WHAT IF Check report

This file was created 2012-01-25 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 pdb2j9x.ent

Checks that need to be done early-on in validation

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected.

 661  CS   (1398-)  B  -  CS       2

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.

 663 DMS   (1400-)  B  -
 664 DMS   (1401-)  B  -
 665 DMS   (1402-)  B  -
 666 P1T   (1396-)  B  -
 667 G3P   (1268-)  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

Note: Ramachandran plot

Chain identifier: B

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

Warning: Missing atoms

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

   1 GLU   (   2-)  A      CG
   1 GLU   (   2-)  A      CD
   1 GLU   (   2-)  A      OE1
   1 GLU   (   2-)  A      OE2
   4 GLU   (   5-)  A      CG
   4 GLU   (   5-)  A      CD
   4 GLU   (   5-)  A      OE1
   4 GLU   (   5-)  A      OE2
  13 ARG   (  14-)  A      CG
  13 ARG   (  14-)  A      CD
  13 ARG   (  14-)  A      NE
  13 ARG   (  14-)  A      CZ
  13 ARG   (  14-)  A      NH1
  13 ARG   (  14-)  A      NH2
  14 ARG   (  15-)  A      CG
  14 ARG   (  15-)  A      CD
  14 ARG   (  15-)  A      NE
  14 ARG   (  15-)  A      CZ
  14 ARG   (  15-)  A      NH1
  14 ARG   (  15-)  A      NH2
 108 ASN   ( 109-)  A      CG
 108 ASN   ( 109-)  A      OD1
 108 ASN   ( 109-)  A      ND2
 119 GLN   ( 120-)  A      CG
 119 GLN   ( 120-)  A      CD
And so on for a total of 87 lines.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 659 GLU   ( 396-)  B
 264 ALA   ( 268-)  A

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 : 11.92

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.

 252 ARG   ( 256-)  A
 403 ARG   ( 141-)  B

Warning: Tyrosine convention problem

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

 270 TYR   (   8-)  B
 278 TYR   (  16-)  B
 336 TYR   (  74-)  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.

 300 ASP   (  38-)  B
 309 ASP   (  47-)  B
 643 ASP   ( 381-)  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.

  48 GLU   (  49-)  A
 434 GLU   ( 172-)  B

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.

 402 GLU   ( 140-)  B      CD   OE2   1.33    4.2
 553 ASP   ( 291-)  B      CG   OD2   1.33    4.5

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.314
RMS-deviation in bond distances: 0.007

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.

 135 SER   ( 136-)  A      N    CA   C   122.61    4.1
 271 PHE   (   9-)  B      N    CA   C    97.86   -4.8
 549 MET   ( 287-)  B      N    CA   C    94.01   -6.1

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.655
RMS-deviation in bond angles: 1.462

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.

  48 GLU   (  49-)  A
 252 ARG   ( 256-)  A
 300 ASP   (  38-)  B
 309 ASP   (  47-)  B
 403 ARG   ( 141-)  B
 434 GLU   ( 172-)  B
 643 ASP   ( 381-)  B

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.

 549 MET   ( 287-)  B    5.20
 271 PHE   (   9-)  B    5.12
 102 ALA   ( 103-)  A    5.11
 135 SER   ( 136-)  A    4.20
 388 LEU   ( 126-)  B    4.18
 405 SER   ( 143-)  B    4.11
 646 ILE   ( 384-)  B    4.04

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.

 542 PHE   ( 280-)  B    -2.9
 458 PRO   ( 196-)  B    -2.9
 208 PHE   ( 212-)  A    -2.8
 372 THR   ( 110-)  B    -2.5
  52 PRO   (  53-)  A    -2.3
 282 ILE   (  20-)  B    -2.2
 571 VAL   ( 309-)  B    -2.2
 170 ARG   ( 171-)  A    -2.1
 413 LEU   ( 151-)  B    -2.1
 230 GLY   ( 234-)  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.

  26 ASP   (  27-)  A  PRO omega poor
 200 HIS   ( 204-)  A  Poor phi/psi
 208 PHE   ( 212-)  A  Poor phi/psi
 317 ARG   (  55-)  B  PRO omega poor
 339 ARG   (  77-)  B  Poor phi/psi
 453 ALA   ( 191-)  B  Poor phi/psi
 457 HIS   ( 195-)  B  PRO omega poor
 542 PHE   ( 280-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.587

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.

 580 SER   ( 318-)  B    0.35
 256 SER   ( 260-)  A    0.36
 440 SER   ( 178-)  B    0.39
 253 SER   ( 257-)  A    0.40

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!

  24 LEU   (  25-)  A      0
  26 ASP   (  27-)  A      0
  27 PRO   (  28-)  A      0
  42 ALA   (  43-)  A      0
  44 ALA   (  45-)  A      0
  56 PRO   (  57-)  A      0
 107 ASN   ( 108-)  A      0
 108 ASN   ( 109-)  A      0
 110 ILE   ( 111-)  A      0
 120 VAL   ( 121-)  A      0
 129 ASP   ( 130-)  A      0
 131 PRO   ( 132-)  A      0
 168 TYR   ( 169-)  A      0
 170 ARG   ( 171-)  A      0
 172 TYR   ( 173-)  A      0
 177 SER   ( 178-)  A      0
 178 ARG   ( 179-)  A      0
 179 SER   ( 180-)  A      0
 181 VAL   ( 182-)  A      0
 182 THR   ( 183-)  A      0
 187 ARG   ( 188-)  A      0
 188 GLY   ( 189-)  A      0
 189 LEU   ( 193-)  A      0
 190 HIS   ( 194-)  A      0
 208 PHE   ( 212-)  A      0
And so on for a total of 179 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 : 1.266

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]

  52 PRO   (  53-)  A    0.46 HIGH
 609 PRO   ( 347-)  B    0.46 HIGH

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.

 324 CYS   (  62-)  B      O   <->  667 HOH   (2057 )  B      O      0.22    2.18  INTRA
 309 ASP   (  47-)  B      OD1 <->  313 ASN   (  51-)  B      ND2    0.21    2.49  INTRA BL
 208 PHE   ( 212-)  A      N   <->  666 HOH   (2132 )  A      O      0.21    2.49  INTRA
 404 GLN   ( 142-)  B      NE2 <->  667 HOH   (2126 )  B      O      0.21    2.49  INTRA
 139 ARG   ( 140-)  A      NH2 <->  666 HOH   (2097 )  A      O      0.21    2.49  INTRA
  26 ASP   (  27-)  A      OD1 <->   69 ARG   (  70-)  A      NE     0.20    2.50  INTRA
 212 SER   ( 216-)  A      C   <->  258 MET   ( 262-)  A      SD     0.18    3.22  INTRA
 173 THR   ( 174-)  A      N   <->  203 PRO   ( 207-)  A      O      0.17    2.53  INTRA
 412 ARG   ( 150-)  B      NH1 <->  667 HOH   (2130 )  B      O      0.17    2.53  INTRA
 373 GLY   ( 111-)  B      N   <->  664 P1T   (1396-)  B      O2     0.17    2.53  INTRA
 479 LEU   ( 217-)  B      O   <->  483 GLY   ( 221-)  B      N      0.16    2.54  INTRA BL
 291 GLU   (  29-)  B      OE2 <->  457 HIS   ( 195-)  B      NE2    0.14    2.56  INTRA BL
 560 TYR   ( 298-)  B      CG  <->  561 SER   ( 299-)  B      N      0.14    2.86  INTRA BL
 111 ASP   ( 112-)  A      OD1 <->  144 ARG   ( 145-)  A      NH2    0.13    2.57  INTRA
 317 ARG   (  55-)  B      NE  <->  473 GLU   ( 211-)  B      OE2    0.12    2.58  INTRA BL
  65 ASN   (  66-)  A      ND2 <->  666 HOH   (2050 )  A      O      0.11    2.59  INTRA
  45 ASP   (  46-)  A      OD2 <->  259 LYS   ( 263-)  A      NZ     0.10    2.60  INTRA
 399 LYS   ( 137-)  B      NZ  <->  667 HOH   (2115 )  B      O      0.10    2.60  INTRA
 535 HIS   ( 273-)  B      ND1 <->  667 HOH   (2201 )  B      O      0.10    2.60  INTRA
 324 CYS   (  62-)  B      SG  <->  337 LEU   (  75-)  B      CG     0.09    3.31  INTRA
 434 GLU   ( 172-)  B      OE2 <->  667 HOH   (2139 )  B      O      0.09    2.31  INTRA
 532 PRO   ( 270-)  B      O   <->  536 GLY   ( 274-)  B      N      0.09    2.61  INTRA BL
 498 ASN   ( 236-)  B      N   <->  664 P1T   (1396-)  B      OP3    0.09    2.61  INTRA
 352 GLN   (  90-)  B      OE1 <->  356 GLN   (  94-)  B      NE2    0.08    2.62  INTRA BL
 284 MET   (  22-)  B      N   <->  285 PRO   (  23-)  B      CD     0.08    2.92  INTRA BL
And so on for a total of 67 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.

 187 ARG   ( 188-)  A      -7.96
 656 ARG   ( 394-)  B      -7.10
 604 HIS   ( 342-)  B      -6.21
 535 HIS   ( 273-)  B      -6.20
 422 HIS   ( 160-)  B      -5.93
 178 ARG   ( 179-)  A      -5.92
 170 ARG   ( 171-)  A      -5.59
 484 ARG   ( 222-)  B      -5.56
  11 ASN   (  12-)  A      -5.47
 362 ARG   ( 100-)  B      -5.33
 537 ARG   ( 275-)  B      -5.16
 198 GLU   ( 202-)  A      -5.05
 626 GLU   ( 364-)  B      -5.01
 525 GLU   ( 263-)  B      -5.01

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.

 186 ASN   ( 187-)  A       188 - GLY    189- ( A)         -5.69
 603 ARG   ( 341-)  B       605 - GLU    343- ( B)         -5.36

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 566 LEU   ( 304-)  B   -2.76
  14 ARG   (  15-)  A   -2.76
 200 HIS   ( 204-)  A   -2.67

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.

 131 PRO   ( 132-)  A     -  134 GLU   ( 135-)  A        -1.13

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: 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.

 666 HOH   (2015 )  A      O
 666 HOH   (2137 )  A      O
 667 HOH   (2116 )  B      O
 667 HOH   (2160 )  B      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   (  68-)  A
 103 ASN   ( 104-)  A
 304 GLN   (  42-)  B
 326 ASN   (  64-)  B
 407 ASN   ( 145-)  B
 522 HIS   ( 260-)  B
 579 ASN   ( 317-)  B
 604 HIS   ( 342-)  B

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  28 GLY   (  29-)  A      N
  46 ALA   (  47-)  A      N
  55 ASP   (  56-)  A      N
 174 TYR   ( 175-)  A      OH
 178 ARG   ( 179-)  A      N
 183 GLY   ( 184-)  A      N
 209 GLY   ( 213-)  A      N
 230 GLY   ( 234-)  A      N
 231 SER   ( 235-)  A      N
 265 THR   (   3-)  B      N
 317 ARG   (  55-)  B      NH2
 339 ARG   (  77-)  B      NH2
 349 LYS   (  87-)  B      N
 352 GLN   (  90-)  B      N
 372 THR   ( 110-)  B      OG1
 373 GLY   ( 111-)  B      N
 374 ALA   ( 112-)  B      N
 376 GLN   ( 114-)  B      N
 377 HIS   ( 115-)  B      N
 437 ARG   ( 175-)  B      NH1
 444 GLU   ( 182-)  B      N
 448 TYR   ( 186-)  B      N
 452 THR   ( 190-)  B      N
 452 THR   ( 190-)  B      OG1
 484 ARG   ( 222-)  B      N
 494 GLY   ( 232-)  B      N
 496 GLY   ( 234-)  B      N
 570 SER   ( 308-)  B      N
 637 ASN   ( 375-)  B      ND2
 639 SER   ( 377-)  B      OG
 647 PHE   ( 385-)  B      N
 656 ARG   ( 394-)  B      N

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.

  31 GLN   (  32-)  A      OE1
  48 GLU   (  49-)  A      OE2

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Unusual water packing

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

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

 666 HOH   (2041 )  A      O  0.89  K  4
 666 HOH   (2091 )  A      O  0.85  K  4 ION-B
 667 HOH   (2211 )  B      O  1.10  K  4 Ion-B
 667 HOH   (2230 )  B      O  1.09  K  4
 667 HOH   (2266 )  B      O  0.99  K  4

Warning: Possible wrong residue type

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

 430 ASP   ( 168-)  B   H-bonding suggests Asn
 567 ASP   ( 305-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.033
  2nd generation packing quality :  -1.081
  Ramachandran plot appearance   :  -0.908
  chi-1/chi-2 rotamer normality  :  -1.587
  Backbone conformation          :   0.545

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.314 (tight)
  Bond angles                    :   0.655 (tight)
  Omega angle restraints         :   0.230 (tight)
  Side chain planarity           :   0.261 (tight)
  Improper dihedral distribution :   0.601
  Inside/Outside distribution    :   1.009

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.314 (tight)
  Bond angles                    :   0.655 (tight)
  Omega angle restraints         :   0.230 (tight)
  Side chain planarity           :   0.261 (tight)
  Improper dihedral distribution :   0.601
  Inside/Outside distribution    :   1.009
==============

WHAT IF
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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Ramachandran plot
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Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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Ion Checks
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      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
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      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
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      Who checks the checkers
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