-)  E    37.3 envelop C-delta (36 degrees)
 656 PRO   ( 100-)  E    47.8 half-chair C-delta/C-gamma (54 degrees)
 661 PRO   ( 113-)  E    51.0 half-chair C-delta/C-gamma (54 degrees)
 665 PRO   ( 117-)  E    41.6 envelop C-delta (36 degrees)
 748 PRO   (  51-)  F    50.3 half-chair C-delta/C-gamma (54 degrees)
 797 PRO   ( 100-)  F    48.2 half-chair C-delta/C-gamma (54 degrees)
 806 PRO   ( 117-)  F    29.2 envelop C-delta (36 degrees)
 960 PRO   ( 130-)  R    48.4 half-chair C-delta/C-gamma (54 degrees)
 974 PRO   ( 144-)  R   100.0 envelop C-beta (108 degrees)
1193 PRO   (  37-)  T    99.8 envelop C-beta (108 degrees)
1677 PRO   (  37-)  W    99.9 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.

1817 VAL   ( 177-)  W      C   <-> 1818 CYS   ( 178-)  W      SG     0.29    3.01  INTRA BF
1301 GLY   ( 145-)  T      C   <-> 1316 HIS   ( 160-)  T      ND1    0.28    2.82  INTRA BF
1333 VAL   ( 177-)  T      C   <-> 1334 CYS   ( 178-)  T      SG     0.26    3.04  INTRA BF
 252 GLU   ( 127-)  B      N   <->  255 ASP   ( 130-)  B      OD2    0.26    2.44  INTRA BL
 295 GLN   (  21-)  C      O   <->  297 GLU   (  23-)  C      N      0.25    2.45  INTRA BL
 571 HIS   (  15-)  E      ND1 <->  615 TYR   (  59-)  E      OH     0.24    2.46  INTRA BL
1318 ILE   ( 162-)  T      C   <-> 1319 CYS   ( 163-)  T      SG     0.23    3.07  INTRA BF
1254 CYS   (  98-)  T      SG  <-> 1268 CYS   ( 112-)  T      SG     0.23    3.22  INTRA BF
1733 ASN   (  93-)  W      CG  <-> 1734 ARG   (  94-)  W      N      0.19    2.81  INTRA BF
1139 GLY   ( 145-)  S      C   <-> 1154 HIS   ( 160-)  S      ND1    0.19    2.91  INTRA BF
1752 CYS   ( 112-)  W      SG  <-> 1753 ARG   ( 113-)  W      N      0.19    3.01  INTRA BF
 923 ASN   (  93-)  R      CG  <->  924 ARG   (  94-)  R      N      0.18    2.82  INTRA BF
 714 VAL   (  17-)  F      O   <->  726 LEU   (  29-)  F      N      0.17    2.53  INTRA BL
 794 ILE   (  97-)  F      CD1 <-> 1591 ARG   ( 113-)  V      NE     0.17    2.93  INTRA BF
 566 ASP   (  10-)  E      C   <->  595 ASN   (  39-)  E      ND2    0.17    2.93  INTRA BF
1789 ASN   ( 149-)  W      OD1 <-> 1798 ARG   ( 158-)  W      NH2    0.16    2.54  INTRA BF
1305 ASN   ( 149-)  T      OD1 <-> 1314 ARG   ( 158-)  T      NH2    0.16    2.54  INTRA BL
1785 GLY   ( 145-)  W      O   <-> 1800 HIS   ( 160-)  W      N      0.16    2.54  INTRA BF
1071 ARG   (  77-)  S      NH2 <-> 1491 MET   ( 174-)  U      SD     0.16    3.14  INTRA BF
1044 ASP   (  50-)  S      CG  <-> 1045 THR   (  51-)  S      N      0.15    2.85  INTRA BF
1462 GLY   ( 145-)  U      O   <-> 1477 HIS   ( 160-)  U      N      0.15    2.55  INTRA BF
 165 ARG   (  32-)  B      NE  <-> 1067 SER   (  73-)  S      OG     0.14    2.56  INTRA BL
 556 GLN   ( 149-)  D      OE1 <-> 1430 ARG   ( 113-)  U      NH1    0.14    2.56  INTRA BF
1610 THR   ( 132-)  V      CG2 <-> 1611 GLU   ( 133-)  V      N      0.14    2.86  INTRA BF
  74 ARG   (  82-)  A      NH2 <->  114 ASP   ( 130-)  A      OD2    0.14    2.56  INTRA BL
And so on for a total of 192 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: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

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.

1749 GLN   ( 109-)  W      -7.09
1426 GLN   ( 109-)  U      -6.88
1587 GLN   ( 109-)  V      -6.88
 939 GLN   ( 109-)  R      -6.86
 587 ARG   (  31-)  E      -6.82
1103 GLN   ( 109-)  S      -6.67
1265 GLN   ( 109-)  T      -6.60
1014 LEU   (  20-)  S      -5.93
1498 LEU   (  20-)  V      -5.91
 850 LEU   (  20-)  R      -5.91
1739 ARG   (  99-)  W      -5.91
 728 ARG   (  31-)  F      -5.91
 446 ARG   (  31-)  D      -5.90
1577 ARG   (  99-)  V      -5.90
1337 LEU   (  20-)  U      -5.87
1255 ARG   (  99-)  T      -5.87
  23 ARG   (  31-)  A      -5.80
1660 LEU   (  20-)  W      -5.71
1176 LEU   (  20-)  T      -5.71
1156 ILE   ( 162-)  S      -5.68
 200 GLN   (  67-)  B      -5.64
1416 ARG   (  99-)  U      -5.50
 482 GLN   (  67-)  D      -5.49
 164 ARG   (  31-)  B      -5.42
 341 GLN   (  67-)  C      -5.42
1318 ILE   ( 162-)  T      -5.42
1093 ARG   (  99-)  S      -5.40
 305 ARG   (  31-)  C      -5.35
1555 ARG   (  77-)  V      -5.33
1802 ILE   ( 162-)  W      -5.33
 644 GLN   (  88-)  E      -5.28
1364 LYS   (  47-)  U      -5.27
  59 GLN   (  67-)  A      -5.26
 623 GLN   (  67-)  E      -5.20
1057 GLN   (  63-)  S      -5.18
1336 ARG   (  19-)  U      -5.17
1380 GLN   (  63-)  U      -5.10
1541 GLN   (  63-)  V      -5.08
1123 ARG   ( 129-)  S      -5.04

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.

 938 LYS   ( 108-)  R       940 - GLU    110- ( R)         -5.17
1586 LYS   ( 108-)  V      1588 - GLU    110- ( V)         -5.05
1748 LYS   ( 108-)  W      1750 - GLU    110- ( W)         -5.14

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: R

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: S

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: T

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: U

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: V

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: W

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.

1184 ALA   (  28-)  T   -2.65
1022 ALA   (  28-)  S   -2.62
  94 GLN   ( 102-)  A   -2.57
1345 ALA   (  28-)  U   -2.56
1469 SER   ( 152-)  U   -2.56
1146 SER   ( 152-)  S   -2.52
  13 GLN   (  21-)  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.

 853 TYR   (  23-)  R     -  856 GLN   (  26-)  R        -1.82
1663 TYR   (  23-)  W     - 1666 GLN   (  26-)  W        -1.69

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: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

  80 GLN   (  88-)  A
 221 GLN   (  88-)  B
 362 GLN   (  88-)  C
 503 GLN   (  88-)  D
 785 GLN   (  88-)  F
 859 GLN   (  29-)  R
 916 GLN   (  86-)  R
 994 ASN   ( 164-)  R
1080 GLN   (  86-)  S
1086 GLN   (  92-)  S
1242 GLN   (  86-)  T
1320 ASN   ( 164-)  T
1426 GLN   ( 109-)  U
1507 GLN   (  29-)  V
1726 GLN   (  86-)  W

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.

  13 GLN   (  21-)  A      NE2
  19 GLN   (  27-)  A      N
  44 SER   (  52-)  A      N
  55 LEU   (  63-)  A      N
  65 HIS   (  73-)  A      N
  66 VAL   (  74-)  A      N
  89 ILE   (  97-)  A      N
  91 SER   (  99-)  A      N
  93 CYS   ( 101-)  A      N
 130 GLU   ( 146-)  A      N
 133 GLN   ( 149-)  A      N
 154 GLN   (  21-)  B      NE2
 156 GLU   (  23-)  B      N
 160 GLN   (  27-)  B      N
 164 ARG   (  31-)  B      N
 185 SER   (  52-)  B      N
 192 TYR   (  59-)  B      OH
 196 LEU   (  63-)  B      N
 207 VAL   (  74-)  B      N
 215 ARG   (  82-)  B      NE
 230 ILE   (  97-)  B      N
 232 SER   (  99-)  B      N
 234 CYS   ( 101-)  B      N
 274 GLN   ( 149-)  B      N
 295 GLN   (  21-)  C      NE2
And so on for a total of 141 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
  84 ASN   (  92-)  A      OD1
 393 GLU   ( 127-)  C      OE1
 789 ASN   (  92-)  F      OD1

Warning: Possible wrong residue type

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

 393 GLU   ( 127-)  C   H-bonding suggests Gln
 396 ASP   ( 130-)  C   H-bonding suggests Asn
 598 GLU   (  42-)  E   H-bonding suggests Gln
 678 ASP   ( 130-)  E   H-bonding suggests Asn; but Alt-Rotamer
 816 GLU   ( 127-)  F   H-bonding suggests Gln; but Alt-Rotamer
1289 GLU   ( 133-)  T   H-bonding suggests Gln
1387 GLU   (  70-)  U   H-bonding suggests Gln
1535 GLU   (  57-)  V   H-bonding suggests Gln; but Alt-Rotamer
1569 GLU   (  91-)  V   H-bonding suggests Gln
1815 ASP   ( 175-)  W   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 :  -1.447
  2nd generation packing quality :  -1.395
  Ramachandran plot appearance   :  -2.647
  chi-1/chi-2 rotamer normality  :  -3.134 (poor)
  Backbone conformation          :  -0.881

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.197 (tight)
  Bond angles                    :   0.435 (tight)
  Omega angle restraints         :   0.852
  Side chain planarity           :   0.174 (tight)
  Improper dihedral distribution :   0.423
  B-factor distribution          :   0.954
  Inside/Outside distribution    :   1.025

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.197 (tight)
  Bond angles                    :   0.435 (tight)
  Omega angle restraints         :   0.852
  Side chain planarity           :   0.174 (tight)
  Improper dihedral distribution :   0.423
  B-factor distribution          :   0.954
  Inside/Outside distribution    :   1.025
==============

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.