WHAT IF Check report

This file was created 2011-12-28 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 pdb1i0h.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 : 0.677
CA-only RMS fit for the two chains : 0.599

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

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  29 LYS   (  29-)  A  -   CD
  29 LYS   (  29-)  A  -   CE
  29 LYS   (  29-)  A  -   NZ
  43 GLU   (  43-)  A  -   CG
  43 GLU   (  43-)  A  -   CD
  43 GLU   (  43-)  A  -   OE1
  43 GLU   (  43-)  A  -   OE2
  47 GLU   (  47-)  A  -   CG
  47 GLU   (  47-)  A  -   CD
  47 GLU   (  47-)  A  -   OE1
  47 GLU   (  47-)  A  -   OE2
  50 ASN   (  50-)  A  -   CG
  50 ASN   (  50-)  A  -   OD1
  50 ASN   (  50-)  A  -   ND2
  54 GLU   (  54-)  A  -   CG
  54 GLU   (  54-)  A  -   CD
  54 GLU   (  54-)  A  -   OE1
  54 GLU   (  54-)  A  -   OE2
  56 LEU   (  56-)  A  -   CG
  56 LEU   (  56-)  A  -   CD1
  56 LEU   (  56-)  A  -   CD2
  59 LYS   (  59-)  A  -   CG
  59 LYS   (  59-)  A  -   CD
  59 LYS   (  59-)  A  -   CE
  59 LYS   (  59-)  A  -   NZ
And so on for a total of 88 lines.

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: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 122 SER   ( 122-)  A    0.50
 206 SER   (   1-)  B    0.50

Warning: What type of B-factor?

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

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

Crystal temperature (K) :110.000

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 : 6.46

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: Tyrosine convention problem

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

 378 TYR   ( 173-)  B

Warning: Phenylalanine convention problem

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

 177 PHE   ( 177-)  A
 321 PHE   ( 116-)  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.

  54 GLU   (  54-)  A
 187 GLU   ( 187-)  A
 358 GLU   ( 153-)  B
 392 GLU   ( 187-)  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: 0.232
RMS-deviation in bond distances: 0.005

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.

  26 HIS   (  26-)  A      CG   ND1  CE1 109.88    4.3
  27 HIS   (  27-)  A      CA   CB   CG  117.85    4.1
  78 HIS   (  78-)  A      CG   ND1  CE1 109.75    4.1
  81 HIS   (  81-)  A      CA   CB   CG  109.78   -4.0
 112 PHE   ( 112-)  A      CA   CB   CG  109.79   -4.0
 171 HIS   ( 171-)  A      CG   ND1  CE1 110.18    4.6
 283 HIS   (  78-)  B      CG   ND1  CE1 109.73    4.1
 286 HIS   (  81-)  B      CA   CB   CG  109.66   -4.1
 376 HIS   ( 171-)  B      CA   CB   CG  117.97    4.2
 376 HIS   ( 171-)  B      CG   ND1  CE1 110.60    5.0
 409 LYS   ( 204-)  B     -C    N    CA  129.16    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.

  54 GLU   (  54-)  A
 187 GLU   ( 187-)  A
 358 GLU   ( 153-)  B
 392 GLU   ( 187-)  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.

  16 PRO   (  16-)  A    -2.8
 221 PRO   (  16-)  B    -2.8
 164 MET   ( 164-)  A    -2.1
 369 MET   ( 164-)  B    -2.1

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  15 GLU   (  15-)  A  PRO omega poor
 130 TRP   ( 130-)  A  omega poor
 135 GLY   ( 135-)  A  Poor phi/psi
 145 ASN   ( 145-)  A  Poor phi/psi
 155 ILE   ( 155-)  A  omega poor
 168 VAL   ( 168-)  A  omega poor
 178 GLN   ( 178-)  A  Poor phi/psi
 210 PRO   (   5-)  B  omega poor
 220 GLU   (  15-)  B  PRO omega poor
 253 PHE   (  48-)  B  Poor phi/psi
 335 TRP   ( 130-)  B  omega poor
 341 ASP   ( 136-)  B  omega poor
 350 ASN   ( 145-)  B  Poor phi/psi
 373 VAL   ( 168-)  B  omega poor
 383 GLN   ( 178-)  B  Poor phi/psi
 409 LYS   ( 204-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.381

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.

  82 SER   (  82-)  A    0.36
 287 SER   (  82-)  B    0.37

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   9 TYR   (   9-)  A      0
  14 LEU   (  14-)  A      0
  15 GLU   (  15-)  A      0
  17 HIS   (  17-)  A      0
  28 THR   (  28-)  A      0
  30 HIS   (  30-)  A      0
  45 LEU   (  45-)  A      0
  59 LYS   (  59-)  A      0
  89 LYS   (  89-)  A      0
  90 LYS   (  90-)  A      0
  94 LEU   (  94-)  A      0
  95 GLN   (  95-)  A      0
 123 ARG   ( 123-)  A      0
 124 PHE   ( 124-)  A      0
 126 SER   ( 126-)  A      0
 128 TRP   ( 128-)  A      0
 130 TRP   ( 130-)  A      0
 134 LYS   ( 134-)  A      0
 136 ASP   ( 136-)  A      0
 144 ALA   ( 144-)  A      0
 145 ASN   ( 145-)  A      0
 146 GLN   ( 146-)  A      0
 151 MET   ( 151-)  A      0
 156 SER   ( 156-)  A      0
 158 ALA   ( 158-)  A      0
And so on for a total of 136 lines.

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

   8 PRO   (   8-)  A    48.5 half-chair C-delta/C-gamma (54 degrees)
 213 PRO   (   8-)  B    37.8 envelop C-delta (36 degrees)
 221 PRO   (  16-)  B   -64.8 envelop C-beta (-72 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

  54 GLU   (  54-)  A      OE2 <->  415 HOH   ( 333 )  A      O      0.34    2.06  INTRA BL
 260 GLU   (  55-)  B      CG  <->  264 LYS   (  59-)  B      CE     0.26    2.94  INTRA
 339 LYS   ( 134-)  B      NZ  <->  416 HOH   ( 285 )  B      O      0.23    2.47  INTRA
 205 LYS   ( 205-)  A      NZ  <->  415 HOH   ( 417 )  A      O      0.23    2.47  INTRA
 236 HIS   (  31-)  B      ND1 <->  290 TRP   (  85-)  B      NE1    0.13    2.87  INTRA BL
  31 HIS   (  31-)  A      NE2 <->   78 HIS   (  78-)  A      ND1    0.13    2.87  INTRA BL
 221 PRO   (  16-)  B      O   <->  381 LYS   ( 176-)  B      NZ     0.11    2.59  INTRA BL
 236 HIS   (  31-)  B      NE2 <->  283 HIS   (  78-)  B      ND1    0.10    2.90  INTRA BL
 181 ARG   ( 181-)  A      N   <->  182 PRO   ( 182-)  A      CD     0.10    2.90  INTRA BL
 254 ALA   (  49-)  B      O   <->  416 HOH   ( 382 )  B      O      0.10    2.30  INTRA
 187 GLU   ( 187-)  A      OE2 <->  415 HOH   ( 460 )  A      O      0.09    2.31  INTRA
  46 PRO   (  46-)  A      O   <->   50 ASN   (  50-)  A      ND2    0.09    2.61  INTRA
 134 LYS   ( 134-)  A      O   <->  136 ASP   ( 136-)  A      N      0.08    2.62  INTRA
 309 ARG   ( 104-)  B      NE  <->  310 ASP   ( 105-)  B      OD1    0.08    2.62  INTRA
 134 LYS   ( 134-)  A      NZ  <->  415 HOH   ( 449 )  A      O      0.07    2.63  INTRA
 113 LYS   ( 113-)  A      NZ  <->  415 HOH   ( 434 )  A      O      0.07    2.63  INTRA
  31 HIS   (  31-)  A      ND1 <->   85 TRP   (  85-)  A      NE1    0.05    2.95  INTRA BL
 386 ARG   ( 181-)  B      N   <->  387 PRO   ( 182-)  B      CD     0.05    2.95  INTRA BL
  25 ILE   (  25-)  A      CD1 <->  383 GLN   ( 178-)  B      NE2    0.04    3.06  INTRA BL
 295 LYS   (  90-)  B      O   <->  416 HOH   ( 400 )  B      O      0.03    2.37  INTRA
 246 ALA   (  41-)  B      O   <->  272 LYS   (  67-)  B      NZ     0.02    2.68  INTRA BL
 315 ASP   ( 110-)  B      OD2 <->  416 HOH   ( 423 )  B      O      0.02    2.38  INTRA
 210 PRO   (   5-)  B      O   <->  232 HIS   (  27-)  B      NE2    0.02    2.68  INTRA BL
 113 LYS   ( 113-)  A      NZ  <->  415 HOH   ( 341 )  A      O      0.01    2.69  INTRA BL
 328 ARG   ( 123-)  B      O   <->  386 ARG   ( 181-)  B      NH1    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

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.

 267 GLN   (  62-)  B      -5.59
  62 GLN   (  62-)  A      -5.54
 329 PHE   ( 124-)  B      -5.13
 124 PHE   ( 124-)  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.

 377 ALA   ( 172-)  B   -2.94
 172 ALA   ( 172-)  A   -2.89
 212 LEU   (   7-)  B   -2.71

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

  11 TYR   (  11-)  A     -   14 LEU   (  14-)  A        -1.75

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.

 415 HOH   ( 374 )  A      O     11.35   46.61   -7.89
 415 HOH   ( 378 )  A      O      2.99   44.47    7.05
 415 HOH   ( 380 )  A      O      0.04   47.42    9.07
 415 HOH   ( 381 )  A      O      1.13   42.52    7.53
 415 HOH   ( 382 )  A      O      1.95   40.97    5.47
 416 HOH   ( 311 )  B      O     -2.43    7.05   51.81
 416 HOH   ( 381 )  B      O     -5.38   28.59   32.54
 416 HOH   ( 404 )  B      O     -5.92   29.70   46.65
 416 HOH   ( 406 )  B      O     -7.73   27.96   43.23
 416 HOH   ( 420 )  B      O     -2.58    5.73   40.24
 416 HOH   ( 442 )  B      O      7.62   20.70   58.57

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.

  73 ASN   (  73-)  A
  74 ASN   (  74-)  A
 350 ASN   ( 145-)  B
 384 ASN   ( 179-)  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.

   9 TYR   (   9-)  A      N
  11 TYR   (  11-)  A      OH
  50 ASN   (  50-)  A      N
  54 GLU   (  54-)  A      N
 108 SER   ( 108-)  A      N
 127 GLY   ( 127-)  A      N
 159 SER   ( 159-)  A      N
 167 ASP   ( 167-)  A      N
 214 TYR   (   9-)  B      N
 236 HIS   (  31-)  B      ND1
 290 TRP   (  85-)  B      NE1
 313 SER   ( 108-)  B      N
 332 GLY   ( 127-)  B      N
 372 ASP   ( 167-)  B      N
 410 LYS   ( 205-)  B      N
Only metal coordination for   26 HIS  (  26-) A      NE2
Only metal coordination for   81 HIS  (  81-) A      NE2
Only metal coordination for  167 ASP  ( 167-) A      OD2
Only metal coordination for  171 HIS  ( 171-) A      NE2
Only metal coordination for  231 HIS  (  26-) B      NE2
Only metal coordination for  286 HIS  (  81-) B      NE2
Only metal coordination for  372 ASP  ( 167-) B      OD2
Only metal coordination for  376 HIS  ( 171-) B      NE2

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.

 415 HOH   ( 251 )  A      O  1.04  K  4
 415 HOH   ( 285 )  A      O  1.05  K  4
 415 HOH   ( 298 )  A      O  1.04  K  4
 416 HOH   ( 238 )  B      O  0.98  K  4
 416 HOH   ( 319 )  B      O  0.96  K  4

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.

 136 ASP   ( 136-)  A   H-bonding suggests Asn; but Alt-Rotamer
 358 GLU   ( 153-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.284
  2nd generation packing quality :  -1.692
  Ramachandran plot appearance   :  -0.445
  chi-1/chi-2 rotamer normality  :  -0.381
  Backbone conformation          :  -1.313

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.232 (tight)
  Bond angles                    :   0.781
  Omega angle restraints         :   1.164
  Side chain planarity           :   0.782
  Improper dihedral distribution :   0.675
  Inside/Outside distribution    :   0.881

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 : 1.35


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.232 (tight)
  Bond angles                    :   0.781
  Omega angle restraints         :   1.164
  Side chain planarity           :   0.782
  Improper dihedral distribution :   0.675
  Inside/Outside distribution    :   0.881
==============

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.