WHAT IF Check report

This file was created 2011-12-21 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 pdb1a0d.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Missing atoms

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

  17 LYS   (  17-)  A      CG
  17 LYS   (  17-)  A      CD
  17 LYS   (  17-)  A      CE
  17 LYS   (  17-)  A      NZ
 110 LYS   ( 110-)  A      CG
 110 LYS   ( 110-)  A      CD
 110 LYS   ( 110-)  A      CE
 110 LYS   ( 110-)  A      NZ
 114 LYS   ( 114-)  A      CG
 114 LYS   ( 114-)  A      CD
 114 LYS   ( 114-)  A      CE
 114 LYS   ( 114-)  A      NZ
 365 LYS   ( 365-)  A      CG
 365 LYS   ( 365-)  A      CD
 365 LYS   ( 365-)  A      CE
 365 LYS   ( 365-)  A      NZ
 414 GLU   ( 414-)  A      CG
 414 GLU   ( 414-)  A      CD
 414 GLU   ( 414-)  A      OE1
 414 GLU   ( 414-)  A      OE2
 454 LYS   (  17-)  B      CG
 454 LYS   (  17-)  B      CD
 454 LYS   (  17-)  B      CE
 454 LYS   (  17-)  B      NZ
 547 LYS   ( 110-)  B      CG
And so on for a total of 80 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

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.

  56 ASP   (  56-)  A      N    CA   CB  102.23   -4.9
  98 HIS   (  98-)  A      CG   ND1  CE1 109.71    4.1
 274 HIS   ( 274-)  A      CG   ND1  CE1 109.86    4.3
 493 ASP   (  56-)  B      N    CA   CB  102.22   -4.9
 535 HIS   (  98-)  B      CG   ND1  CE1 109.67    4.1
 711 HIS   ( 274-)  B      CG   ND1  CE1 109.87    4.3
 930 ASP   (  56-)  C      N    CA   CB  102.23   -4.9
 972 HIS   (  98-)  C      CG   ND1  CE1 109.70    4.1
1148 HIS   ( 274-)  C      CG   ND1  CE1 109.83    4.2
1367 ASP   (  56-)  D      N    CA   CB  102.19   -4.9
1409 HIS   (  98-)  D      CG   ND1  CE1 109.74    4.1
1585 HIS   ( 274-)  D      CG   ND1  CE1 109.87    4.3

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.

1000 TYR   ( 126-)  C    6.52
1437 TYR   ( 126-)  D    6.51
 126 TYR   ( 126-)  A    6.51
 563 TYR   ( 126-)  B    6.49
 127 MET   ( 127-)  A    4.46
1001 MET   ( 127-)  C    4.45
 564 MET   ( 127-)  B    4.45
1438 MET   ( 127-)  D    4.45

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.

1449 THR   ( 138-)  D    -2.4
 575 THR   ( 138-)  B    -2.4
1012 THR   ( 138-)  C    -2.4
 138 THR   ( 138-)  A    -2.4
 630 THR   ( 193-)  B    -2.3
1067 THR   ( 193-)  C    -2.3
 193 THR   ( 193-)  A    -2.3
1504 THR   ( 193-)  D    -2.3
1649 LYS   ( 338-)  D    -2.3
1212 LYS   ( 338-)  C    -2.3
 775 LYS   ( 338-)  B    -2.3
 338 LYS   ( 338-)  A    -2.3
1641 ARG   ( 330-)  D    -2.2
 767 ARG   ( 330-)  B    -2.2
 330 ARG   ( 330-)  A    -2.2
1204 ARG   ( 330-)  C    -2.2
  95 PHE   (  95-)  A    -2.2
1406 PHE   (  95-)  D    -2.2
 969 PHE   (  95-)  C    -2.2
 532 PHE   (  95-)  B    -2.2
1273 THR   ( 399-)  C    -2.1
 399 THR   ( 399-)  A    -2.1
1710 THR   ( 399-)  D    -2.1
 836 THR   ( 399-)  B    -2.1
 811 ARG   ( 374-)  B    -2.1
1248 ARG   ( 374-)  C    -2.1
 374 ARG   ( 374-)  A    -2.1
1685 ARG   ( 374-)  D    -2.1
 964 LEU   (  90-)  C    -2.1
1401 LEU   (  90-)  D    -2.1
 527 LEU   (  90-)  B    -2.1
  90 LEU   (  90-)  A    -2.1
1339 GLU   (  28-)  D    -2.1
 465 GLU   (  28-)  B    -2.1
 902 GLU   (  28-)  C    -2.1
  28 GLU   (  28-)  A    -2.1
1264 GLY   ( 390-)  C    -2.1
 827 GLY   ( 390-)  B    -2.1
1701 GLY   ( 390-)  D    -2.1
 390 GLY   ( 390-)  A    -2.1
 445 THR   (   8-)  B    -2.0
   8 THR   (   8-)  A    -2.0
 882 THR   (   8-)  C    -2.0
1319 THR   (   8-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  24 PHE   (  24-)  A  Poor phi/psi
  55 SER   (  55-)  A  omega poor
  72 GLY   (  72-)  A  Poor phi/psi
  91 ASN   (  91-)  A  Poor phi/psi
 142 PHE   ( 142-)  A  Poor phi/psi
 151 ALA   ( 151-)  A  Poor phi/psi
 223 ASP   ( 223-)  A  Poor phi/psi
 234 GLU   ( 234-)  A  Poor phi/psi, PRO omega poor
 295 ASN   ( 295-)  A  Poor phi/psi
 336 ASP   ( 336-)  A  Poor phi/psi
 390 GLY   ( 390-)  A  Poor phi/psi
 421 ARG   ( 421-)  A  Poor phi/psi
 461 PHE   (  24-)  B  Poor phi/psi
 492 SER   (  55-)  B  omega poor
 509 GLY   (  72-)  B  Poor phi/psi
 528 ASN   (  91-)  B  Poor phi/psi
 579 PHE   ( 142-)  B  Poor phi/psi
 588 ALA   ( 151-)  B  Poor phi/psi
 660 ASP   ( 223-)  B  Poor phi/psi
 671 GLU   ( 234-)  B  Poor phi/psi, PRO omega poor
 732 ASN   ( 295-)  B  Poor phi/psi
 773 ASP   ( 336-)  B  Poor phi/psi
 827 GLY   ( 390-)  B  Poor phi/psi
 858 ARG   ( 421-)  B  Poor phi/psi
 898 PHE   (  24-)  C  Poor phi/psi
 929 SER   (  55-)  C  omega poor
 946 GLY   (  72-)  C  Poor phi/psi
 965 ASN   (  91-)  C  Poor phi/psi
1016 PHE   ( 142-)  C  Poor phi/psi
1025 ALA   ( 151-)  C  Poor phi/psi
1097 ASP   ( 223-)  C  Poor phi/psi
1108 GLU   ( 234-)  C  Poor phi/psi, PRO omega poor
1169 ASN   ( 295-)  C  Poor phi/psi
1210 ASP   ( 336-)  C  Poor phi/psi
1264 GLY   ( 390-)  C  Poor phi/psi
1295 ARG   ( 421-)  C  Poor phi/psi
1335 PHE   (  24-)  D  Poor phi/psi
1366 SER   (  55-)  D  omega poor
1383 GLY   (  72-)  D  Poor phi/psi
1402 ASN   (  91-)  D  Poor phi/psi
1453 PHE   ( 142-)  D  Poor phi/psi
1462 ALA   ( 151-)  D  Poor phi/psi
1534 ASP   ( 223-)  D  Poor phi/psi
1545 GLU   ( 234-)  D  Poor phi/psi, PRO omega poor
1606 ASN   ( 295-)  D  Poor phi/psi
1647 ASP   ( 336-)  D  Poor phi/psi
1701 GLY   ( 390-)  D  Poor phi/psi
1732 ARG   ( 421-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.001

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 : -3.001

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.

 314 SER   ( 314-)  A    0.38
 751 SER   ( 314-)  B    0.38
1188 SER   ( 314-)  C    0.38
1625 SER   ( 314-)  D    0.38

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 PHE   (   3-)  A      0
   4 ASP   (   4-)  A      0
   7 SER   (   7-)  A      0
   8 THR   (   8-)  A      0
  12 GLU   (  12-)  A      0
  15 ALA   (  15-)  A      0
  20 LEU   (  20-)  A      0
  24 PHE   (  24-)  A      0
  28 GLU   (  28-)  A      0
  29 GLU   (  29-)  A      0
  31 VAL   (  31-)  A      0
  33 ASP   (  33-)  A      0
  36 MET   (  36-)  A      0
  41 ARG   (  41-)  A      0
  42 PHE   (  42-)  A      0
  49 THR   (  49-)  A      0
  50 PHE   (  50-)  A      0
  53 ASP   (  53-)  A      0
  55 SER   (  55-)  A      0
  56 ASP   (  56-)  A      0
  58 PHE   (  58-)  A      0
  62 ASN   (  62-)  A      0
  63 MET   (  63-)  A      0
  65 ARG   (  65-)  A      0
  67 TRP   (  67-)  A      0
And so on for a total of 600 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 3.333

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].

 232 PRO   ( 232-)  A    36.9 envelop C-delta (36 degrees)
 669 PRO   ( 232-)  B    37.0 envelop C-delta (36 degrees)
1106 PRO   ( 232-)  C    36.9 envelop C-delta (36 degrees)
1543 PRO   ( 232-)  D    37.0 envelop C-delta (36 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.

 874 CYS   ( 437-)  B      SG   <->  1311 CYS   ( 437-)  C      SG   0.86    2.59  INTRA BF
 437 CYS   ( 437-)  A      SG   <->  1748 CYS   ( 437-)  D      SG   0.85    2.60  INTRA BF
1126 GLN   ( 252-)  C      NE2  <->  1563 GLN   ( 252-)  D      NE2  0.19    2.66  INTRA
1267 ARG   ( 393-)  C      CZ   <->  1271 GLU   ( 397-)  C      CG   0.19    3.01  INTRA BF
 393 ARG   ( 393-)  A      CZ   <->   397 GLU   ( 397-)  A      CG   0.19    3.01  INTRA BF
1704 ARG   ( 393-)  D      CZ   <->  1708 GLU   ( 397-)  D      CG   0.19    3.01  INTRA BF
 830 ARG   ( 393-)  B      CZ   <->   834 GLU   ( 397-)  B      CG   0.19    3.01  INTRA BF
 737 LEU   ( 300-)  B      CD2  <->  1173 MET   ( 299-)  C      SD   0.14    3.26  INTRA
1097 ASP   ( 223-)  C      O    <->  1204 ARG   ( 330-)  C      NH2  0.14    2.56  INTRA BF
 223 ASP   ( 223-)  A      O    <->   330 ARG   ( 330-)  A      NH2  0.14    2.56  INTRA BF
 660 ASP   ( 223-)  B      O    <->   767 ARG   ( 330-)  B      NH2  0.14    2.56  INTRA BF
1534 ASP   ( 223-)  D      O    <->  1641 ARG   ( 330-)  D      NH2  0.14    2.56  INTRA BF
 252 GLN   ( 252-)  A      NE2  <->   689 GLN   ( 252-)  B      NE2  0.13    2.72  INTRA
 736 MET   ( 299-)  B      SD   <->  1174 LEU   ( 300-)  C      CD2  0.13    3.27  INTRA
 934 ALA   (  60-)  C      O    <->  1215 ARG   ( 341-)  C      NH1  0.12    2.58  INTRA BL
1371 ALA   (  60-)  D      O    <->  1652 ARG   ( 341-)  D      NH1  0.12    2.58  INTRA BL
 497 ALA   (  60-)  B      O    <->   778 ARG   ( 341-)  B      NH1  0.12    2.58  INTRA BL
 299 MET   ( 299-)  A      SD   <->  1611 LEU   ( 300-)  D      CD2  0.12    3.28  INTRA
  60 ALA   (  60-)  A      O    <->   341 ARG   ( 341-)  A      NH1  0.12    2.58  INTRA BL
 238 HIS   ( 238-)  A      ND1  <->  1757 HOH   ( 546 )  A      O    0.11    2.59  INTRA BL
1549 HIS   ( 238-)  D      ND1  <->  1760 HOH   ( 496 )  D      O    0.11    2.59  INTRA BL
1158 ARG   ( 284-)  C      NH1  <->  1195 GLU   ( 321-)  C      OE1  0.10    2.60  INTRA
 721 ARG   ( 284-)  B      NH1  <->   758 GLU   ( 321-)  B      OE1  0.10    2.60  INTRA
 284 ARG   ( 284-)  A      NH1  <->   321 GLU   ( 321-)  A      OE1  0.10    2.60  INTRA
1595 ARG   ( 284-)  D      NH1  <->  1632 GLU   ( 321-)  D      OE1  0.10    2.60  INTRA
And so on for a total of 149 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 853 GLN   ( 416-)  B      -6.20
1727 GLN   ( 416-)  D      -6.20
 416 GLN   ( 416-)  A      -6.20
1290 GLN   ( 416-)  C      -6.20
1062 ARG   ( 188-)  C      -6.03
 188 ARG   ( 188-)  A      -6.02
1499 ARG   ( 188-)  D      -5.91
 625 ARG   ( 188-)  B      -5.88
 855 GLN   ( 418-)  B      -5.75
 418 GLN   ( 418-)  A      -5.71
1729 GLN   ( 418-)  D      -5.70
1292 GLN   ( 418-)  C      -5.69
1641 ARG   ( 330-)  D      -5.37
1204 ARG   ( 330-)  C      -5.37
 767 ARG   ( 330-)  B      -5.37
 330 ARG   ( 330-)  A      -5.31
 176 ARG   ( 176-)  A      -5.26
 613 ARG   ( 176-)  B      -5.26
1050 ARG   ( 176-)  C      -5.26
1487 ARG   ( 176-)  D      -5.26
 544 GLU   ( 107-)  B      -5.14
 981 GLU   ( 107-)  C      -5.14
1418 GLU   ( 107-)  D      -5.13
 107 GLU   ( 107-)  A      -5.13
1507 ASN   ( 196-)  D      -5.05
 196 ASN   ( 196-)  A      -5.04
 633 ASN   ( 196-)  B      -5.04
1070 ASN   ( 196-)  C      -5.02

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

1505 LEU   ( 194-)  D   -2.62
 328 LEU   ( 328-)  A   -2.62
1202 LEU   ( 328-)  C   -2.62
1639 LEU   ( 328-)  D   -2.62
 765 LEU   ( 328-)  B   -2.62
 631 LEU   ( 194-)  B   -2.61
1068 LEU   ( 194-)  C   -2.61
 194 LEU   ( 194-)  A   -2.60
 939 ARG   (  65-)  C   -2.51
 502 ARG   (  65-)  B   -2.51
  65 ARG   (  65-)  A   -2.51
1376 ARG   (  65-)  D   -2.51

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

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

1757 HOH   ( 533 )  A      O
1758 HOH   ( 537 )  B      O
1759 HOH   ( 536 )  C      O
1760 HOH   ( 539 )  D      O

Error: HIS, ASN, GLN side chain flips

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

  39 HIS   (  39-)  A
 140 ASN   ( 140-)  A
 156 ASN   ( 156-)  A
 196 ASN   ( 196-)  A
 205 ASN   ( 205-)  A
 263 ASN   ( 263-)  A
 295 ASN   ( 295-)  A
 334 ASN   ( 334-)  A
 408 HIS   ( 408-)  A
 417 ASN   ( 417-)  A
 430 ASN   ( 430-)  A
 476 HIS   (  39-)  B
 577 ASN   ( 140-)  B
 593 ASN   ( 156-)  B
 633 ASN   ( 196-)  B
 642 ASN   ( 205-)  B
 732 ASN   ( 295-)  B
 771 ASN   ( 334-)  B
 854 ASN   ( 417-)  B
 867 ASN   ( 430-)  B
 900 ASN   (  26-)  C
 913 HIS   (  39-)  C
1014 ASN   ( 140-)  C
1030 ASN   ( 156-)  C
1070 ASN   ( 196-)  C
1079 ASN   ( 205-)  C
1137 ASN   ( 263-)  C
1169 ASN   ( 295-)  C
1208 ASN   ( 334-)  C
1282 HIS   ( 408-)  C
1291 ASN   ( 417-)  C
1304 ASN   ( 430-)  C
1350 HIS   (  39-)  D
1451 ASN   ( 140-)  D
1467 ASN   ( 156-)  D
1507 ASN   ( 196-)  D
1516 ASN   ( 205-)  D
1574 ASN   ( 263-)  D
1606 ASN   ( 295-)  D
1645 ASN   ( 334-)  D
1719 HIS   ( 408-)  D
1741 ASN   ( 430-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   6 ILE   (   6-)  A      N
  20 LEU   (  20-)  A      N
  21 ALA   (  21-)  A      N
  28 GLU   (  28-)  A      N
  47 TRP   (  47-)  A      N
  48 HIS   (  48-)  A      N
  65 ARG   (  65-)  A      NH1
  67 TRP   (  67-)  A      N
 108 THR   ( 108-)  A      N
 132 THR   ( 132-)  A      N
 137 ASN   ( 137-)  A      N
 146 ARG   ( 146-)  A      NE
 157 ALA   ( 157-)  A      N
 188 ARG   ( 188-)  A      NH2
 224 GLY   ( 224-)  A      N
 231 LYS   ( 231-)  A      NZ
 233 LYS   ( 233-)  A      N
 236 THR   ( 236-)  A      OG1
 239 GLN   ( 239-)  A      NE2
 243 ASP   ( 243-)  A      N
 246 THR   ( 246-)  A      OG1
 252 GLN   ( 252-)  A      NE2
 263 ASN   ( 263-)  A      ND2
 274 HIS   ( 274-)  A      NE2
 277 GLU   ( 277-)  A      N
And so on for a total of 138 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.

 137 ASN   ( 137-)  A      OD1
 181 ASN   ( 181-)  A      OD1
 241 ASP   ( 241-)  A      OD1
 243 ASP   ( 243-)  A      OD1
 304 ASP   ( 304-)  A      OD1
 574 ASN   ( 137-)  B      OD1
 678 ASP   ( 241-)  B      OD1
 680 ASP   ( 243-)  B      OD1
 700 ASN   ( 263-)  B      OD1
 741 ASP   ( 304-)  B      OD1
 845 HIS   ( 408-)  B      ND1
1011 ASN   ( 137-)  C      OD1
1115 ASP   ( 241-)  C      OD1
1117 ASP   ( 243-)  C      OD1
1178 ASP   ( 304-)  C      OD1
1448 ASN   ( 137-)  D      OD1
1492 ASN   ( 181-)  D      OD1
1552 ASP   ( 241-)  D      OD1
1554 ASP   ( 243-)  D      OD1
1615 ASP   ( 304-)  D      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

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

1749  MN   ( 491-)  A   -.-  -.-  Part of ionic cluster
1750  MN   ( 492-)  A   -.-  -.-  Low probability ion. Occ=0.50
1751  MN   ( 491-)  B   -.-  -.-  Part of ionic cluster
1752  MN   ( 492-)  B   -.-  -.-  Low probability ion. Occ=0.50
1753  MN   ( 491-)  C   -.-  -.-  Part of ionic cluster
1754  MN   ( 492-)  C   -.-  -.-  Low probability ion. Occ=0.50
1755  MN   ( 491-)  D   -.-  -.-  Part of ionic cluster
1756  MN   ( 492-)  D   -.-  -.-  Low probability ion. Occ=0.50

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.

 223 ASP   ( 223-)  A   H-bonding suggests Asn
 660 ASP   ( 223-)  B   H-bonding suggests Asn
1097 ASP   ( 223-)  C   H-bonding suggests Asn
1534 ASP   ( 223-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.124
  2nd generation packing quality :  -1.193
  Ramachandran plot appearance   :  -1.634
  chi-1/chi-2 rotamer normality  :  -3.001 (poor)
  Backbone conformation          :  -0.088

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.381 (tight)
  Bond angles                    :   0.649 (tight)
  Omega angle restraints         :   0.606 (tight)
  Side chain planarity           :   0.523 (tight)
  Improper dihedral distribution :   0.829
  B-factor distribution          :   1.310
  Inside/Outside distribution    :   0.993

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 :   0.9
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.381 (tight)
  Bond angles                    :   0.649 (tight)
  Omega angle restraints         :   0.606 (tight)
  Side chain planarity           :   0.523 (tight)
  Improper dihedral distribution :   0.829
  B-factor distribution          :   1.310
  Inside/Outside distribution    :   0.993
==============

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.