WHAT IF Check report

This file was created 2012-01-31 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 pdb2vcq.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.192
CA-only RMS fit for the two chains : 0.908

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 1.340
CA-only RMS fit for the two chains : 1.028

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.985
CA-only RMS fit for the two chains : 0.629

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 788 GSH   (1200-)  A  -         OK
 789 D25   (1201-)  A  -
 790 GSH   (1200-)  B  -         OK
 791 D25   (1201-)  B  -
 792 GSH   (1200-)  C  -         OK
 793 GSH   (1200-)  D  -         OK
 794 GSH   (1201-)  C  -         OK

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 172 ARG   ( 173-)  A
 192 ARG   ( 193-)  A
 266 ARG   (  69-)  B
 390 ARG   ( 193-)  B
 464 ARG   (  69-)  C
 757 ARG   ( 173-)  D

Warning: Tyrosine convention problem

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

 121 TYR   ( 122-)  A
 221 TYR   (  24-)  B
 319 TYR   ( 122-)  B
 517 TYR   ( 122-)  C

Warning: Phenylalanine convention problem

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

  47 PHE   (  48-)  A
 101 PHE   ( 102-)  A
 162 PHE   ( 163-)  A
 245 PHE   (  48-)  B
 299 PHE   ( 102-)  B
 360 PHE   ( 163-)  B
 443 PHE   (  48-)  C
 497 PHE   ( 102-)  C
 558 PHE   ( 163-)  C
 641 PHE   (  48-)  D

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.

  37 ASP   (  38-)  A
 131 ASP   ( 132-)  A
 235 ASP   (  38-)  B
 273 ASP   (  76-)  B
 329 ASP   ( 132-)  B
 433 ASP   (  38-)  C
 471 ASP   (  76-)  C
 505 ASP   ( 110-)  C
 527 ASP   ( 132-)  C
 631 ASP   (  38-)  D
 716 ASP   ( 132-)  D

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  54 GLU   (  55-)  A
 153 GLU   ( 154-)  A
 351 GLU   ( 154-)  B
 450 GLU   (  55-)  C
 479 GLU   (  84-)  C
 549 GLU   ( 154-)  C
 648 GLU   (  55-)  D
 677 GLU   (  84-)  D
 738 GLU   ( 154-)  D

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: 0.456
RMS-deviation in bond distances: 0.011

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

 |  0.996764 -0.000296 -0.000138|
 | -0.000296  0.997177 -0.000150|
 | -0.000138 -0.000150  0.996668|
Proposed new scale matrix

 |  0.008243  0.000002  0.000001|
 |  0.000002  0.008239  0.000001|
 |  0.000001  0.000001  0.009505|
With corresponding cell

    A    = 121.320  B   = 121.370  C    = 105.211
    Alpha=  90.017  Beta=  90.016  Gamma=  90.034

The CRYST1 cell dimensions

    A    = 121.720  B   = 121.720  C    = 105.566
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 265.640
(Under-)estimated Z-score: 12.012

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.

  61 HIS   (  62-)  A      CG   ND1  CE1 109.63    4.0
  78 GLY   (  79-)  A      N    CA   C    99.49   -4.5
 482 HIS   (  87-)  C      CG   ND1  CE1 109.64    4.0
 676 MET   (  83-)  D      CA   CB   CG  103.64   -5.2
 755 HIS   ( 171-)  D      CG   ND1  CE1 109.71    4.1

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.

  37 ASP   (  38-)  A
  54 GLU   (  55-)  A
 131 ASP   ( 132-)  A
 153 GLU   ( 154-)  A
 172 ARG   ( 173-)  A
 192 ARG   ( 193-)  A
 235 ASP   (  38-)  B
 266 ARG   (  69-)  B
 273 ASP   (  76-)  B
 329 ASP   ( 132-)  B
 351 GLU   ( 154-)  B
 390 ARG   ( 193-)  B
 433 ASP   (  38-)  C
 450 GLU   (  55-)  C
 464 ARG   (  69-)  C
 471 ASP   (  76-)  C
 479 GLU   (  84-)  C
 505 ASP   ( 110-)  C
 527 ASP   ( 132-)  C
 549 GLU   ( 154-)  C
 631 ASP   (  38-)  D
 648 GLU   (  55-)  D
 677 GLU   (  84-)  D
 716 ASP   ( 132-)  D
 738 GLU   ( 154-)  D
 757 ARG   ( 173-)  D

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.

  78 GLY   (  79-)  A    5.05
 390 ARG   ( 193-)  B    4.61

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.

 300 PRO   ( 103-)  B    -2.4
  46 PRO   (  47-)  A    -2.2
 601 TYR   (   8-)  D    -2.1
 403 TYR   (   8-)  C    -2.1
 244 PRO   (  47-)  B    -2.1
 408 GLY   (  13-)  C    -2.1
  34 GLU   (  35-)  A    -2.0
 457 HIS   (  62-)  C    -2.0
  12 GLY   (  13-)  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.

  12 GLY   (  13-)  A  Poor phi/psi
  25 ASP   (  26-)  A  Poor phi/psi
  50 ILE   (  51-)  A  PRO omega poor
  62 GLN   (  63-)  A  Poor phi/psi
  73 ASN   (  74-)  A  Poor phi/psi
 102 PRO   ( 103-)  A  Poor phi/psi
 210 GLY   (  13-)  B  Poor phi/psi
 248 ILE   (  51-)  B  PRO omega poor
 260 GLN   (  63-)  B  Poor phi/psi
 271 ASN   (  74-)  B  Poor phi/psi
 398 ASN   (   3-)  C  Poor phi/psi
 408 GLY   (  13-)  C  Poor phi/psi
 421 ASP   (  26-)  C  Poor phi/psi
 446 ILE   (  51-)  C  PRO omega poor
 458 GLN   (  63-)  C  Poor phi/psi
 469 ASN   (  74-)  C  Poor phi/psi
 619 ASP   (  26-)  D  Poor phi/psi
 644 ILE   (  51-)  D  PRO omega poor
 656 GLN   (  63-)  D  Poor phi/psi
 667 ASN   (  74-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.591

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!

   6 THR   (   7-)  A      0
   7 TYR   (   8-)  A      0
   8 PHE   (   9-)  A      0
   9 ASN   (  10-)  A      0
  10 MET   (  11-)  A      0
  11 ARG   (  12-)  A      0
  13 ARG   (  14-)  A      0
  27 GLN   (  28-)  A      0
  30 ASP   (  31-)  A      0
  50 ILE   (  51-)  A      0
  55 VAL   (  56-)  A      0
  61 HIS   (  62-)  A      0
  62 GLN   (  63-)  A      0
  72 LYS   (  73-)  A      0
  77 ALA   (  78-)  A      0
  79 ASN   (  80-)  A      0
 100 CYS   ( 101-)  A      0
 101 PHE   ( 102-)  A      0
 102 PRO   ( 103-)  A      0
 103 TRP   ( 104-)  A      0
 106 LYS   ( 107-)  A      0
 120 THR   ( 121-)  A      0
 121 TYR   ( 122-)  A      0
 122 ASN   ( 123-)  A      0
 134 LEU   ( 135-)  A      0
And so on for a total of 244 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 : 2.779

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]

 756 PRO   ( 172-)  D    0.14 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].

  39 PRO   (  40-)  A  -137.1 envelop C-delta (-144 degrees)
  46 PRO   (  47-)  A   116.0 envelop C-beta (108 degrees)
 171 PRO   ( 172-)  A  -116.7 envelop C-gamma (-108 degrees)
 199 PRO   (   2-)  B    39.1 envelop C-delta (36 degrees)
 244 PRO   (  47-)  B   101.3 envelop C-beta (108 degrees)
 397 PRO   (   2-)  C   109.1 envelop C-beta (108 degrees)
 567 PRO   ( 172-)  C  -113.8 envelop C-gamma (-108 degrees)
 595 PRO   (   2-)  D   103.2 envelop C-beta (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.

 499 TRP   ( 104-)  C      CE2 <->  794 GSH   (1201-)  C      N3     1.85    0.35  INTRA B2
 409 ARG   (  14-)  C      N   <->  794 GSH   (1201-)  C      O11    1.51    0.79  INTRA BL
 499 TRP   ( 104-)  C      NE1 <->  794 GSH   (1201-)  C      C2     1.44    1.66  INTRA
 499 TRP   ( 104-)  C      CE2 <->  794 GSH   (1201-)  C      C2     1.37    1.43  INTRA B3
 409 ARG   (  14-)  C      N   <->  794 GSH   (1201-)  C      C1     1.26    0.94  INTRA BL
 499 TRP   ( 104-)  C      NE1 <->  794 GSH   (1201-)  C      N3     1.18    1.42  INTRA B3
 409 ARG   (  14-)  C      CA  <->  794 GSH   (1201-)  C      O11    1.17    0.73  INTRA BL
 499 TRP   ( 104-)  C      CZ2 <->  794 GSH   (1201-)  C      C2     1.11    2.09  INTRA
 499 TRP   ( 104-)  C      CZ2 <->  794 GSH   (1201-)  C      N3     1.06    1.64  INTRA B3
 408 GLY   (  13-)  C      CA  <->  794 GSH   (1201-)  C      CA1    1.04    1.76  INTRA BL
 408 GLY   (  13-)  C      C   <->  794 GSH   (1201-)  C      O11    1.03    1.77  INTRA BL
 499 TRP   ( 104-)  C      CH2 <->  794 GSH   (1201-)  C      O32    0.98    0.92  INTRA B2
 499 TRP   ( 104-)  C      CD1 <->  794 GSH   (1201-)  C      CB2    0.96    2.24  INTRA
 499 TRP   ( 104-)  C      CZ2 <->  794 GSH   (1201-)  C      CA3    0.94    1.36  INTRA B2
 499 TRP   ( 104-)  C      CZ2 <->  794 GSH   (1201-)  C      C3     0.89    1.41  INTRA B2
 403 TYR   (   8-)  C      OH  <->  794 GSH   (1201-)  C      CB1    0.83    1.97  INTRA BL
 403 TYR   (   8-)  C      CZ  <->  794 GSH   (1201-)  C      O12    0.77    2.03  INTRA BL
 499 TRP   ( 104-)  C      CD1 <->  794 GSH   (1201-)  C      C2     0.76    2.44  INTRA
 408 GLY   (  13-)  C      C   <->  794 GSH   (1201-)  C      C1     0.75    2.05  INTRA BL
 403 TYR   (   8-)  C      OH  <->  794 GSH   (1201-)  C      CA1    0.67    2.13  INTRA BL
 403 TYR   (   8-)  C      CZ  <->  794 GSH   (1201-)  C      C1     0.64    2.56  INTRA BL
 792 GSH   (1200-)  C      SG2 <->  794 GSH   (1201-)  C      SG2    0.63    2.97  INTRA
 497 PHE   ( 102-)  C      CB  <->  794 GSH   (1201-)  C      CA3    0.62    2.58  INTRA BL
 499 TRP   ( 104-)  C      CD1 <->  794 GSH   (1201-)  C      N3     0.62    2.08  INTRA B3
 409 ARG   (  14-)  C      C   <->  794 GSH   (1201-)  C      O11    0.54    1.86  INTRA BL
And so on for a total of 129 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 780 GLN   ( 196-)  D      -7.17
 591 GLN   ( 196-)  C      -7.09
 195 GLN   ( 196-)  A      -6.85
 621 GLN   (  28-)  D      -6.10
 393 GLN   ( 196-)  B      -5.96
 225 GLN   (  28-)  B      -5.86
 197 LYS   ( 198-)  A      -5.84
 593 LYS   ( 198-)  C      -5.79
  27 GLN   (  28-)  A      -5.74
 395 LYS   ( 198-)  B      -5.71
 782 LYS   ( 198-)  D      -5.67
 777 ARG   ( 193-)  D      -5.64
 390 ARG   ( 193-)  B      -5.63
 192 ARG   ( 193-)  A      -5.56
 247 LYS   (  50-)  B      -5.43
 588 ARG   ( 193-)  C      -5.34
 722 ARG   ( 138-)  D      -5.32
  49 LYS   (  50-)  A      -5.29
 341 ASN   ( 144-)  B      -5.29
 728 ASN   ( 144-)  D      -5.21
 539 ASN   ( 144-)  C      -5.21
 643 LYS   (  50-)  D      -5.15
 469 ASN   (  74-)  C      -5.11
 335 ARG   ( 138-)  B      -5.04

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 727 GLY   ( 143-)  D   -2.58
 364 LEU   ( 167-)  B   -2.55
 166 LEU   ( 167-)  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.

 749 PRO   ( 165-)  D     -  752 LEU   ( 168-)  D        -1.50

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

 796 HOH   (2008 )  B      O
 796 HOH   (2104 )  B      O
Strange Type 7 donor in HBO012
Acidic oxygen connectivity expected for:  794 GSH  (1201-) C      O11
Bound atom  794 GSH  (1201-) C      C1
This atom does not have 3 bonds but 4

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.

 707 ASN   ( 123-)  D

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.

   7 TYR   (   8-)  A      OH
   8 PHE   (   9-)  A      N
  13 ARG   (  14-)  A      NE
  34 GLU   (  35-)  A      N
  50 ILE   (  51-)  A      N
  80 THR   (  81-)  A      N
 137 ARG   ( 138-)  A      NE
 139 TRP   ( 140-)  A      N
 165 ASP   ( 166-)  A      N
 169 ASN   ( 170-)  A      N
 205 TYR   (   8-)  B      OH
 206 PHE   (   9-)  B      N
 246 GLY   (  49-)  B      N
 248 ILE   (  51-)  B      N
 259 HIS   (  62-)  B      NE2
 261 SER   (  64-)  B      N
 266 ARG   (  69-)  B      NH1
 278 THR   (  81-)  B      N
 280 MET   (  83-)  B      N
 404 PHE   (   9-)  C      N
 443 PHE   (  48-)  C      N
 446 ILE   (  51-)  C      N
 459 SER   (  64-)  C      N
 464 ARG   (  69-)  C      NH2
 476 THR   (  81-)  C      N
 477 GLU   (  82-)  C      N
 505 ASP   ( 110-)  C      N
 535 TRP   ( 140-)  C      N
 597 TYR   (   4-)  D      N
 602 PHE   (   9-)  D      N
 607 ARG   (  14-)  D      NE
 622 TYR   (  29-)  D      OH
 625 HIS   (  32-)  D      ND1
 630 ALA   (  37-)  D      N
 641 PHE   (  48-)  D      N
 644 ILE   (  51-)  D      N
 657 SER   (  64-)  D      N
 674 THR   (  81-)  D      N
 696 LYS   ( 112-)  D      N
 710 HIS   ( 126-)  D      N

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.

  96 ASP   (  97-)  A   H-bonding suggests Asn; Ligand-contact
 294 ASP   (  97-)  B   H-bonding suggests Asn
 436 GLU   (  41-)  C   H-bonding suggests Gln
 492 ASP   (  97-)  C   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact

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 :   0.247
  2nd generation packing quality :  -0.863
  Ramachandran plot appearance   :   0.220
  chi-1/chi-2 rotamer normality  :   0.591
  Backbone conformation          :   0.127

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.456 (tight)
  Bond angles                    :   0.673
  Omega angle restraints         :   0.505 (tight)
  Side chain planarity           :   0.606 (tight)
  Improper dihedral distribution :   0.704
  B-factor distribution          :   0.409
  Inside/Outside distribution    :   0.973

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 : 1.95


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :   0.9
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.456 (tight)
  Bond angles                    :   0.673
  Omega angle restraints         :   0.505 (tight)
  Side chain planarity           :   0.606 (tight)
  Improper dihedral distribution :   0.704
  B-factor distribution          :   0.409
  Inside/Outside distribution    :   0.973
==============

WHAT IF
    G.Vriend,
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    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    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.