WHAT IF Check report

This file was created 2012-01-25 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 pdb2hck.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.634
CA-only RMS fit for the two chains : 0.536

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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.

 880 QUE   (   1-)  A  -
 882 QUE   ( 532-)  B  -

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

 881  CA   (   1-)  A  -

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 434 PTR   ( 527-)  A
 872 PTR   ( 527-)  B

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'.

   1 GLU   (  82-)  A      CG
   1 GLU   (  82-)  A      CD
   1 GLU   (  82-)  A      OE1
   1 GLU   (  82-)  A      OE2
   2 ASP   (  83-)  A      CG
   2 ASP   (  83-)  A      OD1
   2 ASP   (  83-)  A      OD2
 110 ASP   ( 192-)  A      CG
 110 ASP   ( 192-)  A      OD1
 110 ASP   ( 192-)  A      OD2
 112 ARG   ( 194-)  A      CG
 112 ARG   ( 194-)  A      CD
 112 ARG   ( 194-)  A      NE
 112 ARG   ( 194-)  A      CZ
 112 ARG   ( 194-)  A      NH1
 112 ARG   ( 194-)  A      NH2
 113 GLN   ( 195-)  A      CG
 113 GLN   ( 195-)  A      CD
 113 GLN   ( 195-)  A      OE1
 113 GLN   ( 195-)  A      NE2
 127 ASN   ( 209-)  A      CG
 127 ASN   ( 209-)  A      OD1
 127 ASN   ( 209-)  A      ND2
 143 GLU   ( 225-)  A      CG
 143 GLU   ( 225-)  A      CD
And so on for a total of 100 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. 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

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.

  29 VAL   ( 110-)  A      CA   CB    1.62    4.6
  36 TRP   ( 118-)  A      CG   CD2   1.35   -4.3
 199 TRP   ( 282-)  A      CG   CD2   1.35   -4.5
 281 ILE   ( 364-)  A      CA   CB    1.63    5.0
 418 TYR   ( 511-)  A      CA   CB    1.62    4.3
 637 TRP   ( 282-)  B      CG   CD2   1.36   -4.3
 729 MET   ( 374-)  B      CA   CB    1.45   -4.0
 797 LEU   ( 452-)  B      CB   CG    1.45   -4.1
 817 ILE   ( 472-)  B      CA   CB    1.61    4.1
 844 TRP   ( 499-)  B      CG   CD2   1.36   -4.3

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.

   2 ASP   (  83-)  A     -CA  -C    N   125.56    4.7
   3 ILE   (  84-)  A     -CA  -C    N   125.14    4.5
  10 ASP   (  91-)  A      CA   CB   CG  118.92    6.3
  12 GLU   (  93-)  A      CA   CB   CG  122.40    4.1
  12 GLU   (  93-)  A      CB   CG   CD  122.46    5.8
  15 HIS   (  96-)  A      CA   CB   CG  109.39   -4.4
  15 HIS   (  96-)  A      CB   CG   ND1 128.32    4.5
  15 HIS   (  96-)  A      CB   CG   CD2 123.25   -4.5
  18 ASP   (  99-)  A      CA   CB   CG  118.70    6.1
  22 GLN   ( 103-)  A      CA   CB   CG  123.27    4.6
  22 GLN   ( 103-)  A      NE2  CD   OE1 117.08   -5.5
  23 LYS   ( 104-)  A      CB   CG   CD  121.40    4.4
  32 GLU   ( 113-)  A      CA   CB   CG  101.71   -6.2
  36 TRP   ( 118-)  A      CD1  CG   CD2 113.24    4.3
  36 TRP   ( 118-)  A      CG   CD2  CE2 101.27   -4.9
  37 TRP   ( 119-)  A      CG   CD2  CE2 101.77   -4.5
  42 LEU   ( 124-)  A      CD1  CG   CD2 120.46    4.4
  46 LYS   ( 128-)  A      CA   CB   CG  122.53    4.2
  47 GLU   ( 129-)  A      CB   CG   CD  120.35    4.6
  50 ILE   ( 132-)  A      N    CA   CB  101.33   -5.4
  53 ASN   ( 135-)  A      CA   CB   CG  121.97    9.4
  53 ASN   ( 135-)  A      ND2  CG   OD1 118.36   -4.2
  54 TYR   ( 136-)  A     -O   -C    N   116.44   -4.1
  57 ARG   ( 139-)  A      CA   CB   CG  122.97    4.4
  65 GLU   ( 147-)  A      N    CA   C   122.61    4.1
And so on for a total of 366 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

 617 ILE   ( 262-)  B      C     -6.1    -7.99     0.03
 689 ILE   ( 334-)  B      CB     8.5    43.34    32.31
 812 SER   ( 467-)  B      C     -6.1    -9.68     0.37
 857 ILE   ( 512-)  B      CB    10.0    45.36    32.31
The average deviation= 1.579

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.

 499 LEU   ( 143-)  B    8.86
 771 ILE   ( 426-)  B    8.63
 333 ILE   ( 426-)  A    7.60
 285 ALA   ( 368-)  A    7.20
 332 PRO   ( 425-)  A    7.20
  61 LEU   ( 143-)  A    6.60
 681 HIS   ( 326-)  B    6.49
 144 LEU   ( 226-)  A    6.00
 243 HIS   ( 326-)  A    5.91
 490 SER   ( 134-)  B    5.90
 487 TYR   ( 131-)  B    5.61
 187 GLU   ( 270-)  A    5.52
  69 LYS   ( 151-)  A    5.45
 788 SER   ( 443-)  B    5.44
 450 GLU   (  93-)  B    5.37
 193 GLY   ( 276-)  A    5.24
 739 HIS   ( 384-)  B    5.23
 770 PRO   ( 425-)  B    5.20
 181 ARG   ( 264-)  A    5.12
 398 LEU   ( 491-)  A    5.06
 858 GLN   ( 513-)  B    4.85
 503 GLU   ( 147-)  B    4.85
 189 LYS   ( 272-)  A    4.59
 715 LEU   ( 360-)  B    4.57
 279 LYS   ( 362-)  A    4.48
 358 LEU   ( 451-)  A    4.45
 259 ALA   ( 342-)  A    4.43
 856 TYR   ( 511-)  B    4.40
 747 ILE   ( 392-)  B    4.39
 677 LEU   ( 322-)  B    4.38
   6 VAL   (  87-)  A    4.24
 449 TYR   (  92-)  B    4.24
  79 GLN   ( 161-)  A    4.24
 287 ILE   ( 370-)  A    4.22
 540 TYR   ( 184-)  B    4.18
 212 LYS   ( 295-)  A    4.16
 122 ILE   ( 204-)  A    4.16
 239 LEU   ( 322-)  A    4.16
 214 MET   ( 297-)  A    4.14
 665 GLU   ( 310-)  B    4.14
 616 GLU   ( 261-)  B    4.11
 845 LYS   ( 500-)  B    4.06
 623 LYS   ( 268-)  B    4.04
 410 PRO   ( 503-)  A    4.02
 113 GLN   ( 195-)  A    4.01

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 2.077

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.296

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.

 760 PHE   ( 405-)  B    -3.1
 333 ILE   ( 426-)  A    -3.0
 771 ILE   ( 426-)  B    -3.0
 785 THR   ( 440-)  B    -2.9
 332 PRO   ( 425-)  A    -2.8
 322 PHE   ( 405-)  A    -2.8
 347 THR   ( 440-)  A    -2.8
 410 PRO   ( 503-)  A    -2.7
 131 TYR   ( 213-)  A    -2.7
 743 ARG   ( 388-)  B    -2.6
 299 TYR   ( 382-)  A    -2.6
  14 ILE   (  95-)  A    -2.6
 808 TYR   ( 463-)  B    -2.5
 430 THR   ( 523-)  A    -2.5
  93 ARG   ( 175-)  A    -2.5
 241 LYS   ( 324-)  A    -2.5
 742 LEU   ( 387-)  B    -2.4
 209 VAL   ( 292-)  A    -2.4
 679 LYS   ( 324-)  B    -2.4
  16 HIS   (  97-)  A    -2.4
 536 THR   ( 180-)  B    -2.4
 737 TYR   ( 382-)  B    -2.4
 441 ILE   (  84-)  B    -2.4
 647 VAL   ( 292-)  B    -2.4
 452 ILE   (  95-)  B    -2.3
And so on for a total of 58 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

  30 LEU   ( 111-)  A  Poor phi/psi
  45 ARG   ( 127-)  A  Poor phi/psi
  59 ASP   ( 141-)  A  Poor phi/psi
  61 LEU   ( 143-)  A  Poor phi/psi
  65 GLU   ( 147-)  A  Poor phi/psi
  69 LYS   ( 151-)  A  Poor phi/psi
  91 MET   ( 173-)  A  Poor phi/psi
 110 ASP   ( 192-)  A  PRO omega poor
 113 GLN   ( 195-)  A  Poor phi/psi
 127 ASN   ( 209-)  A  Poor phi/psi
 128 GLY   ( 210-)  A  Poor phi/psi
 152 ASN   ( 234-)  A  Poor phi/psi
 160 SER   ( 242-)  A  Poor phi/psi
 175 ASP   ( 258-)  A  Poor phi/psi
 176 ALA   ( 259-)  A  Poor phi/psi
 205 LYS   ( 288-)  A  Poor phi/psi
 209 VAL   ( 292-)  A  Poor phi/psi
 215 LYS   ( 298-)  A  PRO omega poor
 234 LEU   ( 317-)  A  Poor phi/psi
 249 GLU   ( 332-)  A  PRO omega poor
 298 ASN   ( 381-)  A  Poor phi/psi
 302 ARG   ( 385-)  A  Poor phi/psi
 315 LEU   ( 398-)  A  Poor phi/psi
 321 ASP   ( 404-)  A  omega poor
 332 PRO   ( 425-)  A  Poor phi/psi
And so on for a total of 60 lines.

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

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

chi-1/chi-2 correlation Z-score : -5.108

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.

 421 SER   ( 514-)  A    0.39

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!

   9 TYR   (  90-)  A      0
  14 ILE   (  95-)  A      0
  15 HIS   (  96-)  A      0
  16 HIS   (  97-)  A      0
  30 LEU   ( 111-)  A      0
  31 GLU   ( 112-)  A      0
  32 GLU   ( 113-)  A      0
  33 SER   ( 114-)  A      0
  35 GLU   ( 117-)  A      0
  36 TRP   ( 118-)  A      0
  45 ARG   ( 127-)  A      0
  47 GLU   ( 129-)  A      0
  49 TYR   ( 131-)  A      0
  54 TYR   ( 136-)  A      0
  55 VAL   ( 137-)  A      0
  58 VAL   ( 140-)  A      0
  65 GLU   ( 147-)  A      0
  66 TRP   ( 148-)  A      0
  83 PRO   ( 165-)  A      0
  86 MET   ( 168-)  A      0
  87 LEU   ( 169-)  A      0
  89 SER   ( 171-)  A      0
  90 PHE   ( 172-)  A      0
  92 ILE   ( 174-)  A      0
  93 ARG   ( 175-)  A      0
And so on for a total of 374 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!

 372 GLY   ( 465-)  A   1.71   80
 776 PRO   ( 431-)  B   1.62   14

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...

  65 GLU   ( 147-)  A   1.78
 499 LEU   ( 143-)  B   1.51
 500 GLU   ( 144-)  B   1.52
 712 LYS   ( 357-)  B   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]

  83 PRO   ( 165-)  A    0.45 HIGH
 180 PRO   ( 263-)  A    0.46 HIGH
 332 PRO   ( 425-)  A    0.49 HIGH
 338 PRO   ( 431-)  A    0.48 HIGH
 376 PRO   ( 469-)  A    0.45 HIGH
 521 PRO   ( 165-)  B    0.48 HIGH
 600 PRO   ( 244-)  B    0.45 HIGH
 618 PRO   ( 263-)  B    0.50 HIGH
 776 PRO   ( 431-)  B    0.46 HIGH
 814 PRO   ( 469-)  B    0.47 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].

 216 PRO   ( 299-)  A    43.2 envelop C-delta (36 degrees)
 278 PRO   ( 361-)  A  -125.4 half-chair C-delta/C-gamma (-126 degrees)
 332 PRO   ( 425-)  A  -120.5 half-chair C-delta/C-gamma (-126 degrees)
 389 PRO   ( 482-)  A    42.1 envelop C-delta (36 degrees)
 410 PRO   ( 503-)  A   109.8 envelop C-beta (108 degrees)
 521 PRO   ( 165-)  B  -114.2 envelop C-gamma (-108 degrees)
 600 PRO   ( 244-)  B    99.6 envelop C-beta (108 degrees)
 618 PRO   ( 263-)  B  -120.7 half-chair C-delta/C-gamma (-126 degrees)
 716 PRO   ( 361-)  B  -122.4 half-chair C-delta/C-gamma (-126 degrees)
 770 PRO   ( 425-)  B  -124.8 half-chair C-delta/C-gamma (-126 degrees)
 776 PRO   ( 431-)  B  -114.1 envelop C-gamma (-108 degrees)
 807 PRO   ( 462-)  B  -125.5 half-chair C-delta/C-gamma (-126 degrees)
 833 PRO   ( 488-)  B   -63.8 envelop C-beta (-72 degrees)
 876 PRO   ( 531-)  B    52.7 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.

 219 MET   ( 302-)  A      SD  <->  224 PHE   ( 307-)  A      CB     0.27    3.13  INTRA BF
 181 ARG   ( 264-)  A      NH2 <->  250 PRO   ( 333-)  A      O      0.23    2.47  INTRA BF
 387 ARG   ( 480-)  A      NH1 <->  406 TRP   ( 499-)  A      O      0.21    2.49  INTRA BF
 808 TYR   ( 463-)  B      CD1 <->  826 MET   ( 481-)  B      SD     0.20    3.20  INTRA BF
 354 SER   ( 447-)  A      O   <->  357 ILE   ( 450-)  A      N      0.19    2.51  INTRA BL
 138 PHE   ( 220-)  A      CZ  <->  147 HIS   ( 229-)  A      ND1    0.19    2.91  INTRA BF
 534 GLU   ( 178-)  B      N   <->  872 PTR   ( 527-)  B      O1P    0.18    2.52  INTRA BL
  86 MET   ( 168-)  A      SD  <->  160 SER   ( 242-)  A      CB     0.16    3.24  INTRA BF
 387 ARG   ( 480-)  A      NH1 <->  406 TRP   ( 499-)  A      CB     0.16    2.94  INTRA BF
 374 SER   ( 467-)  A      O   <->  377 GLU   ( 470-)  A      N      0.16    2.54  INTRA BF
 842 ARG   ( 497-)  B      NH1 <->  856 TYR   ( 511-)  B      CE2    0.15    2.95  INTRA BL
 619 ARG   ( 264-)  B      NH2 <->  688 PRO   ( 333-)  B      O      0.15    2.55  INTRA BL
 479 SER   ( 123-)  B      O   <->  483 ARG   ( 127-)  B      N      0.13    2.57  INTRA BL
 785 THR   ( 440-)  B      N   <->  788 SER   ( 443-)  B      OG     0.12    2.58  INTRA BF
 347 THR   ( 440-)  A      O   <->  350 SER   ( 443-)  A      N      0.12    2.58  INTRA BF
 376 PRO   ( 469-)  A      O   <->  379 ILE   ( 472-)  A      N      0.11    2.59  INTRA BF
 398 LEU   ( 491-)  A      O   <->  401 ILE   ( 494-)  A      N      0.11    2.59  INTRA BL
 728 GLY   ( 373-)  B      O   <->  731 PHE   ( 376-)  B      N      0.11    2.59  INTRA BL
 283 PHE   ( 366-)  A      O   <->  286 GLN   ( 369-)  A      N      0.11    2.59  INTRA BL
 577 SER   ( 221-)  B      N   <->  578 THR   ( 222-)  B      N      0.11    2.49  INTRA BF
 283 PHE   ( 366-)  A      CD1 <->  317 CYS   ( 400-)  A      SG     0.11    3.29  INTRA BL
 546 ASP   ( 190-)  B      CG  <->  547 TYR   ( 191-)  B      N      0.10    2.90  INTRA BF
 719 ILE   ( 364-)  B      O   <->  723 ALA   ( 368-)  B      N      0.10    2.60  INTRA BL
 808 TYR   ( 463-)  B      CE1 <->  826 MET   ( 481-)  B      SD     0.10    3.30  INTRA BF
  64 GLU   ( 146-)  A      O   <->   66 TRP   ( 148-)  A      N      0.09    2.61  INTRA BF
And so on for a total of 84 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 547 TYR   ( 191-)  B      -7.86
 135 ARG   ( 217-)  A      -7.70
 109 TYR   ( 191-)  A      -7.61
 607 GLN   ( 251-)  B      -7.16
 169 GLN   ( 251-)  A      -7.12
 573 ARG   ( 217-)  B      -7.03
 125 LEU   ( 207-)  A      -6.91
 805 ARG   ( 460-)  B      -6.57
 387 ARG   ( 480-)  A      -6.57
 563 LEU   ( 207-)  B      -6.56
 825 ARG   ( 480-)  B      -6.54
 436 GLN   ( 529-)  A      -6.44
 875 GLN   ( 530-)  B      -6.44
 824 TYR   ( 479-)  B      -6.43
 437 GLN   ( 530-)  A      -6.42
 874 GLN   ( 529-)  B      -6.40
 367 ARG   ( 460-)  A      -6.35
 386 TYR   ( 479-)  A      -6.13
 740 ARG   ( 385-)  B      -5.99
 324 LEU   ( 407-)  A      -5.95
 384 ARG   ( 477-)  A      -5.90
 302 ARG   ( 385-)  A      -5.84
 826 MET   ( 481-)  B      -5.82
 525 LEU   ( 169-)  B      -5.75
 388 MET   ( 481-)  A      -5.66
 822 ARG   ( 477-)  B      -5.65
 784 PHE   ( 439-)  B      -5.64
 762 LEU   ( 407-)  B      -5.64
 331 PHE   ( 424-)  A      -5.58
 248 LYS   ( 331-)  A      -5.57
 686 LYS   ( 331-)  B      -5.53
 780 ASN   ( 435-)  B      -5.42
 342 ASN   ( 435-)  A      -5.40
 769 PHE   ( 424-)  B      -5.39
 390 ARG   ( 483-)  A      -5.33
 828 ARG   ( 483-)  B      -5.30
 687 GLU   ( 332-)  B      -5.26
 346 PHE   ( 439-)  A      -5.25
 594 CYS   ( 238-)  B      -5.24
 368 ILE   ( 461-)  A      -5.24
 335 TRP   ( 428-)  A      -5.23
 773 TRP   ( 428-)  B      -5.20
 343 PHE   ( 436-)  A      -5.16
 249 GLU   ( 332-)  A      -5.16
 781 PHE   ( 436-)  B      -5.15
 195 PHE   ( 278-)  A      -5.12
 608 LYS   ( 252-)  B      -5.09
 235 GLN   ( 318-)  A      -5.07
 150 LYS   ( 232-)  A      -5.04

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.

 386 TYR   ( 479-)  A       388 - MET    481- ( A)         -6.12
 824 TYR   ( 479-)  B       826 - MET    481- ( B)         -6.26

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.

 326 ARG   ( 409-)  A   -3.33
 632 GLN   ( 277-)  B   -2.73
 194 GLN   ( 277-)  A   -2.71
 550 ARG   ( 194-)  B   -2.64
 764 ARG   ( 409-)  B   -2.56
  86 MET   ( 168-)  A   -2.54
 112 ARG   ( 194-)  A   -2.53

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 325 ALA   ( 408-)  A     -  328 GLY   ( 411-)  A        -2.19
 763 ALA   ( 408-)  B     -  766 GLY   ( 411-)  B        -1.95

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

 883 HOH   ( 532 )  A      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 204 ASN   ( 287-)  A

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.

   3 ILE   (  84-)  A      N
   9 TYR   (  90-)  A      N
  10 ASP   (  91-)  A      N
  12 GLU   (  93-)  A      N
  31 GLU   ( 112-)  A      N
  33 SER   ( 114-)  A      N
  36 TRP   ( 118-)  A      N
  41 SER   ( 123-)  A      OG
  44 THR   ( 126-)  A      OG1
  59 ASP   ( 141-)  A      N
  66 TRP   ( 148-)  A      N
  73 ARG   ( 155-)  A      N
  78 ARG   ( 160-)  A      NE
  78 ARG   ( 160-)  A      NH2
  87 LEU   ( 169-)  A      N
  89 SER   ( 171-)  A      OG
  93 ARG   ( 175-)  A      NH1
  93 ARG   ( 175-)  A      NH2
  94 ASP   ( 176-)  A      N
  96 GLU   ( 178-)  A      N
  97 THR   ( 179-)  A      OG1
 102 TYR   ( 184-)  A      N
 103 SER   ( 185-)  A      OG
 119 HIS   ( 201-)  A      N
 121 LYS   ( 203-)  A      NZ
And so on for a total of 107 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  15 HIS   (  96-)  A      ND1
 147 HIS   ( 229-)  A      ND1
 236 HIS   ( 319-)  A      ND1
 243 HIS   ( 326-)  A      ND1
 301 HIS   ( 384-)  A      NE2
 361 GLU   ( 454-)  A      OE1
 424 ASP   ( 517-)  A      OD1
 453 HIS   (  96-)  B      ND1
 532 ASP   ( 176-)  B      OD1
 585 HIS   ( 229-)  B      ND1
 681 HIS   ( 326-)  B      ND1
 739 HIS   ( 384-)  B      NE2
 799 GLU   ( 454-)  B      OE2
 834 GLU   ( 489-)  B      OE2
 862 ASP   ( 517-)  B      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 879  CA   (   2-)  B     0.35   0.83 Is perhaps  K
 881  CA   (   1-)  A     0.46   1.27 Scores about as good as  K (Few ligands (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.

  18 ASP   (  99-)  A   H-bonding suggests Asn; but Alt-Rotamer
 146 ASP   ( 228-)  A   H-bonding suggests Asn; but Alt-Rotamer
 351 ASP   ( 444-)  A   H-bonding suggests Asn; but Alt-Rotamer
 456 ASP   (  99-)  B   H-bonding suggests Asn; but Alt-Rotamer
 463 ASP   ( 106-)  B   H-bonding suggests Asn
 532 ASP   ( 176-)  B   H-bonding suggests Asn
 584 ASP   ( 228-)  B   H-bonding suggests Asn; but Alt-Rotamer
 789 ASP   ( 444-)  B   H-bonding suggests Asn; but Alt-Rotamer
 862 ASP   ( 517-)  B   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 :  -2.003
  2nd generation packing quality :  -2.482
  Ramachandran plot appearance   :  -3.296 (poor)
  chi-1/chi-2 rotamer normality  :  -5.108 (bad)
  Backbone conformation          :  -0.833

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.924
  Bond angles                    :   1.805
  Omega angle restraints         :   1.123
  Side chain planarity           :   0.574 (tight)
  Improper dihedral distribution :   1.350
  B-factor distribution          :   0.536
  Inside/Outside distribution    :   1.037

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.924
  Bond angles                    :   1.805
  Omega angle restraints         :   1.123
  Side chain planarity           :   0.574 (tight)
  Improper dihedral distribution :   1.350
  B-factor distribution          :   0.536
  Inside/Outside distribution    :   1.037
==============

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.