WHAT IF Check report

This file was created 2012-10-25 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 pdb4gg6.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 C

All-atom RMS fit for the two chains : 3.228
CA-only RMS fit for the two chains : 2.983

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: E and G

All-atom RMS fit for the two chains : 6.613
CA-only RMS fit for the two chains : 6.431

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: E and G

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: I and J

All-atom RMS fit for the two chains : 0.439
CA-only RMS fit for the two chains : 0.305

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 ASP   (   0-)  A      CG
   1 ASP   (   0-)  A      OD1
   1 ASP   (   0-)  A      OD2
   2 ILE   (   1-)  A      CG1
   2 ILE   (   1-)  A      CG2
   2 ILE   (   1-)  A      CD1
   3 VAL   (   2-)  A      CG1
   3 VAL   (   2-)  A      CG2
  42 GLU   (  40-)  A      CG
  42 GLU   (  40-)  A      CD
  42 GLU   (  40-)  A      OE1
  42 GLU   (  40-)  A      OE2
  51 ARG   (  49-)  A      CG
  51 ARG   (  49-)  A      CD
  51 ARG   (  49-)  A      NE
  51 ARG   (  49-)  A      CZ
  51 ARG   (  49-)  A      NH1
  51 ARG   (  49-)  A      NH2
  52 ARG   (  50-)  A      CG
  52 ARG   (  50-)  A      CD
  52 ARG   (  50-)  A      NE
  52 ARG   (  50-)  A      CZ
  52 ARG   (  50-)  A      NH1
  52 ARG   (  50-)  A      NH2
  55 ARG   (  53-)  A      CG
And so on for a total of 727 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: 14

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.

1077 ARG   ( 206-)  F
1079 ARG   ( 208-)  F
1093 ARG   ( 222-)  F
1497 ARG   ( 206-)  H
1499 ARG   ( 208-)  H
1513 ARG   ( 222-)  H

Warning: Tyrosine convention problem

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

  24 TYR   (  22-)  A
  35 TYR   (  33-)  A
 152 TYR   ( 150-)  A
 187 TYR   (   9-)  B
 215 TYR   (  37-)  B
 261 TYR   (  83-)  B
 367 TYR   (  22-)  C
 378 TYR   (  33-)  C
 495 TYR   ( 150-)  C
 532 TYR   (   9-)  D
 570 TYR   (  47-)  D
 606 TYR   (  83-)  D
 727 TYR   (  38-)  E
 781 TYR   ( 102-)  E
 782 TYR   ( 103-)  E
 817 TYR   ( 138-)  E
 916 TYR   (  40-)  F
 932 TYR   (  56-)  F
 985 TYR   ( 114-)  F
 988 TYR   ( 117-)  F
1035 TYR   ( 164-)  F
1099 TYR   ( 228-)  F
1157 TYR   (  38-)  G
1211 TYR   ( 102-)  G
1212 TYR   ( 103-)  G
1247 TYR   ( 138-)  G
1336 TYR   (  40-)  H
1352 TYR   (  56-)  H
1405 TYR   ( 114-)  H
1408 TYR   ( 117-)  H
1455 TYR   ( 164-)  H
1519 TYR   ( 228-)  H

Warning: Phenylalanine convention problem

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

  94 PHE   (  92-)  A
 139 PHE   ( 137-)  A
 148 PHE   ( 146-)  A
 155 PHE   ( 153-)  A
 185 PHE   (   7-)  B
 319 PHE   ( 155-)  B
 371 PHE   (  26-)  C
 437 PHE   (  92-)  C
 482 PHE   ( 137-)  C
 491 PHE   ( 146-)  C
 498 PHE   ( 153-)  C
 563 PHE   (  40-)  D
 636 PHE   ( 122-)  D
 666 PHE   ( 155-)  D
 831 PHE   ( 156-)  E
 871 PHE   ( 199-)  E
 989 PHE   ( 118-)  F
1005 PHE   ( 134-)  F
1034 PHE   ( 163-)  F
1084 PHE   ( 213-)  F
1261 PHE   ( 156-)  G
1409 PHE   ( 118-)  H
1454 PHE   ( 163-)  H
1504 PHE   ( 213-)  H
1553 PHE   (   6-)  I
1566 PHE   (   6-)  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.

 184 ASP   (   6-)  B
 529 ASP   (   6-)  D
 777 ASP   (  98-)  E
 787 ASP   ( 108-)  E
 832 ASP   ( 157-)  E
 851 ASP   ( 179-)  E
1069 ASP   ( 198-)  F
1105 ASP   ( 234-)  F
1207 ASP   (  98-)  G
1217 ASP   ( 108-)  G
1262 ASP   ( 157-)  G
1280 ASP   ( 179-)  G
1489 ASP   ( 198-)  H
1525 ASP   ( 234-)  H

Warning: Glutamic acid convention problem

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

 136 GLU   ( 134-)  A
 244 GLU   (  66-)  B
 247 GLU   (  69-)  B
 479 GLU   ( 134-)  C
 589 GLU   (  66-)  D
 592 GLU   (  69-)  D
 706 GLU   (  12-)  E
 709 GLU   (  15-)  E
 986 GLU   ( 115-)  F
1008 GLU   ( 137-)  F
1063 GLU   ( 192-)  F
1122 GLU   ( 251-)  F
1139 GLU   (  15-)  G
1191 GLU   (  82-)  G
1406 GLU   ( 115-)  H
1428 GLU   ( 137-)  H
1483 GLU   ( 192-)  H
1542 GLU   ( 251-)  H

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.997923 -0.000118  0.000026|
 | -0.000118  0.998207 -0.000001|
 |  0.000026 -0.000001  0.997923|
Proposed new scale matrix

 |  0.008971  0.000001  0.000000|
 |  0.000000  0.007458  0.000000|
 |  0.000000  0.000000  0.007142|
With corresponding cell

    A    = 111.475  B   = 134.078  C    = 140.020
    Alpha=  90.002  Beta=  90.001  Gamma=  90.008

The CRYST1 cell dimensions

    A    = 111.708  B   = 134.325  C    = 140.304
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 201.342
(Under-)estimated Z-score: 10.458

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.

 136 GLU   ( 134-)  A
 184 ASP   (   6-)  B
 244 GLU   (  66-)  B
 247 GLU   (  69-)  B
 479 GLU   ( 134-)  C
 529 ASP   (   6-)  D
 589 GLU   (  66-)  D
 592 GLU   (  69-)  D
 706 GLU   (  12-)  E
 709 GLU   (  15-)  E
 777 ASP   (  98-)  E
 787 ASP   ( 108-)  E
 832 ASP   ( 157-)  E
 851 ASP   ( 179-)  E
 986 GLU   ( 115-)  F
1008 GLU   ( 137-)  F
1063 GLU   ( 192-)  F
1069 ASP   ( 198-)  F
1077 ARG   ( 206-)  F
1079 ARG   ( 208-)  F
1093 ARG   ( 222-)  F
1105 ASP   ( 234-)  F
1122 GLU   ( 251-)  F
1139 GLU   (  15-)  G
1191 GLU   (  82-)  G
1207 ASP   (  98-)  G
1217 ASP   ( 108-)  G
1262 ASP   ( 157-)  G
1280 ASP   ( 179-)  G
1406 GLU   ( 115-)  H
1428 GLU   ( 137-)  H
1483 GLU   ( 192-)  H
1489 ASP   ( 198-)  H
1497 ARG   ( 206-)  H
1499 ARG   ( 208-)  H
1513 ARG   ( 222-)  H
1525 ASP   ( 234-)  H
1542 GLU   ( 251-)  H

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.

1165 PRO   (  46-)  G    -3.0
 735 PRO   (  46-)  E    -3.0
 527 PRO   (   4-)  D    -2.8
1036 PRO   ( 165-)  F    -2.7
1456 PRO   ( 165-)  H    -2.6
 641 ILE   ( 127-)  D    -2.6
 296 ILE   ( 127-)  B    -2.5
1149 HIS   (  25-)  G    -2.4
 268 THR   (  90-)  B    -2.4
 719 HIS   (  25-)  E    -2.4
  81 SER   (  79-)  A    -2.4
 424 SER   (  79-)  C    -2.4
 544 THR   (  21-)  D    -2.3
 304 THR   ( 140-)  B    -2.3
 313 ARG   ( 149-)  B    -2.3
1155 THR   (  36-)  G    -2.2
 293 PRO   ( 124-)  B    -2.2
 725 THR   (  36-)  E    -2.2
  11 GLY   (   9-)  A    -2.2
 354 GLY   (   9-)  C    -2.1
 680 THR   ( 172-)  D    -2.1
 233 PRO   (  55-)  B    -2.1
 362 GLY   (  17-)  C    -2.1
1114 PRO   ( 243-)  F    -2.1
 119 VAL   ( 117-)  A    -2.1
 462 VAL   ( 117-)  C    -2.1
  19 GLY   (  17-)  A    -2.1
1030 LEU   ( 159-)  F    -2.1
 305 GLY   ( 141-)  B    -2.1
1450 LEU   ( 159-)  H    -2.0
   9 SER   (   8-)  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.

  11 GLY   (   9-)  A  omega poor
  19 GLY   (  17-)  A  PRO omega poor
  34 PHE   (  32-)  A  omega poor
  53 PHE   (  51-)  A  Poor phi/psi
 113 ASN   ( 111-)  A  Poor phi/psi
 115 PHE   ( 113-)  A  PRO omega poor
 117 PRO   ( 115-)  A  Poor phi/psi
 126 ASN   ( 124-)  A  Poor phi/psi
 145 HIS   ( 143-)  A  Poor phi/psi
 147 PHE   ( 145-)  A  omega poor
 211 ASN   (  33-)  B  Poor phi/psi
 267 THR   (  89-)  B  Poor phi/psi
 290 ASP   ( 121-)  B  Poor phi/psi
 292 TYR   ( 123-)  B  PRO omega poor
 293 PRO   ( 124-)  B  Poor phi/psi
 305 GLY   ( 141-)  B  omega poor
 317 TRP   ( 153-)  B  Poor phi/psi
 336 GLN   ( 181-)  B  Poor phi/psi
 354 GLY   (   9-)  C  omega poor
 362 GLY   (  17-)  C  PRO omega poor
 377 PHE   (  32-)  C  omega poor
 396 PHE   (  51-)  C  Poor phi/psi
 456 ASN   ( 111-)  C  Poor phi/psi
 458 PHE   ( 113-)  C  PRO omega poor
 460 PRO   ( 115-)  C  Poor phi/psi
And so on for a total of 57 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.

1020 SER   ( 149-)  F    0.36
1440 SER   ( 149-)  H    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!

   5 ASP   (   4-)  A      0
  10 TYR   (   9-)  A      0
  13 ASN   (  11-)  A      0
  18 TYR   (  16-)  A      0
  20 PRO   (  18-)  A      0
  21 SER   (  19-)  A      0
  33 GLU   (  31-)  A      0
  34 PHE   (  32-)  A      0
  46 GLN   (  44-)  A      0
  52 ARG   (  50-)  A      0
  53 PHE   (  51-)  A      0
  54 ARG   (  52-)  A      0
  81 SER   (  79-)  A      0
 101 LEU   (  99-)  A      0
 112 ASP   ( 110-)  A      0
 115 PHE   ( 113-)  A      0
 116 PRO   ( 114-)  A      0
 117 PRO   ( 115-)  A      0
 118 VAL   ( 116-)  A      0
 125 SER   ( 123-)  A      0
 126 ASN   ( 124-)  A      0
 132 GLU   ( 130-)  A      0
 134 VAL   ( 132-)  A      0
 145 HIS   ( 143-)  A      0
 154 THR   ( 152-)  A      0
And so on for a total of 664 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!

1228 GLY   ( 119-)  G   1.61   29
 798 GLY   ( 119-)  E   1.53   29

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].

  20 PRO   (  18-)  A    37.9 envelop C-delta (36 degrees)
 104 PRO   ( 102-)  A   105.3 envelop C-beta (108 degrees)
 180 PRO   ( 180-)  A   -14.1 half-chair C-alpha/N (-18 degrees)
 182 PRO   (   4-)  B   102.3 envelop C-beta (108 degrees)
 293 PRO   ( 124-)  B   -65.1 envelop C-beta (-72 degrees)
 310 PRO   ( 146-)  B  -130.8 half-chair C-delta/C-gamma (-126 degrees)
 333 PRO   ( 178-)  B   148.8 envelop C-alpha (144 degrees)
 363 PRO   (  18-)  C    34.3 envelop C-delta (36 degrees)
 447 PRO   ( 102-)  C   106.3 envelop C-beta (108 degrees)
 524 PRO   ( 180-)  C   -15.3 half-chair C-alpha/N (-18 degrees)
 527 PRO   (   4-)  D   138.5 envelop C-alpha (144 degrees)
 686 PRO   ( 178-)  D   107.3 envelop C-beta (108 degrees)
 716 PRO   (  22-)  E   -46.5 half-chair C-beta/C-alpha (-54 degrees)
 735 PRO   (  46-)  E  -167.0 half-chair N/C-delta (-162 degrees)
 739 PRO   (  50-)  E   -58.3 half-chair C-beta/C-alpha (-54 degrees)
 878 PRO   ( 211-)  E   -24.8 half-chair C-alpha/N (-18 degrees)
 884 PRO   ( 217-)  E   -16.6 half-chair C-alpha/N (-18 degrees)
 908 PRO   (  25-)  F   -63.4 envelop C-beta (-72 degrees)
1006 PRO   ( 135-)  F    48.8 half-chair C-delta/C-gamma (54 degrees)
1014 PRO   ( 143-)  F  -117.9 half-chair C-delta/C-gamma (-126 degrees)
1036 PRO   ( 165-)  F   -47.2 half-chair C-beta/C-alpha (-54 degrees)
1114 PRO   ( 243-)  F   -49.5 half-chair C-beta/C-alpha (-54 degrees)
1146 PRO   (  22-)  G   -49.0 half-chair C-beta/C-alpha (-54 degrees)
1165 PRO   (  46-)  G  -171.1 envelop N (180 degrees)
1169 PRO   (  50-)  G   -58.0 half-chair C-beta/C-alpha (-54 degrees)
1328 PRO   (  25-)  H   -63.7 envelop C-beta (-72 degrees)
1426 PRO   ( 135-)  H    51.8 half-chair C-delta/C-gamma (54 degrees)
1434 PRO   ( 143-)  H  -116.7 envelop C-gamma (-108 degrees)
1456 PRO   ( 165-)  H   -49.9 half-chair C-beta/C-alpha (-54 degrees)
1534 PRO   ( 243-)  H   -48.0 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

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

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

1004 VAL   ( 133-)  F      O    <->  1111 ARG   ( 240-)  F      NH2  0.35    2.35  INTRA BL
1277 CYS   ( 176-)  G      SG   <->  1278 VAL   ( 177-)  G      N    0.29    2.91  INTRA BF
1424 VAL   ( 133-)  H      O    <->  1531 ARG   ( 240-)  H      NH2  0.29    2.41  INTRA BF
 239 TRP   (  61-)  B      NE1  <->  1570 GLN   (  10-)  J      O    0.25    2.45  INTRA BL
 215 TYR   (  37-)  B      O    <->   228 VAL   (  50-)  B      N    0.23    2.47  INTRA BL
 848 CYS   ( 176-)  E      SG   <->   849 VAL   ( 177-)  E      N    0.22    2.98  INTRA BL
1481 LEU   ( 190-)  H      N    <->  1493 ALA   ( 202-)  H      O    0.22    2.48  INTRA BF
 741 TYR   (  52-)  E      OH   <->   744 HIS   (  55-)  E      ND1  0.17    2.53  INTRA BL
 560 TYR   (  37-)  D      O    <->   573 VAL   (  50-)  D      N    0.17    2.53  INTRA BL
1157 TYR   (  38-)  G      N    <->  1216 ARG   ( 107-)  G      O    0.16    2.54  INTRA BL
 685 HIS   ( 177-)  D      ND1  <->   687 SER   ( 179-)  D      N    0.16    2.84  INTRA BF
1061 LEU   ( 190-)  F      N    <->  1073 ALA   ( 202-)  F      O    0.15    2.55  INTRA BL
 577 GLY   (  54-)  D      N    <->   578 PRO   (  55-)  D      CD   0.14    2.86  INTRA BL
1171 TYR   (  52-)  G      OH   <->  1174 HIS   (  55-)  G      ND1  0.14    2.56  INTRA BL
 397 ARG   (  52-)  C      NE   <->  1550 GLU   (   3-)  I      OE2  0.13    2.57  INTRA BL
 969 SER   (  99-)  F      OG   <->   997 VAL   ( 126-)  F      N    0.12    2.58  INTRA BL
  29 ASP   (  27-)  A      O    <->   313 ARG   ( 149-)  B      NH1  0.12    2.58  INTRA BF
 727 TYR   (  38-)  E      N    <->   786 ARG   ( 107-)  E      O    0.11    2.59  INTRA BL
 839 ASP   ( 167-)  E      CG   <->   840 SER   ( 168-)  E      N    0.10    2.90  INTRA BF
 135 SER   ( 133-)  A      O    <->   152 TYR   ( 150-)  A      N    0.10    2.60  INTRA BF
 478 SER   ( 133-)  C      O    <->   495 TYR   ( 150-)  C      N    0.10    2.60  INTRA BL
 232 GLY   (  54-)  B      N    <->   233 PRO   (  55-)  B      CD   0.10    2.90  INTRA BL
1504 PHE   ( 213-)  H      O    <->  1510 ASN   ( 219-)  H      ND2  0.10    2.60  INTRA BF
 137 THR   ( 135-)  A      O    <->   149 LYS   ( 147-)  A      NZ   0.09    2.61  INTRA BL
1389 SER   (  99-)  H      OG   <->  1417 VAL   ( 126-)  H      N    0.09    2.61  INTRA BF
And so on for a total of 95 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

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.

1529 GLN   ( 238-)  H   -3.69
1282 ARG   ( 181-)  G   -3.38
 103 GLN   ( 101-)  A   -3.35
 868 LYS   ( 196-)  E   -3.33
1126 ARG   ( 255-)  F   -3.32
1546 ARG   ( 255-)  H   -3.31
1002 LYS   ( 131-)  F   -2.99
 834 GLN   ( 159-)  E   -2.95
1509 ARG   ( 218-)  H   -2.85
1089 ARG   ( 218-)  F   -2.84
 398 ARG   (  53-)  C   -2.77
  55 ARG   (  53-)  A   -2.75
1183 ARG   (  74-)  G   -2.74
 753 ARG   (  74-)  E   -2.73
1479 GLN   ( 188-)  H   -2.73
1059 GLN   ( 188-)  F   -2.72
1276 LYS   ( 175-)  G   -2.72
 689 GLN   ( 181-)  D   -2.70
 156 LEU   ( 154-)  A   -2.68
 222 VAL   (  44-)  B   -2.67
 847 LYS   ( 175-)  E   -2.62
 284 LEU   ( 115-)  B   -2.61
 337 ASN   ( 182-)  B   -2.61
 647 GLN   ( 136-)  D   -2.60
 567 VAL   (  44-)  D   -2.57
 675 ARG   ( 167-)  D   -2.56
 646 PHE   ( 132-)  D   -2.53
 274 GLU   (  96-)  B   -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.

 154 THR   ( 152-)  A     -  157 PRO   ( 155-)  A        -1.82

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: 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.

 113 ASN   ( 111-)  A
 126 ASN   ( 124-)  A
1097 GLN   ( 226-)  F
1179 ASN   (  65-)  G

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.

   2 ILE   (   1-)  A      N
  13 ASN   (  11-)  A      ND2
  23 GLN   (  21-)  A      NE2
  26 HIS   (  24-)  A      ND1
  50 PHE   (  48-)  A      N
  54 ARG   (  52-)  A      NH2
 113 ASN   ( 111-)  A      N
 115 PHE   ( 113-)  A      N
 168 TRP   ( 168-)  A      N
 206 THR   (  28-)  B      OG1
 224 VAL   (  46-)  B      N
 260 ASN   (  82-)  B      ND2
 291 PHE   ( 122-)  B      N
 314 ASN   ( 150-)  B      ND2
 315 GLY   ( 151-)  B      N
 325 LEU   ( 161-)  B      N
 354 GLY   (   9-)  C      N
 356 ASN   (  11-)  C      ND2
 366 GLN   (  21-)  C      NE2
 367 TYR   (  22-)  C      N
 369 HIS   (  24-)  C      ND1
 375 GLU   (  30-)  C      N
 393 PHE   (  48-)  C      N
 398 ARG   (  53-)  C      N
 458 PHE   ( 113-)  C      N
And so on for a total of 98 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.

  16 GLN   (  14-)  A      OE1
  31 ASP   (  29-)  A      OD2
  33 GLU   (  31-)  A      OE1
 184 ASP   (   6-)  B      OD2
 188 GLN   (  10-)  B      OE1
 252 GLU   (  74-)  B      OE1
 290 ASP   ( 121-)  B      OD1
 359 GLN   (  14-)  C      OE1
 374 ASP   (  29-)  C      OD1
 456 ASN   ( 111-)  C      OD1
 529 ASP   (   6-)  D      OD2
 533 GLN   (  10-)  D      OE1
 677 ASP   ( 169-)  D      OD1
 729 HIS   (  40-)  E      ND1
1038 HIS   ( 167-)  F      ND1
1159 HIS   (  40-)  G      ND1
1458 HIS   ( 167-)  H      ND1
1517 GLN   ( 226-)  H      OE1
1563 GLU   (   3-)  J      OE1

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.

  29 ASP   (  27-)  A   H-bonding suggests Asn
 372 ASP   (  27-)  C   H-bonding suggests Asn
1057 ASP   ( 186-)  F   H-bonding suggests Asn; but Alt-Rotamer
1477 ASP   ( 186-)  H   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:

  2nd generation packing quality :  -1.958
  Ramachandran plot appearance   :  -1.816
  chi-1/chi-2 rotamer normality  :  -2.884
  Backbone conformation          :  -0.427

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.340 (tight)
  Bond angles                    :   0.528 (tight)
  Omega angle restraints         :   0.950
  Side chain planarity           :   0.221 (tight)
  Improper dihedral distribution :   0.482
  B-factor distribution          :   0.422
  Inside/Outside distribution    :   1.056

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.20


Structure Z-scores, positive is better than average:

  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.340 (tight)
  Bond angles                    :   0.528 (tight)
  Omega angle restraints         :   0.950
  Side chain planarity           :   0.221 (tight)
  Improper dihedral distribution :   0.482
  B-factor distribution          :   0.422
  Inside/Outside distribution    :   1.056
==============

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.