WHAT IF Check report

This file was created 2011-12-15 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 pdb1geh.ent

Checks that need to be done early-on in validation

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.

2136 SO4   ( 445-)  A  -
2137 SO4   ( 446-)  A  -
2138 SO4   (1445-)  B  -
2139 SO4   (1446-)  B  -
2140 SO4   (2445-)  C  -
2141 SO4   (2446-)  C  -
2142 SO4   (3445-)  D  -
2143 SO4   (3446-)  D  -
2144 SO4   (4445-)  E  -
2145 SO4   (4446-)  E  -

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

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

  76 VAL   (  87-)  A
1784 VAL   (  87-)  E

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.

   1 TYR   (  12-)  A    High
   3 ASP   (  14-)  A    High
   5 GLY   (  16-)  A    High
   6 TYR   (  17-)  A    High
   7 GLU   (  18-)  A    High
  10 LYS   (  21-)  A    High
  23 ALA   (  34-)  A    High
  24 GLU   (  35-)  A    High
  25 GLY   (  36-)  A    High
  29 GLU   (  40-)  A    High
  34 ALA   (  45-)  A    High
  42 GLY   (  53-)  A    High
  43 THR   (  54-)  A    High
  44 TRP   (  55-)  A    High
  45 THR   (  56-)  A    High
  46 THR   (  57-)  A    High
  47 LEU   (  58-)  A    High
  48 TYR   (  59-)  A    High
  49 PRO   (  60-)  A    High
  53 GLN   (  64-)  A    High
  54 GLU   (  65-)  A    High
  69 MET   (  80-)  A    High
  74 TRP   (  85-)  A    High
  88 ALA   (  99-)  A    High
  96 SER   ( 107-)  A    High
And so on for a total of 464 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :293.000

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

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

   1 TYR   (  12-)  A
   6 TYR   (  17-)  A
  26 TYR   (  37-)  A
  51 TYR   (  62-)  A
  80 TYR   (  91-)  A
 157 TYR   ( 168-)  A
 255 TYR   ( 266-)  A
 282 TYR   ( 293-)  A
 341 TYR   ( 357-)  A
 428 TYR   (  12-)  B
 433 TYR   (  17-)  B
 453 TYR   (  37-)  B
 507 TYR   (  91-)  B
 584 TYR   ( 168-)  B
 682 TYR   ( 266-)  B
 709 TYR   ( 293-)  B
 768 TYR   ( 357-)  B
 855 TYR   (  12-)  C
 860 TYR   (  17-)  C
 880 TYR   (  37-)  C
 934 TYR   (  91-)  C
1011 TYR   ( 168-)  C
1109 TYR   ( 266-)  C
1136 TYR   ( 293-)  C
1195 TYR   ( 357-)  C
1282 TYR   (  12-)  D
1287 TYR   (  17-)  D
1307 TYR   (  37-)  D
1361 TYR   (  91-)  D
1438 TYR   ( 168-)  D
1536 TYR   ( 266-)  D
1563 TYR   ( 293-)  D
1622 TYR   ( 357-)  D
1709 TYR   (  12-)  E
1714 TYR   (  17-)  E
1734 TYR   (  37-)  E
1788 TYR   (  91-)  E
1865 TYR   ( 168-)  E
1963 TYR   ( 266-)  E
1990 TYR   ( 293-)  E
2049 TYR   ( 357-)  E

Warning: Phenylalanine convention problem

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

 102 PHE   ( 113-)  A
 347 PHE   ( 363-)  A
 529 PHE   ( 113-)  B
 774 PHE   ( 363-)  B
 956 PHE   ( 113-)  C
1201 PHE   ( 363-)  C
1383 PHE   ( 113-)  D
1628 PHE   ( 363-)  D
1810 PHE   ( 113-)  E
2055 PHE   ( 363-)  E

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.

  58 ASP   (  69-)  A
  65 ASP   (  76-)  A
  68 ASP   (  79-)  A
  71 ASP   (  82-)  A
 222 ASP   ( 233-)  A
 332 ASP   ( 348-)  A
 383 ASP   ( 399-)  A
 406 ASP   ( 422-)  A
 485 ASP   (  69-)  B
 492 ASP   (  76-)  B
 495 ASP   (  79-)  B
 498 ASP   (  82-)  B
 649 ASP   ( 233-)  B
 759 ASP   ( 348-)  B
 810 ASP   ( 399-)  B
 833 ASP   ( 422-)  B
 912 ASP   (  69-)  C
 919 ASP   (  76-)  C
 922 ASP   (  79-)  C
 925 ASP   (  82-)  C
1076 ASP   ( 233-)  C
1186 ASP   ( 348-)  C
1237 ASP   ( 399-)  C
1260 ASP   ( 422-)  C
1339 ASP   (  69-)  D
1346 ASP   (  76-)  D
1349 ASP   (  79-)  D
1352 ASP   (  82-)  D
1503 ASP   ( 233-)  D
1613 ASP   ( 348-)  D
1664 ASP   ( 399-)  D
1687 ASP   ( 422-)  D
1766 ASP   (  69-)  E
1773 ASP   (  76-)  E
1776 ASP   (  79-)  E
1779 ASP   (  82-)  E
1930 ASP   ( 233-)  E
2040 ASP   ( 348-)  E
2091 ASP   ( 399-)  E
2114 ASP   ( 422-)  E

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.

   7 GLU   (  18-)  A
  29 GLU   (  40-)  A
 133 GLU   ( 144-)  A
 140 GLU   ( 151-)  A
 160 GLU   ( 171-)  A
 161 GLU   ( 172-)  A
 227 GLU   ( 238-)  A
 323 GLU   ( 339-)  A
 434 GLU   (  18-)  B
 456 GLU   (  40-)  B
 560 GLU   ( 144-)  B
 567 GLU   ( 151-)  B
 587 GLU   ( 171-)  B
 588 GLU   ( 172-)  B
 654 GLU   ( 238-)  B
 750 GLU   ( 339-)  B
 861 GLU   (  18-)  C
 883 GLU   (  40-)  C
 987 GLU   ( 144-)  C
 994 GLU   ( 151-)  C
1014 GLU   ( 171-)  C
1015 GLU   ( 172-)  C
1081 GLU   ( 238-)  C
1177 GLU   ( 339-)  C
1288 GLU   (  18-)  D
1310 GLU   (  40-)  D
1414 GLU   ( 144-)  D
1421 GLU   ( 151-)  D
1441 GLU   ( 171-)  D
1442 GLU   ( 172-)  D
1508 GLU   ( 238-)  D
1604 GLU   ( 339-)  D
1715 GLU   (  18-)  E
1737 GLU   (  40-)  E
1841 GLU   ( 144-)  E
1848 GLU   ( 151-)  E
1868 GLU   ( 171-)  E
1869 GLU   ( 172-)  E
1935 GLU   ( 238-)  E
2031 GLU   ( 339-)  E

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.

   4 LYS   (  15-)  A      N    CA   C   124.54    4.8
   5 GLY   (  16-)  A      N    CA   C    95.02   -6.0
  72 GLY   (  83-)  A      N    CA   C   100.68   -4.1
 263 TYR   ( 274-)  A      N    CA   C    99.00   -4.4
 431 LYS   (  15-)  B      N    CA   C   124.82    4.9
 432 GLY   (  16-)  B      N    CA   C    95.58   -5.8
 690 TYR   ( 274-)  B      N    CA   C    99.00   -4.4
 858 LYS   (  15-)  C      N    CA   C   124.30    4.7
 859 GLY   (  16-)  C      N    CA   C    95.16   -6.0
 926 GLY   (  83-)  C      N    CA   C   100.72   -4.1
1117 TYR   ( 274-)  C      N    CA   C    99.23   -4.3
1285 LYS   (  15-)  D      N    CA   C   124.31    4.7
1286 GLY   (  16-)  D      N    CA   C    95.67   -5.8
1544 TYR   ( 274-)  D      N    CA   C    99.56   -4.2
1712 LYS   (  15-)  E      N    CA   C   124.52    4.8
1713 GLY   (  16-)  E      N    CA   C    95.19   -6.0
1780 GLY   (  83-)  E      N    CA   C   100.76   -4.0
1971 TYR   ( 274-)  E      N    CA   C    99.55   -4.2

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.

   7 GLU   (  18-)  A
  29 GLU   (  40-)  A
  58 ASP   (  69-)  A
  65 ASP   (  76-)  A
  68 ASP   (  79-)  A
  71 ASP   (  82-)  A
 133 GLU   ( 144-)  A
 140 GLU   ( 151-)  A
 160 GLU   ( 171-)  A
 161 GLU   ( 172-)  A
 222 ASP   ( 233-)  A
 227 GLU   ( 238-)  A
 323 GLU   ( 339-)  A
 332 ASP   ( 348-)  A
 383 ASP   ( 399-)  A
 406 ASP   ( 422-)  A
 434 GLU   (  18-)  B
 456 GLU   (  40-)  B
 485 ASP   (  69-)  B
 492 ASP   (  76-)  B
 495 ASP   (  79-)  B
 498 ASP   (  82-)  B
 560 GLU   ( 144-)  B
 567 GLU   ( 151-)  B
 587 GLU   ( 171-)  B
And so on for a total of 80 lines.

Error: Tau angle problems

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

   5 GLY   (  16-)  A    6.66
 859 GLY   (  16-)  C    6.61
1713 GLY   (  16-)  E    6.60
 432 GLY   (  16-)  B    6.46
1286 GLY   (  16-)  D    6.42
1106 ALA   ( 263-)  C    5.88
2030 ARG   ( 338-)  E    5.80
 252 ALA   ( 263-)  A    5.77
 749 ARG   ( 338-)  B    5.73
1603 ARG   ( 338-)  D    5.72
 679 ALA   ( 263-)  B    5.72
1176 ARG   ( 338-)  C    5.65
 322 ARG   ( 338-)  A    5.63
1953 VAL   ( 256-)  E    5.50
 672 VAL   ( 256-)  B    5.38
1533 ALA   ( 263-)  D    5.31
1099 VAL   ( 256-)  C    5.27
 245 VAL   ( 256-)  A    5.24
 431 LYS   (  15-)  B    5.20
1960 ALA   ( 263-)  E    5.15
   4 LYS   (  15-)  A    5.09
1712 LYS   (  15-)  E    5.08
1285 LYS   (  15-)  D    5.00
 858 LYS   (  15-)  C    5.00
1526 VAL   ( 256-)  D    4.71
 690 TYR   ( 274-)  B    4.65
 263 TYR   ( 274-)  A    4.65
  72 GLY   (  83-)  A    4.63
 926 GLY   (  83-)  C    4.61
1780 GLY   (  83-)  E    4.60
1117 TYR   ( 274-)  C    4.56
1353 GLY   (  83-)  D    4.52
1971 TYR   ( 274-)  E    4.44
1544 TYR   ( 274-)  D    4.44
 499 GLY   (  83-)  B    4.44
 447 VAL   (  31-)  B    4.30
1728 VAL   (  31-)  E    4.30
 874 VAL   (  31-)  C    4.24
  20 VAL   (  31-)  A    4.21
1301 VAL   (  31-)  D    4.15

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.561

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.409

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.

1736 ILE   (  39-)  E    -2.7
 882 ILE   (  39-)  C    -2.7
 455 ILE   (  39-)  B    -2.7
1309 ILE   (  39-)  D    -2.7
  28 ILE   (  39-)  A    -2.6
1931 LEU   ( 234-)  E    -2.6
 223 LEU   ( 234-)  A    -2.6
1922 THR   ( 225-)  E    -2.6
1504 LEU   ( 234-)  D    -2.6
 650 LEU   ( 234-)  B    -2.6
 641 THR   ( 225-)  B    -2.6
 214 THR   ( 225-)  A    -2.6
1068 THR   ( 225-)  C    -2.6
1077 LEU   ( 234-)  C    -2.5
1495 THR   ( 225-)  D    -2.5
 889 VAL   (  46-)  C    -2.2
1327 THR   (  57-)  D    -2.2
 900 THR   (  57-)  C    -2.2
1754 THR   (  57-)  E    -2.2
  46 THR   (  57-)  A    -2.2
  48 TYR   (  59-)  A    -2.2
 902 TYR   (  59-)  C    -2.2
1756 TYR   (  59-)  E    -2.2
1329 TYR   (  59-)  D    -2.2
  35 VAL   (  46-)  A    -2.2
And so on for a total of 69 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.

   4 LYS   (  15-)  A  Poor phi/psi
  10 LYS   (  21-)  A  Poor phi/psi
  23 ALA   (  34-)  A  Poor phi/psi
  24 GLU   (  35-)  A  Poor phi/psi
  25 GLY   (  36-)  A  Poor phi/psi
  40 SER   (  51-)  A  Poor phi/psi
  42 GLY   (  53-)  A  Poor phi/psi
  44 TRP   (  55-)  A  Poor phi/psi
  47 LEU   (  58-)  A  Poor phi/psi
  48 TYR   (  59-)  A  Poor phi/psi
  62 LYS   (  73-)  A  Poor phi/psi
 106 ARG   ( 117-)  A  Poor phi/psi
 140 GLU   ( 151-)  A  Poor phi/psi
 154 LYS   ( 165-)  A  Poor phi/psi
 184 THR   ( 195-)  A  Poor phi/psi
 221 ALA   ( 232-)  A  Poor phi/psi
 273 MET   ( 284-)  A  Poor phi/psi
 277 PHE   ( 288-)  A  Poor phi/psi
 298 GLY   ( 309-)  A  Poor phi/psi
 341 TYR   ( 357-)  A  Poor phi/psi
 358 ASN   ( 374-)  A  Poor phi/psi
 360 GLN   ( 376-)  A  Poor phi/psi
 363 ILE   ( 379-)  A  Poor phi/psi
 388 GLY   ( 404-)  A  Poor phi/psi
 402 GLY   ( 418-)  A  Poor phi/psi
And so on for a total of 141 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 : -3.745

Warning: Unusual backbone conformations

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

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

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

   3 ASP   (  14-)  A      0
   4 LYS   (  15-)  A      0
   5 GLY   (  16-)  A      0
   6 TYR   (  17-)  A      0
  12 ARG   (  23-)  A      0
  24 GLU   (  35-)  A      0
  26 TYR   (  37-)  A      0
  28 ILE   (  39-)  A      0
  39 SER   (  50-)  A      0
  40 SER   (  51-)  A      0
  41 THR   (  52-)  A      0
  44 TRP   (  55-)  A      0
  47 LEU   (  58-)  A      0
  48 TYR   (  59-)  A      0
  49 PRO   (  60-)  A      0
  50 TRP   (  61-)  A      0
  51 TYR   (  62-)  A      0
  53 GLN   (  64-)  A      0
  64 TYR   (  75-)  A      0
  65 ASP   (  76-)  A      0
  69 MET   (  80-)  A      0
  71 ASP   (  82-)  A      0
  73 SER   (  84-)  A      0
  83 HIS   (  94-)  A      0
  84 ALA   (  95-)  A      0
And so on for a total of 750 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.130

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!

 402 GLY   ( 418-)  A   1.76   80
 829 GLY   ( 418-)  B   1.76   80
2110 GLY   ( 418-)  E   1.75   80
1256 GLY   ( 418-)  C   1.75   80
1683 GLY   ( 418-)  D   1.75   80
2065 GLY   ( 373-)  E   1.71   80
1638 GLY   ( 373-)  D   1.68   80
1211 GLY   ( 373-)  C   1.67   80
 357 GLY   ( 373-)  A   1.67   80
 784 GLY   ( 373-)  B   1.66   80
2084 GLY   ( 392-)  E   1.63   11
1657 GLY   ( 392-)  D   1.63   11
 376 GLY   ( 392-)  A   1.62   11
1230 GLY   ( 392-)  C   1.61   11
 803 GLY   ( 392-)  B   1.61   11

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.

 184 THR   ( 195-)  A      O   <->  194 ARG   ( 205-)  A      NH2    0.46    2.24  INTRA BL
1038 THR   ( 195-)  C      O   <-> 1048 ARG   ( 205-)  C      NH2    0.46    2.24  INTRA BL
1892 THR   ( 195-)  E      O   <-> 1902 ARG   ( 205-)  E      NH2    0.45    2.25  INTRA BL
1465 THR   ( 195-)  D      O   <-> 1475 ARG   ( 205-)  D      NH2    0.44    2.26  INTRA BL
   5 GLY   (  16-)  A      N   <->    6 TYR   (  17-)  A      N      0.43    2.17  INTRA BF
 859 GLY   (  16-)  C      N   <->  860 TYR   (  17-)  C      N      0.43    2.17  INTRA BF
1713 GLY   (  16-)  E      N   <-> 1714 TYR   (  17-)  E      N      0.43    2.17  INTRA BF
 611 THR   ( 195-)  B      O   <->  621 ARG   ( 205-)  B      NH2    0.43    2.27  INTRA BL
 432 GLY   (  16-)  B      N   <->  433 TYR   (  17-)  B      N      0.42    2.18  INTRA BF
1286 GLY   (  16-)  D      N   <-> 1287 TYR   (  17-)  D      N      0.42    2.18  INTRA BF
1948 HIS   ( 251-)  E      CE1 <-> 2009 GLN   ( 312-)  E      NE2    0.35    2.75  INTRA BL
 240 HIS   ( 251-)  A      CE1 <->  301 GLN   ( 312-)  A      NE2    0.34    2.76  INTRA BL
 667 HIS   ( 251-)  B      CE1 <->  728 GLN   ( 312-)  B      NE2    0.31    2.79  INTRA BL
1094 HIS   ( 251-)  C      CE1 <-> 1155 GLN   ( 312-)  C      NE2    0.31    2.79  INTRA BL
1521 HIS   ( 251-)  D      CE1 <-> 1582 GLN   ( 312-)  D      NE2    0.29    2.81  INTRA BL
 387 ALA   ( 403-)  A      CA  <->  390 ARG   ( 406-)  A      NH2    0.29    2.81  INTRA BF
  72 GLY   (  83-)  A      N   <->   73 SER   (  84-)  A      N      0.28    2.32  INTRA BF
 926 GLY   (  83-)  C      N   <->  927 SER   (  84-)  C      N      0.28    2.32  INTRA BF
1780 GLY   (  83-)  E      N   <-> 1781 SER   (  84-)  E      N      0.27    2.33  INTRA BF
1353 GLY   (  83-)  D      N   <-> 1354 SER   (  84-)  D      N      0.27    2.33  INTRA BF
 280 ASN   ( 291-)  A      OD1 <->  282 TYR   ( 293-)  A      N      0.26    2.44  INTRA BL
 499 GLY   (  83-)  B      N   <->  500 SER   (  84-)  B      N      0.26    2.34  INTRA BF
1134 ASN   ( 291-)  C      OD1 <-> 1136 TYR   ( 293-)  C      N      0.26    2.44  INTRA BL
2095 ALA   ( 403-)  E      CA  <-> 2098 ARG   ( 406-)  E      NH2    0.25    2.85  INTRA BF
1668 ALA   ( 403-)  D      CA  <-> 1671 ARG   ( 406-)  D      NH2    0.25    2.85  INTRA BF
And so on for a total of 650 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

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.

  48 TYR   (  59-)  A      -6.93
 475 TYR   (  59-)  B      -6.92
1329 TYR   (  59-)  D      -6.91
 902 TYR   (  59-)  C      -6.91
1756 TYR   (  59-)  E      -6.91
1133 ARG   ( 290-)  C      -6.82
 279 ARG   ( 290-)  A      -6.81
1560 ARG   ( 290-)  D      -6.81
 706 ARG   ( 290-)  B      -6.81
1987 ARG   ( 290-)  E      -6.79
   6 TYR   (  17-)  A      -5.82
1714 TYR   (  17-)  E      -5.81
 860 TYR   (  17-)  C      -5.79
 433 TYR   (  17-)  B      -5.79
1287 TYR   (  17-)  D      -5.76
1328 LEU   (  58-)  D      -5.62
 474 LEU   (  58-)  B      -5.57
1755 LEU   (  58-)  E      -5.57
  47 LEU   (  58-)  A      -5.56
 901 LEU   (  58-)  C      -5.56
 429 VAL   (  13-)  B      -5.25
1710 VAL   (  13-)  E      -5.25
1283 VAL   (  13-)  D      -5.24
   2 VAL   (  13-)  A      -5.24
 856 VAL   (  13-)  C      -5.22
 431 LYS   (  15-)  B      -5.20
1285 LYS   (  15-)  D      -5.18
   4 LYS   (  15-)  A      -5.18
 858 LYS   (  15-)  C      -5.14
1712 LYS   (  15-)  E      -5.13
 864 LYS   (  21-)  C      -5.12
1718 LYS   (  21-)  E      -5.10
  10 LYS   (  21-)  A      -5.10
2030 ARG   ( 338-)  E      -5.09
 749 ARG   ( 338-)  B      -5.09
1603 ARG   ( 338-)  D      -5.08
 322 ARG   ( 338-)  A      -5.08
1291 LYS   (  21-)  D      -5.08
1176 ARG   ( 338-)  C      -5.07

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.

 424 HIS   ( 440-)  A       427 - PRO    443- ( A)         -4.38
 851 HIS   ( 440-)  B       854 - PRO    443- ( B)         -4.39
1278 HIS   ( 440-)  C      1281 - PRO    443- ( C)         -4.38
1705 HIS   ( 440-)  D      1708 - PRO    443- ( D)         -4.38
2132 HIS   ( 440-)  E      2135 - PRO    443- ( E)         -4.38

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

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.

1756 TYR   (  59-)  E   -2.79
 902 TYR   (  59-)  C   -2.77
  48 TYR   (  59-)  A   -2.77
1329 TYR   (  59-)  D   -2.76
1233 LEU   ( 395-)  C   -2.62
 379 LEU   ( 395-)  A   -2.61
 806 LEU   ( 395-)  B   -2.60
2087 LEU   ( 395-)  E   -2.60
1660 LEU   ( 395-)  D   -2.59

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

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.

 218 ASN   ( 229-)  A
 240 HIS   ( 251-)  A
 335 HIS   ( 351-)  A
 394 GLN   ( 410-)  A
 645 ASN   ( 229-)  B
 667 HIS   ( 251-)  B
 762 HIS   ( 351-)  B
 821 GLN   ( 410-)  B
1072 ASN   ( 229-)  C
1094 HIS   ( 251-)  C
1189 HIS   ( 351-)  C
1248 GLN   ( 410-)  C
1499 ASN   ( 229-)  D
1521 HIS   ( 251-)  D
1616 HIS   ( 351-)  D
1675 GLN   ( 410-)  D
1926 ASN   ( 229-)  E
1948 HIS   ( 251-)  E
2043 HIS   ( 351-)  E
2102 GLN   ( 410-)  E

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.

  19 ARG   (  30-)  A      NH1
  21 THR   (  32-)  A      OG1
  40 SER   (  51-)  A      N
  42 GLY   (  53-)  A      N
  46 THR   (  57-)  A      N
  50 TRP   (  61-)  A      N
  55 ARG   (  66-)  A      NH1
  63 ALA   (  74-)  A      N
  67 HIS   (  78-)  A      N
  71 ASP   (  82-)  A      N
  73 SER   (  84-)  A      OG
  89 ASN   ( 100-)  A      ND2
 101 ILE   ( 112-)  A      N
 106 ARG   ( 117-)  A      N
 111 ARG   ( 122-)  A      N
 120 LYS   ( 131-)  A      N
 126 ASP   ( 137-)  A      N
 129 ALA   ( 140-)  A      N
 152 LYS   ( 163-)  A      N
 154 LYS   ( 165-)  A      N
 157 TYR   ( 168-)  A      N
 157 TYR   ( 168-)  A      OH
 160 GLU   ( 171-)  A      N
 180 ASP   ( 191-)  A      N
 181 GLU   ( 192-)  A      N
And so on for a total of 299 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.

  67 HIS   (  78-)  A      ND1
 179 ASP   ( 190-)  A      OD1
 182 ASN   ( 193-)  A      OD1
 244 ASP   ( 255-)  A      OD1
 244 ASP   ( 255-)  A      OD2
 303 HIS   ( 314-)  A      ND1
 494 HIS   (  78-)  B      ND1
 606 ASP   ( 190-)  B      OD1
 609 ASN   ( 193-)  B      OD1
 671 ASP   ( 255-)  B      OD1
 671 ASP   ( 255-)  B      OD2
 730 HIS   ( 314-)  B      ND1
 921 HIS   (  78-)  C      ND1
1033 ASP   ( 190-)  C      OD1
1036 ASN   ( 193-)  C      OD1
1098 ASP   ( 255-)  C      OD1
1098 ASP   ( 255-)  C      OD2
1157 HIS   ( 314-)  C      ND1
1348 HIS   (  78-)  D      ND1
1463 ASN   ( 193-)  D      OD1
1525 ASP   ( 255-)  D      OD1
1525 ASP   ( 255-)  D      OD2
1584 HIS   ( 314-)  D      ND1
1775 HIS   (  78-)  E      ND1
1890 ASN   ( 193-)  E      OD1
1952 ASP   ( 255-)  E      OD1
1952 ASP   ( 255-)  E      OD2
2011 HIS   ( 314-)  E      ND1

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.

  65 ASP   (  76-)  A   H-bonding suggests Asn
 244 ASP   ( 255-)  A   H-bonding suggests Asn; but Alt-Rotamer
 313 ASP   ( 329-)  A   H-bonding suggests Asn
 397 ASP   ( 413-)  A   H-bonding suggests Asn
 492 ASP   (  76-)  B   H-bonding suggests Asn
 671 ASP   ( 255-)  B   H-bonding suggests Asn; but Alt-Rotamer
 740 ASP   ( 329-)  B   H-bonding suggests Asn
 824 ASP   ( 413-)  B   H-bonding suggests Asn
 919 ASP   (  76-)  C   H-bonding suggests Asn
1098 ASP   ( 255-)  C   H-bonding suggests Asn; but Alt-Rotamer
1167 ASP   ( 329-)  C   H-bonding suggests Asn
1251 ASP   ( 413-)  C   H-bonding suggests Asn
1346 ASP   (  76-)  D   H-bonding suggests Asn
1525 ASP   ( 255-)  D   H-bonding suggests Asn
1594 ASP   ( 329-)  D   H-bonding suggests Asn
1678 ASP   ( 413-)  D   H-bonding suggests Asn
1773 ASP   (  76-)  E   H-bonding suggests Asn
1952 ASP   ( 255-)  E   H-bonding suggests Asn
2021 ASP   ( 329-)  E   H-bonding suggests Asn
2105 ASP   ( 413-)  E   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 :  -1.071
  2nd generation packing quality :  -1.542
  Ramachandran plot appearance   :  -4.409 (bad)
  chi-1/chi-2 rotamer normality  :  -3.745 (poor)
  Backbone conformation          :  -0.273

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.322 (tight)
  Bond angles                    :   0.684
  Omega angle restraints         :   0.206 (tight)
  Side chain planarity           :   0.225 (tight)
  Improper dihedral distribution :   0.633
  B-factor distribution          :   1.376
  Inside/Outside distribution    :   1.019

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -1.9
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.322 (tight)
  Bond angles                    :   0.684
  Omega angle restraints         :   0.206 (tight)
  Side chain planarity           :   0.225 (tight)
  Improper dihedral distribution :   0.633
  B-factor distribution          :   1.376
  Inside/Outside distribution    :   1.019
==============

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.