WHAT IF Check report

This file was created 2012-01-29 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 pdb3bsh.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.

 408 BGC   (4000-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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

Warning: 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.

   2 GLN   (   2-)  A    0.52
  22 MET   (  22-)  A    0.52
  53 MET   (  53-)  A    0.54
  64 LYS   (  64-)  A    0.51
  73 SER   (  73-)  A    0.49
  84 GLN   (  84-)  A    0.48
 107 ILE   ( 107-)  A    0.55
 160 GLU   ( 160-)  A    0.50
 171 ASP   ( 171-)  A    0.55
 183 ARG   ( 183-)  A    0.50
 210 MET   ( 210-)  A    0.54
 230 VAL   ( 230-)  A    0.53
 235 LYS   ( 235-)  A    0.50
 298 MET   ( 298-)  A    0.54
 317 PRO   ( 317-)  A    0.16
 345 ARG   ( 345-)  A    0.60

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) :100.000

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 : 13.35

Note: B-factor plot

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

Chain identifier: A

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.

 156 ARG   ( 156-)  A
 345 ARG   ( 345-)  A

Warning: Tyrosine convention problem

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

  98 TYR   (  98-)  A
 185 TYR   ( 185-)  A

Warning: Phenylalanine convention problem

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

 301 PHE   ( 301-)  A
 390 PHE   ( 390-)  A

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 155 ASP   ( 155-)  A
 221 ASP   ( 221-)  A
 369 ASP   ( 369-)  A

Geometric checks

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.

 155 ASP   ( 155-)  A
 156 ARG   ( 156-)  A
 221 ASP   ( 221-)  A
 345 ARG   ( 345-)  A
 369 ASP   ( 369-)  A

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.

  98 TYR   (  98-)  A    5.32
  12 SER   (  12-)  A    4.65
 195 ASP   ( 195-)  A    4.47
  11 GLU   (  11-)  A    4.43
 187 PRO   ( 187-)  A    4.41
  99 LYS   (  99-)  A    4.33
 328 PHE   ( 328-)  A    4.30
 178 ARG   ( 178-)  A    4.26
 311 ALA   ( 311-)  A    4.21
 313 ILE   ( 313-)  A    4.12
 257 ALA   ( 257-)  A    4.09

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.680

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.556

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.

 395 HIS   ( 395-)  A    -2.7
 397 ASN   ( 397-)  A    -2.6
 181 PHE   ( 181-)  A    -2.5
 294 SER   ( 294-)  A    -2.5
 299 TRP   ( 299-)  A    -2.5
 386 ILE   ( 386-)  A    -2.4
 201 LEU   ( 201-)  A    -2.4
  10 TRP   (  10-)  A    -2.4
 238 GLY   ( 238-)  A    -2.4
 279 TRP   ( 279-)  A    -2.3
 197 THR   ( 197-)  A    -2.3
 244 MET   ( 244-)  A    -2.3
 305 LYS   ( 305-)  A    -2.2
 387 PRO   ( 387-)  A    -2.2
 199 PRO   ( 199-)  A    -2.2
  55 GLY   (  55-)  A    -2.2
   8 PHE   (   8-)  A    -2.1
 205 GLU   ( 205-)  A    -2.0
 155 ASP   ( 155-)  A    -2.0
 382 VAL   ( 382-)  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.

   2 GLN   (   2-)  A  Poor phi/psi
   8 PHE   (   8-)  A  Poor phi/psi
 111 GLY   ( 111-)  A  Poor phi/psi
 114 ASP   ( 114-)  A  Poor phi/psi
 117 LEU   ( 117-)  A  Poor phi/psi
 197 THR   ( 197-)  A  Poor phi/psi
 198 SER   ( 198-)  A  Poor phi/psi
 201 LEU   ( 201-)  A  Poor phi/psi
 216 GLY   ( 216-)  A  Poor phi/psi
 238 GLY   ( 238-)  A  Poor phi/psi
 289 ASN   ( 289-)  A  Poor phi/psi
 294 SER   ( 294-)  A  Poor phi/psi
 315 THR   ( 315-)  A  Poor phi/psi
 324 TYR   ( 324-)  A  Poor phi/psi
 361 GLY   ( 361-)  A  Poor phi/psi
 369 ASP   ( 369-)  A  Poor phi/psi
 371 LYS   ( 371-)  A  Poor phi/psi
 383 GLY   ( 383-)  A  Poor phi/psi
 387 PRO   ( 387-)  A  Poor phi/psi
 393 SER   ( 393-)  A  Poor phi/psi
 394 ALA   ( 394-)  A  Poor phi/psi
 395 HIS   ( 395-)  A  Poor phi/psi
 397 ASN   ( 397-)  A  Poor phi/psi
 398 ASP   ( 398-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.015

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

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

chi-1/chi-2 correlation Z-score : -4.015

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.

  38 VAL   (  38-)  A    0.38

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!

   8 PHE   (   8-)  A      0
  16 SER   (  16-)  A      0
  43 PRO   (  43-)  A      0
  44 SER   (  44-)  A      0
  45 HIS   (  45-)  A      0
  50 GLU   (  50-)  A      0
  52 TYR   (  52-)  A      0
  53 MET   (  53-)  A      0
  54 PRO   (  54-)  A      0
  56 ARG   (  56-)  A      0
  60 ILE   (  60-)  A      0
  65 TYR   (  65-)  A      0
  81 LYS   (  81-)  A      0
  90 VAL   (  90-)  A      0
  91 ILE   (  91-)  A      0
  92 ASN   (  92-)  A      0
  93 HIS   (  93-)  A      0
  98 TYR   (  98-)  A      0
 102 ARG   ( 102-)  A      0
 104 ILE   ( 104-)  A      0
 105 ALA   ( 105-)  A      0
 106 CYS   ( 106-)  A      0
 114 ASP   ( 114-)  A      0
 116 ARG   ( 116-)  A      0
 117 LEU   ( 117-)  A      0
And so on for a total of 163 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 : 1.361

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!

 361 GLY   ( 361-)  A   1.53   18
 196 GLY   ( 196-)  A   1.51   33

Warning: Unusual peptide bond conformations

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

  98 TYR   (  98-)  A   1.54

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.

 341 ALA   ( 341-)  A      O   <->  345 ARG   ( 345-)  A      N      0.35    2.35  INTRA BL
  45 HIS   (  45-)  A      ND1 <->   56 ARG   (  56-)  A      N      0.31    2.69  INTRA BL
 339 LEU   ( 339-)  A      O   <->  342 ILE   ( 342-)  A      N      0.31    2.39  INTRA BL
 114 ASP   ( 114-)  A      OD2 <->  116 ARG   ( 116-)  A      NE     0.27    2.43  INTRA BL
 117 LEU   ( 117-)  A      N   <->  160 GLU   ( 160-)  A      OE1    0.26    2.44  INTRA BL
 183 ARG   ( 183-)  A      NH1 <->  206 VAL   ( 206-)  A      CG1    0.25    2.85  INTRA BL
  53 MET   (  53-)  A      N   <->   54 PRO   (  54-)  A      CD     0.24    2.76  INTRA BL
 143 ASP   ( 143-)  A      CG  <->  144 PHE   ( 144-)  A      N      0.24    2.76  INTRA BL
  92 ASN   (  92-)  A      ND2 <->   93 HIS   (  93-)  A      ND1    0.19    2.81  INTRA BL
 345 ARG   ( 345-)  A      NH1 <->  403 GLU   ( 403-)  A      OE2    0.19    2.51  INTRA BL
 162 LYS   ( 162-)  A      O   <->  166 LEU   ( 166-)  A      N      0.18    2.52  INTRA BL
 307 MET   ( 307-)  A      CE  <->  335 GLN   ( 335-)  A      NE2    0.17    2.93  INTRA BL
 316 HIS   ( 316-)  A      NE2 <->  364 TYR   ( 364-)  A      OH     0.16    2.54  INTRA BL
 289 ASN   ( 289-)  A      OD1 <->  292 THR   ( 292-)  A      N      0.15    2.55  INTRA BL
 304 ASP   ( 304-)  A      OD2 <->  305 LYS   ( 305-)  A      NZ     0.15    2.55  INTRA BL
  35 VAL   (  35-)  A      CG1 <->   36 THR   (  36-)  A      N      0.14    2.86  INTRA BL
 339 LEU   ( 339-)  A      C   <->  341 ALA   ( 341-)  A      N      0.14    2.76  INTRA BL
 152 HIS   ( 152-)  A      O   <->  158 GLN   ( 158-)  A      NE2    0.14    2.56  INTRA BL
 262 LEU   ( 262-)  A      N   <->  361 GLY   ( 361-)  A      O      0.14    2.56  INTRA BL
 133 ASP   ( 133-)  A      N   <->  134 GLY   ( 134-)  A      N      0.14    2.46  INTRA BL
 346 ASN   ( 346-)  A      ND2 <->  372 VAL   ( 372-)  A      CG2    0.13    2.97  INTRA BL
  23 MET   (  23-)  A      C   <->   25 GLY   (  25-)  A      N      0.13    2.77  INTRA BL
  28 ASP   (  28-)  A      O   <->   32 ALA   (  32-)  A      N      0.13    2.57  INTRA BL
 102 ARG   ( 102-)  A      NH2 <->  106 CYS   ( 106-)  A      SG     0.13    3.17  INTRA BL
  20 TYR   (  20-)  A      CZ  <->   71 LEU   (  71-)  A      CD1    0.13    3.07  INTRA BL
And so on for a total of 121 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

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.

 345 ARG   ( 345-)  A      -5.67
 269 GLN   ( 269-)  A      -5.27

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.

  14 LYS   (  14-)  A        16 - SER     16- ( A)         -4.39

Note: Quality value plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 409 HOH   (1459 )  A      O    -29.47   -5.56   25.94

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.

 409 HOH   ( 625 )  A      O
 409 HOH   ( 675 )  A      O
 409 HOH   ( 841 )  A      O
 409 HOH   ( 853 )  A      O
 409 HOH   ( 865 )  A      O
 409 HOH   ( 868 )  A      O
 409 HOH   ( 897 )  A      O
 409 HOH   (1053 )  A      O
 409 HOH   (1142 )  A      O
 409 HOH   (1268 )  A      O
 409 HOH   (1283 )  A      O
 409 HOH   (1298 )  A      O
 409 HOH   (1316 )  A      O
 409 HOH   (1321 )  A      O
 409 HOH   (1391 )  A      O
 409 HOH   (7004 )  A      O
 409 HOH   (7005 )  A      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  67 ASN   (  67-)  A
 227 GLN   ( 227-)  A
 397 ASN   ( 397-)  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 PHE   (   8-)  A      N
  12 SER   (  12-)  A      OG
  13 TRP   (  13-)  A      N
  21 ASN   (  21-)  A      N
  44 SER   (  44-)  A      N
  46 SER   (  46-)  A      N
  50 GLU   (  50-)  A      N
  51 GLY   (  51-)  A      N
  61 ASP   (  61-)  A      N
  91 ILE   (  91-)  A      N
  92 ASN   (  92-)  A      N
  93 HIS   (  93-)  A      N
  94 ARG   (  94-)  A      NH1
  97 ASP   (  97-)  A      N
 102 ARG   ( 102-)  A      N
 112 THR   ( 112-)  A      OG1
 119 TRP   ( 119-)  A      N
 126 ARG   ( 126-)  A      NH1
 136 ALA   ( 136-)  A      N
 138 LEU   ( 138-)  A      N
 178 ARG   ( 178-)  A      NE
 178 ARG   ( 178-)  A      NH1
 183 ARG   ( 183-)  A      N
 201 LEU   ( 201-)  A      N
 208 ASP   ( 208-)  A      N
 217 LYS   ( 217-)  A      N
 226 ARG   ( 226-)  A      NE
 249 THR   ( 249-)  A      OG1
 251 LYS   ( 251-)  A      NZ
 255 ASN   ( 255-)  A      ND2
 263 TRP   ( 263-)  A      N
 266 ILE   ( 266-)  A      N
 283 ALA   ( 283-)  A      N
 286 PHE   ( 286-)  A      N
 287 VAL   ( 287-)  A      N
 288 ASP   ( 288-)  A      N
 330 TRP   ( 330-)  A      N
 332 PHE   ( 332-)  A      N
 343 ARG   ( 343-)  A      NE
 343 ARG   ( 343-)  A      NH1
 343 ARG   ( 343-)  A      NH2
 381 ASP   ( 381-)  A      N
Only metal coordination for   92 ASN  (  92-) A      OD1
Only metal coordination for  143 ASP  ( 143-) A      OD1

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

   1 HIS   (   1-)  A      ND1
  88 ASP   (  88-)  A      OD1
 180 ASP   ( 180-)  A      OD2
 259 GLU   ( 259-)  A      OE1
 290 HIS   ( 290-)  A      NE2
 291 ASP   ( 291-)  A      OD2
 359 HIS   ( 359-)  A      ND1

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+.

 405  CA   ( 500-)  A     0.74   0.96 Scores about as good as NA
 406  CA   ( 501-)  A     0.72   0.94 Scores about as good as NA
 407  CA   ( 502-)  A     0.73   0.94 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.

 100 ASP   ( 100-)  A   H-bonding suggests Asn; but Alt-Rotamer
 259 GLU   ( 259-)  A   H-bonding suggests Gln
 267 ASP   ( 267-)  A   H-bonding suggests Asn; but Alt-Rotamer
 288 ASP   ( 288-)  A   H-bonding suggests Asn
 291 ASP   ( 291-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.297
  2nd generation packing quality :  -2.418
  Ramachandran plot appearance   :  -4.556 (bad)
  chi-1/chi-2 rotamer normality  :  -4.015 (bad)
  Backbone conformation          :  -1.008

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.429 (tight)
  Bond angles                    :   0.724
  Omega angle restraints         :   0.247 (tight)
  Side chain planarity           :   0.273 (tight)
  Improper dihedral distribution :   0.672
  Inside/Outside distribution    :   0.953

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -1.9
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.429 (tight)
  Bond angles                    :   0.724
  Omega angle restraints         :   0.247 (tight)
  Side chain planarity           :   0.273 (tight)
  Improper dihedral distribution :   0.672
  Inside/Outside distribution    :   0.953
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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
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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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DSSP
    W.Kabsch and C.Sander,
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      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.