WHAT IF Check report

This file was created 2012-04-04 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 pdb3o5q.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

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

 130 DMS   (   1-)  A  -
 131 DMS   (   2-)  A  -

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

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'.

  46 LYS   (  58-)  A      CD
  46 LYS   (  58-)  A      CE
  46 LYS   (  58-)  A      NZ
  53 LYS   (  65-)  A      CG
  53 LYS   (  65-)  A      CD
  53 LYS   (  65-)  A      CE
  53 LYS   (  65-)  A      NZ
 126 LYS   ( 138-)  A      CG
 126 LYS   ( 138-)  A      CD
 126 LYS   ( 138-)  A      CE
 126 LYS   ( 138-)  A      NZ
 128 GLU   ( 140-)  A      CG
 128 GLU   ( 140-)  A      CD
 128 GLU   ( 140-)  A      OE1
 128 GLU   ( 140-)  A      OE2

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 35.32

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

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

  42 TYR   (  54-)  A
  45 TYR   (  57-)  A
  99 TYR   ( 111-)  A

Warning: Phenylalanine convention problem

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

  65 PHE   (  77-)  A
  67 PHE   (  79-)  A
 125 PHE   ( 137-)  A

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.

  18 ASP   (  30-)  A

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.

 119 GLU   ( 131-)  A

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.557
RMS-deviation in bond distances: 0.013

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.

  18 ASP   (  30-)  A
 119 GLU   ( 131-)  A

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  63 GLU   (  75-)  A    4.84

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.

 108 PRO   ( 120-)  A    -2.3

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.

  19 ARG   (  31-)  A  Poor phi/psi
  23 LYS   (  35-)  A  omega poor
  29 GLY   (  41-)  A  omega poor
  43 VAL   (  55-)  A  omega poor
  62 ASN   (  74-)  A  Poor phi/psi
  94 LEU   ( 106-)  A  omega poor
 100 ALA   ( 112-)  A  Poor phi/psi
 107 LEU   ( 119-)  A  PRO omega poor
 108 PRO   ( 120-)  A  omega poor
 109 LYS   ( 121-)  A  omega poor
 113 ASN   ( 125-)  A  Poor phi/psi
 118 PHE   ( 130-)  A  omega poor
 chi-1/chi-2 correlation Z-score : 1.538

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!

  23 LYS   (  35-)  A      0
  26 LYS   (  38-)  A      0
  27 ARG   (  39-)  A      0
  30 ASN   (  42-)  A      0
  32 GLU   (  44-)  A      0
  36 MET   (  48-)  A      0
  37 ILE   (  49-)  A      0
  49 LEU   (  61-)  A      0
  56 ASP   (  68-)  A      0
  61 ARG   (  73-)  A      0
  62 ASN   (  74-)  A      0
  69 LEU   (  81-)  A      0
  73 GLN   (  85-)  A      0
  74 VAL   (  86-)  A      0
  87 LYS   (  99-)  A      0
  99 TYR   ( 111-)  A      0
 100 ALA   ( 112-)  A      0
 101 TYR   ( 113-)  A      0
 103 SER   ( 115-)  A      0
 104 ALA   ( 116-)  A      0
 112 SER   ( 124-)  A      0
 113 ASN   ( 125-)  A      0
 124 ASP   ( 136-)  A      0
   9 GLN   (  21-)  A      1
  13 ILE   (  25-)  A      1
  19 ARG   (  31-)  A      1
  33 GLU   (  45-)  A      1
  44 HIS   (  56-)  A      1
  53 LYS   (  65-)  A      1
  55 PHE   (  67-)  A      1
  57 SER   (  69-)  A      1
  75 ILE   (  87-)  A      1
  86 LYS   (  98-)  A      1
  95 CYS   ( 107-)  A      1
  96 LYS   ( 108-)  A      1
 106 SER   ( 118-)  A      1
 107 LEU   ( 119-)  A      1
 108 PRO   ( 120-)  A      1
 109 LYS   ( 121-)  A      1
 110 ILE   ( 122-)  A      1
  14 THR   (  26-)  A      2
  17 LYS   (  29-)  A      2
  51 ASN   (  63-)  A      2
  54 LYS   (  66-)  A      2
  58 SER   (  70-)  A      2
  71 LYS   (  83-)  A      2
  91 CYS   ( 103-)  A      2
 119 GLU   ( 131-)  A      2
 121 GLU   ( 133-)  A      2
 123 LEU   ( 135-)  A      2

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.259

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

  35 PRO   (  47-)  A    0.13 LOW
  97 PRO   ( 109-)  A    0.05 LOW

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.

 132 HOH   ( 233 )  A    B O   <->  132 HOH   ( 369 )  A    B O      0.69    1.51  INTRA BL
  19 ARG   (  31-)  A    A NH2 <->  132 HOH   ( 343 )  A      O      0.46    2.24  INTRA BL
  80 ILE   (  92-)  A    A CD1 <->  132 HOH   ( 235 )  A    A O      0.45    2.35  INTRA BL
  17 LYS   (  29-)  A    A CE  <->  132 HOH   ( 308 )  A      O      0.35    2.45  INTRA BL
 132 HOH   ( 181 )  A      O   <->  132 HOH   ( 318 )  A      O      0.31    1.89  INTRA BL
 132 HOH   ( 337 )  A    A O   <->  132 HOH   ( 345 )  A      O      0.30    1.90  INTRA BL
 132 HOH   ( 233 )  A    A O   <->  132 HOH   ( 328 )  A    B O      0.19    2.01  INTRA BL
  45 TYR   (  57-)  A    A OH  <->   56 ASP   (  68-)  A    A OD2    0.15    2.25  INTRA BL
  54 LYS   (  66-)  A    A CG  <->  132 HOH   ( 191 )  A      O      0.14    2.66  INTRA
  44 HIS   (  56-)  A      ND1 <->   58 SER   (  70-)  A      OG     0.10    2.60  INTRA BL
 132 HOH   ( 176 )  A      O   <->  132 HOH   ( 348 )  A    A O      0.06    2.14  INTRA BL
  45 TYR   (  57-)  A    A OH  <->   56 ASP   (  68-)  A    A CG     0.04    2.76  INTRA BL
 132 HOH   ( 345 )  A      O   <->  132 HOH   ( 356 )  A      O      0.04    2.16  INTRA
  77 ALA   (  89-)  A      CB  <->   95 CYS   ( 107-)  A      SG     0.04    3.36  INTRA BL
   2 ALA   (  14-)  A      N   <->    3 PRO   (  15-)  A      CD     0.01    2.99  INTRA BL

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

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.

 107 LEU   ( 119-)  A      -6.53
  36 MET   (  48-)  A      -5.73
   9 GLN   (  21-)  A      -5.67
  61 ARG   (  73-)  A      -5.58
  73 GLN   (  85-)  A      -5.46

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

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.

 128 GLU   ( 140-)  A   -3.08
  53 LYS   (  65-)  A   -2.71

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 125 PHE   ( 137-)  A     -  128 GLU   ( 140-)  A        -1.93

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

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.

 132 HOH   ( 144 )  A    B O     -4.95   -4.01   -8.75
 132 HOH   ( 151 )  A    A O     15.97    3.34  -22.22
 132 HOH   ( 151 )  A    B O     25.00  -23.74   -6.27
 132 HOH   ( 160 )  A      O     10.68   -5.69  -28.34
 132 HOH   ( 211 )  A      O     -7.44    0.82   -6.56
 132 HOH   ( 231 )  A      O     -5.06  -17.12   -8.95
 132 HOH   ( 239 )  A      O     24.34    0.76   -2.20
 132 HOH   ( 247 )  A      O     -3.53  -10.67   -7.89
 132 HOH   ( 248 )  A      O     -1.13  -22.54   -6.21
 132 HOH   ( 249 )  A      O     23.25   -8.85  -12.15
 132 HOH   ( 372 )  A      O     11.93    5.32  -19.80

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.

  21 VAL   (  33-)  A      N
  74 VAL   (  86-)  A      N
  78 TRP   (  90-)  A      NE1

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.

 132 HOH   ( 148 )  A      O  0.91  K  4
 132 HOH   ( 255 )  A      O  1.07  K  4
 132 HOH   ( 276 )  A      O  0.86  K  4
 132 HOH   ( 284 )  A      O  1.11  K  4
 132 HOH   ( 317 )  A      O  1.09  K  4
 132 HOH   ( 335 )  A      O  1.07  K  4
 132 HOH   ( 345 )  A      O  0.92 NA  7 Ion-B
 132 HOH   ( 354 )  A      O  1.09  K  5 Ion-B
 132 HOH   ( 356 )  A      O  1.03 NA  4 ION-B H2O-B

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 :  -0.948
  2nd generation packing quality :  -2.537
  Ramachandran plot appearance   :   0.458
  chi-1/chi-2 rotamer normality  :   1.538
  Backbone conformation          :  -0.075

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.557 (tight)
  Bond angles                    :   0.763
  Omega angle restraints         :   1.320 (loose)
  Side chain planarity           :   1.033
  Improper dihedral distribution :   0.854
  Inside/Outside distribution    :   0.968

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 : 0.96


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -1.9
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :   1.0
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.557 (tight)
  Bond angles                    :   0.763
  Omega angle restraints         :   1.320 (loose)
  Side chain planarity           :   1.033
  Improper dihedral distribution :   0.854
  Inside/Outside distribution    :   0.968
==============

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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Quality Control
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Ion Checks
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    M.Nayal and E.Di Cera,
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      Is the bond-valence method able to identify metal atoms in protein
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Checking checks
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      Who checks the checkers
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