WHAT IF Check report

This file was created 2011-12-18 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 pdb4tsv.ent

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

  61 PRO   (  70-)  A  -

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 147 LEU   ( 157-)  A  -

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 ASP   (  10-)  A      CG
   1 ASP   (  10-)  A      OD1
   1 ASP   (  10-)  A      OD2
  14 GLU   (  23-)  A      CG
  14 GLU   (  23-)  A      CD
  14 GLU   (  23-)  A      OE1
  14 GLU   (  23-)  A      OE2
  16 GLN   (  25-)  A      CG
  16 GLN   (  25-)  A      CD
  16 GLN   (  25-)  A      OE1
  16 GLN   (  25-)  A      NE2
  77 TYR   (  87-)  A      CG
  77 TYR   (  87-)  A      CD1
  77 TYR   (  87-)  A      CD2
  77 TYR   (  87-)  A      CE1
  77 TYR   (  87-)  A      CE2
  77 TYR   (  87-)  A      CZ
  77 TYR   (  87-)  A      OH
  78 GLN   (  88-)  A      CG
  78 GLN   (  88-)  A      CD
  78 GLN   (  88-)  A      OE1
  78 GLN   (  88-)  A      NE2
  93 ARG   ( 103-)  A      CG
  93 ARG   ( 103-)  A      CD
  93 ARG   ( 103-)  A      NE
  93 ARG   ( 103-)  A      CZ
  93 ARG   ( 103-)  A      NH1
  93 ARG   ( 103-)  A      NH2
  97 GLU   ( 107-)  A      CG
  97 GLU   ( 107-)  A      CD
  97 GLU   ( 107-)  A      OE1
  97 GLU   ( 107-)  A      OE2
 100 GLU   ( 110-)  A      CG
 100 GLU   ( 110-)  A      CD
 100 GLU   ( 110-)  A      OE1
 100 GLU   ( 110-)  A      OE2
 136 GLU   ( 146-)  A      CG
 136 GLU   ( 146-)  A      CD
 136 GLU   ( 146-)  A      OE1
 136 GLU   ( 146-)  A      OE2
 147 LEU   ( 157-)  A      O

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) :298.000

Note: B-factor plot

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

Chain identifier: A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

  64 VAL   (  74-)  A      N   -C     1.25   -4.1
  74 ALA   (  84-)  A      N   -C     1.49    8.2
  82 ASN   (  92-)  A      N   -C     1.21   -5.9
  95 THR   ( 105-)  A      CA   CB    1.63    5.2
  95 THR   ( 105-)  A      N   -C     1.99   33.2
 101 ALA   ( 111-)  A      N   -C     1.74   20.4

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998637  0.000964  0.000044|
 |  0.000964  0.995550 -0.000539|
 |  0.000044 -0.000539  0.997973|
Proposed new scale matrix

 |  0.015000  0.008677  0.000004|
 | -0.000017  0.017384  0.000009|
 |  0.000000  0.000006  0.011776|
With corresponding cell

    A    =  66.629  B   =  66.417  C    =  84.919
    Alpha=  90.055  Beta=  89.998  Gamma= 119.993

The CRYST1 cell dimensions

    A    =  66.720  B   =  66.720  C    =  85.090
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 36.591
(Under-)estimated Z-score: 4.458

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   6 HIS   (  15-)  A      CG   ND1  CE1 109.81    4.2
  24 ALA   (  33-)  A      N    CA   C    97.94   -4.7
  74 ALA   (  84-)  A     -O   -C    N    78.92  -27.5
  74 ALA   (  84-)  A     -CA  -C    N   125.49    4.6
  74 ALA   (  84-)  A     -C    N    CA  135.45    7.6
  82 ASN   (  92-)  A     -O   -C    N   115.35   -4.8
  82 ASN   (  92-)  A     -CA  -C    N   124.50    4.2
  82 ASN   (  92-)  A     -C    N    CA  129.50    4.3
  94 GLU   ( 104-)  A     -C    N    CA  129.80    4.5
  95 THR   ( 105-)  A     -O   -C    N    70.83  -32.6
  95 THR   ( 105-)  A     -CA  -C    N   104.21   -6.0
  95 THR   ( 105-)  A     -C    N    CA  130.10    4.7
  96 PRO   ( 106-)  A      N    CA   C   126.17    5.7
 101 ALA   ( 111-)  A     -C    N    CA  108.95   -7.1
 137 SER   ( 147-)  A      N    CA   C   126.37    5.4

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

  73 ILE   (  83-)  A      C    -34.1   -44.63     0.03
  94 GLU   ( 104-)  A      C    -52.3   -75.81    -0.03
The average deviation= 1.881

Error: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.5 worries us. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 3.427

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.

 137 SER   ( 147-)  A    5.63
  24 ALA   (  33-)  A    5.58
  96 PRO   ( 106-)  A    5.22
  76 SER   (  86-)  A    4.41
  98 GLY   ( 108-)  A    4.01

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.916

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.

  96 PRO   ( 106-)  A    -3.1
  76 SER   (  86-)  A    -2.7
 137 SER   ( 147-)  A    -2.6
  94 GLU   ( 104-)  A    -2.5
  95 THR   ( 105-)  A    -2.5
  22 ARG   (  31-)  A    -2.4
  69 THR   (  79-)  A    -2.2
 145 ILE   ( 155-)  A    -2.2
 110 LEU   ( 120-)  A    -2.2
   4 VAL   (  13-)  A    -2.1
  58 GLN   (  67-)  A    -2.1
  28 LEU   (  37-)  A    -2.1

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.

  25 ASN   (  34-)  A  Poor phi/psi
  37 ASN   (  46-)  A  Poor phi/psi
  75 VAL   (  85-)  A  Poor phi/psi
  76 SER   (  86-)  A  Poor phi/psi
  77 TYR   (  87-)  A  Poor phi/psi
  78 GLN   (  88-)  A  Poor phi/psi
  94 GLU   ( 104-)  A  Poor phi/psi, omega poor
  95 THR   ( 105-)  A  Poor phi/psi
  96 PRO   ( 106-)  A  Poor phi/psi
  97 GLU   ( 107-)  A  Poor phi/psi
 100 GLU   ( 110-)  A  Poor phi/psi, omega poor
 101 ALA   ( 111-)  A  Poor phi/psi
 137 SER   ( 147-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.480

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.480

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!

  13 ALA   (  22-)  A      0
  14 GLU   (  23-)  A      0
  22 ARG   (  31-)  A      0
  23 ARG   (  32-)  A      0
  24 ALA   (  33-)  A      0
  25 ASN   (  34-)  A      0
  26 ALA   (  35-)  A      0
  27 LEU   (  36-)  A      0
  28 LEU   (  37-)  A      0
  29 ALA   (  38-)  A      0
  30 ASN   (  39-)  A      0
  35 ARG   (  44-)  A      0
  37 ASN   (  46-)  A      0
  42 PRO   (  51-)  A      0
  43 ILE   (  52-)  A      0
  44 GLU   (  53-)  A      0
  46 LEU   (  55-)  A      0
  50 TYR   (  59-)  A      0
  58 GLN   (  67-)  A      0
  60 CYS   (  69-)  A      0
  61 PRO   (  70-)  A      0
  62 THR   (  72-)  A      0
  63 HIS   (  73-)  A      0
  64 VAL   (  74-)  A      0
  74 ALA   (  84-)  A      0
And so on for a total of 73 lines.

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].

  61 PRO   (  70-)  A   105.3 envelop C-beta (108 degrees)
  96 PRO   ( 106-)  A   110.7 envelop C-beta (108 degrees)
 107 PRO   ( 117-)  A   -62.4 half-chair C-beta/C-alpha (-54 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.

  62 THR   (  72-)  A      C   <->   63 HIS   (  73-)  A      ND1    0.86    2.14  INTRA BF
  62 THR   (  72-)  A      O   <->   63 HIS   (  73-)  A      ND1    0.80    1.80  INTRA BF
  95 THR   ( 105-)  A      CA  <->  149 HOH   ( 261 )  A      O      0.62    2.18  INTRA BF
  62 THR   (  72-)  A      CG2 <->  149 HOH   ( 259 )  A      O      0.58    2.22  INTRA BF
  88 LYS   (  98-)  A      NZ  <->  107 PRO   ( 117-)  A      O      0.51    2.19  INTRA
  75 VAL   (  85-)  A      CG1 <->   76 SER   (  86-)  A      N      0.38    2.62  INTRA BF
  95 THR   ( 105-)  A      CB  <->   96 PRO   ( 106-)  A      CD     0.27    2.83  INTRA BF
  62 THR   (  72-)  A      OG1 <->  149 HOH   ( 259 )  A      O      0.20    2.20  INTRA BF
  59 GLY   (  68-)  A      N   <->  102 LYS   ( 112-)  A      O      0.19    2.51  INTRA BF
  80 LYS   (  90-)  A      NZ  <->  125 GLU   ( 135-)  A      OE2    0.18    2.52  INTRA BF
  62 THR   (  72-)  A      O   <->   63 HIS   (  73-)  A      CE1    0.16    2.54  INTRA BF
 134 PHE   ( 144-)  A      C   <->  136 GLU   ( 146-)  A      N      0.15    2.75  INTRA
 137 SER   ( 147-)  A      CB  <->  138 GLY   ( 148-)  A      N      0.15    2.55  INTRA B3
  62 THR   (  72-)  A      C   <->   63 HIS   (  73-)  A      CG     0.15    2.95  INTRA BF
  41 VAL   (  50-)  A      CG2 <->   47 PHE   (  56-)  A      CZ     0.14    3.06  INTRA BL
  62 THR   (  72-)  A      CB  <->  149 HOH   ( 259 )  A      O      0.14    2.66  INTRA BF
  41 VAL   (  50-)  A      CG1 <->  117 GLU   ( 127-)  A      O      0.13    2.67  INTRA BL
 134 PHE   ( 144-)  A      N   <->  135 ALA   ( 145-)  A      N      0.08    2.52  INTRA B3
  59 GLY   (  68-)  A      CA  <->  102 LYS   ( 112-)  A      NZ     0.08    3.02  INTRA BF
  62 THR   (  72-)  A      C   <->   63 HIS   (  73-)  A      CE1    0.08    3.02  INTRA BF
  60 CYS   (  69-)  A      CB  <->   94 GLU   ( 104-)  A      CB     0.07    3.13  INTRA BF
   2 LYS   (  11-)  A      O   <->   30 ASN   (  39-)  A      ND2    0.06    2.64  INTRA BL
  45 GLY   (  54-)  A      C   <->  115 GLN   ( 125-)  A      NE2    0.06    3.04  INTRA
  68 HIS   (  78-)  A      ND1 <->  110 LEU   ( 120-)  A      CD2    0.06    3.04  INTRA BL
  73 ILE   (  83-)  A      O   <->   74 ALA   (  84-)  A      N      0.06    1.74  INTRA B2
  41 VAL   (  50-)  A      O   <->  119 GLY   ( 129-)  A      N      0.05    2.65  INTRA BL
 137 SER   ( 147-)  A      CA  <->  149 HOH   ( 266 )  A      O      0.04    2.76  INTRA BF
  16 GLN   (  25-)  A      CB  <->  149 HOH   ( 249 )  A      O      0.03    2.77  INTRA
 134 PHE   ( 144-)  A      O   <->  136 GLU   ( 146-)  A      N      0.03    2.67  INTRA
  62 THR   (  72-)  A      C   <->   63 HIS   (  73-)  A      N      0.03    2.87  INTRA BF
   8 VAL   (  17-)  A      O   <->   20 SER   (  29-)  A      N      0.03    2.67  INTRA BL
 137 SER   ( 147-)  A      OG  <->  138 GLY   ( 148-)  A      N      0.02    2.58  INTRA
  23 ARG   (  32-)  A      C   <->   24 ALA   (  33-)  A      C      0.01    2.79  INTRA BL
  87 ILE   (  97-)  A      CG2 <->   88 LYS   (  98-)  A      N      0.01    2.99  INTRA BL
  63 HIS   (  73-)  A      CD2 <->   91 CYS   ( 101-)  A      O      0.01    2.79  INTRA BF

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

  92 GLN   ( 102-)  A      -7.42
  22 ARG   (  31-)  A      -6.85
  12 GLN   (  21-)  A      -6.47
  94 GLU   ( 104-)  A      -5.40
  43 ILE   (  52-)  A      -5.02

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

  94 GLU   ( 104-)  A        96 - PRO    106- ( A)         -4.85

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.

  93 ARG   ( 103-)  A   -3.62
  97 GLU   ( 107-)  A   -2.52
 100 GLU   ( 110-)  A   -2.52
  16 GLN   (  25-)  A   -2.51

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.

  11 PRO   (  20-)  A     -   14 GLU   (  23-)  A        -1.90

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 149 HOH   ( 215 )  A      O    138.46   20.89   10.25
 149 HOH   ( 225 )  A      O    144.64   42.80   18.68
 149 HOH   ( 242 )  A      O    145.69   35.87  -22.93
 149 HOH   ( 244 )  A      O    150.00   48.35  -19.98
 149 HOH   ( 248 )  A      O    149.91   46.67  -21.92
 149 HOH   ( 252 )  A      O    150.18   44.39   -4.07
 149 HOH   ( 253 )  A      O    154.66   44.48    0.05
 149 HOH   ( 254 )  A      O    156.85   40.17    4.13
 149 HOH   ( 269 )  A      O    146.90   26.62   -8.51

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.

 149 HOH   ( 226 )  A      O
 149 HOH   ( 228 )  A      O
 149 HOH   ( 240 )  A      O
 149 HOH   ( 247 )  A      O
 149 HOH   ( 256 )  A      O
 149 HOH   ( 263 )  A      O

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.

  58 GLN   (  67-)  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.

  16 GLN   (  25-)  A      N
  22 ARG   (  31-)  A      NE
  43 ILE   (  52-)  A      N
  54 LEU   (  63-)  A      N
  87 ILE   (  97-)  A      N
 102 LYS   ( 112-)  A      N
 121 ARG   ( 131-)  A      NH1
 127 ASN   ( 137-)  A      ND2
 136 GLU   ( 146-)  A      N
 137 SER   ( 147-)  A      OG
 139 GLN   ( 149-)  A      NE2

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.

  68 HIS   (  78-)  A      ND1

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.035
  2nd generation packing quality :  -2.300
  Ramachandran plot appearance   :  -2.544
  chi-1/chi-2 rotamer normality  :  -3.480 (poor)
  Backbone conformation          :  -0.191

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.874
  Bond angles                    :   1.087
  Omega angle restraints         :   0.875
  Side chain planarity           :   0.744
  Improper dihedral distribution :   3.427 (loose)
  B-factor distribution          :   0.957
  Inside/Outside distribution    :   1.020

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -1.7
  Ramachandran plot appearance   :  -2.5
  chi-1/chi-2 rotamer normality  :  -3.0
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.874
  Bond angles                    :   1.087
  Omega angle restraints         :   0.875
  Side chain planarity           :   0.744
  Improper dihedral distribution :   3.427 (loose)
  B-factor distribution          :   0.957
  Inside/Outside distribution    :   1.020
==============

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.