WHAT IF Check report

This file was created 2013-01-10 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb4fqx.ent

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 752 NAG   ( 201-)  A  -   O4  bound to  753 NAG   ( 202-)  A  -   C1

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: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Missing atoms

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

 131 PHE   ( 145-)  C      CG
 131 PHE   ( 145-)  C      CD1
 131 PHE   ( 145-)  C      CD2
 131 PHE   ( 145-)  C      CE1
 131 PHE   ( 145-)  C      CE2
 131 PHE   ( 145-)  C      CZ
 524 GLU   ( 141-)  A      CG
 524 GLU   ( 141-)  A      CD
 524 GLU   ( 141-)  A      OE1
 524 GLU   ( 141-)  A      OE2
 635 LYS   (  65-)  B      CG
 635 LYS   (  65-)  B      CD
 635 LYS   (  65-)  B      CE
 635 LYS   (  65-)  B      NZ

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   (  15-)  C    High
   2 HIS   (  16-)  C    High
  30 PHE   (  44-)  C    High
  31 PHE   (  45-)  C    High
  32 ASP   (  46-)  C    High
  34 SER   (  48-)  C    High
  35 GLN   (  49-)  C    High
  36 ASN   (  50-)  C    High
  37 THR   (  51-)  C    High
  42 LEU   (  56-)  C    High
  44 GLU   (  58-)  C    High
  45 PHE   (  59-)  C    High
  46 ALA   (  60-)  C    High
  47 ASP   (  61-)  C    High
  48 TRP   (  62-)  C    High
  49 ALA   (  63-)  C    High
  50 GLN   (  64-)  C    High
  51 GLU   (  65-)  C    High
  52 GLN   (  66-)  C    High
  53 GLY   (  67-)  C    High
  54 ASP   (  68-)  C    High
  55 ALA   (  69-)  C    High
  56 PRO   (  70-)  C    High
  57 ALA   (  71-)  C    High
  63 GLU   (  77-)  C    High
And so on for a total of 110 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: 18

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: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  84 ARG   (  98-)  C

Warning: Tyrosine convention problem

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

 176 TYR   ( 190-)  C
 356 TYR   ( 172-)  D
 533 TYR   ( 150-)  A

Warning: Phenylalanine convention problem

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

 212 PHE   (  28-)  D
 587 PHE   (  17-)  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.

  54 ASP   (  68-)  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.

  98 GLU   ( 112-)  C
 155 GLU   ( 169-)  C
 167 GLU   ( 181-)  C
 386 GLU   (   3-)  A
 387 GLU   (   4-)  A
 481 GLU   (  98-)  A
 517 GLU   ( 134-)  A
 541 GLU   ( 158-)  A
 549 GLU   ( 166-)  A
 657 GLU   (  87-)  B
 666 GLU   (  96-)  B
 689 GLU   ( 128-)  B
 748 GLU   ( 187-)  B

Geometric checks

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.

  54 ASP   (  68-)  C
  84 ARG   (  98-)  C
  98 GLU   ( 112-)  C
 155 GLU   ( 169-)  C
 167 GLU   ( 181-)  C
 386 GLU   (   3-)  A
 387 GLU   (   4-)  A
 481 GLU   (  98-)  A
 517 GLU   ( 134-)  A
 541 GLU   ( 158-)  A
 549 GLU   ( 166-)  A
 657 GLU   (  87-)  B
 666 GLU   (  96-)  B
 689 GLU   ( 128-)  B
 748 GLU   ( 187-)  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.

  55 ALA   (  69-)  C    5.32

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.

 329 HIS   ( 145-)  D    -3.3
 342 THR   ( 158-)  D    -2.9
 343 LEU   ( 159-)  D    -2.7
 133 PRO   ( 147-)  C    -2.7
 348 LEU   ( 164-)  D    -2.6
 399 PRO   (  16-)  A    -2.6
 152 PHE   ( 166-)  C    -2.6
 226 LYS   (  42-)  D    -2.5
 685 PRO   ( 124-)  B    -2.4
 129 GLU   ( 143-)  C    -2.4
 422 LYS   (  39-)  A    -2.3
 475 LEU   (  92-)  A    -2.3
 657 GLU   (  87-)  B    -2.3
 496 THR   ( 113-)  A    -2.3
  73 GLY   (  87-)  C    -2.3
 688 ILE   ( 127-)  B    -2.3
 718 THR   ( 157-)  B    -2.3
 170 ARG   ( 184-)  C    -2.2
 125 SER   ( 139-)  C    -2.2
 569 GLY   (  -1-)  B    -2.2
 529 ARG   ( 146-)  A    -2.2
 293 THR   ( 109-)  D    -2.2
 605 GLU   (  35-)  B    -2.2
 431 PHE   (  48-)  A    -2.1
 322 VAL   ( 138-)  D    -2.1
 311 VAL   ( 127-)  D    -2.1
 558 LEU   ( 175-)  A    -2.1
 500 VAL   ( 117-)  A    -2.1
 608 VAL   (  38-)  B    -2.1
 115 PRO   ( 129-)  C    -2.1
 324 PRO   ( 140-)  D    -2.1
 288 THR   ( 104-)  D    -2.0
 597 LEU   (  27-)  B    -2.0
 537 LEU   ( 154-)  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.

  14 SER   (  28-)  C  PRO omega poor
  25 GLU   (  39-)  C  Poor phi/psi
  29 PHE   (  43-)  C  omega poor
  73 GLY   (  87-)  C  Poor phi/psi
 111 ASN   ( 125-)  C  Poor phi/psi
 113 PHE   ( 127-)  C  Poor phi/psi, PRO omega poor
 125 SER   ( 139-)  C  Poor phi/psi
 142 LEU   ( 156-)  C  Poor phi/psi
 170 ARG   ( 184-)  C  Poor phi/psi
 181 ASN   ( 195-)  C  Poor phi/psi
 197 LEU   (  13-)  D  Poor phi/psi
 201 GLY   (  17-)  D  Poor phi/psi
 205 ASP   (  21-)  D  Poor phi/psi
 214 LYS   (  30-)  D  Poor phi/psi
 292 ASN   ( 108-)  D  Poor phi/psi
 307 TYR   ( 123-)  D  PRO omega poor
 327 SER   ( 143-)  D  Poor phi/psi
 328 ALA   ( 144-)  D  Poor phi/psi
 338 TRP   ( 154-)  D  Poor phi/psi
 398 ASN   (  15-)  A  PRO omega poor
 401 GLN   (  18-)  A  Poor phi/psi
 407 PHE   (  24-)  A  omega poor
 416 HIS   (  33-)  A  omega poor
 461 ASN   (  78-)  A  Poor phi/psi
 462 TYR   (  79-)  A  Poor phi/psi
 470 PRO   (  87-)  A  omega poor
 483 ARG   ( 100-)  A  Poor phi/psi
 496 THR   ( 113-)  A  PRO omega poor
 526 HIS   ( 143-)  A  Poor phi/psi
 569 GLY   (  -1-)  B  Poor phi/psi
 572 ASP   (   2-)  B  Poor phi/psi
 603 ASN   (  33-)  B  Poor phi/psi
 657 GLU   (  87-)  B  Poor phi/psi, omega poor
 660 THR   (  90-)  B  Poor phi/psi
 661 VAL   (  91-)  B  omega poor
 667 PRO   (  97-)  B  omega poor
 684 TYR   ( 123-)  B  PRO omega poor
 685 PRO   ( 124-)  B  omega poor
 696 GLY   ( 135-)  B  Poor phi/psi
 714 TRP   ( 153-)  B  Poor phi/psi
 724 THR   ( 163-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -3.082

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

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

chi-1/chi-2 correlation Z-score : -3.082

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.

 237 SER   (  53-)  D    0.36
 243 SER   (  59-)  D    0.38

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  12 ASP   (  26-)  C      0
  14 SER   (  28-)  C      0
  15 PRO   (  29-)  C      0
  16 SER   (  30-)  C      0
  17 VAL   (  31-)  C      0
  23 TYR   (  37-)  C      0
  25 GLU   (  39-)  C      0
  31 PHE   (  45-)  C      0
  34 SER   (  48-)  C      0
  35 GLN   (  49-)  C      0
  37 THR   (  51-)  C      0
  48 TRP   (  62-)  C      0
  50 GLN   (  64-)  C      0
  51 GLU   (  65-)  C      0
  52 GLN   (  66-)  C      0
  77 ASP   (  91-)  C      0
  83 SER   (  97-)  C      0
  99 PHE   ( 113-)  C      0
 102 PRO   ( 116-)  C      0
 112 LEU   ( 126-)  C      0
 113 PHE   ( 127-)  C      0
 114 PRO   ( 128-)  C      0
 115 PRO   ( 129-)  C      0
 116 MET   ( 130-)  C      0
 124 HIS   ( 138-)  C      0
And so on for a total of 315 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!

 156 PRO   ( 170-)  C   1.67   15

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].

  81 PRO   (  95-)  C    23.2 half-chair N/C-delta (18 degrees)
 133 PRO   ( 147-)  C   -61.4 half-chair C-beta/C-alpha (-54 degrees)
 203 PRO   (  19-)  D  -121.3 half-chair C-delta/C-gamma (-126 degrees)
 269 PRO   (  85-)  D  -113.0 envelop C-gamma (-108 degrees)
 685 PRO   ( 124-)  B   -48.5 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 294 ARG   ( 110-)  D      NH1  <->   748 GLU   ( 187-)  B      OE1  0.60    2.10  INTRA BF
 254 GLN   (  70-)  D      O    <->   258 ASN   (  74-)  D      ND2  0.52    2.18  INTRA BF
 167 GLU   ( 181-)  C      OE1  <->   170 ARG   ( 184-)  C      NH1  0.51    2.19  INTRA BF
 461 ASN   (  78-)  A      ND2  <->   757 HOH   ( 339 )  A      O    0.40    2.30  INTRA BF
  38 ARG   (  52-)  C      NH2  <->    54 ASP   (  68-)  C      OD2  0.40    2.30  INTRA BF
  32 ASP   (  46-)  C      N    <->    37 THR   (  51-)  C      O    0.33    2.37  INTRA BF
 413 GLU   (  30-)  A      OE2  <->   416 HIS   (  33-)  A      ND1  0.29    2.41  INTRA BL
 666 GLU   (  96-)  B      N    <->   758 HOH   ( 327 )  B      O    0.24    2.46  INTRA BL
 198 ASP   (  14-)  D      OD1  <->   199 ASP   (  15-)  D      N    0.21    2.39  INTRA BF
 436 SER   (  53-)  A      O    <->   440 GLN   (  57-)  A      NE2  0.20    2.50  INTRA BF
 572 ASP   (   2-)  B      OD1  <->   576 ARG   (   6-)  B      NH2  0.20    2.50  INTRA BL
 604 GLN   (  34-)  B      OE1  <->   758 HOH   ( 305 )  B      O    0.20    2.20  INTRA BL
 611 ASP   (  41-)  B      O    <->   614 VAL   (  44-)  B      N    0.18    2.52  INTRA BL
  21 GLU   (  35-)  C      OE1  <->    38 ARG   (  52-)  C      NE   0.15    2.55  INTRA BF
  20 SER   (  34-)  C      OG   <->    27 GLN   (  41-)  C      NE2  0.15    2.55  INTRA BF
 294 ARG   ( 110-)  D      NH2  <->   733 THR   ( 172-)  B      OG1  0.14    2.56  INTRA BF
 504 TRP   ( 121-)  A      N    <->   757 HOH   ( 331 )  A      O    0.14    2.56  INTRA BL
 421 LYS   (  38-)  A      NZ   <->   423 GLU   (  40-)  A      OE2  0.14    2.56  INTRA BL
 595 ARG   (  25-)  B      NH2  <->   611 ASP   (  41-)  B      OD2  0.14    2.56  INTRA BL
 526 HIS   ( 143-)  A      CE1  <->   599 ARG   (  29-)  B      NH2  0.14    2.96  INTRA BL
 205 ASP   (  21-)  D      OD1  <->   206 PHE   (  22-)  D      N    0.14    2.46  INTRA BF
 542 ASP   ( 159-)  A      O    <->   757 HOH   ( 343 )  A      O    0.13    2.27  INTRA BL
 118 THR   ( 132-)  C      O    <->   165 THR   ( 179-)  C      N    0.13    2.57  INTRA BL
 580 GLN   (  10-)  B      NE2  <->   758 HOH   ( 307 )  B      O    0.13    2.57  INTRA BL
 526 HIS   ( 143-)  A      ND1  <->   582 LYS   (  12-)  B      NZ   0.12    2.88  INTRA BL
And so on for a total of 73 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

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.

 568 GLN   (  -2-)  B      -6.98
 323 MET   ( 139-)  D      -6.82
 352 TYR   ( 168-)  D      -6.81
 294 ARG   ( 110-)  D      -6.29
 567 PHE   (  -3-)  B      -6.24
 232 PHE   (  48-)  D      -6.14
 180 ARG   ( 194-)  C      -6.14
  41 ARG   (  55-)  C      -6.08
 129 GLU   ( 143-)  C      -5.96
 750 ARG   ( 189-)  B      -5.84
 483 ARG   ( 100-)  A      -5.80
 291 PHE   ( 107-)  D      -5.71
 279 ARG   (  95-)  D      -5.67
 401 GLN   (  18-)  A      -5.67
 727 ARG   ( 166-)  B      -5.48
 363 ILE   ( 179-)  D      -5.40
  71 GLN   (  85-)  C      -5.29
 330 LYS   ( 146-)  D      -5.25
  99 PHE   ( 113-)  C      -5.11
 700 LYS   ( 139-)  B      -5.07
 310 GLU   ( 126-)  D      -5.06
 725 VAL   ( 164-)  B      -5.05

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.

  50 GLN   (  64-)  C        52 - GLN     66- ( C)         -4.67
 566 LEU   (  -4-)  B       569 - GLY     -1- ( B)         -5.57

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: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

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

 131 PHE   ( 145-)  C   -3.05

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: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 758 HOH   ( 306 )  B      O
Bound group on Asn; dont flip  501 ASN  ( 118-) A
Bound to:  752 NAG  ( 201-) 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.

   6 HIS   (  20-)  C
  35 GLN   (  49-)  C
  71 GLN   (  85-)  C
 236 ASN   (  52-)  D
 461 ASN   (  78-)  A
 532 HIS   ( 149-)  A
 580 GLN   (  10-)  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.

  17 VAL   (  31-)  C      N
  38 ARG   (  52-)  C      NH2
  42 LEU   (  56-)  C      N
  47 ASP   (  61-)  C      N
  50 GLN   (  64-)  C      N
 130 GLY   ( 144-)  C      N
 142 LEU   ( 156-)  C      N
 151 ASP   ( 165-)  C      N
 159 ILE   ( 173-)  C      N
 168 ILE   ( 182-)  C      N
 190 HIS   (   6-)  D      NE2
 198 ASP   (  14-)  D      N
 200 ALA   (  16-)  D      N
 201 GLY   (  17-)  D      N
 202 THR   (  18-)  D      N
 205 ASP   (  21-)  D      N
 214 LYS   (  30-)  D      N
 220 TRP   (  36-)  D      NE1
 224 GLU   (  40-)  D      N
 233 GLY   (  49-)  D      N
 248 GLN   (  64-)  D      N
 257 ARG   (  73-)  D      N
 270 PHE   (  86-)  D      N
 271 TRP   (  87-)  D      N
 275 THR   (  91-)  D      OG1
 291 PHE   ( 107-)  D      N
 326 SER   ( 142-)  D      N
 337 ASP   ( 153-)  D      N
 338 TRP   ( 154-)  D      N
 339 THR   ( 155-)  D      N
 351 SER   ( 167-)  D      N
 364 GLY   ( 180-)  D      N
 421 LYS   (  38-)  A      N
 423 GLU   (  40-)  A      N
 426 TRP   (  43-)  A      N
 428 LEU   (  45-)  A      N
 440 GLN   (  57-)  A      N
 443 LEU   (  60-)  A      N
 504 TRP   ( 121-)  A      NE1
 531 PHE   ( 148-)  A      N
 551 TRP   ( 168-)  A      N
 607 SER   (  37-)  B      OG
 616 GLU   (  46-)  B      N
 645 VAL   (  75-)  B      N
 657 GLU   (  87-)  B      N
 660 THR   (  90-)  B      N
 660 THR   (  90-)  B      OG1
 662 GLN   (  92-)  B      N
 724 THR   ( 163-)  B      OG1

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.

  27 GLN   (  41-)  C      OE1
 190 HIS   (   6-)  D      ND1
 199 ASP   (  15-)  D      OD1
 215 ASP   (  31-)  D      OD2
 266 HIS   (  82-)  D      ND1
 345 HIS   ( 161-)  D      ND1
 362 HIS   ( 178-)  D      ND1
 408 ASP   (  25-)  A      OD2
 449 ASP   (  66-)  A      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.

 757 HOH   ( 302 )  A      O  0.90  K  4

Warning: Possible wrong residue type

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

  51 GLU   (  65-)  C   H-bonding suggests Gln; but Alt-Rotamer
  66 GLU   (  80-)  C   H-bonding suggests Gln
 215 ASP   (  31-)  D   H-bonding suggests Asn; but Alt-Rotamer
 276 ASP   (  92-)  D   H-bonding suggests Asn
 372 ASP   ( 188-)  D   H-bonding suggests Asn
 404 GLU   (  21-)  A   H-bonding suggests Gln
 449 ASP   (  66-)  A   H-bonding suggests Asn
 564 ASP   ( 181-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.428
  2nd generation packing quality :  -1.271
  Ramachandran plot appearance   :  -1.456
  chi-1/chi-2 rotamer normality  :  -3.082 (poor)
  Backbone conformation          :  -0.378

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.404 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   1.073
  Side chain planarity           :   0.368 (tight)
  Improper dihedral distribution :   0.647
  B-factor distribution          :   0.510
  Inside/Outside distribution    :   1.048

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 :   0.6
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.404 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   1.073
  Side chain planarity           :   0.368 (tight)
  Improper dihedral distribution :   0.647
  B-factor distribution          :   0.510
  Inside/Outside distribution    :   1.048
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
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Quality Control
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      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.