WHAT IF Check report

This file was created 2013-12-10 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 pdb4ic7.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 D

All-atom RMS fit for the two chains : 1.236
CA-only RMS fit for the two chains : 0.953

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 D

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: E and B

All-atom RMS fit for the two chains : 1.289
CA-only RMS fit for the two chains : 0.776

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: E and B

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 943 ANP   ( 501-)  A  -
 944 ANP   ( 501-)  D  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

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'.

  11 GLU   (  56-)  A      CG
  11 GLU   (  56-)  A      CD
  11 GLU   (  56-)  A      OE1
  11 GLU   (  56-)  A      OE2
  65 LYS   ( 110-)  A      CG
  65 LYS   ( 110-)  A      CD
  65 LYS   ( 110-)  A      CE
  65 LYS   ( 110-)  A      NZ
  77 ARG   ( 122-)  A      CG
  77 ARG   ( 122-)  A      CD
  77 ARG   ( 122-)  A      NE
  77 ARG   ( 122-)  A      CZ
  77 ARG   ( 122-)  A      NH1
  77 ARG   ( 122-)  A      NH2
  80 VAL   ( 125-)  A      CG1
  80 VAL   ( 125-)  A      CG2
  84 GLU   ( 129-)  A      CG
  84 GLU   ( 129-)  A      CD
  84 GLU   ( 129-)  A      OE1
  84 GLU   ( 129-)  A      OE2
  86 LYS   ( 131-)  A      CG
  86 LYS   ( 131-)  A      CD
  86 LYS   ( 131-)  A      CE
  86 LYS   ( 131-)  A      NZ
 162 LEU   ( 207-)  A      CG
And so on for a total of 317 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.

   1 ASP   (  46-)  A    High
   2 VAL   (  47-)  A    High
   3 THR   (  48-)  A    High
   4 PHE   (  49-)  A    High
   5 ASP   (  50-)  A    High
   6 VAL   (  51-)  A    High
   7 GLY   (  52-)  A    High
   8 ASP   (  53-)  A    High
   9 GLU   (  54-)  A    High
  28 ARG   (  73-)  A    High
  30 ARG   (  75-)  A    High
  40 LYS   (  85-)  A    High
  43 ASN   (  88-)  A    High
  44 ALA   (  89-)  A    High
  45 PHE   (  90-)  A    High
  46 ASP   (  91-)  A    High
  47 VAL   (  92-)  A    High
  48 VAL   (  93-)  A    High
  49 THR   (  94-)  A    High
  50 ASN   (  95-)  A    High
  52 LYS   (  97-)  A    High
  59 LYS   ( 104-)  A    High
  77 ARG   ( 122-)  A    High
  78 PRO   ( 123-)  A    High
  79 THR   ( 124-)  A    High
And so on for a total of 394 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: 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

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

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.

  30 ARG   (  75-)  A
 281 ARG   ( 326-)  A
 701 ARG   ( 392-)  D
 919 ARG   ( 115-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

   9 GLU   (  54-)  A
  14 GLU   (  59-)  A
 112 GLU   ( 157-)  A
 147 GLU   ( 192-)  A
 168 GLU   ( 213-)  A
 193 GLU   ( 238-)  A
 265 GLU   ( 310-)  A
 334 GLU   ( 379-)  A
 341 GLU   ( 386-)  A
 348 GLU   ( 393-)  A
 466 GLU   ( 157-)  D
 501 GLU   ( 192-)  D
 547 GLU   ( 238-)  D
 695 GLU   ( 386-)  D
 702 GLU   ( 393-)  D
 749 GLU   (  54-)  E
 760 GLU   (  65-)  E
 772 GLU   (  77-)  E
 865 GLU   (  61-)  B
 869 GLU   (  65-)  B
 881 GLU   (  77-)  B

Geometric checks

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.

 104 HIS   ( 149-)  A      CG   ND1  CE1 109.62    4.0
 162 LEU   ( 207-)  A      C    CA   CB  121.09    5.8
 163 CYS   ( 208-)  A     -CA  -C    N   126.04    4.9
 163 CYS   ( 208-)  A     -C    N    CA  129.97    4.6
 177 VAL   ( 222-)  A     -C    N    CA  129.45    4.3
 177 VAL   ( 222-)  A      N    CA   C    97.35   -4.9
 247 GLU   ( 292-)  A     -C    N    CA  130.43    4.9
 247 GLU   ( 292-)  A      N    CA   C   126.97    5.6
 349 GLY   ( 394-)  A      N    CA   C    98.27   -4.9
 505 LEU   ( 196-)  D      CA   CB   CG  132.67    4.7
 517 CYS   ( 208-)  D     -C    N    CA  130.11    4.7
 601 GLU   ( 292-)  D      N    CA   C   123.35    4.3
 603 VAL   ( 294-)  D      N    CA   C    99.35   -4.2
 606 TYR   ( 297-)  D      N    CA   C    98.15   -4.7
 702 GLU   ( 393-)  D     -C    N    CA  134.42    7.1
 702 GLU   ( 393-)  D      N    CA   C   122.50    4.0
 808 GLY   ( 113-)  E     -C    N    CA  129.07    5.0
 813 HIS   ( 118-)  E      N    CA   C   125.57    5.1
 839 SER   (  35-)  B     -C    N    CA  130.34    4.8
 921 ILE   ( 117-)  B      N    CA   C   122.43    4.0
 922 HIS   ( 118-)  B      N    CA   C   125.15    5.0
 941 HIS   ( 137-)  B      CG   ND1  CE1 109.69    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.

   9 GLU   (  54-)  A
  14 GLU   (  59-)  A
  30 ARG   (  75-)  A
 112 GLU   ( 157-)  A
 147 GLU   ( 192-)  A
 168 GLU   ( 213-)  A
 193 GLU   ( 238-)  A
 265 GLU   ( 310-)  A
 281 ARG   ( 326-)  A
 334 GLU   ( 379-)  A
 341 GLU   ( 386-)  A
 348 GLU   ( 393-)  A
 466 GLU   ( 157-)  D
 501 GLU   ( 192-)  D
 547 GLU   ( 238-)  D
 695 GLU   ( 386-)  D
 701 ARG   ( 392-)  D
 702 GLU   ( 393-)  D
 749 GLU   (  54-)  E
 760 GLU   (  65-)  E
 772 GLU   (  77-)  E
 865 GLU   (  61-)  B
 869 GLU   (  65-)  B
 881 GLU   (  77-)  B
 919 ARG   ( 115-)  B

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 601 GLU   ( 292-)  D      CA   -10.2    17.23    33.96
The average deviation= 0.955

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.

 606 TYR   ( 297-)  D    7.63
 341 GLU   ( 386-)  A    5.64
 349 GLY   ( 394-)  A    5.49
 677 ASP   ( 368-)  D    5.38
 247 GLU   ( 292-)  A    5.30
 177 VAL   ( 222-)  A    4.90
 813 HIS   ( 118-)  E    4.64
 930 ALA   ( 126-)  B    4.53
 922 HIS   ( 118-)  B    4.50
 921 ILE   ( 117-)  B    4.30
 585 MET   ( 276-)  D    4.17
 603 VAL   ( 294-)  D    4.13
 601 GLU   ( 292-)  D    4.06
 929 ARG   ( 125-)  B    4.04

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 919 ARG   ( 115-)  B    7.82

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 : -3.358

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.

 674 PHE   ( 365-)  D    -3.3
 921 ILE   ( 117-)  B    -2.9
 435 PRO   ( 126-)  D    -2.9
  81 PRO   ( 126-)  A    -2.8
 322 PHE   ( 367-)  A    -2.7
 572 PRO   ( 263-)  D    -2.7
 941 HIS   ( 137-)  B    -2.7
 938 HIS   ( 134-)  B    -2.7
 812 ILE   ( 117-)  E    -2.6
 190 SER   ( 235-)  A    -2.6
 807 PRO   ( 112-)  E    -2.6
 549 THR   ( 240-)  D    -2.6
 732 PRO   (  37-)  E    -2.6
 701 ARG   ( 392-)  D    -2.5
 368 GLU   (  59-)  D    -2.5
 793 LEU   (  98-)  E    -2.5
 747 LEU   (  52-)  E    -2.5
 924 LEU   ( 120-)  B    -2.5
 348 GLU   ( 393-)  A    -2.5
 686 ILE   ( 377-)  D    -2.4
 328 THR   ( 373-)  A    -2.4
 677 ASP   ( 368-)  D    -2.4
 815 LEU   ( 120-)  E    -2.4
 375 TYR   (  66-)  D    -2.4
 856 LEU   (  52-)  B    -2.4
And so on for a total of 66 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.

   6 VAL   (  51-)  A  omega poor
   8 ASP   (  53-)  A  Poor phi/psi, omega poor
  14 GLU   (  59-)  A  Poor phi/psi
  19 GLY   (  64-)  A  omega poor
  29 ARG   (  74-)  A  omega poor
  43 ASN   (  88-)  A  omega poor
  64 PHE   ( 109-)  A  omega poor
  80 VAL   ( 125-)  A  PRO omega poor
  81 PRO   ( 126-)  A  omega poor
  84 GLU   ( 129-)  A  Poor phi/psi
 132 GLN   ( 177-)  A  Poor phi/psi
 136 ARG   ( 181-)  A  Poor phi/psi, omega poor
 149 CYS   ( 194-)  A  Poor phi/psi
 155 ASP   ( 200-)  A  Poor phi/psi
 162 LEU   ( 207-)  A  Poor phi/psi, omega poor
 164 THR   ( 209-)  A  Poor phi/psi
 166 PRO   ( 211-)  A  omega poor
 167 ALA   ( 212-)  A  omega poor
 168 GLU   ( 213-)  A  omega poor
 170 GLN   ( 215-)  A  Poor phi/psi
 171 TYR   ( 216-)  A  Poor phi/psi, omega poor
 174 THR   ( 219-)  A  omega poor
 176 TYR   ( 221-)  A  Poor phi/psi, omega poor
 177 VAL   ( 222-)  A  Poor phi/psi
 192 HIS   ( 237-)  A  Poor phi/psi
And so on for a total of 133 lines.

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

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

chi-1/chi-2 correlation Z-score : -4.269

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.

 277 SER   ( 322-)  A    0.37

Warning: Unusual backbone conformations

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

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

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

   8 ASP   (  53-)  A      0
   9 GLU   (  54-)  A      0
  13 ILE   (  58-)  A      0
  14 GLU   (  59-)  A      0
  15 THR   (  60-)  A      0
  16 ILE   (  61-)  A      0
  18 ASN   (  63-)  A      0
  20 ALA   (  65-)  A      0
  21 TYR   (  66-)  A      0
  31 LEU   (  76-)  A      0
  43 ASN   (  88-)  A      0
  44 ALA   (  89-)  A      0
  46 ASP   (  91-)  A      0
  63 HIS   ( 108-)  A      0
  64 PHE   ( 109-)  A      0
  65 LYS   ( 110-)  A      0
  66 HIS   ( 111-)  A      0
  79 THR   ( 124-)  A      0
  80 VAL   ( 125-)  A      0
  81 PRO   ( 126-)  A      0
  82 TYR   ( 127-)  A      0
  84 GLU   ( 129-)  A      0
  85 PHE   ( 130-)  A      0
  86 LYS   ( 131-)  A      0
  87 SER   ( 132-)  A      0
And so on for a total of 399 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.927

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!

 831 GLY   (  27-)  B   2.01   12
 185 PRO   ( 230-)  A   1.58   15

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...

 246 ALA   ( 291-)  A   2.49

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].

  78 PRO   ( 123-)  A   107.6 envelop C-beta (108 degrees)
  81 PRO   ( 126-)  A   -10.7 half-chair C-alpha/N (-18 degrees)
 166 PRO   ( 211-)  A  -132.4 half-chair C-delta/C-gamma (-126 degrees)
 185 PRO   ( 230-)  A   109.7 envelop C-beta (108 degrees)
 218 PRO   ( 263-)  A    -9.5 half-chair C-alpha/N (-18 degrees)
 300 PRO   ( 345-)  A   103.1 envelop C-beta (108 degrees)
 432 PRO   ( 123-)  D   145.9 envelop C-alpha (144 degrees)
 435 PRO   ( 126-)  D    17.6 half-chair N/C-delta (18 degrees)
 539 PRO   ( 230-)  D   111.3 envelop C-beta (108 degrees)
 572 PRO   ( 263-)  D     2.7 envelop N (0 degrees)
 915 PRO   ( 111-)  B   -60.3 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 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.

   3 THR   (  48-)  A      O   <->   40 LYS   (  85-)  A      NZ     0.71    1.99  INTRA BF
 346 ARG   ( 391-)  A      NH2 <->  850 ASP   (  46-)  B      OD2    0.54    2.16  INTRA BF
 702 GLU   ( 393-)  D      OE1 <->  703 GLY   ( 394-)  D      N      0.53    2.07  INTRA BF
 195 THR   ( 240-)  A      N   <->  945 HOH   ( 604 )  A      O      0.44    2.26  INTRA BF
 880 GLU   (  76-)  B      O   <->  883 LYS   (  79-)  B      N      0.42    2.28  INTRA BF
 917 GLY   ( 113-)  B      N   <->  948 HOH   ( 204 )  B      O      0.39    2.31  INTRA BL
 374 ALA   (  65-)  D      O   <->  944 ANP   ( 501-)  D      O2B    0.38    2.02  INTRA BF
 931 GLY   ( 127-)  B      O   <->  933 SER   ( 129-)  B      N      0.34    2.36  INTRA BL
 107 GLN   ( 152-)  A      OE1 <->  925 LYS   ( 121-)  B      N      0.34    2.36  INTRA BL
 540 GLU   ( 231-)  D      OE2 <->  644 ARG   ( 335-)  D      NH1    0.33    2.37  INTRA BL
 540 GLU   ( 231-)  D      OE1 <->  644 ARG   ( 335-)  D      NH2    0.32    2.38  INTRA BL
 736 PHE   (  41-)  E      N   <->  770 ASP   (  75-)  E      OD1    0.32    2.38  INTRA BF
 112 GLU   ( 157-)  A      OE2 <->  115 ARG   ( 160-)  A      NH1    0.32    2.38  INTRA BL
 945 HOH   ( 614 )  A      O   <->  948 HOH   ( 201 )  B      O      0.31    2.09  INTRA BL
 493 LYS   ( 184-)  D      NZ  <->  946 HOH   ( 614 )  D      O      0.31    2.39  INTRA BL
  96 GLU   ( 141-)  A      OE1 <->  147 GLU   ( 192-)  A      N      0.30    2.40  INTRA BF
 461 GLN   ( 152-)  D      OE1 <->  816 LYS   ( 121-)  E      N      0.30    2.40  INTRA BF
 126 LYS   ( 171-)  A      NZ  <->  311 GLU   ( 356-)  A      O      0.30    2.40  INTRA BL
 555 TRP   ( 246-)  D      NE1 <->  946 HOH   ( 602 )  D      O      0.29    2.41  INTRA BL
 310 ASP   ( 355-)  A      OD2 <->  945 HOH   ( 612 )  A      O      0.28    2.12  INTRA BL
  66 HIS   ( 111-)  A      CE1 <->  123 ARG   ( 168-)  A      NH1    0.27    2.83  INTRA BL
 670 PRO   ( 361-)  D      CD  <->  737 ARG   (  42-)  E      NH1    0.26    2.84  INTRA BF
 451 SER   ( 142-)  D      OG  <->  452 ASP   ( 143-)  D      N      0.26    2.34  INTRA BL
 702 GLU   ( 393-)  D      O   <->  704 ILE   ( 395-)  D      N      0.25    2.45  INTRA BF
 186 GLU   ( 231-)  A      OE1 <->  290 ARG   ( 335-)  A      NH2    0.25    2.45  INTRA BL
And so on for a total of 202 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: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

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.

 431 ARG   ( 122-)  D      -8.62
 375 TYR   (  66-)  D      -7.99
  82 TYR   ( 127-)  A      -7.70
 701 ARG   ( 392-)  D      -7.14
 938 HIS   ( 134-)  B      -6.77
 347 ARG   ( 392-)  A      -6.73
 941 HIS   ( 137-)  B      -6.73
 364 TYR   (  55-)  D      -6.55
 929 ARG   ( 125-)  B      -6.54
 838 HIS   (  34-)  B      -6.52
 934 GLN   ( 130-)  B      -6.39
 220 LYS   ( 265-)  A      -6.36
 925 LYS   ( 121-)  B      -6.26
 816 LYS   ( 121-)  E      -6.26
 574 LYS   ( 265-)  D      -6.17
 729 HIS   (  34-)  E      -6.16
 613 ARG   ( 304-)  D      -6.11
 417 HIS   ( 108-)  D      -6.10
 939 HIS   ( 135-)  B      -6.07
 652 ARG   ( 343-)  D      -5.98
  21 TYR   (  66-)  A      -5.95
 388 GLN   (  79-)  D      -5.93
  63 HIS   ( 108-)  A      -5.92
 914 LYS   ( 110-)  B      -5.79
 254 GLN   ( 299-)  A      -5.76
 793 LEU   (  98-)  E      -5.72
 812 ILE   ( 117-)  E      -5.65
 298 ARG   ( 343-)  A      -5.62
 529 GLU   ( 220-)  D      -5.59
 706 GLN   ( 397-)  D      -5.58
 877 ARG   (  73-)  B      -5.54
 921 ILE   ( 117-)  B      -5.52
 829 ASN   (  25-)  B      -5.45
 869 GLU   (  65-)  B      -5.45
 792 GLN   (  97-)  E      -5.42
 354 ILE   ( 399-)  A      -5.33
 568 ARG   ( 259-)  D      -5.33
 768 ARG   (  73-)  E      -5.29
  18 ASN   (  63-)  A      -5.26
 720 ASN   (  25-)  E      -5.19
 805 LYS   ( 110-)  E      -5.19
 176 TYR   ( 221-)  A      -5.19
 327 LEU   ( 372-)  A      -5.18
 372 ASN   (  63-)  D      -5.07
 248 ARG   ( 293-)  A      -5.06
 749 GLU   (  54-)  E      -5.06
 760 GLU   (  65-)  E      -5.04
 700 ARG   ( 391-)  D      -5.03

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.

 174 THR   ( 219-)  A       176 - TYR    221- ( A)         -4.73
 792 GLN   (  97-)  E       794 - ILE     99- ( E)         -5.10
 810 ARG   ( 115-)  E       812 - ILE    117- ( E)         -4.87
 919 ARG   ( 115-)  B       922 - HIS    118- ( B)         -4.69
 934 GLN   ( 130-)  B       936 - GLY    132- ( B)         -5.25

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: D

Note: Quality value plot

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

Chain identifier: E

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.

 937 ARG   ( 133-)  B   -3.67
 355 ARG   ( 400-)  A   -3.53
 602 ARG   ( 293-)  D   -3.44
 683 ARG   ( 374-)  D   -3.41
 324 ARG   ( 369-)  A   -3.40
 259 ARG   ( 304-)  A   -3.36
 705 ARG   ( 396-)  D   -3.31
 940 HIS   ( 136-)  B   -3.14
 383 ARG   (  74-)  D   -3.07
 247 GLU   ( 292-)  A   -3.06
 439 PHE   ( 130-)  D   -2.99
  65 LYS   ( 110-)  A   -2.98
 440 LYS   ( 131-)  D   -2.96
 842 GLN   (  38-)  B   -2.90
 601 GLU   ( 292-)  D   -2.86
 942 HIS   ( 138-)  B   -2.86
 600 ALA   ( 291-)  D   -2.84
  86 LYS   ( 131-)  A   -2.83
 384 ARG   (  75-)  D   -2.72
 358 PHE   (  49-)  D   -2.72
 105 SER   ( 150-)  A   -2.67
  77 ARG   ( 122-)  A   -2.65
 436 TYR   ( 127-)  D   -2.58
 927 ASN   ( 123-)  B   -2.57
 514 ARG   ( 205-)  D   -2.54
 424 ILE   ( 115-)  D   -2.52
 173 MET   ( 218-)  A   -2.51

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.

 381 ALA   (  72-)  D     -  385 LEU   (  76-)  D        -1.96
 437 GLY   ( 128-)  D     -  440 LYS   ( 131-)  D        -2.33
 513 ALA   ( 204-)  D     -  517 CYS   ( 208-)  D        -1.29
 599 GLY   ( 290-)  D     -  602 ARG   ( 293-)  D        -2.67
 938 HIS   ( 134-)  B     -  942 HIS   ( 138-)  B        -2.43

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: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

 455 GLN   ( 146-)  D
 720 ASN   (  25-)  E
 897 GLN   (  93-)  B
 938 HIS   ( 134-)  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.

  10 TYR   (  55-)  A      N
  26 SER   (  71-)  A      N
  32 THR   (  77-)  A      N
  45 PHE   (  90-)  A      N
  47 VAL   (  92-)  A      N
  53 ARG   (  98-)  A      NE
  56 ARG   ( 101-)  A      NH2
  66 HIS   ( 111-)  A      NE2
  85 PHE   ( 130-)  A      N
  95 MET   ( 140-)  A      N
  96 GLU   ( 141-)  A      N
  97 SER   ( 142-)  A      OG
 136 ARG   ( 181-)  A      NH2
 139 LYS   ( 184-)  A      N
 157 GLY   ( 202-)  A      N
 158 MET   ( 203-)  A      N
 160 ARG   ( 205-)  A      NE
 172 PHE   ( 217-)  A      N
 176 TYR   ( 221-)  A      N
 177 VAL   ( 222-)  A      N
 182 TYR   ( 227-)  A      N
 183 ARG   ( 228-)  A      N
 183 ARG   ( 228-)  A      NE
 193 GLU   ( 238-)  A      N
 221 ASN   ( 266-)  A      N
And so on for a total of 91 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.

 509 ASP   ( 200-)  D      OD2
 664 ASP   ( 355-)  D      OD2
 788 GLN   (  93-)  E      OE1
 899 ASN   (  95-)  B      OD1
 920 ASN   ( 116-)  B      OD1
 922 HIS   ( 118-)  B      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.

   8 ASP   (  53-)  A   H-bonding suggests Asn; but Alt-Rotamer
 168 GLU   ( 213-)  A   H-bonding suggests Gln
 311 GLU   ( 356-)  A   H-bonding suggests Gln
 348 GLU   ( 393-)  A   H-bonding suggests Gln
 368 GLU   (  59-)  D   H-bonding suggests Gln
 509 ASP   ( 200-)  D   H-bonding suggests Asn; Ligand-contact
 738 ASP   (  43-)  E   H-bonding suggests Asn
 760 GLU   (  65-)  E   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.180
  2nd generation packing quality :  -3.049 (poor)
  Ramachandran plot appearance   :  -3.358 (poor)
  chi-1/chi-2 rotamer normality  :  -4.269 (bad)
  Backbone conformation          :  -1.062

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.397 (tight)
  Bond angles                    :   0.776
  Omega angle restraints         :   1.441 (loose)
  Side chain planarity           :   0.549 (tight)
  Improper dihedral distribution :   0.857
  B-factor distribution          :   0.967
  Inside/Outside distribution    :   1.042

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.8
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.397 (tight)
  Bond angles                    :   0.776
  Omega angle restraints         :   1.441 (loose)
  Side chain planarity           :   0.549 (tight)
  Improper dihedral distribution :   0.857
  B-factor distribution          :   0.967
  Inside/Outside distribution    :   1.042
==============

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.