WHAT IF Check report

This file was created 2013-12-09 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 pdb3tnx.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 C

All-atom RMS fit for the two chains : 1.405
CA-only RMS fit for the two chains : 1.151

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 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: A

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'.

  88 TYR   (  97-)  A      CG
  88 TYR   (  97-)  A      CD1
  88 TYR   (  97-)  A      CD2
  88 TYR   (  97-)  A      CE1
  88 TYR   (  97-)  A      CE2
  88 TYR   (  97-)  A      CZ
  88 TYR   (  97-)  A      OH
 398 TYR   (  97-)  C      CG
 398 TYR   (  97-)  C      CD1
 398 TYR   (  97-)  C      CD2
 398 TYR   (  97-)  C      CE1
 398 TYR   (  97-)  C      CE2
 398 TYR   (  97-)  C      CZ
 398 TYR   (  97-)  C      OH
 403 ASN   ( 102-)  C      CG
 403 ASN   ( 102-)  C      OD1
 403 ASN   ( 102-)  C      ND2

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 ASN   (  10-)  A    High
   2 ASP   (  11-)  A    High
   8 ARG   (  17-)  A    High
  80 ASN   (  89-)  A    High
  81 TYR   (  90-)  A    High
  82 THR   (  91-)  A    High
  83 THR   (  92-)  A    High
  84 THR   (  93-)  A    High
  85 GLU   (  94-)  A    High
  86 LEU   (  95-)  A    High
  87 SER   (  96-)  A    High
  88 TYR   (  97-)  A    High
  89 GLU   (  98-)  A    High
  90 GLU   (  99-)  A    High
  91 VAL   ( 100-)  A    High
  92 LEU   ( 101-)  A    High
  93 ASN   ( 102-)  A    High
  94 ASP   ( 103-)  A    High
  95 GLY   ( 104-)  A    High
  96 ASP   ( 105-)  A    High
  97 VAL   ( 106-)  A    High
  98 ASN   ( 107-)  A    High
 311 ASN   (  10-)  C    High
 312 ASP   (  11-)  C    High
 313 LEU   (  12-)  C    High
And so on for a total of 74 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: 4

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: 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

 102 TYR   ( 111-)  A
 146 TYR   ( 155-)  A
 159 TYR   ( 168-)  A
 165 TYR   ( 174-)  A
 184 TYR   ( 193-)  A
 201 TYR   ( 210-)  A
 242 TYR   ( 251-)  A
 268 TYR   ( 277-)  A
 284 TYR   ( 293-)  A
 301 TYR   ( 310-)  A
 306 TYR   ( 315-)  A
 383 TYR   (  82-)  C
 391 TYR   (  90-)  C
 456 TYR   ( 155-)  C
 475 TYR   ( 174-)  C
 486 TYR   ( 185-)  C
 494 TYR   ( 193-)  C
 502 TYR   ( 201-)  C
 511 TYR   ( 210-)  C
 552 TYR   ( 251-)  C
 574 TYR   ( 273-)  C
 578 TYR   ( 277-)  C
 594 TYR   ( 293-)  C
 605 TYR   ( 304-)  C
 611 TYR   ( 310-)  C

Warning: Phenylalanine convention problem

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

 239 PHE   ( 248-)  A
 549 PHE   ( 248-)  C

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.

  45 ASP   (  54-)  A
 312 ASP   (  11-)  C
 355 ASP   (  54-)  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.

   7 GLU   (  16-)  A
  71 GLU   (  80-)  A
  89 GLU   (  98-)  A
 145 GLU   ( 154-)  A
 187 GLU   ( 196-)  A
 197 GLU   ( 206-)  A
 216 GLU   ( 225-)  A
 381 GLU   (  80-)  C
 395 GLU   (  94-)  C
 399 GLU   (  98-)  C
 400 GLU   (  99-)  C
 455 GLU   ( 154-)  C
 497 GLU   ( 196-)  C
 526 GLU   ( 225-)  C
 543 GLU   ( 242-)  C

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.

 216 GLU   ( 225-)  A      CD   OE1   1.35    5.2
 233 GLU   ( 242-)  A      CD   OE2   1.33    4.3
 455 GLU   ( 154-)  C      CD   OE1   1.34    4.7
 526 GLU   ( 225-)  C      CD   OE1   1.34    4.7
 543 GLU   ( 242-)  C      CD   OE1   1.34    4.6

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.

  20 HIS   (  29-)  A      CG   ND1  CE1 109.83    4.2
  60 VAL   (  69-)  A      C    CA   CB   99.86   -5.4
  63 ASP   (  72-)  A     -C    N    CA  133.49    6.5
  63 ASP   (  72-)  A      N    CA   CB  101.38   -5.4
  63 ASP   (  72-)  A      C    CA   CB  102.02   -4.3
 130 SER   ( 139-)  A     -C    N    CA  113.79   -4.4
 293 ASN   ( 302-)  A      N    CA   C    97.50   -4.9
 373 ASP   (  72-)  C     -C    N    CA  129.14    4.1
 373 ASP   (  72-)  C      N    CA   CB  102.54   -4.7
 396 LEU   (  95-)  C      N    CA   C    98.28   -4.6

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.

   7 GLU   (  16-)  A
  45 ASP   (  54-)  A
  71 GLU   (  80-)  A
  89 GLU   (  98-)  A
 145 GLU   ( 154-)  A
 187 GLU   ( 196-)  A
 197 GLU   ( 206-)  A
 216 GLU   ( 225-)  A
 312 ASP   (  11-)  C
 355 ASP   (  54-)  C
 381 GLU   (  80-)  C
 395 GLU   (  94-)  C
 399 GLU   (  98-)  C
 400 GLU   (  99-)  C
 455 GLU   ( 154-)  C
 497 GLU   ( 196-)  C
 526 GLU   ( 225-)  C
 543 GLU   ( 242-)  C

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.

  63 ASP   (  72-)  A      CA     6.2    46.01    33.73
The average deviation= 1.001

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.

 357 THR   (  56-)  C    6.00
 396 LEU   (  95-)  C    5.26
 293 ASN   ( 302-)  A    4.65
 402 LEU   ( 101-)  C    4.38

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.510

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.

 392 THR   (  91-)  C    -3.7
  82 THR   (  91-)  A    -3.6
  83 THR   (  92-)  A    -3.6
 394 THR   (  93-)  C    -3.5
 494 TYR   ( 193-)  C    -3.4
 184 TYR   ( 193-)  A    -3.1
 214 TYR   ( 223-)  A    -2.8
 402 LEU   ( 101-)  C    -2.7
 357 THR   (  56-)  C    -2.7
 524 TYR   ( 223-)  C    -2.6
 397 SER   (  96-)  C    -2.6
 152 LEU   ( 161-)  A    -2.6
 542 LEU   ( 241-)  C    -2.5
  89 GLU   (  98-)  A    -2.5
 333 ILE   (  32-)  C    -2.5
 409 ILE   ( 108-)  C    -2.4
 611 TYR   ( 310-)  C    -2.4
 356 GLU   (  55-)  C    -2.4
  85 GLU   (  94-)  A    -2.4
 395 GLU   (  94-)  C    -2.4
  84 THR   (  93-)  A    -2.4
 313 LEU   (  12-)  C    -2.4
 619 LYS   ( 318-)  C    -2.3
 368 LEU   (  67-)  C    -2.3
 259 VAL   ( 268-)  A    -2.3
And so on for a total of 63 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   2 ASP   (  11-)  A  Poor phi/psi
  51 ASN   (  60-)  A  Poor phi/psi
  59 ASN   (  68-)  A  Poor phi/psi
  63 ASP   (  72-)  A  omega poor
  78 ALA   (  87-)  A  Poor phi/psi
  79 GLY   (  88-)  A  omega poor
  82 THR   (  91-)  A  Poor phi/psi, omega poor
  83 THR   (  92-)  A  Poor phi/psi
  84 THR   (  93-)  A  Poor phi/psi
  85 GLU   (  94-)  A  Poor phi/psi
  87 SER   (  96-)  A  Poor phi/psi
  89 GLU   (  98-)  A  Poor phi/psi
  91 VAL   ( 100-)  A  omega poor
  93 ASN   ( 102-)  A  Poor phi/psi
  94 ASP   ( 103-)  A  Poor phi/psi
  96 ASP   ( 105-)  A  Poor phi/psi
 146 TYR   ( 155-)  A  omega poor
 153 ASP   ( 162-)  A  omega poor
 226 GLN   ( 235-)  A  Poor phi/psi
 247 PHE   ( 256-)  A  omega poor
 249 GLY   ( 258-)  A  PRO omega poor
 256 ASP   ( 265-)  A  Poor phi/psi
 291 THR   ( 300-)  A  omega poor
 298 CYS   ( 307-)  A  Poor phi/psi
 312 ASP   (  11-)  C  Poor phi/psi
And so on for a total of 52 lines.

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

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

chi-1/chi-2 correlation Z-score : -4.438

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.

 440 SER   ( 139-)  C    0.37

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!

   3 LEU   (  12-)  A      0
   4 THR   (  13-)  A      0
  22 LYS   (  31-)  A      0
  25 LYS   (  34-)  A      0
  26 ASN   (  35-)  A      0
  50 LYS   (  59-)  A      0
  51 ASN   (  60-)  A      0
  52 ASN   (  61-)  A      0
  58 LEU   (  67-)  A      0
  59 ASN   (  68-)  A      0
  60 VAL   (  69-)  A      0
  61 PHE   (  70-)  A      0
  63 ASP   (  72-)  A      0
  73 TYR   (  82-)  A      0
  74 THR   (  83-)  A      0
  76 SER   (  85-)  A      0
  77 ILE   (  86-)  A      0
  78 ALA   (  87-)  A      0
  80 ASN   (  89-)  A      0
  82 THR   (  91-)  A      0
  83 THR   (  92-)  A      0
  84 THR   (  93-)  A      0
  85 GLU   (  94-)  A      0
  86 LEU   (  95-)  A      0
  87 SER   (  96-)  A      0
And so on for a total of 288 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!

 280 GLY   ( 289-)  A   1.60   12
 590 GLY   ( 289-)  C   1.53   16

Warning: Unusual peptide bond conformations

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

  84 THR   (  93-)  A   1.84

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].

 185 PRO   ( 194-)  A    14.7 half-chair N/C-delta (18 degrees)
 200 PRO   ( 209-)  A   103.7 envelop C-beta (108 degrees)
 213 PRO   ( 222-)  A   -60.5 half-chair C-beta/C-alpha (-54 degrees)
 523 PRO   ( 222-)  C    47.0 half-chair C-delta/C-gamma (54 degrees)
 560 PRO   ( 259-)  C   -43.9 envelop C-alpha (-36 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.

 332 LYS   (  31-)  C      NZ  <->  625 HOH   ( 346 )  C      O      0.61    2.09  INTRA BF
 112 THR   ( 121-)  A      O   <->  272 ARG   ( 281-)  A      NH2    0.61    2.09  INTRA BL
 318 ARG   (  17-)  C      CD  <->  625 HOH   ( 342 )  C      O      0.42    2.38  INTRA BF
   4 THR   (  13-)  A      CG2 <->  624 HOH   ( 420 )  A      O      0.41    2.39  INTRA BF
 390 ASN   (  89-)  C      O   <->  392 THR   (  91-)  C      N      0.41    2.29  INTRA BF
  97 VAL   ( 106-)  A      CG2 <->  624 HOH   ( 415 )  A      O      0.40    2.40  INTRA BF
 181 ARG   ( 190-)  A      CD  <->  624 HOH   ( 411 )  A      O      0.38    2.42  INTRA BL
 288 LYS   ( 297-)  A      NZ  <->  624 HOH   ( 370 )  A      O      0.35    2.35  INTRA BL
 115 LYS   ( 124-)  A      NZ  <->  145 GLU   ( 154-)  A      OE2    0.34    2.36  INTRA BL
 520 GLN   ( 219-)  C      CB  <->  615 PHE   ( 314-)  C      CE2    0.32    2.88  INTRA BF
 150 GLU   ( 159-)  A      OE2 <->  179 HIS   ( 188-)  A      ND1    0.32    2.38  INTRA BL
 243 ARG   ( 252-)  A      NH2 <->  624 HOH   ( 407 )  A      O      0.31    2.39  INTRA BL
 384 THR   (  83-)  C      CG2 <->  385 GLY   (  84-)  C      N      0.30    2.70  INTRA BF
 462 LEU   ( 161-)  C      O   <->  500 GLN   ( 199-)  C      NE2    0.29    2.41  INTRA BF
 390 ASN   (  89-)  C      C   <->  392 THR   (  91-)  C      N      0.29    2.61  INTRA BF
 315 SER   (  14-)  C      C   <->  625 HOH   ( 327 )  C      O      0.28    2.52  INTRA BF
   4 THR   (  13-)  A      OG1 <->    8 ARG   (  17-)  A      NH1    0.26    2.44  INTRA BF
 251 CYS   ( 260-)  A      SG  <->  298 CYS   ( 307-)  A      N      0.25    3.05  INTRA BL
 426 ASN   ( 125-)  C      OD1 <->  428 GLY   ( 127-)  C      N      0.25    2.45  INTRA BL
 609 GLY   ( 308-)  C      O   <->  611 TYR   ( 310-)  C      N      0.25    2.45  INTRA BF
 135 ILE   ( 144-)  A      CG2 <->  136 ILE   ( 145-)  A      N      0.24    2.76  INTRA BL
 440 SER   ( 139-)  C      OG  <->  582 ARG   ( 281-)  C      NH1    0.23    2.47  INTRA BL
 315 SER   (  14-)  C      O   <->  319 LEU   (  18-)  C      CD1    0.22    2.58  INTRA BF
 315 SER   (  14-)  C      CA  <->  625 HOH   ( 327 )  C      O      0.22    2.58  INTRA BF
 525 ASN   ( 224-)  C      OD1 <->  527 GLY   ( 226-)  C      N      0.22    2.48  INTRA BF
And so on for a total of 127 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: 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.

  86 LEU   (  95-)  A      -6.93
 502 TYR   ( 201-)  C      -6.87
  81 TYR   (  90-)  A      -6.06
  89 GLU   (  98-)  A      -5.85
 335 LYS   (  34-)  C      -5.74
 192 TYR   ( 201-)  A      -5.72
 391 TYR   (  90-)  C      -5.68
 313 LEU   (  12-)  C      -5.61
 417 GLN   ( 116-)  C      -5.61
 399 GLU   (  98-)  C      -5.61
 485 GLN   ( 184-)  C      -5.58
 107 GLN   ( 116-)  A      -5.58
 396 LEU   (  95-)  C      -5.55
  25 LYS   (  34-)  A      -5.50
 175 GLN   ( 184-)  A      -5.43
 449 ARG   ( 148-)  C      -5.41
 469 TYR   ( 168-)  C      -5.33
 159 TYR   ( 168-)  A      -5.32
  93 ASN   ( 102-)  A      -5.29
 412 TYR   ( 111-)  C      -5.20
  98 ASN   ( 107-)  A      -5.16
 511 TYR   ( 210-)  C      -5.10
 162 ASN   ( 171-)  A      -5.07
 139 ARG   ( 148-)  A      -5.07
 190 GLN   ( 199-)  A      -5.03

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.

  92 LEU   ( 101-)  A        94 - ASP    103- ( A)         -4.54
 500 GLN   ( 199-)  C       502 - TYR    201- ( C)         -5.21

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: 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.

  88 TYR   (  97-)  A   -3.29
 559 GLY   ( 258-)  C   -3.11
 398 TYR   (  97-)  C   -3.03
 249 GLY   ( 258-)  A   -2.89
 142 ASN   ( 151-)  A   -2.85

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: 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.

 624 HOH   ( 404 )  A      O
 624 HOH   ( 416 )  A      O
 625 HOH   ( 341 )  C      O
 625 HOH   ( 347 )  C      O
Marked this atom as acceptor  623  CL  ( 320-) A     CL

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.

  20 HIS   (  29-)  A
  26 ASN   (  35-)  A
  51 ASN   (  60-)  A
 142 ASN   ( 151-)  A
 190 GLN   ( 199-)  A
 376 ASN   (  75-)  C
 536 GLN   ( 235-)  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.

   2 ASP   (  11-)  A      N
   8 ARG   (  17-)  A      NH1
  26 ASN   (  35-)  A      N
  48 ASN   (  57-)  A      ND2
  49 LYS   (  58-)  A      N
  51 ASN   (  60-)  A      N
  54 TYR   (  63-)  A      N
  63 ASP   (  72-)  A      N
  65 SER   (  74-)  A      N
  74 THR   (  83-)  A      OG1
  76 SER   (  85-)  A      OG
  78 ALA   (  87-)  A      N
  83 THR   (  92-)  A      N
  84 THR   (  93-)  A      N
  86 LEU   (  95-)  A      N
  87 SER   (  96-)  A      N
  88 TYR   (  97-)  A      N
  91 VAL   ( 100-)  A      N
  92 LEU   ( 101-)  A      N
 111 VAL   ( 120-)  A      N
 124 TRP   ( 133-)  A      N
 148 GLU   ( 157-)  A      N
 157 ARG   ( 166-)  A      NH1
 167 TRP   ( 176-)  A      N
 188 GLY   ( 197-)  A      N
And so on for a total of 74 lines.

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.

  35 GLU   (  44-)  A      OE2
 179 HIS   ( 188-)  A      ND1
 210 GLN   ( 219-)  A      OE1
 257 HIS   ( 266-)  A      ND1
 404 ASP   ( 103-)  C      OD1
 489 HIS   ( 188-)  C      ND1
 567 HIS   ( 266-)  C      ND1

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.

  85 GLU   (  94-)  A   H-bonding suggests Gln
  90 GLU   (  99-)  A   H-bonding suggests Gln; but Alt-Rotamer
 256 ASP   ( 265-)  A   H-bonding suggests Asn
 404 ASP   ( 103-)  C   H-bonding suggests Asn; but Alt-Rotamer
 406 ASP   ( 105-)  C   H-bonding suggests Asn; but Alt-Rotamer
 443 GLU   ( 142-)  C   H-bonding suggests Gln; but Alt-Rotamer
 566 ASP   ( 265-)  C   H-bonding suggests Asn
 591 GLU   ( 290-)  C   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.215
  2nd generation packing quality :  -2.168
  Ramachandran plot appearance   :  -3.510 (poor)
  chi-1/chi-2 rotamer normality  :  -4.438 (bad)
  Backbone conformation          :  -0.837

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.741
  Bond angles                    :   0.799
  Omega angle restraints         :   1.117
  Side chain planarity           :   0.552 (tight)
  Improper dihedral distribution :   0.882
  B-factor distribution          :   0.468
  Inside/Outside distribution    :   1.082

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 : 2.62


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.741
  Bond angles                    :   0.799
  Omega angle restraints         :   1.117
  Side chain planarity           :   0.552 (tight)
  Improper dihedral distribution :   0.882
  B-factor distribution          :   0.468
  Inside/Outside distribution    :   1.082
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

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Bond lengths and angles, DNA/RNA
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    Acta Crystallogr. D52, 57--64 (1996).

DSSP
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      Dictionary of protein secondary structure: pattern
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    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
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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.