WHAT IF Check report

This file was created 2013-12-10 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 pdb4dm9.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.128
CA-only RMS fit for the two chains : 0.795

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

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

 455 CF0   (   5-)  Y  B

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.

 452 PHQ   (   1-)  X  -
 453 GME   (   4-)  X  -
 456 GME   (   4-)  Y  -
 457 PHQ   (   1-)  Y  -

Administrative problems that can generate validation failures

Warning: Amino acids observed inside ligands

Ligands were detected that contain amino acids. This is not a wise thing to do. Please rename those ligand fragments and call them DRG, XXX, or whatever, but do not give them the name of a valid amino acid, nucleotide, or sugar.

Crystallographers and NMR spectroscopists have an understandable dislike for organic chemistry and quantum chemistry. And they hate making topology entries for small molecules. So, if they find a funny small molecular ligand in their molecule, they generally try to 'recycle' old topologies. If the ligand contains a group that, for example, looks like an amino acid, it is common practice to split the ligand into several 'ligand-residues' and use the amino acid topology for the amino acid fragment. This is all fine, but please change the name into DRG, XXX, or whatever, before depositing the ligand. If you think that the validation software makes errors that are related to these ligands, I suggest you first change the name of the ligand (and make one ligand out of the fragments) and run the validation again. The table lists the residues, or residue-like things, that are found bound between ligands or unrecognized things, and that thus are suspect of actually being part of one big ligand.

 447 VAL   (   2-)  X  -
 449 VAL   (   2-)  Y  -

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.

 447 VAL   (   2-)  X  -   N   bound to  452 PHQ   (   1-)  X  -   C1
 449 VAL   (   2-)  Y  -   N   bound to  457 PHQ   (   1-)  Y  -   C1

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: B-factors outside the range 0.0 - 100.0

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

   1 MET   (   1-)  A    High
   2 GLN   (   2-)  A    High
   7 GLU   (   7-)  A    High
  11 GLU   (  11-)  A    High
  12 MET   (  12-)  A    High
  23 ALA   (  23-)  A    High
  24 GLY   (  24-)  A    High
  25 GLN   (  25-)  A    High
  27 ARG   (  27-)  A    High
  35 GLU   (  35-)  A    High
  36 GLU   (  36-)  A    High
  37 GLU   (  37-)  A    High
  38 SER   (  38-)  A    High
  39 LEU   (  39-)  A    High
  40 GLY   (  40-)  A    High
  41 SER   (  41-)  A    High
  42 VAL   (  42-)  A    High
  43 PRO   (  43-)  A    High
  44 ALA   (  44-)  A    High
  45 PRO   (  45-)  A    High
  58 GLN   (  58-)  A    High
  59 HIS   (  59-)  A    High
  61 ASN   (  61-)  A    High
  62 PHE   (  62-)  A    High
  63 ARG   (  63-)  A    High
And so on for a total of 150 lines.

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 11

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 153 ARG   ( 153-)  A
 178 ARG   ( 178-)  A
 250 ARG   (  27-)  B

Warning: Phenylalanine convention problem

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

  28 PHE   (  28-)  A
 108 PHE   ( 108-)  A
 165 PHE   ( 165-)  A
 181 PHE   ( 181-)  A
 204 PHE   ( 204-)  A
 251 PHE   (  28-)  B
 331 PHE   ( 108-)  B
 404 PHE   ( 181-)  B
 427 PHE   ( 204-)  B
 437 PHE   ( 214-)  B

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.

 104 ASP   ( 104-)  A
 110 ASP   ( 110-)  A
 144 ASP   ( 144-)  A
 156 ASP   ( 156-)  A
 176 ASP   ( 176-)  A
 196 ASP   ( 196-)  A
 327 ASP   ( 104-)  B
 333 ASP   ( 110-)  B
 367 ASP   ( 144-)  B
 379 ASP   ( 156-)  B
 399 ASP   ( 176-)  B
 419 ASP   ( 196-)  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.

  36 GLU   (  36-)  A
  60 GLU   (  60-)  A
  69 GLU   (  69-)  A
 137 GLU   ( 137-)  A
 203 GLU   ( 203-)  A
 211 GLU   ( 211-)  A
 258 GLU   (  35-)  B
 283 GLU   (  60-)  B
 292 GLU   (  69-)  B
 360 GLU   ( 137-)  B
 434 GLU   ( 211-)  B

Geometric checks

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.

 433 GLY   ( 210-)  B     -C    N    CA  127.78    4.2
 449 VAL   (   2-)  Y      N    CA   C   125.35    5.1

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.

  36 GLU   (  36-)  A
  60 GLU   (  60-)  A
  69 GLU   (  69-)  A
 104 ASP   ( 104-)  A
 110 ASP   ( 110-)  A
 137 GLU   ( 137-)  A
 144 ASP   ( 144-)  A
 153 ARG   ( 153-)  A
 156 ASP   ( 156-)  A
 176 ASP   ( 176-)  A
 178 ARG   ( 178-)  A
 196 ASP   ( 196-)  A
 203 GLU   ( 203-)  A
 211 GLU   ( 211-)  A
 250 ARG   (  27-)  B
 258 GLU   (  35-)  B
 283 GLU   (  60-)  B
 292 GLU   (  69-)  B
 327 ASP   ( 104-)  B
 333 ASP   ( 110-)  B
 360 GLU   ( 137-)  B
 367 ASP   ( 144-)  B
 379 ASP   ( 156-)  B
 399 ASP   ( 176-)  B
 419 ASP   ( 196-)  B
 434 GLU   ( 211-)  B

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 152 CYS   ( 152-)  A      CA    -7.2    21.58    34.33
 375 CYS   ( 152-)  B      CA    -7.6    20.82    34.33
The average deviation= 0.638

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.

 449 VAL   (   2-)  Y    5.91
 152 CYS   ( 152-)  A    4.21

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.

 162 PHE   ( 162-)  A    -2.3
 385 PHE   ( 162-)  B    -2.3
 210 GLY   ( 210-)  A    -2.3
 153 ARG   ( 153-)  A    -2.3
 376 ARG   ( 153-)  B    -2.3
 231 ILE   (   8-)  B    -2.1
 431 GLU   ( 208-)  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.

  23 ALA   (  23-)  A  omega poor
  44 ALA   (  44-)  A  PRO omega poor
  71 LYS   (  71-)  A  Poor phi/psi
  88 ASN   (  88-)  A  Poor phi/psi
 152 CYS   ( 152-)  A  Poor phi/psi
 155 ASP   ( 155-)  A  Poor phi/psi
 156 ASP   ( 156-)  A  Poor phi/psi
 157 LYS   ( 157-)  A  Poor phi/psi
 159 ASN   ( 159-)  A  Poor phi/psi
 169 ASP   ( 169-)  A  Poor phi/psi
 206 GLU   ( 206-)  A  Poor phi/psi
 208 GLU   ( 208-)  A  omega poor
 210 GLY   ( 210-)  A  Poor phi/psi
 214 PHE   ( 214-)  A  Poor phi/psi
 246 ALA   (  23-)  B  omega poor
 267 ALA   (  44-)  B  PRO omega poor
 293 LEU   (  70-)  B  Poor phi/psi
 311 ASN   (  88-)  B  Poor phi/psi
 375 CYS   ( 152-)  B  Poor phi/psi
 377 VAL   ( 154-)  B  Poor phi/psi
 380 LYS   ( 157-)  B  Poor phi/psi
 382 ASN   ( 159-)  B  Poor phi/psi
 392 ASP   ( 169-)  B  Poor phi/psi
 429 GLU   ( 206-)  B  Poor phi/psi, omega poor
 431 GLU   ( 208-)  B  Poor phi/psi, omega poor
 437 PHE   ( 214-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.195

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.

  18 SER   (  18-)  A    0.36
 342 SER   ( 119-)  B    0.36

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 ILE   (   8-)  A      0
   9 ASN   (   9-)  A      0
  20 LEU   (  20-)  A      0
  25 GLN   (  25-)  A      0
  32 LEU   (  32-)  A      0
  34 LEU   (  34-)  A      0
  35 GLU   (  35-)  A      0
  44 ALA   (  44-)  A      0
  47 CYS   (  47-)  A      0
  71 LYS   (  71-)  A      0
  88 ASN   (  88-)  A      0
  89 SER   (  89-)  A      0
  90 CYS   (  90-)  A      0
 102 ASN   ( 102-)  A      0
 105 LYS   ( 105-)  A      0
 110 ASP   ( 110-)  A      0
 123 LYS   ( 123-)  A      0
 124 MET   ( 124-)  A      0
 151 GLN   ( 151-)  A      0
 152 CYS   ( 152-)  A      0
 154 VAL   ( 154-)  A      0
 155 ASP   ( 155-)  A      0
 156 ASP   ( 156-)  A      0
 157 LYS   ( 157-)  A      0
 166 ASN   ( 166-)  A      0
And so on for a total of 146 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  77 PRO   (  77-)  A    0.16 LOW
 300 PRO   (  77-)  B    0.16 LOW

Warning: Unusual PRO puckering phases

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

  45 PRO   (  45-)  A    16.9 half-chair N/C-delta (18 degrees)
 268 PRO   (  45-)  B    16.9 half-chair N/C-delta (18 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 313 CYS   (  90-)  B      SG   <->   455 CF0   (   5-)  Y      C1   1.60    1.80  INTRA BF
  90 CYS   (  90-)  A      SG   <->   454 CF0   (   5-)  X      C1   1.60    1.80  INTRA BF
 450 ALA   (   3-)  Y      C    <->   456 GME   (   4-)  Y      N    1.37    1.33  INTRA BF
 449 VAL   (   2-)  Y      N    <->   457 PHQ   (   1-)  Y      C1   1.27    1.43  INTRA BF
 455 CF0   (   5-)  Y      C1   <->   456 GME   (   4-)  Y      C    1.26    1.54  INTRA BF
  90 CYS   (  90-)  A      SG   <->   453 GME   (   4-)  X      C    0.85    2.55  INTRA BF
 313 CYS   (  90-)  B      SG   <->   456 GME   (   4-)  Y      C    0.70    2.70  INTRA BL
 450 ALA   (   3-)  Y      CA   <->   456 GME   (   4-)  Y      N    0.65    2.45  INTRA BF
 449 VAL   (   2-)  Y      CA   <->   457 PHQ   (   1-)  Y      C1   0.63    2.57  INTRA BF
 450 ALA   (   3-)  Y      O    <->   456 GME   (   4-)  Y      N    0.45    2.25  INTRA BF
  83 LYS   (  83-)  A      NZ   <->   127 GLU   ( 127-)  A      OE2  0.41    2.29  INTRA BF
 154 VAL   ( 154-)  A      O    <->   156 ASP   ( 156-)  A      N    0.38    2.32  INTRA BF
   1 MET   (   1-)  A      N    <->   458 HOH   ( 307 )  A      O    0.33    2.37  INTRA BF
 449 VAL   (   2-)  Y      O    <->   456 GME   (   4-)  Y      N    0.33    2.37  INTRA BF
 315 THR   (  92-)  B      OG1  <->   366 HIS   ( 143-)  B      ND1  0.31    2.39  INTRA BL
 286 ARG   (  63-)  B      NH2  <->   397 GLU   ( 174-)  B      OE2  0.30    2.40  INTRA BF
 313 CYS   (  90-)  B      CB   <->   455 CF0   (   5-)  Y      C1   0.28    2.92  INTRA BF
  90 CYS   (  90-)  A      CB   <->   454 CF0   (   5-)  X      C1   0.27    2.93  INTRA BF
  92 THR   (  92-)  A      OG1  <->   143 HIS   ( 143-)  A      ND1  0.27    2.43  INTRA BL
 283 GLU   (  60-)  B      OE1  <->   382 ASN   ( 159-)  B      ND2  0.26    2.44  INTRA BL
  87 GLY   (  87-)  A      N    <->   458 HOH   ( 309 )  A      O    0.24    2.46  INTRA BL
 161 HIS   ( 161-)  A      ND1  <->   176 ASP   ( 176-)  A      OD2  0.21    2.49  INTRA BL
 376 ARG   ( 153-)  B      NH1  <->   456 GME   (   4-)  Y      OE2  0.21    2.49  INTRA BF
 174 GLU   ( 174-)  A      OE1  <->   185 HIS   ( 185-)  A      NE2  0.20    2.50  INTRA BL
 144 ASP   ( 144-)  A      OD2  <->   242 ARG   (  19-)  B      NH2  0.18    2.52  INTRA BL
And so on for a total of 66 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 374 GLN   ( 151-)  B      -7.66
 151 GLN   ( 151-)  A      -7.58
 255 LEU   (  32-)  B      -6.61
  32 LEU   (  32-)  A      -6.59
 401 ARG   ( 178-)  B      -6.47
 178 ARG   ( 178-)  A      -6.34
 209 GLN   ( 209-)  A      -6.19
 123 LYS   ( 123-)  A      -6.05
 153 ARG   ( 153-)  A      -5.93
 346 LYS   ( 123-)  B      -5.92
 430 ARG   ( 207-)  B      -5.81
 213 ARG   ( 213-)  A      -5.46
 436 ARG   ( 213-)  B      -5.34
 376 ARG   ( 153-)  B      -5.20
 432 GLN   ( 209-)  B      -5.10

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: 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.

 152 CYS   ( 152-)  A     -  155 ASP   ( 155-)  A        -1.90

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

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.

  59 HIS   (  59-)  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.

   9 ASN   (   9-)  A      N
  27 ARG   (  27-)  A      NH1
  33 GLY   (  33-)  A      N
  48 ALA   (  48-)  A      N
  58 GLN   (  58-)  A      NE2
  74 GLU   (  74-)  A      N
  89 SER   (  89-)  A      N
  90 CYS   (  90-)  A      N
 113 VAL   ( 113-)  A      N
 123 LYS   ( 123-)  A      NZ
 125 SER   ( 125-)  A      N
 154 VAL   ( 154-)  A      N
 157 LYS   ( 157-)  A      N
 167 ASN   ( 167-)  A      N
 167 ASN   ( 167-)  A      ND2
 181 PHE   ( 181-)  A      N
 211 GLU   ( 211-)  A      N
 225 GLN   (   2-)  B      N
 230 GLU   (   7-)  B      N
 231 ILE   (   8-)  B      N
 256 GLY   (  33-)  B      N
 265 VAL   (  42-)  B      N
 271 ALA   (  48-)  B      N
 289 GLN   (  66-)  B      NE2
 307 GLN   (  84-)  B      NE2
 312 SER   (  89-)  B      N
 313 CYS   (  90-)  B      N
 376 ARG   ( 153-)  B      NH1
 381 VAL   ( 158-)  B      N
 390 ASN   ( 167-)  B      N
 390 ASN   ( 167-)  B      ND2
 404 PHE   ( 181-)  B      N
 407 ASN   ( 184-)  B      N
 432 GLN   ( 209-)  B      N
 432 GLN   ( 209-)  B      NE2

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

 156 ASP   ( 156-)  A      OD1
 378 ASP   ( 155-)  B      OD2
 431 GLU   ( 208-)  B      OE1

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.

 196 ASP   ( 196-)  A   H-bonding suggests Asn
 208 GLU   ( 208-)  A   H-bonding suggests Gln
 419 ASP   ( 196-)  B   H-bonding suggests Asn
 431 GLU   ( 208-)  B   H-bonding suggests Gln; but Alt-Rotamer

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 :   0.009
  2nd generation packing quality :  -1.122
  Ramachandran plot appearance   :   0.094
  chi-1/chi-2 rotamer normality  :  -1.195
  Backbone conformation          :   0.149

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.243 (tight)
  Bond angles                    :   0.542 (tight)
  Omega angle restraints         :   0.786
  Side chain planarity           :   0.431 (tight)
  Improper dihedral distribution :   0.598
  B-factor distribution          :   1.379
  Inside/Outside distribution    :   0.957

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 : 2.35


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.1
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :   1.4
  chi-1/chi-2 rotamer normality  :   0.0
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.243 (tight)
  Bond angles                    :   0.542 (tight)
  Omega angle restraints         :   0.786
  Side chain planarity           :   0.431 (tight)
  Improper dihedral distribution :   0.598
  B-factor distribution          :   1.379
  Inside/Outside distribution    :   0.957
==============

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.