WHAT IF Check report

This file was created 2011-12-13 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 pdb1ain.ent

Checks that need to be done early-on in validation

Warning: Unconventional orthorhombic cell

The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length.

The CRYST1 cell dimensions

    A    = 139.360  B   =  67.500  C    =  42.110
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    = 139.360  B   =  67.500  C    =  42.110
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  42.110  B   =  67.500  C    = 139.360
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  42.110  B   =  67.500  C    = 139.360
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

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 GLY   (   6-)  A  -
   2 SER   (   7-)  A  -
   3 ALA   (   8-)  A  -
   4 VAL   (   9-)  A  -
   5 SER   (  10-)  A  -
   6 PRO   (  11-)  A  -
   7 TYR   (  12-)  A  -
   8 PRO   (  13-)  A  -
   9 THR   (  14-)  A  -
  10 PHE   (  15-)  A  -
  11 ASN   (  16-)  A  -
  12 PRO   (  17-)  A  -
  13 SER   (  18-)  A  -
  14 SER   (  19-)  A  -
  15 ASP   (  20-)  A  -
  16 VAL   (  21-)  A  -
  17 ALA   (  22-)  A  -
  18 ALA   (  23-)  A  -
  19 LEU   (  24-)  A  -
  20 HIS   (  25-)  A  -
  21 LYS   (  26-)  A  -
  22 ALA   (  27-)  A  -
  23 ILE   (  28-)  A  -
  24 MET   (  29-)  A  -
  25 VAL   (  30-)  A  -
And so on for a total of 314 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: 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'.

   1 GLY   (   6-)  A  -   N
   1 GLY   (   6-)  A  -   C
   1 GLY   (   6-)  A  -   O
   2 SER   (   7-)  A  -   N
   2 SER   (   7-)  A  -   C
   2 SER   (   7-)  A  -   O
   2 SER   (   7-)  A  -   CB
   2 SER   (   7-)  A  -   OG
   3 ALA   (   8-)  A  -   N
   3 ALA   (   8-)  A  -   C
   3 ALA   (   8-)  A  -   O
   3 ALA   (   8-)  A  -   CB
   4 VAL   (   9-)  A  -   N
   4 VAL   (   9-)  A  -   C
   4 VAL   (   9-)  A  -   O
   4 VAL   (   9-)  A  -   CB
   4 VAL   (   9-)  A  -   CG1
   4 VAL   (   9-)  A  -   CG2
   5 SER   (  10-)  A  -   N
   5 SER   (  10-)  A  -   C
   5 SER   (  10-)  A  -   O
   5 SER   (  10-)  A  -   CB
   5 SER   (  10-)  A  -   OG
   6 PRO   (  11-)  A  -   N
   6 PRO   (  11-)  A  -   C
And so on for a total of 2143 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. 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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 = 0.046

Note: B-factor plot

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

Chain identifier: A

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 SER   (   7-)  A  - Impossible phi
   3 ALA   (   8-)  A  - Impossible phi
   4 VAL   (   9-)  A  - Impossible phi
   5 SER   (  10-)  A  - Impossible phi
   6 PRO   (  11-)  A  - Impossible phi
   7 TYR   (  12-)  A  - Impossible phi
   8 PRO   (  13-)  A  - Impossible phi
   9 THR   (  14-)  A  - Impossible phi
  10 PHE   (  15-)  A  - Impossible phi
  11 ASN   (  16-)  A  - Impossible phi
  12 PRO   (  17-)  A  - Impossible phi
  13 SER   (  18-)  A  - Impossible phi
  14 SER   (  19-)  A  - Impossible phi
  15 ASP   (  20-)  A  - Impossible phi
  16 VAL   (  21-)  A  - Impossible phi
  17 ALA   (  22-)  A  - Impossible phi
  18 ALA   (  23-)  A  - Impossible phi
  19 LEU   (  24-)  A  - Impossible phi
  20 HIS   (  25-)  A  - Impossible phi
  21 LYS   (  26-)  A  - Impossible phi
  22 ALA   (  27-)  A  - Impossible phi
  23 ILE   (  28-)  A  - Impossible phi
  24 MET   (  29-)  A  - Impossible phi
  25 VAL   (  30-)  A  - Impossible phi
  26 LYS   (  31-)  A  - Impossible phi
And so on for a total of 312 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 169 SER   ( 174-)  A  -   0.39
ERROR. Too many Ca-only residues in this range

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!

 257 VAL   ( 262-)  A  -     0
 274 ILE   ( 279-)  A  -     0
  28 VAL   (  33-)  A  -     1
  71 HIS   (  76-)  A  -     1
  98 LEU   ( 103-)  A  -     1
 160 PHE   ( 165-)  A  -     1
  27 GLY   (  32-)  A  -     2
 275 ASP   ( 280-)  A  -     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]

   6 PRO   (  11-)  A  -   0.00 LOW
   8 PRO   (  13-)  A  -   0.00 LOW
  12 PRO   (  17-)  A  -   0.00 LOW
  59 PRO   (  64-)  A  -   0.00 LOW
  83 PRO   (  88-)  A  -   0.00 LOW
 199 PRO   ( 204-)  A  -   0.00 LOW
 243 PRO   ( 248-)  A  -   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: 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: 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.

  40 ARG   (  45-)  A  -  -2.65
  45 ARG   (  50-)  A  -  -2.65
  92 ARG   (  97-)  A  -  -2.65
 112 ARG   ( 117-)  A  -  -2.65
 118 ARG   ( 123-)  A  -  -2.65
 122 ARG   ( 127-)  A  -  -2.65
 125 ARG   ( 130-)  A  -  -2.65
 130 ARG   ( 135-)  A  -  -2.65
 145 ARG   ( 150-)  A  -  -2.65
 156 ARG   ( 161-)  A  -  -2.65
 172 ARG   ( 177-)  A  -  -2.65
 180 ARG   ( 185-)  A  -  -2.65
 181 ARG   ( 186-)  A  -  -2.65
 196 ARG   ( 201-)  A  -  -2.65
 202 ARG   ( 207-)  A  -  -2.65
 203 ARG   ( 208-)  A  -  -2.65
 260 ARG   ( 265-)  A  -  -2.65
 266 ARG   ( 271-)  A  -  -2.65
 271 ARG   ( 276-)  A  -  -2.65
  95 MET   ( 100-)  A  -  -2.62
 254 MET   ( 259-)  A  -  -2.62

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.

  63 THR   (  68-)  A  -  -   66 LYS   (  71-)  A  -     -1.99
 179 GLU   ( 184-)  A  -  -  182 LYS   ( 187-)  A  -     -2.24
 200 GLN   ( 205-)  A  -  -  203 ARG   ( 208-)  A  -     -2.20
ERROR. Too many Ca-only residues in this range

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: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 315  CA   ( 351-)  A  -  -.-  -.-  Too few ligands (0)
 316  CA   ( 352-)  A  -  -.-  -.-  Too few ligands (0)
 317  CA   ( 353-)  A  -  -.-  -.-  Too few ligands (0)
 318  CA   ( 354-)  A  -  -.-  -.-  Too few ligands (0)
 319  CA   ( 355-)  A  -  -.-  -.-  Too few ligands (0)
 320  CA   ( 356-)  A  -  -.-  -.-  Too few ligands (0)
Since there are no waters, the water check has been skipped.

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 :  -8.438 (bad)
  Backbone conformation          :  15.599

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 : 2.50


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -5.3 (bad)
  Backbone conformation          :  15.0

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.