WHAT IF Check report

This file was created 2012-08-12 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 pdb1qzv.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 182.283  B   = 190.376  C    = 220.253
    Alpha=  90.000  Beta=  90.480  Gamma=  90.000

Dimensions of a reduced cell

    A    = 182.283  B   = 190.376  C    = 220.253
    Alpha=  90.000  Beta=  90.480  Gamma=  90.000

Dimensions of the conventional cell

    A    = 182.283  B   = 190.376  C    = 220.253
    Alpha=  90.000  Beta=  89.520  Gamma=  90.000

Transformation to conventional cell

 | -1.000000  0.000000  0.000000|
 |  0.000000 -1.000000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: P

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
There is also strong SEQRES evidence for a multiplicity of: 2
No explicit MTRIX NCS matrices found in the input file
but NCS matrices (but not the unitary matrix) are found labeled `dont use`: 1
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 2 4
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 116317.563
Volume of the Unit Cell V= 7643300.5
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
but the number of MTRIX matrices flagged as `do not use` = 1
which, by the way, seems inconsistent with the SEQRES multiplicity
Matthews coefficient for observed atoms and Z high: Vm= 65.711
Vm by authors and this calculated Vm do not agree very well
SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and there is further disagreement with the MTRIX record count)

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

  61 CLA   (1011-)  A  -         Atom types
  62 CLA   (1021-)  B  -         Atom types
  63 CLA   (1012-)  A  -         Atom types
  64 CLA   (1022-)  B  -         Atom types
  65 CLA   (1013-)  A  -         Atom types
  66 CLA   (1023-)  B  -         Atom types
  67 CLA   (1101-)  J  -         Atom types
  68 CLA   (1102-)  A  -         Atom types
  69 CLA   (1103-)  A  -         Atom types
  70 CLA   (1104-)  A  -         Atom types
  71 CLA   (1105-)  A  -         Atom types
  72 CLA   (1106-)  A  -         Atom types
  73 CLA   (1107-)  A  -         Atom types
  74 CLA   (1108-)  A  -         Atom types
  75 CLA   (1109-)  A  -         Atom types
  76 CLA   (1110-)  A  -         Atom types
  77 CLA   (1111-)  A  -         Atom types
  78 CLA   (1112-)  A  -         Atom types
  79 CLA   (1113-)  A  -         Atom types
  80 CLA   (1114-)  A  -         Atom types
  81 CLA   (1115-)  A  -         Atom types
  82 CLA   (1116-)  A  -         Atom types
  83 CLA   (1117-)  A  -         Atom types
  84 CLA   (1118-)  A  -         Atom types
  85 CLA   (1119-)  A  -         Atom types
And so on for a total of 344 lines.

Administrative problems that can generate validation failures

Error: Calpha only residues

WHAT IF has detected residues that contain just an alpha carbon atom and nothing else. The many missing atoms make it hard for WHAT IF to properly validate the environment of these residues. Consequently, you are suggested to be careful when using the WHAT CHECK report.

   1 GLU   (  18-)  F  -
   2 LYS   (  19-)  F  -
   3 GLN   (  20-)  F  -
   4 ALA   (  21-)  F  -
   5 LEU   (  22-)  F  -
   6 LYS   (  23-)  F  -
   7 LYS   (  24-)  F  -
   8 LEU   (  25-)  F  -
   9 GLN   (  26-)  F  -
  10 ALA   (  27-)  F  -
  11 SER   (  28-)  F  -
  12 LEU   (  29-)  F  -
  13 LYS   (  30-)  F  -
  14 LEU   (  31-)  F  -
  15 TYR   (  32-)  F  -
  16 ALA   (  33-)  F  -
  17 ASP   (  34-)  F  -
  18 ASP   (  35-)  F  -
  19 SER   (  36-)  F  -
  20 ALA   (  37-)  F  -
  21 PRO   (  38-)  F  -
  22 ALA   (  39-)  F  -
  23 LEU   (  40-)  F  -
  24 ALA   (  41-)  F  -
  25 ILE   (  42-)  F  -
And so on for a total of 60 lines.

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: F

Note: Ramachandran plot

Chain identifier: U

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'.

   1 GLU   (  18-)  F  -   N
   1 GLU   (  18-)  F  -   C
   1 GLU   (  18-)  F  -   O
   1 GLU   (  18-)  F  -   CB
   1 GLU   (  18-)  F  -   CG
   1 GLU   (  18-)  F  -   CD
   1 GLU   (  18-)  F  -   OE1
   1 GLU   (  18-)  F  -   OE2
   2 LYS   (  19-)  F  -   N
   2 LYS   (  19-)  F  -   C
   2 LYS   (  19-)  F  -   O
   2 LYS   (  19-)  F  -   CB
   2 LYS   (  19-)  F  -   CG
   2 LYS   (  19-)  F  -   CD
   2 LYS   (  19-)  F  -   CE
   2 LYS   (  19-)  F  -   NZ
   3 GLN   (  20-)  F  -   N
   3 GLN   (  20-)  F  -   C
   3 GLN   (  20-)  F  -   O
   3 GLN   (  20-)  F  -   CB
   3 GLN   (  20-)  F  -   CG
   3 GLN   (  20-)  F  -   CD
   3 GLN   (  20-)  F  -   OE1
   3 GLN   (  20-)  F  -   NE2
   4 ALA   (  21-)  F  -   N
And so on for a total of 392 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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: 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 = 0.016

Warning: Average B-factor problem

The average B-factor for all buried protein atoms normally lies between 10-30. Values around 3-10 are expected for X-ray studies performed at liquid nitrogen temperature.

Because of the extreme value for the average B-factor, no further analysis of the B-factors is performed.

Average B-factor for buried atoms : 0.000

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: F

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: U

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.

   2 LYS   (  19-)  F  - Impossible phi
   3 GLN   (  20-)  F  - Impossible phi
   4 ALA   (  21-)  F  - Impossible phi
   5 LEU   (  22-)  F  - Impossible phi
   6 LYS   (  23-)  F  - Impossible phi
   7 LYS   (  24-)  F  - Impossible phi
   8 LEU   (  25-)  F  - Impossible phi
   9 GLN   (  26-)  F  - Impossible phi
  10 ALA   (  27-)  F  - Impossible phi
  11 SER   (  28-)  F  - Impossible phi
  12 LEU   (  29-)  F  - Impossible phi
  13 LYS   (  30-)  F  - Impossible phi
  14 LEU   (  31-)  F  - Impossible phi
  15 TYR   (  32-)  F  - Impossible phi
  16 ALA   (  33-)  F  - Impossible phi
  17 ASP   (  34-)  F  - Impossible phi
  18 ASP   (  35-)  F  - Impossible phi
  19 SER   (  36-)  F  - Impossible phi
  20 ALA   (  37-)  F  - Impossible phi
  21 PRO   (  38-)  F  - Impossible phi
  22 ALA   (  39-)  F  - Impossible phi
  23 LEU   (  40-)  F  - Impossible phi
  24 ALA   (  41-)  F  - Impossible phi
  25 ILE   (  42-)  F  - Impossible phi
  26 LYS   (  43-)  F  - Impossible phi
And so on for a total of 56 lines.

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!

  29 MET   (  46-)  F  -     0
  30 GLU   (  47-)  F  -     0
  31 GLU   (  18-)  U  -     0
  32 LYS   (  19-)  U  -     0
  15 TYR   (  32-)  F  -     2
  45 TYR   (  32-)  U  -     2

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]

  21 PRO   (  38-)  F  -   0.00 LOW
  51 PRO   (  38-)  U  -   0.00 LOW

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: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

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: U

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: F

Note: Second generation quality Z-score plot

Chain identifier: U

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:

  2nd generation packing quality :  -7.908 (bad)
  Backbone conformation          :  13.877

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.000 (tight)
  Side chain planarity           :   0.000 (tight)

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 : 4.44


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -4.5 (bad)
  Backbone conformation          :  22.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.000 (tight)
  Side chain planarity           :   0.000 (tight)
==============

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.