WHAT IF Check report

This file was created 2013-12-09 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb3s3p.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 622 XW1   (   2-)  B  -
 623 PHQ   (   1-)  B  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 253 CYS   ( 277-)  A  -   SG   622 XW1   (   2-)  B  -   C15

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.

 612 GLN   (   3-)  B  -   N   bound to  622 XW1   (   2-)  B  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

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'.

  27 ARG   (  28-)  A      CG
  27 ARG   (  28-)  A      CD
  27 ARG   (  28-)  A      NE
  27 ARG   (  28-)  A      CZ
  27 ARG   (  28-)  A      NH1
  27 ARG   (  28-)  A      NH2
  29 LYS   (  30-)  A      CG
  29 LYS   (  30-)  A      CD
  29 LYS   (  30-)  A      CE
  29 LYS   (  30-)  A      NZ
  50 GLU   (  51-)  A      CG
  50 GLU   (  51-)  A      CD
  50 GLU   (  51-)  A      OE1
  50 GLU   (  51-)  A      OE2
  96 ASP   (  97-)  A      CG
  96 ASP   (  97-)  A      OD1
  96 ASP   (  97-)  A      OD2
  97 CYS   (  98-)  A      SG
 119 GLU   ( 120-)  A      CG
 119 GLU   ( 120-)  A      CD
 119 GLU   ( 120-)  A      OE1
 119 GLU   ( 120-)  A      OE2
 124 TYR   ( 125-)  A      CG
 124 TYR   ( 125-)  A      CD1
 124 TYR   ( 125-)  A      CD2
And so on for a total of 154 lines.

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.

 546 GLU   ( 618-)  A    High
 565 GLU   ( 637-)  A    High
 567 PRO   ( 639-)  A    High
 579 ARG   ( 651-)  A    High
 585 LEU   ( 657-)  A    High
 586 HIS   ( 658-)  A    High
 587 MET   ( 659-)  A    High

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

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

 114 TYR   ( 115-)  A
 167 TYR   ( 168-)  A
 287 TYR   ( 315-)  A
 342 TYR   ( 388-)  A
 392 TYR   ( 445-)  A
 440 TYR   ( 503-)  A
 465 TYR   ( 528-)  A

Warning: Phenylalanine convention problem

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

  44 PHE   (  45-)  A
  58 PHE   (  59-)  A
  76 PHE   (  77-)  A
 134 PHE   ( 135-)  A
 165 PHE   ( 166-)  A
 173 PHE   ( 174-)  A
 202 PHE   ( 203-)  A
 256 PHE   ( 280-)  A
 288 PHE   ( 316-)  A
 296 PHE   ( 334-)  A
 346 PHE   ( 392-)  A
 348 PHE   ( 394-)  A
 403 PHE   ( 456-)  A
 429 PHE   ( 492-)  A
 474 PHE   ( 537-)  A
 550 PHE   ( 622-)  A

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.

  24 ASP   (  25-)  A
  54 ASP   (  55-)  A
 150 ASP   ( 151-)  A
 190 ASP   ( 191-)  A
 209 ASP   ( 210-)  A
 381 ASP   ( 434-)  A
 518 ASP   ( 581-)  A
 599 ASP   ( 671-)  A

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.

   3 GLU   (   4-)  A
  14 GLU   (  15-)  A
  69 GLU   (  70-)  A
  83 GLU   (  84-)  A
  84 GLU   (  85-)  A
 152 GLU   ( 153-)  A
 154 GLU   ( 155-)  A
 314 GLU   ( 352-)  A
 398 GLU   ( 451-)  A
 401 GLU   ( 454-)  A
 476 GLU   ( 539-)  A
 506 GLU   ( 569-)  A
 565 GLU   ( 637-)  A
 571 GLU   ( 643-)  A
 597 GLU   ( 669-)  A

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.

 612 GLN   (   3-)  B      CD   NE2   1.49    7.9
 613 PRO   (   4-)  B      N   -C     1.46    6.4
 614 LEU   (   5-)  B      N   -C     1.43    5.0

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.

 613 PRO   (   4-)  B      N    CA   CB  107.48    4.1

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.

   3 GLU   (   4-)  A
  14 GLU   (  15-)  A
  24 ASP   (  25-)  A
  54 ASP   (  55-)  A
  69 GLU   (  70-)  A
  83 GLU   (  84-)  A
  84 GLU   (  85-)  A
 150 ASP   ( 151-)  A
 152 GLU   ( 153-)  A
 154 GLU   ( 155-)  A
 190 ASP   ( 191-)  A
 209 ASP   ( 210-)  A
 314 GLU   ( 352-)  A
 381 ASP   ( 434-)  A
 398 GLU   ( 451-)  A
 401 GLU   ( 454-)  A
 476 GLU   ( 539-)  A
 506 GLU   ( 569-)  A
 518 ASP   ( 581-)  A
 565 GLU   ( 637-)  A
 571 GLU   ( 643-)  A
 597 GLU   ( 669-)  A
 599 ASP   ( 671-)  A

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.

 584 PRO   ( 656-)  A    -3.0
 586 HIS   ( 658-)  A    -2.6
  90 THR   (  91-)  A    -2.5
 466 LEU   ( 529-)  A    -2.5
 375 THR   ( 428-)  A    -2.5
  28 GLU   (  29-)  A    -2.4
 382 GLU   ( 435-)  A    -2.3
 111 ILE   ( 112-)  A    -2.3
 359 ILE   ( 405-)  A    -2.3
 149 LEU   ( 150-)  A    -2.3
  12 GLU   (  13-)  A    -2.3
 182 GLY   ( 183-)  A    -2.2
 558 THR   ( 630-)  A    -2.2
 506 GLU   ( 569-)  A    -2.2
 468 ASN   ( 531-)  A    -2.2
 554 GLY   ( 626-)  A    -2.1
 489 ARG   ( 552-)  A    -2.1
 540 PRO   ( 612-)  A    -2.0
 123 GLY   ( 124-)  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.

  21 HIS   (  22-)  A  Poor phi/psi
  54 ASP   (  55-)  A  omega poor
  95 GLN   (  96-)  A  Poor phi/psi
  96 ASP   (  97-)  A  Poor phi/psi
 123 GLY   ( 124-)  A  Poor phi/psi
 129 PHE   ( 130-)  A  Poor phi/psi
 168 GLN   ( 169-)  A  Poor phi/psi
 182 GLY   ( 183-)  A  Poor phi/psi
 231 ASP   ( 232-)  A  Poor phi/psi
 233 GLN   ( 234-)  A  omega poor
 240 TRP   ( 254-)  A  omega poor
 284 LEU   ( 312-)  A  Poor phi/psi
 288 PHE   ( 316-)  A  Poor phi/psi
 292 MET   ( 330-)  A  Poor phi/psi
 326 GLY   ( 372-)  A  PRO omega poor
 341 LYS   ( 387-)  A  omega poor
 343 ASP   ( 389-)  A  Poor phi/psi
 357 ASP   ( 403-)  A  omega poor
 373 ILE   ( 426-)  A  omega poor
 381 ASP   ( 434-)  A  Poor phi/psi
 427 ASP   ( 490-)  A  omega poor
 429 PHE   ( 492-)  A  omega poor
 435 ASN   ( 498-)  A  Poor phi/psi
 496 ASN   ( 559-)  A  Poor phi/psi
 510 ASN   ( 573-)  A  Poor phi/psi
 573 GLY   ( 645-)  A  Poor phi/psi
 586 HIS   ( 658-)  A  Poor phi/psi
 603 ALA   ( 675-)  A  Poor phi/psi
 604 VAL   ( 676-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -3.553

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 : -3.553

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.

  52 SER   (  53-)  A    0.36

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
   7 GLU   (   8-)  A      0
   8 ARG   (   9-)  A      0
  21 HIS   (  22-)  A      0
  22 THR   (  23-)  A      0
  26 CYS   (  27-)  A      0
  27 ARG   (  28-)  A      0
  28 GLU   (  29-)  A      0
  29 LYS   (  30-)  A      0
  34 ARG   (  35-)  A      0
  39 TRP   (  40-)  A      0
  45 GLU   (  46-)  A      0
  47 ARG   (  48-)  A      0
  49 TYR   (  50-)  A      0
  53 VAL   (  54-)  A      0
  62 THR   (  63-)  A      0
  65 ALA   (  66-)  A      0
  66 PRO   (  67-)  A      0
  72 THR   (  73-)  A      0
  73 LYS   (  74-)  A      0
  79 ARG   (  80-)  A      0
  81 ALA   (  82-)  A      0
  84 GLU   (  85-)  A      0
  87 TRP   (  88-)  A      0
  92 VAL   (  93-)  A      0
And so on for a total of 254 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!

 554 GLY   ( 626-)  A   2.15   15
 556 GLY   ( 628-)  A   1.71   35

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].

 106 PRO   ( 107-)  A  -121.5 half-chair C-delta/C-gamma (-126 degrees)
 200 PRO   ( 201-)  A  -132.7 half-chair C-delta/C-gamma (-126 degrees)
 323 PRO   ( 361-)  A   108.3 envelop C-beta (108 degrees)
 393 PRO   ( 446-)  A  -121.3 half-chair C-delta/C-gamma (-126 degrees)
 584 PRO   ( 656-)  A   117.5 half-chair C-beta/C-alpha (126 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.

 253 CYS   ( 277-)  A      SG   <->   622 XW1   (   2-)  B      C15  1.22    1.78  INTRA BF
 622 XW1   (   2-)  B      N    <->   623 PHQ   (   1-)  B      C1   1.21    1.49  INTRA BL
 612 GLN   (   3-)  B      N    <->   622 XW1   (   2-)  B      C    1.16    1.54  INTRA BF
 612 GLN   (   3-)  B      CA   <->   622 XW1   (   2-)  B      C    0.59    2.61  INTRA BF
 622 XW1   (   2-)  B      CA   <->   623 PHQ   (   1-)  B      C1   0.52    2.48  INTRA BL
 253 CYS   ( 277-)  A      CB   <->   622 XW1   (   2-)  B      C15  0.38    2.82  INTRA BF
 496 ASN   ( 559-)  A      ND2  <->   521 LEU   ( 584-)  A      O    0.31    2.39  INTRA BF
 122 THR   ( 123-)  A      O    <->   124 TYR   ( 125-)  A      N    0.25    2.45  INTRA BF
 352 ASN   ( 398-)  A      C    <->   369 VAL   ( 422-)  A      CG2  0.17    3.03  INTRA BL
 292 MET   ( 330-)  A      CG   <->   293 ILE   ( 331-)  A      N    0.15    2.85  INTRA BF
 418 GLN   ( 481-)  A      CG   <->   419 SER   ( 482-)  A      N    0.15    2.85  INTRA BF
 375 THR   ( 428-)  A      O    <->   384 GLU   ( 437-)  A      N    0.15    2.55  INTRA BL
 364 ASN   ( 417-)  A      OD1  <->   366 SER   ( 419-)  A      N    0.14    2.56  INTRA BF
 168 GLN   ( 169-)  A      NE2  <->   177 ILE   ( 178-)  A      CB   0.14    2.96  INTRA BF
 227 VAL   ( 228-)  A      O    <->   236 LEU   ( 237-)  A      N    0.12    2.58  INTRA BL
 357 ASP   ( 403-)  A      N    <->   362 SER   ( 415-)  A      O    0.12    2.58  INTRA BF
  43 HIS   (  44-)  A      CD2  <->    98 THR   (  99-)  A      CG2  0.12    3.08  INTRA BL
 377 SER   ( 430-)  A      N    <->   382 GLU   ( 435-)  A      O    0.12    2.58  INTRA BL
 575 GLU   ( 647-)  A      OE2  <->   577 LYS   ( 649-)  A      NZ   0.12    2.58  INTRA BF
 529 ARG   ( 592-)  A      O    <->   534 GLU   ( 606-)  A      N    0.12    2.58  INTRA BF
 489 ARG   ( 552-)  A      CG   <->   490 ASP   ( 553-)  A      N    0.10    2.90  INTRA BF
 575 GLU   ( 647-)  A      CG   <->   576 VAL   ( 648-)  A      N    0.10    2.90  INTRA BF
 358 TRP   ( 404-)  A      N    <->   514 LEU   ( 577-)  A      O    0.10    2.60  INTRA BF
 297 HIS   ( 335-)  A      ND1  <->   622 XW1   (   2-)  B      C93  0.10    3.00  INTRA BF
 434 ASN   ( 497-)  A      N    <->   475 SER   ( 538-)  A      O    0.10    2.60  INTRA BF
And so on for a total of 83 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

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.

 453 TYR   ( 516-)  A      -7.59
 586 HIS   ( 658-)  A      -7.24
 237 LEU   ( 238-)  A      -6.59
 560 GLU   ( 632-)  A      -6.09
  95 GLN   (  96-)  A      -6.08
 342 TYR   ( 388-)  A      -6.07
 173 PHE   ( 174-)  A      -5.99
  20 HIS   (  21-)  A      -5.78
 538 GLN   ( 610-)  A      -5.66
 474 PHE   ( 537-)  A      -5.49
 579 ARG   ( 651-)  A      -5.48
 407 ASN   ( 460-)  A      -5.26
 418 GLN   ( 481-)  A      -5.23
 341 LYS   ( 387-)  A      -5.19
  28 GLU   (  29-)  A      -5.15
  47 ARG   (  48-)  A      -5.07

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

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.

 380 ARG   ( 433-)  A   -3.25
 602 LYS   ( 674-)  A   -2.88
 365 ARG   ( 418-)  A   -2.71
 587 MET   ( 659-)  A   -2.70
 124 TYR   ( 125-)  A   -2.65
  27 ARG   (  28-)  A   -2.63
 487 LYS   ( 550-)  A   -2.61
 172 LYS   ( 173-)  A   -2.51

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

Water, ion, and hydrogenbond related checks

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.

  27 ARG   (  28-)  A      N
  30 LEU   (  31-)  A      N
  36 GLN   (  37-)  A      N
  84 GLU   (  85-)  A      N
 105 THR   ( 106-)  A      N
 125 GLN   ( 126-)  A      N
 150 ASP   ( 151-)  A      N
 151 SER   ( 152-)  A      N
 163 GLN   ( 164-)  A      N
 169 GLY   ( 170-)  A      N
 228 ASN   ( 229-)  A      N
 228 ASN   ( 229-)  A    A ND2
 234 GLY   ( 235-)  A      N
 241 ILE   ( 255-)  A      N
 244 VAL   ( 258-)  A      N
 246 ILE   ( 260-)  A      N
 254 TRP   ( 278-)  A      N
 255 VAL   ( 279-)  A      N
 257 ALA   ( 281-)  A      N
 276 ASN   ( 300-)  A      ND2
 284 LEU   ( 312-)  A      N
 285 ILE   ( 313-)  A      N
 293 ILE   ( 331-)  A      N
 295 ASN   ( 333-)  A      ND2
 367 LEU   ( 420-)  A      N
 407 ASN   ( 460-)  A      ND2
 435 ASN   ( 498-)  A      N
 454 ASN   ( 517-)  A      N
 468 ASN   ( 531-)  A      N
 493 THR   ( 556-)  A      OG1
 496 ASN   ( 559-)  A      ND2
 497 LEU   ( 560-)  A      N
 543 VAL   ( 615-)  A      N
 548 CYS   ( 620-)  A      N
 554 GLY   ( 626-)  A      N
 568 ASP   ( 640-)  A      N
 571 GLU   ( 643-)  A      N
 586 HIS   ( 658-)  A      N
 601 LEU   ( 673-)  A      N

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.

  43 HIS   (  44-)  A      ND1
 276 ASN   ( 300-)  A      OD1
 590 HIS   ( 662-)  A      NE2

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.

  86 ASP   (  87-)  A   H-bonding suggests Asn
 197 ASP   ( 198-)  A   H-bonding suggests Asn; but Alt-Rotamer
 597 GLU   ( 669-)  A   H-bonding suggests Gln; but Alt-Rotamer
 599 ASP   ( 671-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.866
  2nd generation packing quality :  -2.076
  Ramachandran plot appearance   :  -2.073
  chi-1/chi-2 rotamer normality  :  -3.553 (poor)
  Backbone conformation          :   0.069

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.382 (tight)
  Bond angles                    :   0.548 (tight)
  Omega angle restraints         :   0.990
  Side chain planarity           :   0.319 (tight)
  Improper dihedral distribution :   0.539
  B-factor distribution          :   0.881
  Inside/Outside distribution    :   1.044

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.382 (tight)
  Bond angles                    :   0.548 (tight)
  Omega angle restraints         :   0.990
  Side chain planarity           :   0.319 (tight)
  Improper dihedral distribution :   0.539
  B-factor distribution          :   0.881
  Inside/Outside distribution    :   1.044
==============

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.