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 pdb1amy.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

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

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 45049.410
Volume of the Unit Cell V= 1260088.3
Space group multiplicity: 6
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.662
Vm by authors and this calculated Vm agree remarkably well
Matthews coefficient read from REMARK 280 Vm= 4.670

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: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

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

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 16.35

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.

   2 VAL   (   2-)  A      CA   CB    1.61    4.2
   9 TRP   (   9-)  A      CG   CD2   1.35   -4.5
 282 VAL   ( 282-)  A      CA   CB    1.62    4.5
 297 TRP   ( 297-)  A      NE1  CE2   1.32   -4.4
 328 TRP   ( 328-)  A      CG   CD2   1.35   -4.6

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

 |  1.005426  0.001006 -0.000300|
 |  0.001006  1.004944  0.000504|
 | -0.000300  0.000504  1.004882|
Proposed new scale matrix

 |  0.007352  0.004242  0.000000|
 | -0.000009  0.008499 -0.000004|
 |  0.000004 -0.000006  0.012502|
With corresponding cell

    A    = 135.942  B   = 135.761  C    =  79.987
    Alpha=  89.933  Beta=  90.034  Gamma= 119.925

The CRYST1 cell dimensions

    A    = 135.200  B   = 135.200  C    =  79.600
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 362.806
(Under-)estimated Z-score: 14.038

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.

   1 GLN   (   1-)  A      N    CA   C    94.24   -6.1
   1 GLN   (   1-)  A      CG   CD   NE2 123.18    4.5
   1 GLN   (   1-)  A      NE2  CD   OE1 116.13   -6.5
   2 VAL   (   2-)  A      N    CA   C    99.12   -4.3
   2 VAL   (   2-)  A      C    CA   CB  117.99    4.2
   5 GLN   (   5-)  A      CG   CD   NE2 124.38    5.3
   5 GLN   (   5-)  A      NE2  CD   OE1 113.67   -8.9
   9 TRP   (   9-)  A      CG   CD2  CE2 101.58   -4.7
  12 TRP   (  12-)  A      CD1  CG   CD2 113.65    4.6
  12 TRP   (  12-)  A      CG   CD1  NE1 103.99   -4.8
  12 TRP   (  12-)  A      CG   CD2  CE2 101.35   -4.9
  14 HIS   (  14-)  A      CB   CG   ND1 128.47    4.6
  18 TRP   (  18-)  A      CD1  CG   CD2 113.94    4.8
  18 TRP   (  18-)  A      CG   CD1  NE1 103.66   -5.0
  18 TRP   (  18-)  A      CG   CD2  CE2 101.22   -5.0
  36 HIS   (  36-)  A     -CA  -C    N   125.52    4.7
  36 HIS   (  36-)  A      CB   CG   ND1 128.39    4.5
  38 TRP   (  38-)  A      CE3  CD2  CG  139.40    5.5
  38 TRP   (  38-)  A      CG   CD2  CE2 101.40   -4.8
  40 PRO   (  40-)  A     -O   -C    N   116.21   -4.1
  41 PRO   (  41-)  A     -CA  -C    N   123.79    4.6
  42 ALA   (  42-)  A     -CA  -C    N   106.99   -4.6
  43 SER   (  43-)  A     -CA  -C    N   125.13    4.5
  45 SER   (  45-)  A      CA   CB   OG  119.34    4.1
  46 VAL   (  46-)  A      N    CA   CB  101.54   -5.3
And so on for a total of 155 lines.

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.

 115 ARG   ( 115-)  A      C     -6.4    -9.66     0.13
 144 GLY   ( 144-)  A      C      6.1     8.18     0.06
The average deviation= 1.573

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.

   1 GLN   (   1-)  A    6.73
 323 ASP   ( 323-)  A    6.01
 382 ASN   ( 382-)  A    5.60
 177 ARG   ( 177-)  A    5.32
 362 TYR   ( 362-)  A    5.09
 169 ALA   ( 169-)  A    5.08
  70 LEU   (  70-)  A    4.99
 306 GLN   ( 306-)  A    4.57
 145 ALA   ( 145-)  A    4.53
 273 MET   ( 273-)  A    4.44
 264 ARG   ( 264-)  A    4.41
   2 VAL   (   2-)  A    4.22
 143 PHE   ( 143-)  A    4.20
 101 ARG   ( 101-)  A    4.02

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 : 1.782

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.

 180 PHE   ( 180-)  A    -3.1
 300 PRO   ( 300-)  A    -2.9
 116 LEU   ( 116-)  A    -2.7
 266 THR   ( 266-)  A    -2.6
 381 GLY   ( 381-)  A    -2.4
 348 ASN   ( 348-)  A    -2.4
 129 PRO   ( 129-)  A    -2.4
  85 ILE   (  85-)  A    -2.4
 297 TRP   ( 297-)  A    -2.4
 292 SER   ( 292-)  A    -2.3
 277 TRP   ( 277-)  A    -2.3
 263 LEU   ( 263-)  A    -2.2
 236 GLY   ( 236-)  A    -2.2
 330 LEU   ( 330-)  A    -2.2
 376 PRO   ( 376-)  A    -2.2
 197 GLU   ( 197-)  A    -2.1
  52 MET   (  52-)  A    -2.1
  54 GLY   (  54-)  A    -2.1
 152 LEU   ( 152-)  A    -2.1
 347 HIS   ( 347-)  A    -2.0
  39 LEU   (  39-)  A    -2.0
 274 ILE   ( 274-)  A    -2.0
 382 ASN   ( 382-)  A    -2.0
 103 ILE   ( 103-)  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.

   6 GLY   (   6-)  A  Poor phi/psi
 101 ARG   ( 101-)  A  Poor phi/psi
 116 LEU   ( 116-)  A  Poor phi/psi
 125 ARG   ( 125-)  A  Poor phi/psi
 128 ARG   ( 128-)  A  PRO omega poor
 133 GLY   ( 133-)  A  Poor phi/psi
 172 GLY   ( 172-)  A  Poor phi/psi
 197 GLU   ( 197-)  A  Poor phi/psi
 214 ASP   ( 214-)  A  Poor phi/psi
 292 SER   ( 292-)  A  Poor phi/psi
 295 HIS   ( 295-)  A  Poor phi/psi
 347 HIS   ( 347-)  A  omega poor
 348 ASN   ( 348-)  A  Poor phi/psi
 379 ASP   ( 379-)  A  Poor phi/psi
 381 GLY   ( 381-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.325

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.325

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!

   7 PHE   (   7-)  A      0
  14 HIS   (  14-)  A      0
  15 ASN   (  15-)  A      0
  18 TRP   (  18-)  A      0
  34 ILE   (  34-)  A      0
  42 ALA   (  42-)  A      0
  43 SER   (  43-)  A      0
  44 GLN   (  44-)  A      0
  49 GLN   (  49-)  A      0
  51 TYR   (  51-)  A      0
  52 MET   (  52-)  A      0
  53 PRO   (  53-)  A      0
  55 ARG   (  55-)  A      0
  64 TYR   (  64-)  A      0
  66 ASN   (  66-)  A      0
  80 LYS   (  80-)  A      0
  89 VAL   (  89-)  A      0
  90 ILE   (  90-)  A      0
  91 ASN   (  91-)  A      0
  97 HIS   (  97-)  A      0
 101 ARG   ( 101-)  A      0
 104 TYR   ( 104-)  A      0
 105 CYS   ( 105-)  A      0
 112 PRO   ( 112-)  A      0
 113 ASP   ( 113-)  A      0
And so on for a total of 170 lines.

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 348 ASN   ( 348-)  A   1.71

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]

 112 PRO   ( 112-)  A    0.48 HIGH
 137 PRO   ( 137-)  A    0.47 HIGH
 198 PRO   ( 198-)  A    0.45 HIGH

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].

  40 PRO   (  40-)  A   -31.9 envelop C-alpha (-36 degrees)
  53 PRO   (  53-)  A    51.5 half-chair C-delta/C-gamma (54 degrees)
 129 PRO   ( 129-)  A   -65.9 envelop C-beta (-72 degrees)
 315 PRO   ( 315-)  A  -114.7 envelop C-gamma (-108 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.

   5 GLN   (   5-)  A      NE2 <->  288 HIS   ( 288-)  A      ND1    0.14    2.86  INTRA BL
  14 HIS   (  14-)  A      NE2 <->   21 PHE   (  21-)  A      CD1    0.14    2.96  INTRA
 101 ARG   ( 101-)  A      N   <->  102 GLY   ( 102-)  A      N      0.13    2.47  INTRA B3
   1 GLN   (   1-)  A      NE2 <->  348 ASN   ( 348-)  A      OD1    0.11    2.59  INTRA BF
  99 ASP   (  99-)  A      CG  <->  105 CYS   ( 105-)  A      SG     0.09    3.31  INTRA BL
 205 ILE   ( 205-)  A      N   <->  408 HOH   ( 614 )  A      O      0.08    2.62  INTRA BL
 225 ARG   ( 225-)  A      NH1 <->  271 PRO   ( 271-)  A      C      0.08    3.02  INTRA BL
 219 LEU   ( 219-)  A      N   <->  220 ASN   ( 220-)  A      N      0.06    2.54  INTRA BL
  75 GLY   (  75-)  A      O   <->   79 GLY   (  79-)  A      N      0.06    2.64  INTRA
  91 ASN   (  91-)  A      ND2 <->   92 HIS   (  92-)  A      ND1    0.05    2.95  INTRA BL
   6 GLY   (   6-)  A      O   <->   18 TRP   (  18-)  A      NE1    0.05    2.65  INTRA BL
 347 HIS   ( 347-)  A      O   <->  349 GLU   ( 349-)  A      N      0.05    2.65  INTRA
 348 ASN   ( 348-)  A      CB  <->  349 GLU   ( 349-)  A      N      0.04    2.66  INTRA B3
 306 GLN   ( 306-)  A      N   <->  307 GLY   ( 307-)  A      N      0.04    2.56  INTRA BL
 396 ASP   ( 396-)  A      N   <->  397 TYR   ( 397-)  A      N      0.03    2.57  INTRA B3
 224 HIS   ( 224-)  A      ND1 <->  247 THR   ( 247-)  A      OG1    0.03    2.67  INTRA BL
 295 HIS   ( 295-)  A      ND1 <->  408 HOH   ( 692 )  A      O      0.03    2.67  INTRA BF
 125 ARG   ( 125-)  A      N   <->  136 ASN   ( 136-)  A      O      0.02    2.68  INTRA BL
 196 SER   ( 196-)  A      N   <->  197 GLU   ( 197-)  A      N      0.02    2.58  INTRA B3
  15 ASN   (  15-)  A      N   <->  408 HOH   ( 707 )  A      O      0.02    2.68  INTRA
 302 ASP   ( 302-)  A      N   <->  303 ARG   ( 303-)  A      N      0.01    2.59  INTRA B3
  64 TYR   (  64-)  A      N   <->   65 GLY   (  65-)  A      N      0.01    2.59  INTRA BL
 347 HIS   ( 347-)  A      O   <->  350 SER   ( 350-)  A      N      0.01    2.69  INTRA
  78 HIS   (  78-)  A      NE2 <->  174 ASP   ( 174-)  A      OD2    0.01    2.69  INTRA BL

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.

 238 LYS   ( 238-)  A      -7.03
 378 TYR   ( 378-)  A      -6.78
 128 ARG   ( 128-)  A      -6.41
  15 ASN   (  15-)  A      -5.95
 343 ARG   ( 343-)  A      -5.61
 211 TYR   ( 211-)  A      -5.48
 395 ASN   ( 395-)  A      -5.10

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: 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.

 408 HOH   ( 660 )  A      O     14.95   78.90   23.39
 408 HOH   ( 680 )  A      O    -12.96   73.73   51.32
 408 HOH   ( 720 )  A      O      3.55   66.24   41.94
 408 HOH   ( 722 )  A      O     16.46   77.46   21.22
 408 HOH   ( 728 )  A      O     -5.73   70.07   51.45
 408 HOH   ( 731 )  A      O     34.04   38.54   12.51
 408 HOH   ( 750 )  A      O     18.46   75.37   21.66

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.

 408 HOH   ( 668 )  A      O
 408 HOH   ( 682 )  A      O
 408 HOH   ( 703 )  A      O
 408 HOH   ( 715 )  A      O
 408 HOH   ( 728 )  A      O
 408 HOH   ( 731 )  A      O
 408 HOH   ( 739 )  A      O
 408 HOH   ( 742 )  A      O
 408 HOH   ( 743 )  A      O
 408 HOH   ( 744 )  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.

  49 GLN   (  49-)  A
  66 ASN   (  66-)  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.

   2 VAL   (   2-)  A      N
   5 GLN   (   5-)  A      NE2
   7 PHE   (   7-)  A      N
  11 SER   (  11-)  A      OG
  20 ASN   (  20-)  A      N
  27 ASP   (  27-)  A      N
  28 ASP   (  28-)  A      N
  48 GLU   (  48-)  A      N
  49 GLN   (  49-)  A      N
  92 HIS   (  92-)  A      N
  93 ARG   (  93-)  A      NH1
 113 ASP   ( 113-)  A      N
 135 GLY   ( 135-)  A      N
 155 ARG   ( 155-)  A      NE
 182 LYS   ( 182-)  A      N
 187 ASP   ( 187-)  A      N
 200 PHE   ( 200-)  A      N
 220 ASN   ( 220-)  A      N
 231 TRP   ( 231-)  A      NE1
 241 ALA   ( 241-)  A      N
 261 TRP   ( 261-)  A      N
 264 ARG   ( 264-)  A      NH2
 267 ASP   ( 267-)  A      N
 279 ALA   ( 279-)  A      N
 331 LYS   ( 331-)  A      N
 348 ASN   ( 348-)  A      N
 357 ALA   ( 357-)  A      N
 377 ARG   ( 377-)  A      NH2
 378 TYR   ( 378-)  A      N
 396 ASP   ( 396-)  A      N
Only metal coordination for   91 ASN  (  91-) 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.

  69 GLN   (  69-)  A      OE1

Warning: No crystallisation information

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

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

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

 407  CA   ( 502-)  A     0.69   0.90 Scores about as good as NA

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.

 214 ASP   ( 214-)  A   H-bonding suggests Asn
 396 ASP   ( 396-)  A   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.836
  2nd generation packing quality :  -2.000
  Ramachandran plot appearance   :  -2.782
  chi-1/chi-2 rotamer normality  :  -4.325 (bad)
  Backbone conformation          :  -1.091

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.947
  Bond angles                    :   1.711
  Omega angle restraints         :   0.900
  Side chain planarity           :   0.645 (tight)
  Improper dihedral distribution :   1.333
  Inside/Outside distribution    :   0.957

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.947
  Bond angles                    :   1.711
  Omega angle restraints         :   0.900
  Side chain planarity           :   0.645 (tight)
  Improper dihedral distribution :   1.333
  Inside/Outside distribution    :   0.957
==============

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.