WHAT IF Check report

This file was created 2011-12-17 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 pdb3qy1.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 : 0.749
CA-only RMS fit for the two chains : 0.449

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

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

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'.

 326 GLU   ( 112-)  B      CG
 326 GLU   ( 112-)  B      CD
 326 GLU   ( 112-)  B      OE1
 326 GLU   ( 112-)  B      OE2

Warning: B-factors outside the range 0.0 - 100.0

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

  14 LYS   (  16-)  A    High
  25 GLU   (  27-)  A    High
  26 LYS   (  28-)  A    High
  29 GLN   (  31-)  A    High
  31 GLN   (  33-)  A    High
 216 LYS   (   2-)  B    High
 230 LYS   (  16-)  B    High
 234 GLU   (  20-)  B    High
 235 GLU   (  21-)  B    High
 236 ASP   (  22-)  B    High
 241 GLU   (  27-)  B    High
 242 LYS   (  28-)  B    High
 245 GLN   (  31-)  B    High

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: 18

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

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.

 265 ARG   (  51-)  B

Warning: Tyrosine convention problem

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

 179 TYR   ( 181-)  A
 395 TYR   ( 181-)  B

Warning: Phenylalanine convention problem

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

  24 PHE   (  26-)  A
  35 PHE   (  37-)  A
 240 PHE   (  26-)  B
 251 PHE   (  37-)  B

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.

  19 GLU   (  21-)  A
  57 GLU   (  59-)  A
  87 GLU   (  89-)  A
 273 GLU   (  59-)  B
 303 GLU   (  89-)  B

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: 0.586
RMS-deviation in bond distances: 0.014

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

 |  0.997697  0.000839  0.000282|
 |  0.000839  0.996831 -0.000082|
 |  0.000282 -0.000082  0.995347|
Proposed new scale matrix

 |  0.008696 -0.000007  0.003779|
 | -0.000017  0.020803  0.000002|
 | -0.000004  0.000001  0.013677|
With corresponding cell

    A    = 114.982  B   =  48.070  C    =  79.714
    Alpha=  90.047  Beta= 113.473  Gamma=  89.904

The CRYST1 cell dimensions

    A    = 115.252  B   =  48.223  C    =  80.072
    Alpha=  90.000  Beta= 113.450  Gamma=  90.000

Variance: 172.624
(Under-)estimated Z-score: 9.683

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.

  19 GLU   (  21-)  A
  57 GLU   (  59-)  A
  87 GLU   (  89-)  A
 265 ARG   (  51-)  B
 273 GLU   (  59-)  B
 303 GLU   (  89-)  B

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.

 330 ILE   ( 116-)  B    -2.4
 114 ILE   ( 116-)  A    -2.3

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.

  65 ALA   (  67-)  A  Poor phi/psi
  87 GLU   (  89-)  A  Poor phi/psi
 183 ASP   ( 185-)  A  Poor phi/psi
 190 ASP   ( 192-)  A  Poor phi/psi
 281 ALA   (  67-)  B  Poor phi/psi
 303 GLU   (  89-)  B  Poor phi/psi
 399 ASP   ( 185-)  B  Poor phi/psi
 406 ASP   ( 192-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.774

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 208 SER   ( 210-)  A    0.35
 424 SER   ( 210-)  B    0.35
 122 ARG   ( 124-)  A    0.36
   7 SER   (   9-)  A    0.36
 164 SER   ( 166-)  A    0.36
 211 SER   ( 213-)  A    0.36
 427 SER   ( 213-)  B    0.37
 229 SER   (  15-)  B    0.39
 380 SER   ( 166-)  B    0.39

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!

  29 GLN   (  31-)  A      0
  42 ASP   (  44-)  A      0
  43 SER   (  45-)  A      0
  44 ARG   (  46-)  A      0
  63 ASN   (  65-)  A      0
  64 VAL   (  66-)  A      0
  65 ALA   (  67-)  A      0
  71 THR   (  73-)  A      0
  84 ASP   (  86-)  A      0
  89 GLU   (  91-)  A      0
  97 SER   (  99-)  A      0
  99 CYS   ( 101-)  A      0
 107 GLU   ( 109-)  A      0
 108 ASN   ( 110-)  A      0
 110 GLU   ( 112-)  A      0
 113 LEU   ( 115-)  A      0
 135 MET   ( 137-)  A      0
 177 TRP   ( 179-)  A      0
 189 LEU   ( 191-)  A      0
 190 ASP   ( 192-)  A      0
 191 VAL   ( 193-)  A      0
 193 ALA   ( 195-)  A      0
 194 THR   ( 196-)  A      0
 195 ASN   ( 197-)  A      0
 214 TYR   ( 216-)  A      0
And so on for a total of 128 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 : 3.611

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.

 167 LYS   ( 169-)  A      NZ  <->  434 HOH   ( 381 )  A      O      0.14    2.56  INTRA BF
 384 ARG   ( 170-)  B      NH2 <->  386 GLN   ( 172-)  B      OE1    0.14    2.56  INTRA BL
 146 GLU   ( 148-)  A      OE2 <->  187 ARG   ( 189-)  A      NH1    0.14    2.56  INTRA BF
 362 GLU   ( 148-)  B      OE2 <->  403 ARG   ( 189-)  B      NH1    0.13    2.57  INTRA
  90 HIS   (  92-)  A      ND1 <->  175 HIS   ( 177-)  A      NE2    0.11    2.89  INTRA BL
 306 HIS   (  92-)  B      ND1 <->  391 HIS   ( 177-)  B      NE2    0.11    2.89  INTRA BL
 168 ARG   ( 170-)  A      NH2 <->  170 GLN   ( 172-)  A      OE1    0.09    2.61  INTRA
 344 HIS   ( 130-)  B      NE2 <->  367 GLU   ( 153-)  B      OE2    0.07    2.63  INTRA BL
 128 HIS   ( 130-)  A      NE2 <->  151 GLU   ( 153-)  A      OE2    0.06    2.64  INTRA BL
  34 ARG   (  36-)  A      NH1 <->  216 LYS   (   2-)  B      O      0.06    2.64  INTRA BF
  70 HIS   (  72-)  A      ND1 <->  434 HOH   ( 225 )  A      O      0.06    2.64  INTRA BL
 286 HIS   (  72-)  B      ND1 <->  435 HOH   ( 227 )  B      O      0.05    2.65  INTRA BL
  34 ARG   (  36-)  A      NH2 <->  434 HOH   ( 240 )  A      O      0.05    2.65  INTRA BF
  40 CYS   (  42-)  A      SG  <->   41 SER   (  43-)  A      N      0.04    3.16  INTRA BL
 256 CYS   (  42-)  B      SG  <->  257 SER   (  43-)  B      N      0.04    3.16  INTRA BL
 391 HIS   ( 177-)  B      ND1 <->  435 HOH   ( 295 )  B      O      0.04    2.66  INTRA BL
  65 ALA   (  67-)  A      C   <->   66 ASN   (  68-)  A      CG     0.04    3.06  INTRA BL
  27 LEU   (  29-)  A      O   <->  260 ARG   (  46-)  B      NH2    0.04    2.66  INTRA BF
 281 ALA   (  67-)  B      C   <->  282 ASN   (  68-)  B      CG     0.03    3.07  INTRA BL
 204 HIS   ( 206-)  A      ND1 <->  434 HOH   ( 412 )  A      O      0.02    2.68  INTRA BF
 338 ARG   ( 124-)  B      NE  <->  435 HOH   ( 379 )  B      O      0.01    2.69  INTRA
 108 ASN   ( 110-)  A      N   <->  109 PRO   ( 111-)  A      CD     0.01    2.99  INTRA BL
 324 ASN   ( 110-)  B      N   <->  325 PRO   ( 111-)  B      CD     0.01    2.99  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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 247 GLN   (  33-)  B      -6.86
  31 GLN   (  33-)  A      -6.74
 260 ARG   (  46-)  B      -6.58
  44 ARG   (  46-)  A      -6.55
 158 HIS   ( 160-)  A      -5.64
 374 HIS   ( 160-)  B      -5.60
 110 GLU   ( 112-)  A      -5.56
 245 GLN   (  31-)  B      -5.53
 235 GLU   (  21-)  B      -5.06
 107 GLU   ( 109-)  A      -5.04
 323 GLU   ( 109-)  B      -5.03
  19 GLU   (  21-)  A      -5.00

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

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.

 386 GLN   ( 172-)  B   -2.73
 170 GLN   ( 172-)  A   -2.68

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

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.

 434 HOH   ( 226 )  A      O     38.65  -14.57  -10.70
 434 HOH   ( 277 )  A      O     37.37   -5.23   -8.34
 434 HOH   ( 287 )  A      O    -13.89  -34.13  -13.97
 434 HOH   ( 317 )  A      O     14.91  -36.44    3.17
 434 HOH   ( 321 )  A      O     12.09   -7.04  -27.91
 434 HOH   ( 390 )  A      O    -17.29  -33.40  -11.92
 434 HOH   ( 418 )  A      O     16.72   -6.88    5.13
 434 HOH   ( 434 )  A      O    -12.61  -10.00  -50.00
 434 HOH   ( 449 )  A      O      9.03   10.18    0.11
 434 HOH   ( 458 )  A      O     30.38    5.62   -4.20
 435 HOH   ( 248 )  B      O    -24.12   -3.59   -6.59
 435 HOH   ( 265 )  B      O    -16.94  -12.85   -5.86
 435 HOH   ( 349 )  B      O     29.11   -4.40   -0.34
 435 HOH   ( 383 )  B      O     30.99  -31.12   -7.28
 435 HOH   ( 393 )  B      O     -0.28   10.67  -10.73
 435 HOH   ( 444 )  B      O     -1.37    9.87  -20.02

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.

 434 HOH   ( 434 )  A      O
 434 HOH   ( 448 )  A      O
 435 HOH   ( 398 )  B      O
 435 HOH   ( 399 )  B      O
 435 HOH   ( 439 )  B      O
Metal-coordinating Histidine residue  96 fixed to   1
Metal-coordinating Histidine residue 312 fixed to   1

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.

 201 ASN   ( 203-)  A
 324 ASN   ( 110-)  B

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.

  71 THR   (  73-)  A      N
 161 ILE   ( 163-)  A      N
 219 ASP   (   5-)  B      N
 240 PHE   (  26-)  B      N
 265 ARG   (  51-)  B      NE
 265 ARG   (  51-)  B      NH1
 274 LEU   (  60-)  B      N
 338 ARG   ( 124-)  B      NH1
 377 ILE   ( 163-)  B      N
 408 THR   ( 194-)  B      N
Only metal coordination for   96 HIS  (  98-) A      NE2
Only metal coordination for  312 HIS  (  98-) B      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.

  20 ASP   (  22-)  A      OD2

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 434 HOH   ( 247 )  A      O  0.92  K  4
 434 HOH   ( 360 )  A      O  1.06  K  4 Ion-B
 434 HOH   ( 418 )  A      O  0.94  K  4 Ion-B
 435 HOH   ( 266 )  B      O  0.93  K  4
 435 HOH   ( 279 )  B      O  1.08  K  4
 435 HOH   ( 319 )  B      O  0.89  K  5

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 123 ASP   ( 125-)  A   H-bonding suggests Asn

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 :   0.547
  2nd generation packing quality :  -1.248
  Ramachandran plot appearance   :   0.801
  chi-1/chi-2 rotamer normality  :  -0.774
  Backbone conformation          :  -0.227

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.586 (tight)
  Bond angles                    :   0.781
  Omega angle restraints         :   0.656 (tight)
  Side chain planarity           :   1.122
  Improper dihedral distribution :   0.884
  B-factor distribution          :   0.924
  Inside/Outside distribution    :   0.974

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 : 1.54


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -1.3
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.586 (tight)
  Bond angles                    :   0.781
  Omega angle restraints         :   0.656 (tight)
  Side chain planarity           :   1.122
  Improper dihedral distribution :   0.884
  B-factor distribution          :   0.924
  Inside/Outside distribution    :   0.974
==============

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.