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 pdb4g3y.ent

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

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. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 582 LEU   ( 157-)  C  -

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: L

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: C

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'.

 512 TYR   (  87-)  C      CG
 512 TYR   (  87-)  C      CD1
 512 TYR   (  87-)  C      CD2
 512 TYR   (  87-)  C      CE1
 512 TYR   (  87-)  C      CE2
 512 TYR   (  87-)  C      CZ
 512 TYR   (  87-)  C      OH
 582 LEU   ( 157-)  C      O

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.

 214 CYS   ( 214-)  L    High

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: 0

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: L

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: C

Nomenclature related problems

Warning: Tyrosine convention problem

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

  50 TYR   (  50-)  L
  87 TYR   (  87-)  L
 192 TYR   ( 192-)  L
 296 TYR   (  82-)  H
 311 TYR   (  97-)  H
 366 TYR   ( 152-)  H
 397 TYR   ( 183-)  H
 415 TYR   ( 201-)  H
 566 TYR   ( 141-)  C

Warning: Phenylalanine convention problem

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

  62 PHE   (  62-)  L
  71 PHE   (  71-)  L
 116 PHE   ( 116-)  L
 118 PHE   ( 118-)  L
 343 PHE   ( 129-)  H

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.

  70 ASP   (  70-)  L
 167 ASP   ( 167-)  L
 470 ASP   (  45-)  C

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.

  17 GLU   (  17-)  L
 105 GLU   ( 105-)  L
 187 GLU   ( 187-)  L
 195 GLU   ( 195-)  L
 220 GLU   (   6-)  H
 256 GLU   (  42-)  H
 264 GLU   (  50-)  H
 433 GLU   ( 219-)  H
 532 GLU   ( 107-)  C
 535 GLU   ( 110-)  C
 571 GLU   ( 146-)  C

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.

 198 HIS   ( 198-)  L      CG   ND1  CE1 109.62    4.0
 440 HIS   (  15-)  C      CG   ND1  CE1 109.61    4.0
 527 GLN   ( 102-)  C     -C    N    CA  130.22    4.7

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.

  17 GLU   (  17-)  L
  70 ASP   (  70-)  L
 105 GLU   ( 105-)  L
 167 ASP   ( 167-)  L
 187 GLU   ( 187-)  L
 195 GLU   ( 195-)  L
 220 GLU   (   6-)  H
 256 GLU   (  42-)  H
 264 GLU   (  50-)  H
 433 GLU   ( 219-)  H
 470 ASP   (  45-)  C
 532 GLU   ( 107-)  C
 535 GLU   ( 110-)  C
 571 GLU   ( 146-)  C

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.

  77 THR   (  77-)  L    -3.1
 368 PRO   ( 154-)  H    -3.0
 370 PRO   ( 156-)  H    -2.7
 528 ARG   ( 103-)  C    -2.7
 338 LYS   ( 124-)  H    -2.7
 352 THR   ( 138-)  H    -2.6
 469 ARG   (  44-)  C    -2.6
 579 ILE   ( 154-)  C    -2.6
 569 PHE   ( 144-)  C    -2.5
 359 LEU   ( 145-)  H    -2.5
 377 SER   ( 163-)  H    -2.5
 353 SER   ( 139-)  H    -2.4
 504 THR   (  79-)  C    -2.4
 219 GLU   (   5-)  H    -2.4
 242 ILE   (  28-)  H    -2.4
 580 ILE   ( 155-)  C    -2.3
 566 TYR   ( 141-)  C    -2.3
 337 THR   ( 123-)  H    -2.3
 171 SER   ( 171-)  L    -2.3
 527 GLN   ( 102-)  C    -2.3
 462 LEU   (  37-)  C    -2.2
 530 THR   ( 105-)  C    -2.2
  48 ILE   (  48-)  L    -2.2
 457 ARG   (  32-)  C    -2.2
 108 ARG   ( 108-)  L    -2.2
 216 VAL   (   2-)  H    -2.1
 537 LYS   ( 112-)  C    -2.1
 156 SER   ( 156-)  L    -2.1
  24 ARG   (  24-)  L    -2.1
 209 PHE   ( 209-)  L    -2.1
 270 ILE   (  56-)  H    -2.1
 141 PRO   ( 141-)  L    -2.1
 396 LEU   ( 182-)  H    -2.1
 220 GLU   (   6-)  H    -2.0
 195 GLU   ( 195-)  L    -2.0
 515 LYS   (  90-)  C    -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.

   7 SER   (   7-)  L  PRO omega poor
  12 SER   (  12-)  L  omega poor
  32 SER   (  32-)  L  Poor phi/psi
  51 ALA   (  51-)  L  Poor phi/psi, omega poor
  52 SER   (  52-)  L  Poor phi/psi
  69 THR   (  69-)  L  Poor phi/psi
  72 THR   (  72-)  L  omega poor
  84 ALA   (  84-)  L  Poor phi/psi
  94 TRP   (  94-)  L  PRO omega poor
 132 VAL   ( 132-)  L  omega poor
 140 TYR   ( 140-)  L  PRO omega poor
 152 ASN   ( 152-)  L  Poor phi/psi
 171 SER   ( 171-)  L  Poor phi/psi
 216 VAL   (   2-)  H  Poor phi/psi
 238 ALA   (  24-)  H  omega poor
 245 ASN   (  31-)  H  omega poor
 249 ASN   (  35-)  H  omega poor
 270 ILE   (  56-)  H  omega poor
 271 ASN   (  57-)  H  Poor phi/psi
 293 SER   (  79-)  H  Poor phi/psi
 311 TYR   (  97-)  H  omega poor
 319 SER   ( 105-)  H  Poor phi/psi
 353 SER   ( 139-)  H  Poor phi/psi
 354 GLY   ( 140-)  H  omega poor
 363 VAL   ( 149-)  H  omega poor
 367 PHE   ( 153-)  H  PRO omega poor
 369 GLU   ( 155-)  H  PRO omega poor
 370 PRO   ( 156-)  H  omega poor
 376 ASN   ( 162-)  H  Poor phi/psi
 447 ALA   (  22-)  C  omega poor
 455 ASN   (  30-)  C  omega poor
 457 ARG   (  32-)  C  Poor phi/psi
 464 ASN   (  39-)  C  Poor phi/psi
 470 ASP   (  45-)  C  Poor phi/psi
 471 ASN   (  46-)  C  Poor phi/psi
 481 TYR   (  56-)  C  omega poor
 489 PHE   (  64-)  C  omega poor
 511 SER   (  86-)  C  Poor phi/psi
 513 GLN   (  88-)  C  Poor phi/psi
 526 CYS   ( 101-)  C  omega poor
 527 GLN   ( 102-)  C  Poor phi/psi
 528 ARG   ( 103-)  C  Poor phi/psi
 532 GLU   ( 107-)  C  Poor phi/psi, omega poor
 533 GLY   ( 108-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.398

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.398

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.

 408 SER   ( 194-)  H    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!

   6 GLN   (   6-)  L      0
   7 SER   (   7-)  L      0
   8 PRO   (   8-)  L      0
   9 ALA   (   9-)  L      0
  10 ILE   (  10-)  L      0
  15 PRO   (  15-)  L      0
  26 SER   (  26-)  L      0
  28 PHE   (  28-)  L      0
  29 VAL   (  29-)  L      0
  31 SER   (  31-)  L      0
  32 SER   (  32-)  L      0
  40 THR   (  40-)  L      0
  41 ASN   (  41-)  L      0
  44 PRO   (  44-)  L      0
  49 LYS   (  49-)  L      0
  50 TYR   (  50-)  L      0
  51 ALA   (  51-)  L      0
  52 SER   (  52-)  L      0
  56 SER   (  56-)  L      0
  62 PHE   (  62-)  L      0
  65 SER   (  65-)  L      0
  67 SER   (  67-)  L      0
  69 THR   (  69-)  L      0
  70 ASP   (  70-)  L      0
  76 ASN   (  76-)  L      0
And so on for a total of 246 lines.

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!

 212 GLY   ( 212-)  L   2.20   69

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].

  15 PRO   (  15-)  L  -117.3 half-chair C-delta/C-gamma (-126 degrees)
 228 PRO   (  14-)  H   113.0 envelop C-beta (108 degrees)
 347 PRO   ( 133-)  H  -116.4 envelop C-gamma (-108 degrees)
 368 PRO   ( 154-)  H   -52.2 half-chair C-beta/C-alpha (-54 degrees)
 370 PRO   ( 156-)  H   -25.7 half-chair C-alpha/N (-18 degrees)
 495 PRO   (  70-)  C    50.7 half-chair C-delta/C-gamma (54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 527 GLN   ( 102-)  C      OE1 <->  528 ARG   ( 103-)  C      NH1    0.47    2.23  INTRA BF
 526 CYS   ( 101-)  C      CA  <->  527 GLN   ( 102-)  C      CB     0.32    2.68  INTRA
 189 HIS   ( 189-)  L      O   <->  211 ARG   ( 211-)  L      NE     0.29    2.41  INTRA BF
 532 GLU   ( 107-)  C      C   <->  534 ALA   ( 109-)  C      N      0.27    2.63  INTRA BF
 494 CYS   (  69-)  C      N   <->  530 THR   ( 105-)  C      CG2    0.24    2.86  INTRA BL
 314 ARG   ( 100-)  H      NH2 <->  322 ASP   ( 108-)  H      OD2    0.24    2.46  INTRA BL
 315 ASN   ( 101-)  H      ND2 <->  319 SER   ( 105-)  H      N      0.23    2.62  INTRA BL
   1 ASP   (   1-)  L      CA  <->  584 HOH   ( 320 )  L      O      0.21    2.59  INTRA
 352 THR   ( 138-)  H      O   <->  353 SER   ( 139-)  H      C      0.20    2.40  INTRA BF
 190 LYS   ( 190-)  L      O   <->  211 ARG   ( 211-)  L      N      0.20    2.50  INTRA BF
 192 TYR   ( 192-)  L      CB  <->  209 PHE   ( 209-)  L      CE1    0.19    3.01  INTRA BF
  37 GLN   (  37-)  L      OE1 <->   39 ARG   (  39-)  L      NH1    0.19    2.51  INTRA
 270 ILE   (  56-)  H      CD1 <->  492 GLN   (  67-)  C      CD     0.19    3.01  INTRA BF
 257 LYS   (  43-)  H      CE  <->  260 GLU   (  46-)  H      OE1    0.18    2.62  INTRA
 119 PRO   ( 119-)  L      CB  <->  209 PHE   ( 209-)  L      CE2    0.18    3.02  INTRA BF
 422 LYS   ( 208-)  H      N   <->  423 PRO   ( 209-)  H      CD     0.18    2.82  INTRA BF
 386 THR   ( 172-)  H      OG1 <->  585 HOH   ( 357 )  H      O      0.17    2.23  INTRA BL
 151 ASP   ( 151-)  L      N   <->  191 VAL   ( 191-)  L      O      0.16    2.54  INTRA BF
  92 HIS   (  92-)  L      CE1 <->  586 HOH   ( 218 )  C      O      0.16    2.64  INTRA BL
 288 ARG   (  74-)  H      NE  <->  290 ASP   (  76-)  H      OD1    0.16    2.54  INTRA BL
 436 LYS   (  11-)  C      O   <->  464 ASN   (  39-)  C      ND2    0.15    2.55  INTRA BF
 357 ALA   ( 143-)  H      N   <->  405 VAL   ( 191-)  H      O      0.14    2.56  INTRA BF
 271 ASN   (  57-)  H      CG  <->  272 SER   (  58-)  H      N      0.13    2.87  INTRA BF
 270 ILE   (  56-)  H      C   <->  271 ASN   (  57-)  H      O      0.13    2.47  INTRA BF
 578 GLY   ( 153-)  C      C   <->  579 ILE   ( 154-)  C      CG2    0.13    2.97  INTRA BL
And so on for a total of 104 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: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 456 ARG   (  31-)  C      -7.60
 527 GLN   ( 102-)  C      -6.32
 528 ARG   ( 103-)  C      -5.64
 532 GLU   ( 107-)  C      -5.60
 213 GLU   ( 213-)  L      -5.54
 326 GLN   ( 112-)  H      -5.50
  28 PHE   (  28-)  L      -5.30
  41 ASN   (  41-)  L      -5.17
 227 GLN   (  13-)  H      -5.17
 376 ASN   ( 162-)  H      -5.16
 448 GLU   (  23-)  C      -5.15
 256 GLU   (  42-)  H      -5.14
 211 ARG   ( 211-)  L      -5.08
 433 GLU   ( 219-)  H      -5.04

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: L

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: H

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: C

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.

 512 TYR   (  87-)  C   -2.96

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: L

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: C

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.

 585 HOH   ( 309 )  H      O
 585 HOH   ( 311 )  H      O
 586 HOH   ( 225 )  C      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.

  92 HIS   (  92-)  L
 158 ASN   ( 158-)  L
 271 ASN   (  57-)  H
 315 ASN   ( 101-)  H
 326 GLN   ( 112-)  H
 498 HIS   (  73-)  C
 503 HIS   (  78-)  C
 574 GLN   ( 149-)  C

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.

   6 GLN   (   6-)  L      NE2
   7 SER   (   7-)  L      N
  10 ILE   (  10-)  L      N
  27 GLN   (  27-)  L      N
  30 GLY   (  30-)  L      N
 121 SER   ( 121-)  L      OG
 143 GLU   ( 143-)  L      N
 147 GLN   ( 147-)  L      N
 158 ASN   ( 158-)  L      ND2
 159 SER   ( 159-)  L      N
 203 SER   ( 203-)  L      N
 247 TRP   (  33-)  H      NE1
 250 TRP   (  36-)  H      NE1
 268 LYS   (  54-)  H      N
 314 ARG   ( 100-)  H      NH1
 315 ASN   ( 101-)  H      ND2
 327 GLY   ( 113-)  H      N
 352 THR   ( 138-)  H      N
 365 ASP   ( 151-)  H      N
 371 VAL   ( 157-)  H      N
 392 GLN   ( 178-)  H      NE2
 394 SER   ( 180-)  H      OG
 422 LYS   ( 208-)  H      N
 430 LYS   ( 216-)  H      N
 448 GLU   (  23-)  C      N
 450 GLN   (  25-)  C      N
 457 ARG   (  32-)  C      NH1
 460 ALA   (  35-)  C      N
 488 LEU   (  63-)  C      N
 494 CYS   (  69-)  C      N
 496 SER   (  71-)  C      N
 514 THR   (  89-)  C      N
 522 ILE   (  97-)  C      N
 527 GLN   ( 102-)  C      N
 530 THR   ( 105-)  C      OG1
 532 GLU   ( 107-)  C      N
 559 ALA   ( 134-)  C      N
 571 GLU   ( 146-)  C      N

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.

 429 ASP   ( 215-)  H   H-bonding suggests Asn; but Alt-Rotamer
 448 GLU   (  23-)  C   H-bonding suggests Gln
 571 GLU   ( 146-)  C   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 :  -0.053
  2nd generation packing quality :  -0.798
  Ramachandran plot appearance   :  -1.464
  chi-1/chi-2 rotamer normality  :  -3.398 (poor)
  Backbone conformation          :  -0.069

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.379 (tight)
  Bond angles                    :   0.622 (tight)
  Omega angle restraints         :   1.200
  Side chain planarity           :   0.363 (tight)
  Improper dihedral distribution :   0.651
  B-factor distribution          :   1.013
  Inside/Outside distribution    :   0.975

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.1
  2nd generation packing quality :   0.6
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.379 (tight)
  Bond angles                    :   0.622 (tight)
  Omega angle restraints         :   1.200
  Side chain planarity           :   0.363 (tight)
  Improper dihedral distribution :   0.651
  B-factor distribution          :   1.013
  Inside/Outside distribution    :   0.975
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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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
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
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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
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    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
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
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