WHAT IF Check report

This file was created 2013-12-09 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 pdb2vrh.ent

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 MSE   (   1-)  A  -
   2 GLN   (   2-)  A  -
   3 VAL   (   3-)  A  -
   4 SER   (   4-)  A  -
   5 VAL   (   5-)  A  -
   6 GLU   (   6-)  A  -
   7 THR   (   7-)  A  -
   8 THR   (   8-)  A  -
   9 GLN   (   9-)  A  -
  10 GLY   (  10-)  A  -
  11 LEU   (  11-)  A  -
  12 GLY   (  12-)  A  -
  13 ARG   (  13-)  A  -
  14 ARG   (  14-)  A  -
  15 VAL   (  15-)  A  -
  16 THR   (  16-)  A  -
  17 ILE   (  17-)  A  -
  18 THR   (  18-)  A  -
  19 ILE   (  19-)  A  -
  20 ALA   (  20-)  A  -
  21 ALA   (  21-)  A  -
  22 ASP   (  22-)  A  -
  23 SER   (  23-)  A  -
  24 ILE   (  24-)  A  -
  25 GLU   (  25-)  A  -
And so on for a total of 695 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

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: 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 MSE   (   1-)  A  -   N
   1 MSE   (   1-)  A  -   C
   1 MSE   (   1-)  A  -   O
   1 MSE   (   1-)  A  -   CB
   1 MSE   (   1-)  A  -   CG
   1 MSE   (   1-)  A  -  SE
   1 MSE   (   1-)  A  -   CE
   2 GLN   (   2-)  A  -   N
   2 GLN   (   2-)  A  -   C
   2 GLN   (   2-)  A  -   O
   2 GLN   (   2-)  A  -   CB
   2 GLN   (   2-)  A  -   CG
   2 GLN   (   2-)  A  -   CD
   2 GLN   (   2-)  A  -   OE1
   2 GLN   (   2-)  A  -   NE2
   3 VAL   (   3-)  A  -   N
   3 VAL   (   3-)  A  -   C
   3 VAL   (   3-)  A  -   O
   3 VAL   (   3-)  A  -   CB
   3 VAL   (   3-)  A  -   CG1
   3 VAL   (   3-)  A  -   CG2
   4 SER   (   4-)  A  -   N
   4 SER   (   4-)  A  -   C
   4 SER   (   4-)  A  -   O
   4 SER   (   4-)  A  -   CB
And so on for a total of 4749 lines.

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 MSE   (   1-)  A  -   High
 151 TRP   ( 151-)  A  -   High
 152 LYS   ( 152-)  A  -   High
 153 GLU   ( 153-)  A  -   High
 154 LYS   ( 154-)  A  -   High
 155 ASP   ( 155-)  A  -   High
 156 GLY   ( 156-)  A  -   High
 157 ALA   ( 157-)  A  -   High
 158 VAL   ( 158-)  A  -   High
 159 GLU   ( 159-)  A  -   High
 161 GLU   ( 161-)  A  -   High
 165 THR   ( 165-)  A  -   High
 166 ILE   ( 166-)  A  -   High
 167 ASP   ( 167-)  A  -   High
 168 PHE   ( 168-)  A  -   High
 170 GLY   ( 170-)  A  -   High
 171 SER   ( 171-)  A  -   High
 172 VAL   ( 172-)  A  -   High
 173 ASP   ( 173-)  A  -   High
 174 GLY   ( 174-)  A  -   High
 175 GLU   ( 175-)  A  -   High
 176 GLU   ( 176-)  A  -   High
 177 PHE   ( 177-)  A  -   High
 178 GLU   ( 178-)  A  -   High
 179 GLY   ( 179-)  A  -   High
And so on for a total of 67 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 not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

Note: B-factor plot

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

Chain identifier: A

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: B

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: C

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: D

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 GLN   (   2-)  A  - Impossible phi
   3 VAL   (   3-)  A  - Impossible phi
   4 SER   (   4-)  A  - Impossible phi
   5 VAL   (   5-)  A  - Impossible phi
   6 GLU   (   6-)  A  - Impossible phi
   7 THR   (   7-)  A  - Impossible phi
   8 THR   (   8-)  A  - Impossible phi
   9 GLN   (   9-)  A  - Impossible phi
  10 GLY   (  10-)  A  - Impossible phi
  11 LEU   (  11-)  A  - Impossible phi
  12 GLY   (  12-)  A  - Impossible phi
  13 ARG   (  13-)  A  - Impossible phi
  14 ARG   (  14-)  A  - Impossible phi
  15 VAL   (  15-)  A  - Impossible phi
  16 THR   (  16-)  A  - Impossible phi
  17 ILE   (  17-)  A  - Impossible phi
  18 THR   (  18-)  A  - Impossible phi
  19 ILE   (  19-)  A  - Impossible phi
  20 ALA   (  20-)  A  - Impossible phi
  21 ALA   (  21-)  A  - Impossible phi
  22 ASP   (  22-)  A  - Impossible phi
  23 SER   (  23-)  A  - Impossible phi
  24 ILE   (  24-)  A  - Impossible phi
  25 GLU   (  25-)  A  - Impossible phi
  26 THR   (  26-)  A  - Impossible phi
And so on for a total of 677 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.

 449 GLU   (  18-)  B  -   0.36
  72 SER   (  72-)  A  -   0.38
  30 SER   (  30-)  A  -   0.39
ERROR. Too many Ca-only residues in this range
ERROR. Too many Ca-only residues in this range
ERROR. Too many Ca-only residues in this range
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!

   9 GLN   (   9-)  A  -     0
  51 MSE   (  51-)  A  -     0
  71 MSE   (  71-)  A  -     0
 140 MSE   ( 140-)  A  -     0
 189 MSE   ( 189-)  A  -     0
 194 MSE   ( 194-)  A  -     0
 246 PRO   ( 246-)  A  -     0
 247 GLU   ( 247-)  A  -     0
 274 MSE   ( 274-)  A  -     0
 322 PHE   ( 322-)  A  -     0
 323 GLY   ( 323-)  A  -     0
 374 MSE   ( 374-)  A  -     0
 395 MSE   ( 395-)  A  -     0
 398 MSE   ( 398-)  A  -     0
 428 MSE   ( 428-)  A  -     0
 430 GLN   ( 430-)  A  -     0
 431 GLN   ( 431-)  A  -     0
 432 MET   (   1-)  B  -     0
 433 ILE   (   2-)  B  -     0
 437 ARG   (   6-)  B  -     0
 503 GLN   (  72-)  B  -     0
 504 ARG   (  73-)  B  -     0
 529 GLY   (  98-)  B  -     0
 530 ALA   (  99-)  B  -     0
 531 ALA   (   1-)  C  -     0
And so on for a total of 61 lines.

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]

  50 PRO   (  50-)  A  -   0.00 LOW
  86 PRO   (  86-)  A  -   0.00 LOW
  90 PRO   (  90-)  A  -   0.00 LOW
  94 PRO   (  94-)  A  -   0.00 LOW
 113 PRO   ( 113-)  A  -   0.00 LOW
 128 PRO   ( 128-)  A  -   0.00 LOW
 196 PRO   ( 196-)  A  -   0.00 LOW
 218 PRO   ( 218-)  A  -   0.00 LOW
 246 PRO   ( 246-)  A  -   0.00 LOW
 303 PRO   ( 303-)  A  -   0.00 LOW
 333 PRO   ( 333-)  A  -   0.00 LOW
 381 PRO   ( 381-)  A  -   0.00 LOW
 445 PRO   (  14-)  B  -   0.00 LOW
 577 PRO   (  47-)  C  -   0.00 LOW
 579 PRO   (  49-)  C  -   0.00 LOW
 584 PRO   (  54-)  C  -   0.00 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.

 537 ASP   (   7-)  C  -   CA  <->  554 VAL   (  24-)  C  -   CA     0.11    3.09  INTRA
ERROR. Skipped check: Too many Ca residues in soup
ERROR. Incorrect unit number passed to GVFFOP: 135733987
ERROR. Too many Ca-only residues in this range
ERROR. Too many Ca-only residues in this range
ERROR. Too many Ca-only residues in this range
ERROR. Too many Ca-only residues in this range

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

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.

  13 ARG   (  13-)  A  -  -2.65
  14 ARG   (  14-)  A  -  -2.65
  40 ARG   (  40-)  A  -  -2.65
  45 ARG   (  45-)  A  -  -2.65
  57 ARG   (  57-)  A  -  -2.65
  63 ARG   (  63-)  A  -  -2.65
  73 ARG   (  73-)  A  -  -2.65
 145 ARG   ( 145-)  A  -  -2.65
 163 ARG   ( 163-)  A  -  -2.65
 193 ARG   ( 193-)  A  -  -2.65
 243 ARG   ( 243-)  A  -  -2.65
 255 ARG   ( 255-)  A  -  -2.65
 267 ARG   ( 267-)  A  -  -2.65
 271 ARG   ( 271-)  A  -  -2.65
 276 ARG   ( 276-)  A  -  -2.65
 283 ARG   ( 283-)  A  -  -2.65
 285 ARG   ( 285-)  A  -  -2.65
 315 ARG   ( 315-)  A  -  -2.65
 316 ARG   ( 316-)  A  -  -2.65
 321 ARG   ( 321-)  A  -  -2.65
 334 ARG   ( 334-)  A  -  -2.65
 343 ARG   ( 343-)  A  -  -2.65
 344 ARG   ( 344-)  A  -  -2.65
 356 ARG   ( 356-)  A  -  -2.65
 366 ARG   ( 366-)  A  -  -2.65
 399 ARG   ( 399-)  A  -  -2.65
 434 ARG   (   3-)  B  -  -2.65
 437 ARG   (   6-)  B  -  -2.65
 443 ARG   (  12-)  B  -  -2.65
 500 ARG   (  69-)  B  -  -2.65
 504 ARG   (  73-)  B  -  -2.65
 507 ARG   (  76-)  B  -  -2.65
 508 ARG   (  77-)  B  -  -2.65
 535 ARG   (   5-)  C  -  -2.65
 536 ARG   (   6-)  C  -  -2.65
 551 ARG   (  21-)  C  -  -2.65
 611 ARG   (  81-)  C  -  -2.65
 615 ARG   (  85-)  C  -  -2.65
 623 ARG   (  93-)  C  -  -2.65
 639 ARG   (   7-)  D  -  -2.65
 655 ARG   (  23-)  D  -  -2.65
 661 ARG   (  29-)  D  -  -2.65
 679 ARG   (  47-)  D  -  -2.65
 680 ARG   (  48-)  D  -  -2.65
 684 ARG   (  52-)  D  -  -2.65

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.

 313 VAL   ( 313-)  A  -  -  316 ARG   ( 316-)  A  -     -2.06
 348 GLY   ( 348-)  A  -  -  351 LEU   ( 351-)  A  -     -2.03
 436 GLU   (   5-)  B  -  -  439 LEU   (   8-)  B  -     -2.01
 652 ASN   (  20-)  D  -  -  655 ARG   (  23-)  D  -     -2.07
ERROR. Too many Ca-only residues in this range
ERROR. Too many Ca-only residues in this range
ERROR. Too many Ca-only residues in this range
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

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: 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.

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 :  -7.894 (bad)
  Backbone conformation          :  11.972

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 : 19.00


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -3.9 (poor)
  Backbone conformation          :   6.0

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

WHAT IF
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    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
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      Accurate bond and angle parameters for X-ray protein structure
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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      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.