WHAT IF Check report

This file was created 2011-12-16 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 pdb2j6f.ent

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  29 LYS   (  30-)  A  -   CD
  29 LYS   (  30-)  A  -   CE
  29 LYS   (  30-)  A  -   NZ
  30 LYS   (  31-)  A  -   CG
  30 LYS   (  31-)  A  -   CD
  30 LYS   (  31-)  A  -   CE
  30 LYS   (  31-)  A  -   NZ
  38 GLU   (  39-)  A  -   CD
  38 GLU   (  39-)  A  -   OE1
  38 GLU   (  39-)  A  -   OE2

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: C

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

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

  58 ARG   (  59-)  A

Warning: Strange distribution of occupancy values

The distribution of the occupancy values in this file differs significantly from distributions commonly observed in well-refined PDB files. This does not need to mean anything, but please look at it. This file is not very suitable for use in training sets that need to hold 'good' PDB files.

Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT IF's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal...

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  47 MET   (  48-)  A    0.76
  58 PRO   ( 905-)  C    0.50
  59 PRO   ( 906-)  C    0.50
  60 LYS   ( 907-)  C    0.50
  61 PRO   ( 908-)  C    0.50
  62 ARG   ( 909-)  C    0.50
  63 PRO   ( 910-)  C    0.50
  64 ARG   ( 911-)  C    0.50
  65 ARG   ( 912-)  C    0.50

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: 1

Crystal temperature (K) :110.000

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.057

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: C

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  20 ARG   (  21-)  A
  26 ARG   (  27-)  A
  65 ARG   ( 912-)  C

Warning: Tyrosine convention problem

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

   3 TYR   (   4-)  A
   7 TYR   (   8-)  A
   9 TYR   (  10-)  A

Warning: Phenylalanine convention problem

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

  48 PHE   (  49-)  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.

  10 ASP   (  11-)  A
  14 ASP   (  15-)  A
  15 ASP   (  16-)  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.

   6 GLU   (   7-)  A
  23 GLU   (  24-)  A
  34 GLU   (  35-)  A
  40 GLU   (  41-)  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: 0.538
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.

   6 GLU   (   7-)  A
  10 ASP   (  11-)  A
  14 ASP   (  15-)  A
  15 ASP   (  16-)  A
  20 ARG   (  21-)  A
  23 GLU   (  24-)  A
  26 ARG   (  27-)  A
  34 GLU   (  35-)  A
  40 GLU   (  41-)  A
  65 ARG   ( 912-)  C

Torsion-related checks

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 ASN   (  28-)  A  Poor phi/psi
  42 ASN   (  43-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 3.087

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!

   7 TYR   (   8-)  A      0
   8 ASP   (   9-)  A      0
  21 VAL   (  22-)  A      0
  26 ARG   (  27-)  A      0
  27 ASN   (  28-)  A      0
  32 GLN   (  33-)  A      0
  34 GLU   (  35-)  A      0
  41 LEU   (  42-)  A      0
  45 ARG   (  46-)  A      0
  47 MET   (  48-)  A      0
  52 PHE   (  53-)  A      0
  53 VAL   (  54-)  A      0
  56 ILE   (  57-)  A      0
  57 LYS   (  58-)  A      0
  58 PRO   ( 905-)  C      0
  59 PRO   ( 906-)  C      0
  63 PRO   ( 910-)  C      0
   6 GLU   (   7-)  A      1
  12 VAL   (  13-)  A      1
  13 HIS   (  14-)  A      1
  40 GLU   (  41-)  A      1
  50 ASP   (  51-)  A      1
  10 ASP   (  11-)  A      2
  23 GLU   (  24-)  A      2
  31 LEU   (  32-)  A      2
  33 GLU   (  34-)  A      2
  36 TRP   (  37-)  A      2
  38 GLU   (  39-)  A      2
  48 PHE   (  49-)  A      2
  51 ASN   (  52-)  A      2
  62 ARG   ( 909-)  C      2

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  63 PRO   ( 910-)  C  -114.9 envelop C-gamma (-108 degrees)

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.

  42 ASN   (  43-)  A      CB  <->   67 HOH   (2044 )  A      O      0.18    2.62  INTRA BF
  16 GLU   (  17-)  A      OE2 <->   60 LYS   ( 907-)  C      NZ     0.18    2.52  INTRA BL
  64 ARG   ( 911-)  C      O   <->   68 HOH   (2005 )  C      O      0.08    2.32  INTRA
  10 ASP   (  11-)  A      OD1 <->   20 ARG   (  21-)  A      NH2    0.04    2.66  INTRA BL
  66 ARG   ( 912-)  C      O'' <->   68 HOH   (2006 )  C      O      0.01    2.39  INTRA BF

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.

  64 ARG   ( 911-)  C      -7.78
  62 ARG   ( 909-)  C      -7.35
  45 ARG   (  46-)  A      -5.31

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: 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.

  67 HOH   (2020 )  A      O     33.91   32.88   25.82

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.

  53 VAL   (  54-)  A      N
  62 ARG   ( 909-)  C      NH1
  65 ARG   ( 912-)  C      N

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.

   2 ASP   (   3-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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

Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.667
  2nd generation packing quality :   1.529
  Ramachandran plot appearance   :   1.053
  chi-1/chi-2 rotamer normality  :   3.087
  Backbone conformation          :  -0.122

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.538 (tight)
  Bond angles                    :   0.682
  Omega angle restraints         :   1.058
  Side chain planarity           :   0.614 (tight)
  Improper dihedral distribution :   0.756
  B-factor distribution          :   0.743
  Inside/Outside distribution    :   1.055

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 : 1.70

Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.5
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :   3.2
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.538 (tight)
  Bond angles                    :   0.682
  Omega angle restraints         :   1.058
  Side chain planarity           :   0.614 (tight)
  Improper dihedral distribution :   0.756
  B-factor distribution          :   0.743
  Inside/Outside distribution    :   1.055

      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
    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).

    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
      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
    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.