WHAT IF Check report

This file was created 2011-12-15 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 pdb1fyt.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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

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'.

 519 GLN   ( 152-)  D      CG
 519 GLN   ( 152-)  D      CD
 519 GLN   ( 152-)  D      OE1
 519 GLN   ( 152-)  D      NE2
 521 LYS   ( 154-)  D      CG
 521 LYS   ( 154-)  D      CD
 521 LYS   ( 154-)  D      CE
 521 LYS   ( 154-)  D      NZ
 524 ASP   ( 157-)  D      CG
 524 ASP   ( 157-)  D      OD1
 524 ASP   ( 157-)  D      OD2

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

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

 225 TYR   (  47-)  B
 280 TYR   ( 102-)  B
 292 TYR   ( 123-)  B
 403 TYR   (  31-)  D
 407 TYR   (  35-)  D
 460 TYR   (  88-)  D
 526 TYR   ( 159-)  D
 618 TYR   (  50-)  E
 782 TYR   ( 218-)  E

Warning: Phenylalanine convention problem

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

 291 PHE   ( 122-)  B
 469 PHE   (  97-)  D
 554 PHE   ( 187-)  D
 588 PHE   (  20-)  E
 616 PHE   (  48-)  E
 672 PHE   ( 108-)  E

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.

 158 ASP   ( 159-)  A
 180 ASP   ( 181-)  A
 492 ASP   ( 122-)  D
 568 ASP   ( 201-)  D
 596 ASP   (  28-)  E
 619 ASP   (  51-)  E
 683 ASP   ( 119-)  E

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.

 165 GLU   ( 166-)  A
 297 GLU   ( 128-)  B
 345 GLU   ( 176-)  B
 356 GLU   ( 187-)  B
 386 GLU   (  14-)  D
 585 GLU   (  17-)  E
 691 GLU   ( 127-)  E

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.

  15 PRO   (  16-)  A      C    O     1.32    4.4

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.

  14 ASN   (  15-)  A     -C    N    CA  111.76   -5.5
  14 ASN   (  15-)  A      N    CA   C   130.57    6.9
  14 ASN   (  15-)  A      CA   CB   CG  108.56   -4.0
  87 GLU   (  88-)  A      N    CA   C    95.46   -5.6
 117 ASN   ( 118-)  A      ND2  CG   OD1 127.71    5.1
 276 LYS   (  98-)  B      N    CA   C    99.80   -4.1
 333 VAL   ( 164-)  B      N    CA   C    99.97   -4.0
 504 SER   ( 137-)  D      N    CA   C    95.93   -5.5
 561 ASN   ( 194-)  D      N    CA   C    97.07   -5.0
 563 SER   ( 196-)  D      N    CA   C   123.81    4.5
 671 THR   ( 107-)  E      N    CA   C    98.76   -4.4
 691 GLU   ( 127-)  E      N    CA   C    96.36   -5.3

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.

 158 ASP   ( 159-)  A
 165 GLU   ( 166-)  A
 180 ASP   ( 181-)  A
 297 GLU   ( 128-)  B
 345 GLU   ( 176-)  B
 356 GLU   ( 187-)  B
 386 GLU   (  14-)  D
 492 ASP   ( 122-)  D
 568 ASP   ( 201-)  D
 585 GLU   (  17-)  E
 596 ASP   (  28-)  E
 619 ASP   (  51-)  E
 683 ASP   ( 119-)  E
 691 GLU   ( 127-)  E

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.

 504 SER   ( 137-)  D    6.19
  14 ASN   (  15-)  A    6.18
  87 GLU   (  88-)  A    6.03
 691 GLU   ( 127-)  E    5.64
 561 ASN   ( 194-)  D    4.80
 563 SER   ( 196-)  D    4.65
 671 THR   ( 107-)  E    4.51
 276 LYS   (  98-)  B    4.43
 433 GLY   (  61-)  D    4.32
 176 HIS   ( 177-)  A    4.04

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 443 THR   (  71-)  D    -3.6
  15 PRO   (  16-)  A    -2.8
 565 ILE   ( 198-)  D    -2.5
 563 SER   ( 196-)  D    -2.5
 142 HIS   ( 143-)  A    -2.5
 419 LEU   (  47-)  D    -2.5
 634 VAL   (  67-)  E    -2.4
 112 THR   ( 113-)  A    -2.4
 809 ARG   ( 245-)  E    -2.4
 748 PRO   ( 184-)  E    -2.4
 400 VAL   (  28-)  D    -2.4
 308 LYS   ( 139-)  B    -2.3
 615 TYR   (  47-)  E    -2.2
 133 GLU   ( 134-)  A    -2.2
 326 THR   ( 157-)  B    -2.1
 207 ARG   (  29-)  B    -2.1
 445 PHE   (  73-)  D    -2.1
 314 THR   ( 145-)  B    -2.1
 690 PRO   ( 126-)  E    -2.1
 509 THR   ( 142-)  D    -2.1
 397 SER   (  25-)  D    -2.1
 423 SER   (  51-)  D    -2.1
 212 GLN   (  34-)  B    -2.1
 182 ARG   (   4-)  B    -2.1
 122 ARG   ( 123-)  A    -2.1
 216 VAL   (  38-)  B    -2.0
 666 LEU   (  99-)  E    -2.0
 375 VAL   (   3-)  D    -2.0
 539 ASP   ( 172-)  D    -2.0
 742 GLN   ( 178-)  E    -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.

  14 ASN   (  15-)  A  Poor phi/psi
  17 GLN   (  18-)  A  Poor phi/psi
  77 ASN   (  78-)  A  Poor phi/psi
  99 ARG   ( 100-)  A  Poor phi/psi
 110 LYS   ( 111-)  A  Poor phi/psi
 112 THR   ( 113-)  A  PRO omega poor
 114 PRO   ( 115-)  A  Poor phi/psi
 123 ASN   ( 124-)  A  Poor phi/psi
 128 THR   ( 129-)  A  Poor phi/psi
 130 GLY   ( 131-)  A  Poor phi/psi
 142 HIS   ( 143-)  A  Poor phi/psi
 197 ASN   (  19-)  B  Poor phi/psi
 212 GLN   (  34-)  B  Poor phi/psi
 268 THR   (  90-)  B  Poor phi/psi
 292 TYR   ( 123-)  B  PRO omega poor
 322 TRP   ( 153-)  B  Poor phi/psi
 387 GLY   (  15-)  D  Poor phi/psi
 412 ASN   (  40-)  D  Poor phi/psi
 423 SER   (  51-)  D  Poor phi/psi
 443 THR   (  71-)  D  Poor phi/psi
 458 ALA   (  86-)  D  Poor phi/psi
 510 ASP   ( 143-)  D  Poor phi/psi
 539 ASP   ( 172-)  D  Poor phi/psi
 562 ASN   ( 195-)  D  Poor phi/psi
 596 ASP   (  28-)  E  Poor phi/psi
 621 LYS   (  53-)  E  Poor phi/psi
 667 PRO   ( 100-)  E  Poor phi/psi
 706 GLN   ( 142-)  E  Poor phi/psi
 718 PHE   ( 154-)  E  PRO omega poor
 720 ASP   ( 156-)  E  Poor phi/psi
 797 PRO   ( 233-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.761

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.

 703 SER   ( 139-)  E    0.33

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 GLU   (   4-)  A      0
   4 HIS   (   5-)  A      0
  10 GLU   (  11-)  A      0
  14 ASN   (  15-)  A      0
  17 GLN   (  18-)  A      0
  22 MET   (  23-)  A      0
  25 PHE   (  26-)  A      0
  31 PHE   (  32-)  A      0
  32 HIS   (  33-)  A      0
  50 PHE   (  51-)  A      0
  52 SER   (  53-)  A      0
  78 TYR   (  79-)  A      0
  93 ASN   (  94-)  A      0
  98 LEU   (  99-)  A      0
 102 ASN   ( 103-)  A      0
 109 ASP   ( 110-)  A      0
 110 LYS   ( 111-)  A      0
 111 PHE   ( 112-)  A      0
 112 THR   ( 113-)  A      0
 113 PRO   ( 114-)  A      0
 114 PRO   ( 115-)  A      0
 115 VAL   ( 116-)  A      0
 122 ARG   ( 123-)  A      0
 128 THR   ( 129-)  A      0
 129 THR   ( 130-)  A      0
And so on for a total of 342 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 : 1.528

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...

 562 ASN   ( 195-)  D   1.76

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]

  15 PRO   (  16-)  A    0.46 HIGH
  95 PRO   (  96-)  A    0.45 HIGH
 719 PRO   ( 155-)  E    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].

 690 PRO   ( 126-)  E    46.7 half-chair C-delta/C-gamma (54 degrees)
 797 PRO   ( 233-)  E    51.1 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.

  38 LYS   (  39-)  A      NZ  <->  815 HOH   ( 512 )  A      O      0.48    2.22  INTRA BF
 569 THR   ( 202-)  D      CG2 <->  819 HOH   ( 288 )  E      O      0.43    2.37  INTRA BF
  14 ASN   (  15-)  A      O   <->   15 PRO   (  16-)  A      C      0.42    2.18  INTRA BF
 146 LYS   ( 147-)  A      NZ  <->  148 HIS   ( 149-)  A      CE1    0.29    2.81  INTRA BL
 656 MET   (  89-)  E      CE  <->  676 THR   ( 112-)  E      C      0.27    2.93  INTRA
 776 ARG   ( 212-)  E      NE  <->  819 HOH   ( 285 )  E      O      0.26    2.44  INTRA BF
  75 ARG   (  76-)  A      NH1 <->  235 ASP   (  57-)  B      OD2    0.25    2.45  INTRA BL
 679 THR   ( 115-)  E      OG1 <->  721 HIS   ( 157-)  E      CE1    0.25    2.55  INTRA BL
  16 ASP   (  17-)  A      CG  <->  184 ARG   (   6-)  B      NH1    0.24    2.86  INTRA
  16 ASP   (  17-)  A      OD1 <->  184 ARG   (   6-)  B      NH1    0.24    2.46  INTRA BL
  14 ASN   (  15-)  A      O   <->   16 ASP   (  17-)  A      N      0.22    2.48  INTRA BF
 432 ASN   (  60-)  D      O   <->  449 LYS   (  77-)  D      NZ     0.22    2.48  INTRA BF
 453 HIS   (  81-)  D      CD2 <->  454 MET   (  82-)  D      N      0.22    2.78  INTRA BF
 400 VAL   (  28-)  D      CG2 <->  401 PRO   (  29-)  D      CD     0.21    2.99  INTRA BF
 656 MET   (  89-)  E      CE  <->  677 ARG   ( 113-)  E      N      0.21    2.89  INTRA
 740 ASP   ( 176-)  E      OD1 <->  760 ARG   ( 196-)  E      NH2    0.20    2.50  INTRA BF
 555 ALA   ( 188-)  D      O   <->  558 ASN   ( 191-)  D      ND2    0.20    2.50  INTRA BF
 558 ASN   ( 191-)  D      ND2 <->  559 ALA   ( 192-)  D      N      0.19    2.56  INTRA BF
  14 ASN   (  15-)  A      O   <->   17 GLN   (  18-)  A      N      0.19    2.51  INTRA BF
 159 VAL   ( 160-)  A      CG1 <->  176 HIS   ( 177-)  A      CE1    0.19    3.01  INTRA BF
 409 GLN   (  37-)  D      NE2 <->  605 GLN   (  37-)  E      NE2    0.18    2.67  INTRA BL
 688 PHE   ( 124-)  E      CZ  <->  754 ARG   ( 190-)  E      NH2    0.18    2.92  INTRA
 776 ARG   ( 212-)  E      NH1 <->  778 GLN   ( 214-)  E      OE1    0.18    2.52  INTRA BF
  61 ASN   (  62-)  A      CG  <->  367 THR   ( 313-)  C      CG2    0.16    3.04  INTRA BL
 181 THR   (   3-)  B      CG2 <->  182 ARG   (   4-)  B      NH1    0.16    2.94  INTRA BF
And so on for a total of 142 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

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.

 182 ARG   (   4-)  B      -7.27
 668 TYR   ( 104-)  E      -7.25
 809 ARG   ( 245-)  E      -6.79
  99 ARG   ( 100-)  A      -6.68
 489 GLN   ( 119-)  D      -6.47
 378 LEU   (   6-)  D      -6.45
 704 HIS   ( 140-)  E      -5.92
 412 ASN   (  40-)  D      -5.78
 308 LYS   ( 139-)  B      -5.60
 358 ARG   ( 189-)  B      -5.53
 335 ARG   ( 166-)  B      -5.22
 742 GLN   ( 178-)  E      -5.17
 432 ASN   (  60-)  D      -5.16
  49 ARG   (  50-)  A      -5.09

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: 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

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: D

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: E

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.

 792 GLN   ( 228-)  E   -2.89
 666 LEU   (  99-)  E   -2.50

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

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

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.

 815 HOH   ( 520 )  A      O
Bound group on Asn; dont flip   77 ASN  (  78-) A
Bound to:  811 NAG  ( 501-) A
Bound group on Asn; dont flip  117 ASN  ( 118-) A
Bound to:  812 NAG  ( 511-) A

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.

 148 HIS   ( 149-)  A
 319 ASN   ( 150-)  B
 325 GLN   ( 156-)  B
 373 GLN   (   1-)  D
 395 ASN   (  23-)  D
 409 GLN   (  37-)  D
 453 HIS   (  81-)  D
 487 ASN   ( 117-)  D
 574 GLN   (   6-)  E
 721 HIS   ( 157-)  E

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.

  44 LEU   (  45-)  A      N
  68 ASN   (  69-)  A      ND2
 120 TRP   ( 121-)  A      NE1
 167 TRP   ( 168-)  A      N
 171 GLU   ( 172-)  A      N
 182 ARG   (   4-)  B      N
 185 PHE   (   7-)  B      N
 215 SER   (  37-)  B      OG
 224 GLU   (  46-)  B      N
 225 TYR   (  47-)  B      OH
 242 GLN   (  64-)  B      NE2
 244 ASP   (  66-)  B      N
 249 ARG   (  71-)  B      NH2
 253 VAL   (  75-)  B      N
 259 HIS   (  81-)  B      N
 278 THR   ( 100-)  B      OG1
 335 ARG   ( 166-)  B      N
 359 ALA   ( 190-)  B      N
 366 ASN   ( 312-)  C      ND2
 378 LEU   (   6-)  D      N
 423 SER   (  51-)  D      N
 471 ASN   (  99-)  D      ND2
 472 GLU   ( 102-)  D      N
 505 VAL   ( 138-)  D      N
 511 PHE   ( 144-)  D      N
 512 ASP   ( 145-)  D      N
 517 VAL   ( 150-)  D      N
 530 LYS   ( 163-)  D      N
 567 GLU   ( 200-)  D      N
 574 GLN   (   6-)  E      NE2
 583 THR   (  15-)  E      OG1
 591 CYS   (  23-)  E      N
 597 HIS   (  29-)  E      N
 611 LEU   (  43-)  E      N
 618 TYR   (  50-)  E      N
 636 ARG   (  69-)  E      N
 647 GLU   (  80-)  E      N
 655 SER   (  88-)  E      OG
 668 TYR   ( 104-)  E      N
 675 GLY   ( 111-)  E      N
 676 THR   ( 112-)  E      OG1
 698 SER   ( 134-)  E      N
 742 GLN   ( 178-)  E      N
 754 ARG   ( 190-)  E      NE
 760 ARG   ( 196-)  E      NE
 760 ARG   ( 196-)  E      NH1
 776 ARG   ( 212-)  E      NH1

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.

  10 GLU   (  11-)  A      OE1
  24 ASP   (  25-)  A      OD2
  65 ASP   (  66-)  A      OD2
 568 ASP   ( 201-)  D      OD2

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.

 816 HOH   ( 202 )  B      O  1.14  K  4 ION-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.

  65 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
  97 GLU   (  98-)  A   H-bonding suggests Gln
 158 ASP   ( 159-)  A   H-bonding suggests Asn; but Alt-Rotamer
 331 GLU   ( 162-)  B   H-bonding suggests Gln
 568 ASP   ( 201-)  D   H-bonding suggests Asn; but Alt-Rotamer
 746 GLU   ( 182-)  E   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 :   0.179
  2nd generation packing quality :  -1.061
  Ramachandran plot appearance   :  -1.156
  chi-1/chi-2 rotamer normality  :  -2.761
  Backbone conformation          :  -0.240

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.379 (tight)
  Bond angles                    :   0.704
  Omega angle restraints         :   0.278 (tight)
  Side chain planarity           :   0.330 (tight)
  Improper dihedral distribution :   0.654
  B-factor distribution          :   0.524
  Inside/Outside distribution    :   1.019

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 :   1.4
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.379 (tight)
  Bond angles                    :   0.704
  Omega angle restraints         :   0.278 (tight)
  Side chain planarity           :   0.330 (tight)
  Improper dihedral distribution :   0.654
  B-factor distribution          :   0.524
  Inside/Outside distribution    :   1.019
==============

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

WHAT_CHECK (verification routines from WHAT IF)
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    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
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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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    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.