WHAT IF Check report

This file was created 2011-12-17 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 pdb1q0k.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.360
CA-only RMS fit for the two chains : 0.192

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.453
CA-only RMS fit for the two chains : 0.229

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.671
CA-only RMS fit for the two chains : 0.211

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.485
CA-only RMS fit for the two chains : 0.213

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.418
CA-only RMS fit for the two chains : 0.213

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and F

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

1418 THJ   (7003-)  A  -
1421 THJ   (7002-)  B  -
1422 THJ   (7005-)  B  -
1425 THJ   (7001-)  A  -
1428 THJ   (7004-)  D  -
1429 THJ   (7006-)  D  -
1436 THJ   (7007-)  G  -
1439 THJ   (7008-)  H  -
1440 THJ   (7011-)  K  -
1443 THJ   (7009-)  I  -
1450 THJ   (7010-)  L  -
1452 THJ   (7012-)  J  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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

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) :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

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

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

 |  0.998576 -0.000513 -0.000005|
 | -0.000513  0.998334 -0.000010|
 | -0.000005 -0.000010  0.998270|
Proposed new scale matrix

 |  0.008971  0.000005  0.000000|
 |  0.000005  0.008814  0.000000|
 |  0.000000  0.000000  0.007744|
With corresponding cell

    A    = 111.473  B   = 113.460  C    = 129.126
    Alpha=  90.001  Beta=  90.001  Gamma=  90.059

The CRYST1 cell dimensions

    A    = 111.635  B   = 113.651  C    = 129.356
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 120.792
(Under-)estimated Z-score: 8.100

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.

  35 HIS   (  35-)  A      CA   CB   CG  108.43   -5.4
 269 HIS   (  35-)  C      CA   CB   CG  107.71   -6.1
 503 HIS   (  35-)  E      CA   CB   CG  108.21   -5.6
 620 HIS   (  35-)  F      CA   CB   CG  107.97   -5.8
 737 HIS   (  35-)  G      CA   CB   CG  109.50   -4.3
 854 HIS   (  35-)  H      CA   CB   CG  107.66   -6.1
1088 HIS   (  35-)  J      CA   CB   CG  108.33   -5.5
1205 HIS   (  35-)  K      CA   CB   CG  109.51   -4.3
1322 HIS   (  35-)  L      CA   CB   CG  107.57   -6.2

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.

 884 PRO   (  65-)  H    -2.4

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.

   3 ASP   (   3-)  A  Poor phi/psi
   4 LEU   (   4-)  A  PRO omega poor
 120 ASP   (   3-)  B  Poor phi/psi
 121 LEU   (   4-)  B  PRO omega poor
 237 ASP   (   3-)  C  Poor phi/psi
 238 LEU   (   4-)  C  PRO omega poor
 354 ASP   (   3-)  D  Poor phi/psi
 355 LEU   (   4-)  D  PRO omega poor
 471 ASP   (   3-)  E  Poor phi/psi
 472 LEU   (   4-)  E  PRO omega poor
 588 ASP   (   3-)  F  Poor phi/psi
 589 LEU   (   4-)  F  PRO omega poor
 705 ASP   (   3-)  G  Poor phi/psi
 706 LEU   (   4-)  G  PRO omega poor
 712 ASP   (  10-)  G  Poor phi/psi
 822 ASP   (   3-)  H  Poor phi/psi
 823 LEU   (   4-)  H  PRO omega poor
 939 ASP   (   3-)  I  Poor phi/psi
 940 LEU   (   4-)  I  PRO omega poor
1056 ASP   (   3-)  J  Poor phi/psi
1057 LEU   (   4-)  J  PRO omega poor
1173 ASP   (   3-)  K  Poor phi/psi
1174 LEU   (   4-)  K  PRO omega poor
1290 ASP   (   3-)  L  Poor phi/psi
1291 LEU   (   4-)  L  PRO omega poor
 chi-1/chi-2 correlation Z-score : 0.581

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.

1139 SER   (  86-)  J    0.35

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   (   3-)  A      0
   4 LEU   (   4-)  A      0
   5 PRO   (   5-)  A      0
   9 TYR   (   9-)  A      0
  62 TYR   (  62-)  A      0
  63 PHE   (  63-)  A      0
  90 ALA   (  90-)  A      0
 116 LYS   ( 116-)  A      0
 117 ALA   ( 117-)  A      0
 118 HIS   (   1-)  B      0
 119 CYS   (   2-)  B      0
 120 ASP   (   3-)  B      0
 121 LEU   (   4-)  B      0
 122 PRO   (   5-)  B      0
 123 CYS   (   6-)  B      0
 179 TYR   (  62-)  B      0
 180 PHE   (  63-)  B      0
 207 ALA   (  90-)  B      0
 209 THR   (  92-)  B      0
 233 LYS   ( 116-)  B      0
 234 ALA   ( 117-)  B      0
 235 HIS   (   1-)  C      0
 236 CYS   (   2-)  C      0
 237 ASP   (   3-)  C      0
 238 LEU   (   4-)  C      0
And so on for a total of 277 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 : 0.965

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.

  47 ARG   (  47-)  A      NH2 <-> 1418 THJ   (7003-)  A      S2     0.76    2.54  INTRA BF
 983 ARG   (  47-)  I      NH2 <-> 1436 THJ   (7007-)  G      S2     0.75    2.55  INTRA BF
 866 ARG   (  47-)  H      NH2 <-> 1440 THJ   (7011-)  K      S2     0.63    2.67  INTRA BF
 164 ARG   (  47-)  B      NH2 <-> 1422 THJ   (7005-)  B      S2     0.60    2.70  INTRA BF
 281 ARG   (  47-)  C      NH2 <-> 1425 THJ   (7001-)  A      S2     0.60    2.70  INTRA BF
1425 THJ   (7001-)  A      S2  <-> 1453 HOH   (9035 )  A      O      0.58    2.42  INTRA BF
1440 THJ   (7011-)  K      S2  <-> 1463 HOH   (9024 )  K      O      0.57    2.43  INTRA BF
 749 ARG   (  47-)  G      NH2 <-> 1443 THJ   (7009-)  I      S2     0.36    2.94  INTRA BF
 883 LYS   (  64-)  H      NZ  <-> 1460 HOH   (9042 )  H      O      0.33    2.37  INTRA BF
  53 HIS   (  53-)  A      NE2 <-> 1425 THJ   (7001-)  A      O1     0.33    2.37  INTRA BF
 404 HIS   (  53-)  D      NE2 <-> 1428 THJ   (7004-)  D      S2     0.32    2.98  INTRA BF
1340 HIS   (  53-)  L      NE2 <-> 1452 THJ   (7012-)  J      S2     0.31    2.99  INTRA BL
1428 THJ   (7004-)  D      S2  <-> 1456 HOH   (9019 )  D      O      0.30    2.70  INTRA BF
 872 HIS   (  53-)  H      NE2 <-> 1439 THJ   (7008-)  H      S2     0.26    3.04  INTRA BF
 398 ARG   (  47-)  D      NH2 <-> 1429 THJ   (7006-)  D      O3     0.25    2.45  INTRA BF
  52 LYS   (  52-)  A      NZ  <->  588 ASP   (   3-)  F      OD2    0.25    2.45  INTRA
 298 LYS   (  64-)  C      N   <->  301 HIS   (  67-)  C      ND1    0.25    2.75  INTRA BF
 148 ASN   (  31-)  B      O   <->  154 GLN   (  37-)  B      NE2    0.25    2.45  INTRA BF
 505 GLN   (  37-)  E      OE1 <->  620 HIS   (  35-)  F      NE2    0.24    2.46  INTRA BL
1219 GLU   (  49-)  K      OE1 <-> 1259 LYS   (  89-)  K      NZ     0.23    2.47  INTRA
1223 HIS   (  53-)  K      NE2 <-> 1440 THJ   (7011-)  K      O1     0.22    2.48  INTRA BF
 850 ASN   (  31-)  H      O   <->  856 GLN   (  37-)  H      NE2    0.22    2.48  INTRA BF
1088 HIS   (  35-)  J      ND1 <-> 1462 HOH   (9014 )  J      O      0.22    2.48  INTRA BF
 586 HIS   (   1-)  F      N   <->  591 CYS   (   6-)  F      SG     0.22    3.08  INTRA BF
 755 HIS   (  53-)  G      NE2 <-> 1436 THJ   (7007-)  G      O2     0.22    2.48  INTRA BF
And so on for a total of 261 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: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

 818 LYS   ( 116-)  G      -5.12
1403 LYS   ( 116-)  L      -5.12

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.

 817 LYS   ( 115-)  G       819 - ALA    117- ( G)         -4.52

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

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: K

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: L

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

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1458 HOH   (9061 )  F      O     58.39   39.59   96.15

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.

 652 HIS   (  67-)  F
 691 GLN   ( 106-)  F
1011 HIS   (  75-)  I

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.

  47 ARG   (  47-)  A      NH2
  79 ASN   (  79-)  A      ND2
 121 LEU   (   4-)  B      N
 164 ARG   (  47-)  B      NH2
 192 HIS   (  75-)  B      N
 196 ASN   (  79-)  B      ND2
 281 ARG   (  47-)  C      NH2
 313 ASN   (  79-)  C      ND2
 398 ARG   (  47-)  D      NH2
 426 HIS   (  75-)  D      N
 430 ASN   (  79-)  D      ND2
 475 GLY   (   7-)  E      N
 515 ARG   (  47-)  E      NH2
 547 ASN   (  79-)  E      ND2
 620 HIS   (  35-)  F      N
 632 ARG   (  47-)  F      NH2
 649 LYS   (  64-)  F      N
 664 ASN   (  79-)  F      ND2
 749 ARG   (  47-)  G      NH2
 781 ASN   (  79-)  G      ND2
 823 LEU   (   4-)  H      N
 866 ARG   (  47-)  H      NH2
 895 THR   (  76-)  H      N
 898 ASN   (  79-)  H      ND2
 940 LEU   (   4-)  I      N
 971 HIS   (  35-)  I      N
 983 ARG   (  47-)  I      NH2
 995 TRP   (  59-)  I      NE1
1015 ASN   (  79-)  I      ND2
1054 HIS   (   1-)  J      N
1057 LEU   (   4-)  J      N
1060 GLY   (   7-)  J      N
1100 ARG   (  47-)  J      NH2
1132 ASN   (  79-)  J      ND2
1174 LEU   (   4-)  K      N
1217 ARG   (  47-)  K      NH2
1249 ASN   (  79-)  K      ND2
1291 LEU   (   4-)  L      N
1334 ARG   (  47-)  L      NH2
1366 ASN   (  79-)  L      ND2

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.

  56 ASP   (  56-)  A      OD1
 287 HIS   (  53-)  C      NE2
 290 ASP   (  56-)  C      OD1
 404 HIS   (  53-)  D      NE2
 407 ASP   (  56-)  D      OD1
 524 ASP   (  56-)  E      OD1
 687 ASP   ( 102-)  F      OD2
 758 ASP   (  56-)  G      OD1
 875 ASP   (  56-)  H      OD1
 992 ASP   (  56-)  I      OD1
1109 ASP   (  56-)  J      OD1
1155 ASP   ( 102-)  J      OD2
1226 ASP   (  56-)  K      OD1
1343 ASP   (  56-)  L      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1464 HOH   (9025 )  L      O  0.98  K  4

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.

  56 ASP   (  56-)  A   H-bonding suggests Asn; but Alt-Rotamer
 102 ASP   ( 102-)  A   H-bonding suggests Asn
 173 ASP   (  56-)  B   H-bonding suggests Asn
 290 ASP   (  56-)  C   H-bonding suggests Asn; but Alt-Rotamer
 407 ASP   (  56-)  D   H-bonding suggests Asn; but Alt-Rotamer
 541 GLU   (  73-)  E   H-bonding suggests Gln
 758 ASP   (  56-)  G   H-bonding suggests Asn
 804 ASP   ( 102-)  G   H-bonding suggests Asn
 992 ASP   (  56-)  I   H-bonding suggests Asn; but Alt-Rotamer
1038 ASP   ( 102-)  I   H-bonding suggests Asn
1343 ASP   (  56-)  L   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   2.046
  2nd generation packing quality :   1.343
  Ramachandran plot appearance   :   0.971
  chi-1/chi-2 rotamer normality  :   0.581
  Backbone conformation          :   0.988

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.311 (tight)
  Bond angles                    :   0.596 (tight)
  Omega angle restraints         :   0.175 (tight)
  Side chain planarity           :   0.292 (tight)
  Improper dihedral distribution :   0.495
  B-factor distribution          :   0.476
  Inside/Outside distribution    :   1.024

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   2.5
  2nd generation packing quality :   1.1
  Ramachandran plot appearance   :   1.6
  chi-1/chi-2 rotamer normality  :   1.3
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.311 (tight)
  Bond angles                    :   0.596 (tight)
  Omega angle restraints         :   0.175 (tight)
  Side chain planarity           :   0.292 (tight)
  Improper dihedral distribution :   0.495
  B-factor distribution          :   0.476
  Inside/Outside distribution    :   1.024
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
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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.