WHAT IF Check report

This file was created 2011-12-21 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 pdb1d3c.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    = 117.791  B   = 109.532  C    =  65.223
    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    = 117.791  B   = 109.532  C    =  65.223
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  65.223  B   = 109.532  C    = 117.791
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  65.223  B   = 109.532  C    = 117.791
    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|

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.

 743 MPD   ( 716-)  A  -

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

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

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'.

 687 GLC   ( 690-)  A      O4
 689 GLC   ( 692-)  A      O4
 690 GLC   ( 693-)  A      O4
 691 GLC   ( 694-)  A      O4
 692 GLC   ( 695-)  A      O4
 693 GLC   ( 696-)  A      O4
 694 GLC   ( 697-)  A      O4
 695 GLC   ( 698-)  A      O4
 696 GLC   ( 699-)  A      O4
 697 GLC   ( 700-)  A      O4
 698 GLC   ( 701-)  A      O4
 699 GLC   ( 702-)  A      O4
 700 GLC   ( 703-)  A      O4
 701 GLC   ( 704-)  A      O4
 702 GLC   ( 705-)  A      O4
 703 GLC   ( 706-)  A      O4
 704 GLC   ( 707-)  A      O4
 705 GLC   ( 708-)  A      O4
 706 GLC   ( 709-)  A      O4
 707 GLC   ( 710-)  A      O4
 708 GLC   ( 711-)  A      O4
 709 GLC   ( 712-)  A      O4
 710 GLC   ( 713-)  A      O4
 711 GLC   ( 714-)  A      O4
 712 GLC   ( 715-)  A      O4

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.

  78 GLN   (  78-)  A    0.46
 128 LYS   ( 128-)  A    0.46
 197 LEU   ( 197-)  A    0.46
 232 LYS   ( 232-)  A    0.46
 331 ARG   ( 331-)  A    0.46
 342 LEU   ( 342-)  A    0.46
 444 ILE   ( 444-)  A    0.46
 478 SER   ( 478-)  A    0.46
 510 LYS   ( 510-)  A    0.46
 552 LYS   ( 552-)  A    0.46
 651 LYS   ( 651-)  A    0.46
 656 GLN   ( 656-)  A    0.46
 675 SER   ( 675-)  A    0.46

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:

Crystal temperature (K) :120.000

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

  49 TYR   (  49-)  A

Warning: Phenylalanine convention problem

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

 105 PHE   ( 105-)  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.

 147 ASP   ( 147-)  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: 0.335
RMS-deviation in bond distances: 0.009

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). 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 angles: 0.498
RMS-deviation in bond angles: 1.168

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.

 147 ASP   ( 147-)  A

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 275 GLU   ( 275-)  A    4.76

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.

 318 ASP   ( 318-)  A    4.11

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.

 372 PRO   ( 372-)  A    -3.1
 195 TYR   ( 195-)  A    -2.5
  90 SER   (  90-)  A    -2.5
  43 CYS   (  43-)  A    -2.5
 414 ILE   ( 414-)  A    -2.4
 545 GLU   ( 545-)  A    -2.4
  76 ILE   (  76-)  A    -2.3
 138 PRO   ( 138-)  A    -2.3
 194 LEU   ( 194-)  A    -2.2
 653 LEU   ( 653-)  A    -2.2
 145 SER   ( 145-)  A    -2.2
 470 SER   ( 470-)  A    -2.1
  24 ARG   (  24-)  A    -2.1
 173 ASN   ( 173-)  A    -2.0
 682 VAL   ( 682-)  A    -2.0
 638 TYR   ( 638-)  A    -2.0

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.

  90 SER   (  90-)  A  Poor phi/psi
 103 ARG   ( 103-)  A  Poor phi/psi
 129 ASN   ( 129-)  A  Poor phi/psi
 141 THR   ( 141-)  A  Poor phi/psi
 152 ALA   ( 152-)  A  Poor phi/psi
 169 ASN   ( 169-)  A  Poor phi/psi
 173 ASN   ( 173-)  A  Poor phi/psi
 183 PHE   ( 183-)  A  Poor phi/psi
 195 TYR   ( 195-)  A  Poor phi/psi
 249 TYR   ( 249-)  A  Poor phi/psi
 263 ASN   ( 263-)  A  Poor phi/psi
 279 SER   ( 279-)  A  Poor phi/psi
 296 ASN   ( 296-)  A  Poor phi/psi
 365 TYR   ( 365-)  A  Poor phi/psi
 371 ASP   ( 371-)  A  PRO omega poor
 465 ASN   ( 465-)  A  Poor phi/psi
 505 GLY   ( 505-)  A  PRO omega poor
 555 ALA   ( 555-)  A  Poor phi/psi
 578 ASN   ( 578-)  A  Poor phi/psi
 595 ASN   ( 595-)  A  Poor phi/psi
 616 TRP   ( 616-)  A  Poor phi/psi
 623 GLY   ( 623-)  A  PRO omega poor
 629 VAL   ( 629-)  A  Poor phi/psi
 633 TYR   ( 633-)  A  PRO omega poor
 chi-1/chi-2 correlation Z-score : -2.982

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 LYS   (   9-)  A      0
  10 GLN   (  10-)  A      0
  11 ASN   (  11-)  A      0
  13 SER   (  13-)  A      0
  25 PHE   (  25-)  A      0
  26 SER   (  26-)  A      0
  33 ASN   (  33-)  A      0
  35 THR   (  35-)  A      0
  38 ALA   (  38-)  A      0
  43 CYS   (  43-)  A      0
  46 LEU   (  46-)  A      0
  49 TYR   (  49-)  A      0
  50 CYS   (  50-)  A      0
  54 TRP   (  54-)  A      0
  69 MET   (  69-)  A      0
  72 THR   (  72-)  A      0
  77 SER   (  77-)  A      0
  78 GLN   (  78-)  A      0
  80 VAL   (  80-)  A      0
  89 TYR   (  89-)  A      0
  90 SER   (  90-)  A      0
  96 ALA   (  96-)  A      0
 100 TYR   ( 100-)  A      0
 101 TRP   ( 101-)  A      0
 103 ARG   ( 103-)  A      0
And so on for a total of 334 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 2.125

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 527 GLY   ( 527-)  A   1.62   10

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]

  30 PRO   (  30-)  A    0.04 LOW
 356 PRO   ( 356-)  A    0.11 LOW
 402 PRO   ( 402-)  A    0.07 LOW
 499 PRO   ( 499-)  A    0.16 LOW
 624 PRO   ( 624-)  A    0.08 LOW
 686 PRO   ( 686-)  A    0.09 LOW

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].

   2 PRO   (   2-)  A   -63.9 envelop C-beta (-72 degrees)
  34 PRO   (  34-)  A   115.9 envelop C-beta (108 degrees)
  79 PRO   (  79-)  A   -48.0 half-chair C-beta/C-alpha (-54 degrees)
 372 PRO   ( 372-)  A   -47.2 half-chair C-beta/C-alpha (-54 degrees)
 379 PRO   ( 379-)  A   -56.7 half-chair C-beta/C-alpha (-54 degrees)
 511 PRO   ( 511-)  A   101.0 envelop C-beta (108 degrees)
 618 PRO   ( 618-)  A    99.0 envelop C-beta (108 degrees)
 634 PRO   ( 634-)  A   -63.3 envelop C-beta (-72 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.

 712 GLC   ( 715-)  A      C4  <->  732 GLC   ( 708-)  A      O1     1.42    1.38  INTRA
 706 GLC   ( 709-)  A      C1  <->  733 GLC   ( 709-)  A      O1     1.42    1.38  INTRA
 712 GLC   ( 715-)  A      C1  <->  742 GLC   ( 715-)  A      O1     1.41    1.39  INTRA
 710 GLC   ( 713-)  A      C4  <->  738 GLC   ( 714-)  A      O1     1.41    1.39  INTRA BF
 696 GLC   ( 699-)  A      C1  <->  723 GLC   ( 699-)  A      O1     1.41    1.39  INTRA
 700 GLC   ( 703-)  A      C1  <->  727 GLC   ( 703-)  A      O1     1.40    1.40  INTRA BF
 698 GLC   ( 701-)  A      C1  <->  725 GLC   ( 701-)  A      O1     1.40    1.40  INTRA BF
 697 GLC   ( 700-)  A      C1  <->  724 GLC   ( 700-)  A      O1     1.40    1.40  INTRA
 693 GLC   ( 696-)  A      C1  <->  720 GLC   ( 696-)  A      O1     1.39    1.41  INTRA BL
 689 GLC   ( 692-)  A      C1  <->  716 GLC   ( 692-)  A      O1     1.39    1.41  INTRA
 702 GLC   ( 705-)  A      C4  <->  730 GLC   ( 706-)  A      O1     1.38    1.42  INTRA
 699 GLC   ( 702-)  A      C1  <->  726 GLC   ( 702-)  A      O1     1.38    1.42  INTRA BF
 706 GLC   ( 709-)  A      C4  <->  734 GLC   ( 710-)  A      O1     1.38    1.42  INTRA
 690 GLC   ( 693-)  A      C1  <->  717 GLC   ( 693-)  A      O1     1.38    1.42  INTRA
 709 GLC   ( 712-)  A      C1  <->  736 GLC   ( 712-)  A      O1     1.37    1.43  INTRA BF
 703 GLC   ( 706-)  A      C4  <->  731 GLC   ( 707-)  A      O1     1.37    1.43  INTRA
 691 GLC   ( 694-)  A      C1  <->  718 GLC   ( 694-)  A      O1     1.37    1.43  INTRA BL
 687 GLC   ( 690-)  A      C4  <->  715 GLC   ( 691-)  A      O1     1.36    1.44  INTRA BL
 695 GLC   ( 698-)  A      C1  <->  722 GLC   ( 698-)  A      O1     1.36    1.44  INTRA
 694 GLC   ( 697-)  A      C1  <->  721 GLC   ( 697-)  A      O1     1.36    1.44  INTRA
 708 GLC   ( 711-)  A      C1  <->  735 GLC   ( 711-)  A      O1     1.35    1.45  INTRA BF
 710 GLC   ( 713-)  A      C1  <->  737 GLC   ( 713-)  A      O1     1.35    1.45  INTRA BF
 702 GLC   ( 705-)  A      C1  <->  729 GLC   ( 705-)  A      O1     1.34    1.46  INTRA BF
 701 GLC   ( 704-)  A      C1  <->  728 GLC   ( 704-)  A      O1     1.33    1.47  INTRA BF
 692 GLC   ( 695-)  A      C1  <->  719 GLC   ( 695-)  A      O1     1.30    1.50  INTRA BL
And so on for a total of 178 lines.

Packing, accessibility and threading

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.

  84 TYR   (  84-)  A      -6.20
 600 LEU   ( 600-)  A      -6.12
 195 TYR   ( 195-)  A      -6.03
 377 ARG   ( 377-)  A      -5.80
 685 GLN   ( 685-)  A      -5.57
 453 GLN   ( 453-)  A      -5.41
  89 TYR   (  89-)  A      -5.41
 233 HIS   ( 233-)  A      -5.39
  32 ASN   (  32-)  A      -5.36
 353 ARG   ( 353-)  A      -5.35
 633 TYR   ( 633-)  A      -5.29
 364 GLN   ( 364-)  A      -5.25
 259 PHE   ( 259-)  A      -5.20
 265 VAL   ( 265-)  A      -5.15
  62 ASN   (  62-)  A      -5.11

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.

 195 TYR   ( 195-)  A   -3.07
 315 ALA   ( 315-)  A   -2.74
 582 LEU   ( 582-)  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.

 402 PRO   ( 402-)  A     -  405 ALA   ( 405-)  A        -1.52

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.

 744 HOH   (1091 )  A      O     77.91   81.34   36.39
 744 HOH   (1134 )  A      O     58.30   53.93    7.70
 744 HOH   (1185 )  A      O     51.27   93.04   -5.90
 744 HOH   (1207 )  A      O     18.65   88.14   29.83
 744 HOH   (1244 )  A      O     62.41   55.99    8.39
 744 HOH   (1352 )  A      O     85.31   64.35   41.33

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 744 HOH   ( 989 )  A      O
 744 HOH   (1208 )  A      O
 744 HOH   (1336 )  A      O
Strange metal coordination for HIS 233
ERROR. No convergence in HB2STD
Old,New value: 987.131 987.142

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 257 GLN   ( 257-)  A
 263 ASN   ( 263-)  A
 578 ASN   ( 578-)  A

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.

  22 THR   (  22-)  A      OG1
  50 CYS   (  50-)  A      N
  80 VAL   (  80-)  A      N
  85 SER   (  85-)  A      OG
  92 VAL   (  92-)  A      N
  94 ASN   (  94-)  A      ND2
  98 HIS   (  98-)  A      N
 140 HIS   ( 140-)  A      N
 185 THR   ( 185-)  A      N
 192 LYS   ( 192-)  A      N
 227 ARG   ( 227-)  A      NE
 229 ASN   ( 229-)  A      ND2
 230 ALA   ( 230-)  A      N
 232 LYS   ( 232-)  A      N
 238 TRP   ( 238-)  A      N
 252 VAL   ( 252-)  A      N
 260 LEU   ( 260-)  A      N
 284 ARG   ( 284-)  A      NH1
 318 ASP   ( 318-)  A      N
 323 PHE   ( 323-)  A      N
 326 ASN   ( 326-)  A      N
 380 SER   ( 380-)  A      N
 385 THR   ( 385-)  A      N
 412 ARG   ( 412-)  A      NE
 445 SER   ( 445-)  A      N
 467 ASN   ( 467-)  A      N
 504 VAL   ( 504-)  A      N
 527 GLY   ( 527-)  A      N
 548 GLN   ( 548-)  A      N
 584 GLY   ( 584-)  A      N
 598 THR   ( 598-)  A      OG1
 604 VAL   ( 604-)  A      N
 610 VAL   ( 610-)  A      N
 627 ASN   ( 627-)  A      ND2
 631 TYR   ( 631-)  A      N
 675 SER   ( 675-)  A      N
 692 GLC   ( 695-)  A      O6
 705 GLC   ( 708-)  A      O3
Only metal coordination for   33 ASN  (  33-) A      OD1
Only metal coordination for  139 ASN  ( 139-) A      OD1

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 233 HIS   ( 233-)  A      ND1
 239 GLN   ( 239-)  A      OE1

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+.

 739  CA   ( 687-)  A     0.89   1.12 Scores about as good as NA
 740  CA   ( 688-)  A     0.79   1.03 Scores about as good as NA
 741  CA   ( 689-)  A     0.78   1.02 Scores about as good as NA

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.

 744 HOH   ( 759 )  A      O  0.99  K  4
 744 HOH   ( 782 )  A      O  0.88  K  4
 744 HOH   ( 808 )  A      O  0.86  K  4
 744 HOH   ( 911 )  A      O  0.89  K  4
 744 HOH   ( 956 )  A      O  1.01  K  4
 744 HOH   ( 984 )  A      O  0.91  K  5

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.

 328 ASP   ( 328-)  A   H-bonding suggests Asn
 411 GLU   ( 411-)  A   H-bonding suggests Gln

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 :  -0.134
  2nd generation packing quality :  -1.178
  Ramachandran plot appearance   :  -1.549
  chi-1/chi-2 rotamer normality  :  -2.982
  Backbone conformation          :  -0.710

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.335 (tight)
  Bond angles                    :   0.498 (tight)
  Omega angle restraints         :   0.386 (tight)
  Side chain planarity           :   1.010
  Improper dihedral distribution :   0.758
  B-factor distribution          :   1.425
  Inside/Outside distribution    :   0.987

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 : 1.78


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -1.6
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.335 (tight)
  Bond angles                    :   0.498 (tight)
  Omega angle restraints         :   0.386 (tight)
  Side chain planarity           :   1.010
  Improper dihedral distribution :   0.758
  B-factor distribution          :   1.425
  Inside/Outside distribution    :   0.987
==============

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.