WHAT IF Check report

This file was created 2012-01-19 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 pdb1xev.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 : 0.656
CA-only RMS fit for the two chains : 0.382

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 : 0.686
CA-only RMS fit for the two chains : 0.340

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 : 0.576
CA-only RMS fit for the two chains : 0.262

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: B and C

All-atom RMS fit for the two chains : 0.667
CA-only RMS fit for the two chains : 0.373

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: B 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: B and D

All-atom RMS fit for the two chains : 0.662
CA-only RMS fit for the two chains : 0.370

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: B and D

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: 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

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

 630 TYR   ( 114-)  C
 643 TYR   ( 128-)  C

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.

 127 ASP   ( 130-)  A
 557 ASP   (  41-)  C
 680 ASP   ( 165-)  C

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.

 236 GLU   ( 239-)  A
 271 GLU   (  14-)  B
 443 GLU   ( 187-)  B
 702 GLU   ( 187-)  C

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

 |  0.996764 -0.000023  0.000448|
 | -0.000023  0.996766  0.000042|
 |  0.000448  0.000042  0.996649|
Proposed new scale matrix

 |  0.021950  0.000000  0.000500|
 |  0.000000  0.006820  0.000000|
 | -0.000006  0.000000  0.013129|
With corresponding cell

    A    =  45.558  B   = 146.626  C    =  76.186
    Alpha=  90.001  Beta=  91.279  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  45.706  B   = 147.100  C    =  76.446
    Alpha=  90.000  Beta=  91.330  Gamma=  90.000

Variance: 386.982
(Under-)estimated Z-score: 14.498

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.

 127 ASP   ( 130-)  A
 236 GLU   ( 239-)  A
 271 GLU   (  14-)  B
 443 GLU   ( 187-)  B
 557 ASP   (  41-)  C
 680 ASP   ( 165-)  C
 702 GLU   ( 187-)  C

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.

 722 VAL   ( 207-)  C    5.60
 204 VAL   ( 207-)  A    5.60
 463 VAL   ( 207-)  B    5.45
  37 LYS   (  39-)  A    4.79
 637 VAL   ( 121-)  C    4.36
 939 SER   ( 166-)  D    4.34
 980 VAL   ( 207-)  D    4.29
 251 ARG   ( 254-)  A    4.22
 594 VAL   (  78-)  C    4.20
 964 TYR   ( 191-)  D    4.17
 852 VAL   (  78-)  D    4.08

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 : 1.500

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.

 340 PRO   (  83-)  B    -3.0
 857 PRO   (  83-)  D    -2.9
 599 PRO   (  83-)  C    -2.8
  81 PRO   (  83-)  A    -2.8
 682 ILE   ( 167-)  C    -2.7
 529 PRO   (  13-)  C    -2.6
 546 PRO   (  30-)  C    -2.6
  28 PRO   (  30-)  A    -2.4
  58 LEU   (  60-)  A    -2.4
 287 PRO   (  30-)  B    -2.4
 576 LEU   (  60-)  C    -2.3
 834 LEU   (  60-)  D    -2.3
  29 VAL   (  31-)  A    -2.2
 804 PRO   (  30-)  D    -2.2
 596 LYS   (  80-)  C    -2.2
 966 THR   ( 193-)  D    -2.1
  57 ILE   (  59-)  A    -2.1
 432 PHE   ( 176-)  B    -2.1
 349 GLN   (  92-)  B    -2.1
 607 ILE   (  91-)  C    -2.1
 590 GLN   (  74-)  C    -2.1
 731 ILE   ( 216-)  C    -2.1
 924 GLY   ( 151-)  D    -2.1
 691 PHE   ( 176-)  C    -2.0
 865 ILE   (  91-)  D    -2.0
 866 GLN   (  92-)  D    -2.0
 989 ILE   ( 216-)  D    -2.0
 317 LEU   (  60-)  B    -2.0
 190 THR   ( 193-)  A    -2.0
 708 THR   ( 193-)  C    -2.0
 279 ILE   (  22-)  B    -2.0
  90 GLN   (  92-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  27 SER   (  29-)  A  PRO omega poor
  63 ALA   (  65-)  A  Poor phi/psi
  73 ASP   (  75-)  A  Poor phi/psi
  74 LYS   (  76-)  A  Poor phi/psi
 108 ASP   ( 110-)  A  Poor phi/psi
 109 LYS   ( 111-)  A  Poor phi/psi
 175 ASN   ( 178-)  A  Poor phi/psi
 198 PRO   ( 201-)  A  PRO omega poor
 240 ASP   ( 243-)  A  Poor phi/psi
 286 SER   (  29-)  B  PRO omega poor
 322 ALA   (  65-)  B  Poor phi/psi
 349 GLN   (  92-)  B  Poor phi/psi
 367 ASP   ( 110-)  B  Poor phi/psi
 368 LYS   ( 111-)  B  Poor phi/psi
 434 ASN   ( 178-)  B  Poor phi/psi
 457 PRO   ( 201-)  B  PRO omega poor
 509 ASN   ( 253-)  B  Poor phi/psi
 545 SER   (  29-)  C  PRO omega poor
 581 ALA   (  65-)  C  Poor phi/psi
 627 LYS   ( 111-)  C  Poor phi/psi
 693 ASN   ( 178-)  C  Poor phi/psi
 716 PRO   ( 201-)  C  PRO omega poor
 718 LEU   ( 203-)  C  Poor phi/psi
 767 LYS   ( 252-)  C  Poor phi/psi
 803 SER   (  29-)  D  PRO omega poor
 839 ALA   (  65-)  D  Poor phi/psi
 866 GLN   (  92-)  D  Poor phi/psi
 884 ASP   ( 110-)  D  Poor phi/psi
 885 LYS   ( 111-)  D  Poor phi/psi
 951 ASN   ( 178-)  D  Poor phi/psi
 974 PRO   ( 201-)  D  PRO omega poor
 976 LEU   ( 203-)  D  Poor phi/psi
1026 ASN   ( 253-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.383

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 TRP   (   5-)  A      0
   5 TYR   (   7-)  A      0
   8 HIS   (  10-)  A      0
  17 ASP   (  19-)  A      0
  18 PHE   (  20-)  A      0
  22 LYS   (  24-)  A      0
  25 ARG   (  27-)  A      0
  26 GLN   (  28-)  A      0
  27 SER   (  29-)  A      0
  28 PRO   (  30-)  A      0
  36 ALA   (  38-)  A      0
  48 SER   (  50-)  A      0
  50 ASP   (  52-)  A      0
  52 ALA   (  54-)  A      0
  60 ASN   (  62-)  A      0
  62 HIS   (  64-)  A      0
  63 ALA   (  65-)  A      0
  70 ASP   (  72-)  A      0
  71 SER   (  73-)  A      0
  73 ASP   (  75-)  A      0
  74 LYS   (  76-)  A      0
  75 ALA   (  77-)  A      0
  78 LYS   (  80-)  A      0
  81 PRO   (  83-)  A      0
  82 LEU   (  84-)  A      0
And so on for a total of 491 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 : 1.433

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!

 126 GLY   ( 129-)  A   2.07   11
 385 GLY   ( 129-)  B   1.85   10

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.

  13 HIS   (  15-)  A      ND1 <->   16 LYS   (  18-)  A      NZ     0.28    2.72  INTRA BL
 332 ASP   (  75-)  B      OD1 <->  346 ARG   (  89-)  B      NE     0.24    2.46  INTRA BL
 291 ASP   (  34-)  B      N   <-> 1044 HOH   ( 669 )  B      O      0.20    2.50  INTRA BL
 513 LYS   ( 257-)  B      NZ  <-> 1044 HOH   ( 665 )  B      O      0.19    2.51  INTRA
 156 LYS   ( 159-)  A      N   <-> 1043 HOH   ( 297 )  A      O      0.17    2.53  INTRA BL
 900 LYS   ( 127-)  D      NZ  <-> 1046 HOH   (1003 )  D      O      0.16    2.54  INTRA
 849 ASP   (  75-)  D      OD1 <->  863 ARG   (  89-)  D      NH2    0.16    2.54  INTRA
 261 HIS   (   4-)  B      NE2 <-> 1044 HOH   ( 705 )  B      O      0.14    2.56  INTRA
 590 GLN   (  74-)  C      NE2 <-> 1045 HOH   ( 949 )  C      O      0.14    2.56  INTRA
 531 HIS   (  15-)  C      ND1 <->  534 LYS   (  18-)  C      NZ     0.14    2.86  INTRA BL
 134 GLN   ( 137-)  A      NE2 <-> 1043 HOH   ( 326 )  A      O      0.13    2.57  INTRA BL
 281 LYS   (  24-)  B      NZ  <-> 1044 HOH   ( 582 )  B      O      0.13    2.57  INTRA BL
 574 ARG   (  58-)  C      NH2 <-> 1038 LYS   ( 261-)  D      O''    0.11    2.59  INTRA
 903 ASP   ( 130-)  D      CG  <-> 1046 HOH   (1078 )  D      O      0.11    2.69  INTRA
 580 HIS   (  64-)  C      CD2 <-> 1045 HOH   ( 941 )  C      O      0.10    2.70  INTRA
 481 LYS   ( 225-)  B      NZ  <-> 1044 HOH   ( 672 )  B      O      0.10    2.60  INTRA
 331 GLN   (  74-)  B      NE2 <-> 1044 HOH   ( 638 )  B      O      0.09    2.61  INTRA
  99 ASP   ( 101-)  A      OD2 <-> 1043 HOH   ( 287 )  A      O      0.09    2.31  INTRA BL
 424 LYS   ( 168-)  B      NZ  <-> 1044 HOH   ( 593 )  B      O      0.09    2.61  INTRA
1001 LYS   ( 228-)  D      NZ  <-> 1046 HOH   (1029 )  D      O      0.08    2.62  INTRA
 284 ARG   (  27-)  B      NH1 <-> 1044 HOH   ( 653 )  B      O      0.08    2.62  INTRA
 541 GLY   (  25-)  C      O   <->  767 LYS   ( 252-)  C      NZ     0.08    2.62  INTRA
 652 GLN   ( 137-)  C      NE2 <-> 1045 HOH   ( 999 )  C      O      0.08    2.62  INTRA
 685 LYS   ( 170-)  C      NZ  <-> 1045 HOH   (1004 )  C      O      0.08    2.62  INTRA
 158 VAL   ( 161-)  A      CG1 <->  222 LYS   ( 225-)  A      CD     0.08    3.12  INTRA
And so on for a total of 55 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.

 261 HIS   (   4-)  B      -6.27
 778 HIS   (   4-)  D      -6.05
 267 HIS   (  10-)  B      -6.04
 526 HIS   (  10-)  C      -6.00
 784 HIS   (  10-)  D      -5.92
   2 HIS   (   4-)  A      -5.70
 357 LEU   ( 100-)  B      -5.51
 616 LEU   ( 100-)  C      -5.51
  98 LEU   ( 100-)  A      -5.49
 874 LEU   ( 100-)  D      -5.46
 519 HIS   (   3-)  C      -5.43
   8 HIS   (  10-)  A      -5.39
 133 GLN   ( 136-)  A      -5.39
 284 ARG   (  27-)  B      -5.28
   7 LYS   (   9-)  A      -5.22
 302 LYS   (  45-)  B      -5.16
 266 LYS   (   9-)  B      -5.08
 651 GLN   ( 136-)  C      -5.08
 260 HIS   (   3-)  B      -5.07
 392 GLN   ( 136-)  B      -5.03

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.

 900 LYS   ( 127-)  D   -2.57

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

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.

1043 HOH   ( 385 )  A      O     58.38   44.22   52.40
1045 HOH   ( 973 )  C      O     -0.66    2.78   33.93

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.

1043 HOH   ( 329 )  A      O
1043 HOH   ( 382 )  A      O
1046 HOH   (1064 )  D      O
Metal-coordinating Histidine residue  92 fixed to   1
Metal-coordinating Histidine residue  94 fixed to   1
Metal-coordinating Histidine residue 117 fixed to   1
Metal-coordinating Histidine residue 351 fixed to   1
Metal-coordinating Histidine residue 353 fixed to   1
Metal-coordinating Histidine residue 376 fixed to   1
Metal-coordinating Histidine residue 610 fixed to   1
Metal-coordinating Histidine residue 612 fixed to   1
Metal-coordinating Histidine residue 635 fixed to   1
Metal-coordinating Histidine residue 868 fixed to   1
Metal-coordinating Histidine residue 870 fixed to   1
Metal-coordinating Histidine residue 893 fixed to   1

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.

  72 GLN   (  74-)  A
 134 GLN   ( 137-)  A
 331 GLN   (  74-)  B
 509 ASN   ( 253-)  B
 519 HIS   (   3-)  C
 768 ASN   ( 253-)  C
 784 HIS   (  10-)  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.

  29 VAL   (  31-)  A      N
  98 LEU   ( 100-)  A      N
 162 ASP   ( 165-)  A      N
 197 THR   ( 200-)  A      N
 201 LEU   ( 204-)  A      N
 241 ASN   ( 244-)  A      ND2
 242 TRP   ( 245-)  A      N
 249 LYS   ( 252-)  A      NZ
 257 PHE   ( 260-)  A      N
 258 LYS   ( 261-)  A      N
 288 VAL   (  31-)  B      N
 331 GLN   (  74-)  B      N
 357 LEU   ( 100-)  B      N
 456 THR   ( 200-)  B      N
 460 LEU   ( 204-)  B      N
 500 ASN   ( 244-)  B      ND2
 501 TRP   ( 245-)  B      N
 509 ASN   ( 253-)  B      N
 516 PHE   ( 260-)  B      N
 547 VAL   (  31-)  C      N
 569 GLN   (  53-)  C      N
 592 LYS   (  76-)  C      N
 616 LEU   ( 100-)  C      N
 645 ASP   ( 130-)  C      N
 715 THR   ( 200-)  C      N
 719 LEU   ( 204-)  C      N
 745 ASN   ( 230-)  C      ND2
 759 ASN   ( 244-)  C      ND2
 760 TRP   ( 245-)  C      N
 775 PHE   ( 260-)  C      N
 805 VAL   (  31-)  D      N
 874 LEU   ( 100-)  D      N
 938 ASP   ( 165-)  D      N
 973 THR   ( 200-)  D      N
 977 LEU   ( 204-)  D      N
 994 GLU   ( 221-)  D      N
1018 TRP   ( 245-)  D      N
1033 PHE   ( 260-)  D      N
Only metal coordination for   94 HIS  (  96-) A      NE2
Only metal coordination for  353 HIS  (  96-) B      NE2
Only metal coordination for  376 HIS  ( 119-) B      ND1
Only metal coordination for  612 HIS  (  96-) C      NE2
Only metal coordination for  870 HIS  (  96-) D      NE2
Only metal coordination for  893 HIS  ( 119-) D      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.

 461 GLU   ( 205-)  B   H-bonding suggests Gln
 530 GLU   (  14-)  C   H-bonding suggests Gln
 677 ASP   ( 162-)  C   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 :  -1.472
  2nd generation packing quality :  -0.612
  Ramachandran plot appearance   :  -2.265
  chi-1/chi-2 rotamer normality  :  -1.383
  Backbone conformation          :  -1.095

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.699
  Omega angle restraints         :   0.260 (tight)
  Side chain planarity           :   0.277 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   0.684
  Inside/Outside distribution    :   0.966

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.391 (tight)
  Bond angles                    :   0.699
  Omega angle restraints         :   0.260 (tight)
  Side chain planarity           :   0.277 (tight)
  Improper dihedral distribution :   0.581
  B-factor distribution          :   0.684
  Inside/Outside distribution    :   0.966
==============

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.