WHAT IF Check report

This file was created 2011-12-13 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 pdb1cpu.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 505 HMC   ( 503-)  A  -
 506 AGL   ( 502-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 497 GLC   ( 501-)  A  -   O4  bound to  506 AGL   ( 502-)  A  -   C1
 498 GLC   ( 504-)  A  -   O4  bound to  499 GLC   ( 505-)  A  -   C1

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

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 PCA   (   1-)  A      OE

Warning: What type of B-factor?

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

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

Crystal temperature (K) :298.000

Geometric checks

Warning: Unusual bond lengths

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

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

 484 GLU   ( 484-)  A      CA   C     1.62    4.5
 484 GLU   ( 484-)  A      CB   CG    1.39   -4.2

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.

 101 HIS   ( 101-)  A      CG   ND1  CE1 109.60    4.0
 115 CYS   ( 115-)  A      CA   CB   SG  124.54    4.4
 116 GLY   ( 116-)  A      N    CA   C   124.26    4.1
 238 GLY   ( 238-)  A      N    CA   C   125.56    4.5
 476 HIS   ( 476-)  A      CG   ND1  CE1 109.63    4.0
 484 GLU   ( 484-)  A      C    CA   CB  119.22    4.8
 491 HIS   ( 491-)  A      CG   ND1  CE1 109.68    4.1

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.

 238 GLY   ( 238-)  A    4.30

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.

 163 THR   ( 163-)  A    -3.5
 407 THR   ( 407-)  A    -2.6
 376 THR   ( 376-)  A    -2.5
 142 LYS   ( 142-)  A    -2.5
 314 THR   ( 314-)  A    -2.4
 124 ARG   ( 124-)  A    -2.3
 440 LEU   ( 440-)  A    -2.2
 329 LEU   ( 329-)  A    -2.2
  45 PRO   (  45-)  A    -2.2
  44 PRO   (  44-)  A    -2.1
 347 GLN   ( 347-)  A    -2.1
 341 SER   ( 341-)  A    -2.1
 438 LEU   ( 438-)  A    -2.1
 343 ARG   ( 343-)  A    -2.1
 466 LYS   ( 466-)  A    -2.1
  66 SER   (  66-)  A    -2.1
 243 LYS   ( 243-)  A    -2.0
 414 SER   ( 414-)  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.

   5 ASN   (   5-)  A  Poor phi/psi
  18 GLU   (  18-)  A  Poor phi/psi
  53 ASN   (  53-)  A  PRO omega poor
 102 MET   ( 102-)  A  Poor phi/psi
 124 ARG   ( 124-)  A  Poor phi/psi
 129 VAL   ( 129-)  A  PRO omega poor
 268 LYS   ( 268-)  A  Poor phi/psi
 350 ASN   ( 350-)  A  Poor phi/psi
 364 ASN   ( 364-)  A  Poor phi/psi
 376 THR   ( 376-)  A  Poor phi/psi
 380 ASN   ( 380-)  A  Poor phi/psi
 381 ASP   ( 381-)  A  Poor phi/psi
 414 SER   ( 414-)  A  Poor phi/psi
 459 ASN   ( 459-)  A  Poor phi/psi
 486 PRO   ( 486-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.400

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!

   5 ASN   (   5-)  A      0
   8 GLN   (   8-)  A      0
  10 ARG   (  10-)  A      0
  12 SER   (  12-)  A      0
  17 PHE   (  17-)  A      0
  18 GLU   (  18-)  A      0
  19 TRP   (  19-)  A      0
  30 ARG   (  30-)  A      0
  31 TYR   (  31-)  A      0
  45 PRO   (  45-)  A      0
  52 TYR   (  52-)  A      0
  53 ASN   (  53-)  A      0
  54 PRO   (  54-)  A      0
  55 PHE   (  55-)  A      0
  56 ARG   (  56-)  A      0
  58 TRP   (  58-)  A      0
  59 TRP   (  59-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  67 TYR   (  67-)  A      0
  69 LEU   (  69-)  A      0
  70 CYS   (  70-)  A      0
  73 SER   (  73-)  A      0
  75 ASN   (  75-)  A      0
And so on for a total of 231 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 : 2.376

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 306 GLY   ( 306-)  A   1.65   11
 110 GLY   ( 110-)  A   1.54   17

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].

 130 PRO   ( 130-)  A   -32.1 envelop C-alpha (-36 degrees)
 361 PRO   ( 361-)  A   100.2 envelop C-beta (108 degrees)
 374 PRO   ( 374-)  A  -117.3 half-chair C-delta/C-gamma (-126 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.

 505 HMC   ( 503-)  A      C1  <->  506 AGL   ( 502-)  A      N4     1.18    1.52  INTRA B3
 497 GLC   ( 501-)  A      O4  <->  506 AGL   ( 502-)  A      C1     0.99    1.41  INTRA B3
 497 GLC   ( 501-)  A      C4  <->  506 AGL   ( 502-)  A      C1     0.82    2.38  INTRA
 505 HMC   ( 503-)  A      C2  <->  506 AGL   ( 502-)  A      N4     0.59    2.51  INTRA
 505 HMC   ( 503-)  A      C6  <->  506 AGL   ( 502-)  A      N4     0.47    2.63  INTRA
 349 GLN   ( 349-)  A      O   <->  352 ASN   ( 352-)  A      ND2    0.24    2.46  INTRA
 325 VAL   ( 325-)  A      O   <->  329 LEU   ( 329-)  A      CD2    0.20    2.60  INTRA
 505 HMC   ( 503-)  A      C6  <->  506 AGL   ( 502-)  A      C4     0.16    3.04  INTRA
  23 ASP   (  23-)  A      O   <->   26 LEU   (  26-)  A      CD2    0.15    2.65  INTRA
 100 ASN   ( 100-)  A      ND2 <->  101 HIS   ( 101-)  A      ND1    0.13    2.87  INTRA BL
 283 GLY   ( 283-)  A      N   <->  507 HOH   ( 723 )  A      O      0.13    2.57  INTRA
 149 GLU   ( 149-)  A      N   <->  156 GLN   ( 156-)  A      OE1    0.13    2.57  INTRA BL
 142 LYS   ( 142-)  A      CG  <->  507 HOH   ( 701 )  A      O      0.10    2.70  INTRA
 331 HIS   ( 331-)  A      O   <->  398 ARG   ( 398-)  A      NH1    0.10    2.60  INTRA BL
 268 LYS   ( 268-)  A      NZ  <->  431 ASN   ( 431-)  A      O      0.09    2.61  INTRA BL
 457 LYS   ( 457-)  A      NZ  <->  495 LYS   ( 495-)  A      O      0.09    2.61  INTRA
 200 LYS   ( 200-)  A      NZ  <->  240 GLU   ( 240-)  A      OE1    0.09    2.61  INTRA
 465 ILE   ( 465-)  A      CG2 <->  466 LYS   ( 466-)  A      N      0.07    2.93  INTRA BL
 410 TYR   ( 410-)  A      N   <->  418 ALA   ( 418-)  A      O      0.07    2.63  INTRA BL
 269 TRP   ( 269-)  A      C   <->  270 ASN   ( 270-)  A      CG     0.07    3.03  INTRA
 441 GLN   ( 441-)  A      OE1 <->  443 GLY   ( 443-)  A      N      0.07    2.63  INTRA
 142 LYS   ( 142-)  A      CE  <->  155 THR   ( 155-)  A      CG2    0.06    3.14  INTRA
 170 LEU   ( 170-)  A      CD1 <->  202 MET   ( 202-)  A      SD     0.06    3.34  INTRA BL
 431 ASN   ( 431-)  A      ND2 <->  507 HOH   ( 573 )  A      O      0.06    2.64  INTRA BL
 258 TYR   ( 258-)  A      CE2 <->  280 TRP   ( 280-)  A      NE1    0.06    3.04  INTRA BL
 216 ASN   ( 216-)  A      N   <->  507 HOH   ( 642 )  A      O      0.05    2.65  INTRA
 231 TYR   ( 231-)  A      CD2 <->  293 LEU   ( 293-)  A      CG     0.05    3.15  INTRA
 460 GLY   ( 460-)  A      C   <->  496 LEU   ( 496-)  A      CD1    0.05    3.15  INTRA
 462 CYS   ( 462-)  A      SG  <->  466 LYS   ( 466-)  A      CG     0.05    3.35  INTRA
 305 HIS   ( 305-)  A      NE2 <->  507 HOH   ( 562 )  A      O      0.04    2.66  INTRA BL
 494 SER   ( 494-)  A      N   <->  495 LYS   ( 495-)  A      N      0.04    2.56  INTRA BL
 195 ARG   ( 195-)  A      CA  <->  231 TYR   ( 231-)  A      CE1    0.03    3.17  INTRA
 480 SER   ( 480-)  A      C   <->  482 SER   ( 482-)  A      N      0.03    2.87  INTRA BL
 458 ILE   ( 458-)  A      N   <->  461 ASN   ( 461-)  A      O      0.03    2.67  INTRA
 314 THR   ( 314-)  A      CG2 <->  316 TRP   ( 316-)  A      CD1    0.03    3.17  INTRA BL
 346 ARG   ( 346-)  A      NH1 <->  507 HOH   ( 603 )  A      O      0.02    2.68  INTRA
 407 THR   ( 407-)  A      O   <->  420 GLY   ( 420-)  A      N      0.02    2.68  INTRA BL
 369 GLU   ( 369-)  A      O   <->  380 ASN   ( 380-)  A      ND2    0.02    2.68  INTRA BL
 194 PHE   ( 194-)  A      O   <->  231 TYR   ( 231-)  A      CD1    0.02    2.78  INTRA
 302 GLN   ( 302-)  A      N   <->  303 ARG   ( 303-)  A      N      0.02    2.58  INTRA BL
 392 ARG   ( 392-)  A      NH2 <->  507 HOH   ( 736 )  A      O      0.02    2.68  INTRA
 308 GLY   ( 308-)  A      N   <->  309 GLY   ( 309-)  A      N      0.01    2.59  INTRA B3
  20 ARG   (  20-)  A      N   <->  507 HOH   ( 547 )  A      O      0.01    2.69  INTRA BL
 436 PHE   ( 436-)  A      O   <->  479 ILE   ( 479-)  A      N      0.01    2.69  INTRA BL
 267 ARG   ( 267-)  A      N   <->  268 LYS   ( 268-)  A      N      0.01    2.59  INTRA BL

Packing, accessibility and threading

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.

  72 ARG   (  72-)  A      -7.06
   2 TYR   (   2-)  A      -6.27
  52 TYR   (  52-)  A      -6.08
 343 ARG   ( 343-)  A      -6.00
   8 GLN   (   8-)  A      -5.95
 118 TYR   ( 118-)  A      -5.81
   7 GLN   (   7-)  A      -5.52
 284 TRP   ( 284-)  A      -5.49
 269 TRP   ( 269-)  A      -5.45
  88 ASN   (  88-)  A      -5.32
 279 ASN   ( 279-)  A      -5.32
 302 GLN   ( 302-)  A      -5.31
 303 ARG   ( 303-)  A      -5.29
 142 LYS   ( 142-)  A      -5.29
 270 ASN   ( 270-)  A      -5.25
  53 ASN   (  53-)  A      -5.23
  30 ARG   (  30-)  A      -5.22
 237 LEU   ( 237-)  A      -5.02

Warning: Abnormal packing environment for sequential residues

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

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

 269 TRP   ( 269-)  A       271 - GLY    271- ( A)         -4.97

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.

 507 HOH   ( 759 )  A      O      8.87   64.22   55.56

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.

 507 HOH   ( 760 )  A      O
Bound group on Asn; dont flip  461 ASN  ( 461-) A
Bound to:  500 NAG  ( 497-) A
Marked this atom as acceptor  504  CL  ( 499-) A     CL
Strange metal coordination for HIS 201

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.

  15 HIS   (  15-)  A
 105 ASN   ( 105-)  A
 349 GLN   ( 349-)  A
 350 ASN   ( 350-)  A
 363 ASN   ( 363-)  A
 415 ASN   ( 415-)  A

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   8 GLN   (   8-)  A      N
  59 TRP   (  59-)  A      N
  87 ASN   (  87-)  A      ND2
 101 HIS   ( 101-)  A      N
 142 LYS   ( 142-)  A      N
 193 GLY   ( 193-)  A      N
 195 ARG   ( 195-)  A      NH2
 273 LYS   ( 273-)  A      N
 281 GLY   ( 281-)  A      N
 295 PHE   ( 295-)  A      N
 299 HIS   ( 299-)  A      NE2
 300 ASP   ( 300-)  A      N
 306 GLY   ( 306-)  A      N
 316 TRP   ( 316-)  A      N
 316 TRP   ( 316-)  A      NE1
 337 ARG   ( 337-)  A      NH2
 344 TRP   ( 344-)  A      N
 353 ASP   ( 353-)  A      N
 357 TRP   ( 357-)  A      N
 370 VAL   ( 370-)  A      N
 382 TRP   ( 382-)  A      NE1
 434 TRP   ( 434-)  A      N
 462 CYS   ( 462-)  A      N
 497 GLC   ( 501-)  A      O3

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.

 201 HIS   ( 201-)  A      NE2

Warning: Unusual ion packing

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

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

 503  CA   ( 498-)  A     0.59   0.82 Scores about as good as NA

Warning: Possible wrong residue type

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

 240 GLU   ( 240-)  A   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 :  -1.044
  2nd generation packing quality :  -1.529
  Ramachandran plot appearance   :  -1.629
  chi-1/chi-2 rotamer normality  :  -2.400
  Backbone conformation          :  -1.174

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.340 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   0.432 (tight)
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.657
  B-factor distribution          :   0.839
  Inside/Outside distribution    :   1.005

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.340 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   0.432 (tight)
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.657
  B-factor distribution          :   0.839
  Inside/Outside distribution    :   1.005
==============

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.