WHAT IF Check report

This file was created 2012-01-05 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 pdb1p15.ent

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: 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) :105.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

  54 TYR   ( 595-)  A
  97 TYR   ( 638-)  A

Warning: Phenylalanine convention problem

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

  23 PHE   ( 564-)  A
 437 PHE   ( 734-)  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.

  38 ASP   ( 579-)  A
  46 ASP   ( 587-)  A
 101 ASP   ( 642-)  A
 312 ASP   ( 608-)  B
 371 ASP   ( 667-)  B
 488 ASP   ( 785-)  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.

  66 GLU   ( 607-)  A
 112 GLU   ( 653-)  A
 118 GLU   ( 659-)  A
 201 GLU   ( 742-)  A
 267 GLU   ( 563-)  B
 280 GLU   ( 576-)  B
 474 GLU   ( 771-)  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.

 377 THR   ( 673-)  B      CA   CB    1.61    4.2

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.

  35 GLU   ( 576-)  A      N    CA   C   123.05    4.2
  35 GLU   ( 576-)  A      N    CA   CB  102.89   -4.5
  36 ASN   ( 577-)  A      N    CA   C   126.39    5.4
  63 HIS   ( 604-)  A      N    CA   C    91.25   -7.1
  63 HIS   ( 604-)  A      C    CA   CB  118.76    4.6
  87 GLU   ( 628-)  A      N    CA   C   124.44    4.7
  88 GLU   ( 629-)  A     -C    N    CA  130.15    4.7
  88 GLU   ( 629-)  A      N    CA   C    82.67  -10.2
  89 ARG   ( 630-)  A      N    CA   C   132.14    7.5
  90 GLY   ( 631-)  A      N    CA   C    80.13  -11.2
  91 GLN   ( 632-)  A     -C    N    CA  113.26   -4.7
  91 GLN   ( 632-)  A      CA   CB   CG  102.62   -5.7
  93 LYS   ( 634-)  A      C    CA   CB  100.67   -5.0
  95 ALA   ( 636-)  A     -C    N    CA  131.98    5.7
  95 ALA   ( 636-)  A      N    CA   C   133.96    8.1
  96 GLN   ( 637-)  A      N    CA   C    87.25   -8.6
 115 LYS   ( 656-)  A      N    CA   C   126.64    5.5
 116 GLU   ( 657-)  A     -C    N    CA  109.38   -6.8
 116 GLU   ( 657-)  A      N    CA   C   123.91    4.5
 133 ARG   ( 674-)  A     -C    N    CA  131.34    5.4
 133 ARG   ( 674-)  A      N    CA   C    86.52   -8.8
 134 GLU   ( 675-)  A     -C    N    CA  131.20    5.3
 134 GLU   ( 675-)  A      N    CA   C   131.15    7.1
 137 SER   ( 678-)  A      N    CA   C   125.43    5.1
 174 SER   ( 715-)  A      N    CA   C    94.31   -6.0
 230 GLU   ( 771-)  A      N    CA   C    96.53   -5.2
 231 GLN   ( 772-)  A      N    CA   C    89.00   -7.9
 294 ARG   ( 590-)  B      CB   CG   CD  105.44   -4.3
 379 ASN   ( 676-)  B      C    CA   CB  117.77    4.0
 380 LYS   ( 677-)  B     -C    N    CA  128.93    4.0
 380 LYS   ( 677-)  B      N    CA   C   124.09    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.

  38 ASP   ( 579-)  A
  46 ASP   ( 587-)  A
  66 GLU   ( 607-)  A
 101 ASP   ( 642-)  A
 112 GLU   ( 653-)  A
 118 GLU   ( 659-)  A
 201 GLU   ( 742-)  A
 267 GLU   ( 563-)  B
 280 GLU   ( 576-)  B
 312 ASP   ( 608-)  B
 371 ASP   ( 667-)  B
 474 GLU   ( 771-)  B
 488 ASP   ( 785-)  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.

  90 GLY   ( 631-)  A   12.00
  88 GLU   ( 629-)  A    9.82
  96 GLN   ( 637-)  A    9.47
  95 ALA   ( 636-)  A    9.36
 133 ARG   ( 674-)  A    9.28
 231 GLN   ( 772-)  A    8.79
  89 ARG   ( 630-)  A    7.80
 233 GLU   ( 774-)  A    7.03
 137 SER   ( 678-)  A    6.94
 134 GLU   ( 675-)  A    6.72
 174 SER   ( 715-)  A    6.60
  63 HIS   ( 604-)  A    6.56
 115 LYS   ( 656-)  A    5.89
 213 GLN   ( 754-)  A    5.25
 230 GLU   ( 771-)  A    5.09
 164 ILE   ( 705-)  A    4.97
 380 LYS   ( 677-)  B    4.91
  36 ASN   ( 577-)  A    4.81
  87 GLU   ( 628-)  A    4.43
 414 GLN   ( 711-)  B    4.33
 116 GLU   ( 657-)  A    4.25
 232 TYR   ( 773-)  A    4.14
  31 LYS   ( 572-)  A    4.01
 315 ARG   ( 611-)  B    4.00

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 2.164

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.598

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.

 282 THR   ( 578-)  B    -3.5
 232 TYR   ( 773-)  A    -3.2
  64 THR   ( 605-)  A    -3.0
 133 ARG   ( 674-)  A    -3.0
  49 ARG   ( 590-)  A    -3.0
  32 ARG   ( 573-)  A    -2.8
 228 THR   ( 769-)  A    -2.8
 138 ARG   ( 679-)  A    -2.7
 113 LEU   ( 654-)  A    -2.7
  84 THR   ( 625-)  A    -2.7
 209 LEU   ( 750-)  A    -2.7
 103 LEU   ( 644-)  A    -2.6
 223 PRO   ( 764-)  A    -2.6
 329 THR   ( 625-)  B    -2.6
  94 CYS   ( 635-)  A    -2.5
  62 LEU   ( 603-)  A    -2.5
  88 GLU   ( 629-)  A    -2.4
  35 GLU   ( 576-)  A    -2.4
 128 LEU   ( 669-)  A    -2.4
  96 GLN   ( 637-)  A    -2.4
  93 LYS   ( 634-)  A    -2.3
 153 ILE   ( 694-)  A    -2.3
 135 ASN   ( 676-)  A    -2.3
  89 ARG   ( 630-)  A    -2.2
 432 GLY   ( 729-)  B    -2.2
 347 GLY   ( 643-)  B    -2.2
 132 THR   ( 673-)  A    -2.2
 239 VAL   ( 780-)  A    -2.2
  90 GLY   ( 631-)  A    -2.2
 280 GLU   ( 576-)  B    -2.2
 118 GLU   ( 659-)  A    -2.2
 336 GLN   ( 632-)  B    -2.2
  34 GLU   ( 575-)  A    -2.1
 362 GLU   ( 658-)  B    -2.1
   2 ARG   ( 543-)  A    -2.1
  87 GLU   ( 628-)  A    -2.0
  52 ASP   ( 593-)  A    -2.0
 158 LYS   ( 699-)  A    -2.0
  92 GLU   ( 633-)  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.

  32 ARG   ( 573-)  A  Poor phi/psi
  35 GLU   ( 576-)  A  Poor phi/psi
  36 ASN   ( 577-)  A  Poor phi/psi
  49 ARG   ( 590-)  A  Poor phi/psi
  52 ASP   ( 593-)  A  Poor phi/psi
  61 LEU   ( 602-)  A  Poor phi/psi
  62 LEU   ( 603-)  A  Poor phi/psi
  64 THR   ( 605-)  A  Poor phi/psi
  92 GLU   ( 633-)  A  Poor phi/psi
  93 LYS   ( 634-)  A  Poor phi/psi
  94 CYS   ( 635-)  A  Poor phi/psi
  95 ALA   ( 636-)  A  Poor phi/psi
  96 GLN   ( 637-)  A  Poor phi/psi
 101 ASP   ( 642-)  A  Poor phi/psi
 103 LEU   ( 644-)  A  Poor phi/psi
 113 LEU   ( 654-)  A  Poor phi/psi
 114 LYS   ( 655-)  A  Poor phi/psi
 115 LYS   ( 656-)  A  Poor phi/psi
 120 GLU   ( 661-)  A  Poor phi/psi
 133 ARG   ( 674-)  A  Poor phi/psi
 134 GLU   ( 675-)  A  Poor phi/psi
 135 ASN   ( 676-)  A  Poor phi/psi
 138 ARG   ( 679-)  A  Poor phi/psi
 139 GLN   ( 680-)  A  Poor phi/psi
 154 PRO   ( 695-)  A  Poor phi/psi
And so on for a total of 58 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 : -4.013

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.

 441 SER   ( 738-)  B    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!

   5 ASN   ( 546-)  A      0
  18 ILE   ( 559-)  A      0
  23 PHE   ( 564-)  A      0
  31 LYS   ( 572-)  A      0
  32 ARG   ( 573-)  A      0
  34 GLU   ( 575-)  A      0
  35 GLU   ( 576-)  A      0
  36 ASN   ( 577-)  A      0
  37 THR   ( 578-)  A      0
  38 ASP   ( 579-)  A      0
  41 ASN   ( 582-)  A      0
  48 TYR   ( 589-)  A      0
  49 ARG   ( 590-)  A      0
  51 LYS   ( 592-)  A      0
  52 ASP   ( 593-)  A      0
  53 SER   ( 594-)  A      0
  60 PRO   ( 601-)  A      0
  61 LEU   ( 602-)  A      0
  62 LEU   ( 603-)  A      0
  63 HIS   ( 604-)  A      0
  64 THR   ( 605-)  A      0
  75 TRP   ( 616-)  A      0
  77 SER   ( 618-)  A      0
  78 CYS   ( 619-)  A      0
  79 SER   ( 620-)  A      0
And so on for a total of 239 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 : 1.688

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!

 347 GLY   ( 643-)  B   2.12   12
 278 GLY   ( 574-)  B   1.84   11

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...

  91 GLN   ( 632-)  A   1.64
 112 GLU   ( 653-)  A   2.21
 113 LEU   ( 654-)  A   1.81

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]

 223 PRO   ( 764-)  A    0.45 HIGH

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].

  29 PRO   ( 570-)  A  -115.0 envelop C-gamma (-108 degrees)
  60 PRO   ( 601-)  A  -116.1 envelop C-gamma (-108 degrees)
 154 PRO   ( 695-)  A  -132.8 half-chair C-delta/C-gamma (-126 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.

  92 GLU   ( 633-)  A      O   <->   94 CYS   ( 635-)  A      N      0.96    1.74  INTRA BF
 138 ARG   ( 679-)  A      O   <->  140 ILE   ( 681-)  A      N      0.62    2.08  INTRA BF
  95 ALA   ( 636-)  A      CB  <->   97 TYR   ( 638-)  A      CD2    0.59    2.61  INTRA BF
 115 LYS   ( 656-)  A      CB  <->  126 ASP   ( 667-)  A      N      0.59    2.51  INTRA BF
  91 GLN   ( 632-)  A      O   <->   93 LYS   ( 634-)  A      N      0.54    2.16  INTRA BF
 113 LEU   ( 654-)  A      CA  <->  115 LYS   ( 656-)  A      NZ     0.51    2.59  INTRA BF
  63 HIS   ( 604-)  A      N   <->   64 THR   ( 605-)  A      N      0.51    2.09  INTRA BF
 232 TYR   ( 773-)  A      O   <->  235 CYS   ( 776-)  A      N      0.49    2.21  INTRA BF
  62 LEU   ( 603-)  A      CA  <->   65 ILE   ( 606-)  A      CG2    0.47    2.73  INTRA BF
   2 ARG   ( 543-)  A      NH1 <->   19 ILE   ( 560-)  A      O      0.45    2.25  INTRA BF
  94 CYS   ( 635-)  A      SG  <->   95 ALA   ( 636-)  A      N      0.43    2.77  INTRA BF
  92 GLU   ( 633-)  A      C   <->   94 CYS   ( 635-)  A      N      0.41    2.49  INTRA BF
  95 ALA   ( 636-)  A      CB  <->   98 TRP   ( 639-)  A      CZ3    0.39    2.81  INTRA BF
  78 CYS   ( 619-)  A      SG  <->  138 ARG   ( 679-)  A      CD     0.38    3.02  INTRA BF
  62 LEU   ( 603-)  A      N   <->   65 ILE   ( 606-)  A      CG2    0.37    2.73  INTRA BF
   5 ASN   ( 546-)  A      ND2 <->  492 HOH   (  34 )  A      O      0.36    2.34  INTRA BF
 174 SER   ( 715-)  A      N   <->  175 GLY   ( 716-)  A      N      0.35    2.25  INTRA BF
 133 ARG   ( 674-)  A      N   <->  134 GLU   ( 675-)  A      N      0.35    2.25  INTRA BF
 377 THR   ( 673-)  B      CG2 <->  379 ASN   ( 676-)  B      ND2    0.34    2.76  INTRA BF
  95 ALA   ( 636-)  A      CB  <->   96 GLN   ( 637-)  A      N      0.34    2.36  INTRA BF
  96 GLN   ( 637-)  A      N   <->   97 TYR   ( 638-)  A      N      0.34    2.26  INTRA BF
 246 MET   ( 542-)  B      SD  <->  247 ARG   ( 543-)  B      CG     0.33    3.07  INTRA BF
 115 LYS   ( 656-)  A      CB  <->  125 ARG   ( 666-)  A      C      0.33    2.87  INTRA BF
  14 ARG   ( 555-)  A      NH1 <->   93 LYS   ( 634-)  A      C      0.33    2.77  INTRA BF
 415 GLN   ( 712-)  B      NE2 <->  421 HIS   ( 718-)  B      O      0.33    2.37  INTRA BF
And so on for a total of 283 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.

  32 ARG   ( 573-)  A      -8.06
 133 ARG   ( 674-)  A      -7.27
 277 ARG   ( 573-)  B      -7.13
  89 ARG   ( 630-)  A      -7.08
 294 ARG   ( 590-)  B      -6.90
 173 GLN   ( 714-)  A      -6.57
 417 GLN   ( 714-)  B      -6.25
  49 ARG   ( 590-)  A      -6.22
 334 ARG   ( 630-)  B      -6.05
 276 LYS   ( 572-)  B      -5.94
 150 GLU   ( 691-)  A      -5.80
 279 GLU   ( 575-)  B      -5.80
  91 GLN   ( 632-)  A      -5.57
 113 LEU   ( 654-)  A      -5.49
 395 VAL   ( 692-)  B      -5.42
 151 VAL   ( 692-)  A      -5.39
  63 HIS   ( 604-)  A      -5.37
   5 ASN   ( 546-)  A      -5.31
 394 GLU   ( 691-)  B      -5.30
  31 LYS   ( 572-)  A      -5.28
  34 GLU   ( 575-)  A      -5.21
 138 ARG   ( 679-)  A      -5.16
 259 ARG   ( 555-)  B      -5.14
 308 HIS   ( 604-)  B      -5.11
 380 LYS   ( 677-)  B      -5.04
 206 GLU   ( 747-)  A      -5.00

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.

 100 SER   ( 641-)  A       102 - GLY    643- ( A)         -4.39
 150 GLU   ( 691-)  A       153 - ILE    694- ( A)         -5.07
 279 GLU   ( 575-)  B       281 - ASN    577- ( B)         -4.86

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

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

Warning: Water molecules need moving

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

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

 492 HOH   (  89 )  A      O      1.39   27.41   50.80
 492 HOH   ( 113 )  A      O     68.66  -32.37   15.31
 492 HOH   ( 115 )  A      O     28.20   25.68   29.02
 493 HOH   (  53 )  B      O     55.29   -0.23   21.48
 493 HOH   (  57 )  B      O     79.48   -7.23   13.46

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.

 492 HOH   (   6 )  A      O
 492 HOH   (  28 )  A      O
 492 HOH   (  38 )  A      O
 492 HOH   (  45 )  A      O
 492 HOH   (  58 )  A      O
 492 HOH   (  75 )  A      O
 492 HOH   (  88 )  A      O
 492 HOH   (  89 )  A      O
 492 HOH   ( 109 )  A      O
 492 HOH   ( 113 )  A      O
 492 HOH   ( 116 )  A      O
 492 HOH   ( 118 )  A      O
 492 HOH   ( 119 )  A      O
 493 HOH   (  17 )  B      O
 493 HOH   (  57 )  B      O
 493 HOH   (  81 )  B      O
 493 HOH   (  87 )  B      O
 493 HOH   (  90 )  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.

  17 GLN   ( 558-)  A
 135 ASN   ( 676-)  A
 142 GLN   ( 683-)  A
 213 GLN   ( 754-)  A
 221 GLN   ( 762-)  A
 240 GLN   ( 781-)  A
 281 ASN   ( 577-)  B
 295 GLN   ( 591-)  B
 376 ASN   ( 672-)  B
 420 ASN   ( 717-)  B
 465 GLN   ( 762-)  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.

   2 ARG   ( 543-)  A      NH1
   4 GLY   ( 545-)  A      N
  18 ILE   ( 559-)  A      N
  31 LYS   ( 572-)  A      N
  37 THR   ( 578-)  A      N
  43 SER   ( 584-)  A      OG
  50 GLN   ( 591-)  A      N
  59 GLY   ( 600-)  A      N
  62 LEU   ( 603-)  A      N
  63 HIS   ( 604-)  A      N
  65 ILE   ( 606-)  A      N
  70 ARG   ( 611-)  A      NE
  84 THR   ( 625-)  A      N
  94 CYS   ( 635-)  A      N
  96 GLN   ( 637-)  A      N
  97 TYR   ( 638-)  A      N
  98 TRP   ( 639-)  A      N
 101 ASP   ( 642-)  A      N
 104 VAL   ( 645-)  A      N
 112 GLU   ( 653-)  A      N
 121 SER   ( 662-)  A      N
 126 ASP   ( 667-)  A      N
 129 VAL   ( 670-)  A      N
 142 GLN   ( 683-)  A      NE2
 148 TRP   ( 689-)  A      N
And so on for a total of 77 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.

  52 ASP   ( 593-)  A      OD2
 120 GLU   ( 661-)  A      OE2
 126 ASP   ( 667-)  A      OD1
 170 GLN   ( 711-)  A      OE1

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.

 493 HOH   (  83 )  B      O  0.96  K  4 ION-B H2O-B

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.

  52 ASP   ( 593-)  A   H-bonding suggests Asn
  87 GLU   ( 628-)  A   H-bonding suggests Gln
 244 ASP   ( 785-)  A   H-bonding suggests Asn
 280 GLU   ( 576-)  B   H-bonding suggests Gln; but Alt-Rotamer
 485 GLU   ( 782-)  B   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 :  -1.565
  2nd generation packing quality :  -2.014
  Ramachandran plot appearance   :  -4.598 (bad)
  chi-1/chi-2 rotamer normality  :  -4.013 (bad)
  Backbone conformation          :  -1.105

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.435 (tight)
  Bond angles                    :   0.909
  Omega angle restraints         :   0.307 (tight)
  Side chain planarity           :   0.333 (tight)
  Improper dihedral distribution :   0.721
  B-factor distribution          :   0.510
  Inside/Outside distribution    :   1.064

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.4
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -3.8 (poor)
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.435 (tight)
  Bond angles                    :   0.909
  Omega angle restraints         :   0.307 (tight)
  Side chain planarity           :   0.333 (tight)
  Improper dihedral distribution :   0.721
  B-factor distribution          :   0.510
  Inside/Outside distribution    :   1.064
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.