WHAT IF Check report

This file was created 2011-12-28 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 pdb1ggt.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 : 0.998
CA-only RMS fit for the two chains : 0.522

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

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

  23 GLU   (  30-)  A  -
 710 PRO   ( 729-)  A  -
 733 GLU   (  30-)  B  -
1418 ARG   ( 727-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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'.

  23 GLU   (  30-)  A      O
 710 PRO   ( 729-)  A      O
 733 GLU   (  30-)  B      O
1418 ARG   ( 727-)  B      O

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 3.72

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.539 over 10237 bonds
Average difference in B over a bond : 3.43
RMS difference in B over a bond : 4.46

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.

 632 GLU   ( 651-)  A      CD   OE2   1.33    4.2
1151 ILE   ( 460-)  B      CA   CB    1.45   -4.1
1342 GLU   ( 651-)  B      CD   OE2   1.34    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.

   2 GLY   (   9-)  A      N    CA   C   100.27   -4.2
  11 ASN   (  18-)  A      N    CA   C   123.30    4.3
  50 TYR   (  69-)  A      N    CA   C    98.53   -4.5
  86 ILE   ( 105-)  A      C    CA   CB  102.28   -4.1
 261 ASP   ( 280-)  A      N    CA   C   122.63    4.1
 291 ARG   ( 310-)  A      N    CA   C   124.59    4.8
 292 TYR   ( 311-)  A      N    CA   C   123.49    4.4
 320 PHE   ( 339-)  A     -C    N    CA  112.65   -5.0
 320 PHE   ( 339-)  A      C    CA   CB  118.62    4.5
 336 GLU   ( 355-)  A      N    CA   C    99.81   -4.1
 346 THR   ( 365-)  A      N    CA   C    84.15   -9.7
 406 GLN   ( 425-)  A      N    CA   C   126.21    5.4
 407 PHE   ( 426-)  A     -CA  -C    N   105.29   -5.5
 407 PHE   ( 426-)  A     -C    N    CA  132.03    5.7
 407 PHE   ( 426-)  A      C    CA   CB  120.29    5.4
 493 MET   ( 512-)  A      N    CA   C    95.72   -5.5
 540 PHE   ( 559-)  A      N    CA   C    95.89   -5.5
 555 ASP   ( 574-)  A      N    CA   C    99.68   -4.1
 655 ARG   ( 674-)  A      N    CA   C    97.62   -4.8
 735 PHE   (  44-)  B      N    CA   C   123.66    4.5
 743 LEU   (  52-)  B      N    CA   C    97.43   -4.9
 766 ILE   (  75-)  B      N    CA   C    99.64   -4.1
 791 ARG   ( 100-)  B      CB   CG   CD  103.08   -5.5
 801 GLN   ( 110-)  B      N    CA   C    98.49   -4.5
 808 ILE   ( 117-)  B      C    CA   CB  102.11   -4.2
 825 ILE   ( 134-)  B      N    CA   C    95.95   -5.4
 892 ARG   ( 201-)  B      CB   CG   CD  106.06   -4.0
 960 LYS   ( 269-)  B      N    CA   C    98.91   -4.4
 964 GLY   ( 273-)  B      N    CA   C   124.21    4.0
1002 TYR   ( 311-)  B     -CA  -C    N   107.67   -4.3
1002 TYR   ( 311-)  B     -C    N    CA  129.08    4.1
1054 LYS   ( 363-)  B      N    CA   C    99.43   -4.2
1056 THR   ( 365-)  B     -C    N    CA  129.63    4.4
1056 THR   ( 365-)  B      N    CA   C    91.07   -7.2
1116 GLN   ( 425-)  B      N    CA   C   129.94    6.7
1117 PHE   ( 426-)  B     -CA  -C    N   105.75   -5.2
1117 PHE   ( 426-)  B     -C    N    CA  131.25    5.3
1117 PHE   ( 426-)  B      C    CA   CB  118.33    4.3
1151 ILE   ( 460-)  B      N    CA   C   133.12    7.8
1252 THR   ( 561-)  B      C    CA   CB  101.48   -4.5
1264 PHE   ( 573-)  B      C    CA   CB  101.34   -4.6
1265 ASP   ( 574-)  B      N    CA   C    95.72   -5.5
1320 ILE   ( 629-)  B      N    CA   C    98.14   -4.7
1323 ILE   ( 632-)  B      N    CA   C    97.00   -5.1
1365 ARG   ( 674-)  B      N    CA   C    99.24   -4.3
1396 LEU   ( 705-)  B      N    CA   C    98.45   -4.6

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.

  72 PRO   (  91-)  A      N      6.2    17.87    -2.48
 319 TYR   ( 338-)  A      CA    -7.6    21.96    34.03
 345 LEU   ( 364-)  A      C     -6.9   -10.68     0.20
 346 THR   ( 365-)  A      C     -7.0   -10.22     0.30
 407 PHE   ( 426-)  A      CA    -7.6    21.78    33.98
1055 LEU   ( 364-)  B      C     -6.6   -10.20     0.20
1056 THR   ( 365-)  B      C     -7.0   -10.19     0.30
1116 GLN   ( 425-)  B      C      6.7    10.64     0.15
1117 PHE   ( 426-)  B      C     -7.4   -11.90     0.23
The average deviation= 1.477

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.

 346 THR   ( 365-)  A    9.10
1151 ILE   ( 460-)  B    7.99
1116 GLN   ( 425-)  B    7.29
 291 ARG   ( 310-)  A    7.13
1056 THR   ( 365-)  B    6.76
 409 ALA   ( 428-)  A    6.75
 292 TYR   ( 311-)  A    6.06
 540 PHE   ( 559-)  A    5.91
 406 GLN   ( 425-)  A    5.83
1207 SER   ( 516-)  B    5.76
 825 ILE   ( 134-)  B    5.66
 655 ARG   ( 674-)  A    5.47
 930 LEU   ( 239-)  B    5.24
1005 CYS   ( 314-)  B    5.23
 743 LEU   (  52-)  B    5.19
1108 ILE   ( 417-)  B    5.17
 295 CYS   ( 314-)  A    5.13
 801 GLN   ( 110-)  B    5.06
1265 ASP   ( 574-)  B    4.97
1259 PHE   ( 568-)  B    4.90
 832 SER   ( 141-)  B    4.86
  50 TYR   (  69-)  A    4.83
 735 PHE   (  44-)  B    4.79
 578 GLN   ( 597-)  A    4.78
   2 GLY   (   9-)  A    4.77
 960 LYS   ( 269-)  B    4.77
1396 LEU   ( 705-)  B    4.74
1365 ARG   ( 674-)  B    4.71
 493 MET   ( 512-)  A    4.69
 395 VAL   ( 414-)  A    4.67
 989 ILE   ( 298-)  B    4.60
1054 LYS   ( 363-)  B    4.57
1001 ARG   ( 310-)  B    4.54
1323 ILE   ( 632-)  B    4.49
 198 VAL   ( 217-)  A    4.46
 345 LEU   ( 364-)  A    4.37
 185 TYR   ( 204-)  A    4.35
 416 VAL   ( 435-)  A    4.32
 460 ASP   ( 479-)  A    4.32
 895 TYR   ( 204-)  B    4.23
1250 PHE   ( 559-)  B    4.21
 159 THR   ( 178-)  A    4.18
 535 SER   ( 554-)  A    4.17
1320 ILE   ( 629-)  B    4.09
 397 ALA   ( 416-)  A    4.09
 766 ILE   (  75-)  B    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 : 1.866

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

1098 TYR   ( 407-)  B      OH   4.25
1063 TYR   ( 372-)  B      OH   4.24
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.152

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 : -3.152

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.

 346 THR   ( 365-)  A    -3.5
 264 TYR   ( 283-)  A    -3.0
  50 TYR   (  69-)  A    -2.9
1151 ILE   ( 460-)  B    -2.9
1002 TYR   ( 311-)  B    -2.8
1307 ARG   ( 616-)  B    -2.8
 809 PRO   ( 118-)  B    -2.7
 553 THR   ( 572-)  A    -2.7
 292 TYR   ( 311-)  A    -2.7
 195 TYR   ( 214-)  A    -2.6
 407 PHE   ( 426-)  A    -2.6
 974 TYR   ( 283-)  B    -2.6
1330 THR   ( 639-)  B    -2.6
 914 ARG   ( 223-)  B    -2.6
1207 SER   ( 516-)  B    -2.6
1270 PRO   ( 579-)  B    -2.4
 561 LEU   ( 580-)  A    -2.4
1074 PRO   ( 383-)  B    -2.4
 819 GLY   ( 128-)  B    -2.4
 497 SER   ( 516-)  A    -2.4
 204 ARG   ( 223-)  A    -2.4
  77 ARG   (  96-)  A    -2.4
 735 PHE   (  44-)  B    -2.4
1263 THR   ( 572-)  B    -2.4
 564 LYS   ( 583-)  A    -2.4
And so on for a total of 98 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.

  25 PHE   (  44-)  A  Poor phi/psi
  46 HIS   (  65-)  A  Poor phi/psi
  50 TYR   (  69-)  A  Poor phi/psi
  72 PRO   (  91-)  A  Poor phi/psi
 119 GLU   ( 138-)  A  Poor phi/psi
 120 ASP   ( 139-)  A  Poor phi/psi
 121 ARG   ( 140-)  A  Poor phi/psi
 195 TYR   ( 214-)  A  Poor phi/psi
 227 GLN   ( 246-)  A  Poor phi/psi
 251 ASP   ( 270-)  A  Poor phi/psi
 252 ASP   ( 271-)  A  Poor phi/psi
 262 ASN   ( 281-)  A  Poor phi/psi
 287 GLU   ( 306-)  A  Poor phi/psi
 292 TYR   ( 311-)  A  Poor phi/psi
 319 TYR   ( 338-)  A  Poor phi/psi
 327 ALA   ( 346-)  A  Poor phi/psi
 339 GLY   ( 358-)  A  Poor phi/psi
 383 ASN   ( 402-)  A  Poor phi/psi
 387 MET   ( 406-)  A  Poor phi/psi
 391 GLY   ( 410-)  A  PRO omega poor
 402 HIS   ( 421-)  A  Poor phi/psi
 407 PHE   ( 426-)  A  Poor phi/psi
 490 GLU   ( 509-)  A  Poor phi/psi
 493 MET   ( 512-)  A  Poor phi/psi
 494 LYS   ( 513-)  A  Poor phi/psi
And so on for a total of 78 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 : -4.445

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!

   4 ARG   (  11-)  A      0
   5 ARG   (  12-)  A      0
  10 ASN   (  17-)  A      0
  15 ALA   (  22-)  A      0
  18 ASP   (  25-)  A      0
  22 VAL   (  29-)  A      0
  23 GLU   (  30-)  A      0
  24 GLU   (  43-)  A      0
  25 PHE   (  44-)  A      0
  26 LEU   (  45-)  A      0
  27 ASN   (  46-)  A      0
  29 THR   (  48-)  A      0
  30 SER   (  49-)  A      0
  34 PHE   (  53-)  A      0
  35 LYS   (  54-)  A      0
  39 ASP   (  58-)  A      0
  46 HIS   (  65-)  A      0
  47 THR   (  66-)  A      0
  48 ASP   (  67-)  A      0
  50 TYR   (  69-)  A      0
  51 GLU   (  70-)  A      0
  52 ASN   (  71-)  A      0
  59 ARG   (  78-)  A      0
  70 SER   (  89-)  A      0
  71 ARG   (  90-)  A      0
And so on for a total of 643 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.864

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!

1360 GLY   ( 669-)  B   2.03   24

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...

 119 GLU   ( 138-)  A   1.90
 291 ARG   ( 310-)  A   3.52
 406 GLN   ( 425-)  A   2.02
 407 PHE   ( 426-)  A   2.04
1001 ARG   ( 310-)  B   2.44

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]

  20 PRO   (  27-)  A    0.45 HIGH
 545 PRO   ( 564-)  A    0.46 HIGH
 719 PRO   (  16-)  B    0.46 HIGH
 946 PRO   ( 255-)  B    0.47 HIGH
1077 PRO   ( 386-)  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].

  72 PRO   (  91-)  A  -122.5 half-chair C-delta/C-gamma (-126 degrees)
 147 PRO   ( 166-)  A  -119.2 half-chair C-delta/C-gamma (-126 degrees)
 269 PRO   ( 288-)  A  -120.5 half-chair C-delta/C-gamma (-126 degrees)
 289 PRO   ( 308-)  A  -112.7 envelop C-gamma (-108 degrees)
 785 PRO   (  94-)  B  -114.5 envelop C-gamma (-108 degrees)
 980 PRO   ( 289-)  B    99.2 envelop C-beta (108 degrees)
1074 PRO   ( 383-)  B    47.3 half-chair C-delta/C-gamma (54 degrees)
1321 PRO   ( 630-)  B   -51.3 half-chair C-beta/C-alpha (-54 degrees)
1366 PRO   ( 675-)  B  -125.0 half-chair C-delta/C-gamma (-126 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.

1361 PRO   ( 670-)  B      O   <-> 1394 ARG   ( 703-)  B      NH1    0.38    2.32  INTRA BL
 344 LYS   ( 363-)  A      CG  <->  345 LEU   ( 364-)  A      N      0.34    2.66  INTRA BF
1285 TYR   ( 594-)  B      CD1 <-> 1286 MET   ( 595-)  B      N      0.31    2.69  INTRA
 155 ARG   ( 174-)  A      NH2 <->  160 ASP   ( 179-)  A      OD1    0.31    2.39  INTRA BL
1073 ARG   ( 382-)  B      NH1 <-> 1075 ASP   ( 384-)  B      OD2    0.31    2.39  INTRA BL
1054 LYS   ( 363-)  B      CG  <-> 1055 LEU   ( 364-)  B      N      0.30    2.70  INTRA BF
 435 ASN   ( 454-)  A      OD1 <->  493 MET   ( 512-)  A      SD     0.29    2.56  INTRA BF
 104 SER   ( 123-)  A      O   <->  114 LYS   ( 133-)  A      NZ     0.28    2.42  INTRA BF
 910 ASP   ( 219-)  B      CG  <->  912 LYS   ( 221-)  B      NZ     0.28    2.82  INTRA
 727 ASP   (  24-)  B      O   <->  849 ARG   ( 158-)  B      NH2    0.25    2.45  INTRA
 337 GLU   ( 356-)  A      CG  <->  426 LYS   ( 445-)  A      NZ     0.25    2.85  INTRA BF
 450 ILE   ( 469-)  A      CG2 <->  451 GLY   ( 470-)  A      N      0.25    2.75  INTRA
1285 TYR   ( 594-)  B      O   <-> 1287 GLY   ( 596-)  B      N      0.24    2.46  INTRA BF
 419 ASP   ( 438-)  A      OD2 <->  485 LYS   ( 504-)  A      NZ     0.24    2.46  INTRA
 179 GLU   ( 198-)  A      OE1 <->  182 ARG   ( 201-)  A      NH1    0.24    2.46  INTRA
 752 LYS   (  61-)  B      NZ  <->  762 ASN   (  71-)  B      O      0.23    2.47  INTRA BL
 813 VAL   ( 122-)  B      CG1 <->  814 SER   ( 123-)  B      N      0.23    2.77  INTRA BF
 334 PHE   ( 353-)  A      CD2 <->  345 LEU   ( 364-)  A      O      0.23    2.57  INTRA BF
 742 HIS   (  51-)  B      N   <->  776 GLN   (  85-)  B      O      0.22    2.48  INTRA
1033 HIS   ( 342-)  B      ND1 <-> 1125 GLU   ( 434-)  B      OE2    0.22    2.48  INTRA BL
  81 ARG   ( 100-)  A      CD  <->  145 TRP   ( 164-)  A      CZ3    0.21    2.99  INTRA BF
  37 ARG   (  56-)  A      NH2 <->   51 GLU   (  70-)  A      OE2    0.21    2.49  INTRA
1005 CYS   ( 314-)  B      SG  <-> 1006 TRP   ( 315-)  B      N      0.20    3.00  INTRA BL
1219 VAL   ( 528-)  B      CG1 <-> 1220 LEU   ( 529-)  B      N      0.20    2.80  INTRA
 494 LYS   ( 513-)  A      NZ  <->  495 SER   ( 514-)  A      O      0.20    2.40  INTRA BF
And so on for a total of 325 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.

 148 TYR   ( 167-)  A      -9.08
   4 ARG   (  11-)  A      -8.68
 714 ARG   (  11-)  B      -8.46
 709 ARG   ( 728-)  A      -7.95
 858 TYR   ( 167-)  B      -7.69
 266 TYR   ( 285-)  A      -7.57
 976 TYR   ( 285-)  B      -7.13
 735 PHE   (  44-)  B      -7.00
 155 ARG   ( 174-)  A      -6.96
1365 ARG   ( 674-)  B      -6.76
 708 ARG   ( 727-)  A      -6.75
 865 ARG   ( 174-)  B      -6.62
  76 ARG   (  95-)  A      -6.62
 799 TYR   ( 108-)  B      -6.38
  25 PHE   (  44-)  A      -6.34
  88 ARG   ( 107-)  A      -6.07
 655 ARG   ( 674-)  A      -6.04
  89 TYR   ( 108-)  A      -5.96
1137 LYS   ( 446-)  B      -5.95
   5 ARG   (  12-)  A      -5.90
 449 GLN   ( 468-)  A      -5.78
1175 GLN   ( 484-)  B      -5.77
 662 ARG   ( 681-)  A      -5.77
1200 GLU   ( 509-)  B      -5.74
1159 GLN   ( 468-)  B      -5.73
And so on for a total of 57 lines.

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.

 387 MET   ( 406-)  A       389 - ARG    408- ( A)         -5.00
1097 MET   ( 406-)  B      1099 - ARG    408- ( B)         -4.84
1202 VAL   ( 511-)  B      1204 - LYS    513- ( B)         -4.68
1206 ARG   ( 515-)  B      1208 - ASN    517- ( B)         -4.57

Note: Quality value plot

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

Chain identifier: 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.

 623 VAL   ( 642-)  A   -2.84
 787 ARG   (  96-)  B   -2.80
 345 LEU   ( 364-)  A   -2.66
 813 VAL   ( 122-)  B   -2.58
 982 ALA   ( 291-)  B   -2.53
1098 TYR   ( 407-)  B   -2.53
 388 TYR   ( 407-)  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

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.

 188 ASN   ( 207-)  A
 417 ASN   ( 436-)  A
 742 HIS   (  51-)  B
 998 ASN   ( 307-)  B
1013 ASN   ( 322-)  B
1028 ASN   ( 337-)  B
1296 HIS   ( 605-)  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.

   4 ARG   (  11-)  A      N
  13 ASN   (  20-)  A      N
  15 ALA   (  22-)  A      N
  26 LEU   (  45-)  A      N
  36 GLU   (  55-)  A      N
  41 ASN   (  60-)  A      N
  41 ASN   (  60-)  A      ND2
  42 LYS   (  61-)  A      N
  49 LYS   (  68-)  A      N
  56 ILE   (  75-)  A      N
  58 ARG   (  77-)  A      NH1
  60 GLY   (  79-)  A      N
  71 ARG   (  90-)  A      N
  73 TYR   (  92-)  A      N
  80 PHE   (  99-)  A      N
  84 TYR   ( 103-)  A      OH
  91 GLN   ( 110-)  A      N
  93 ASN   ( 112-)  A      ND2
  97 TYR   ( 116-)  A      N
 118 ARG   ( 137-)  A      NH1
 119 GLU   ( 138-)  A      N
 121 ARG   ( 140-)  A      N
 129 SER   ( 148-)  A      OG
 130 SER   ( 149-)  A      N
 135 VAL   ( 154-)  A      N
And so on for a total of 176 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.

  61 GLN   (  80-)  A      OE1
 200 ASP   ( 219-)  A      OD2
 294 GLN   ( 313-)  A      OE1
 303 ASN   ( 322-)  A      OD1
 354 HIS   ( 373-)  A      ND1
 400 HIS   ( 419-)  A      ND1
1004 GLN   ( 313-)  B      OE1
1141 HIS   ( 450-)  B      ND1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  44 ASP   (  63-)  A   H-bonding suggests Asn
  68 ASP   (  87-)  A   H-bonding suggests Asn; but Alt-Rotamer
 504 GLU   ( 523-)  A   H-bonding suggests Gln
 574 GLU   ( 593-)  A   H-bonding suggests Gln
 693 ASP   ( 712-)  A   H-bonding suggests Asn
 829 GLU   ( 138-)  B   H-bonding suggests Gln; but Alt-Rotamer
 907 GLU   ( 216-)  B   H-bonding suggests Gln
 963 GLU   ( 272-)  B   H-bonding suggests Gln
1200 GLU   ( 509-)  B   H-bonding suggests Gln
1216 GLU   ( 525-)  B   H-bonding suggests Gln
1403 ASP   ( 712-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.161
  2nd generation packing quality :  -2.135
  Ramachandran plot appearance   :  -3.152 (poor)
  chi-1/chi-2 rotamer normality  :  -4.445 (bad)
  Backbone conformation          :  -0.580

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.591 (tight)
  Bond angles                    :   0.910
  Omega angle restraints         :   0.339 (tight)
  Side chain planarity           :   0.623 (tight)
  Improper dihedral distribution :   1.265
  B-factor distribution          :   1.539 (loose)
  Inside/Outside distribution    :   1.055

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 : 2.65


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.591 (tight)
  Bond angles                    :   0.910
  Omega angle restraints         :   0.339 (tight)
  Side chain planarity           :   0.623 (tight)
  Improper dihedral distribution :   1.265
  B-factor distribution          :   1.539 (loose)
  Inside/Outside distribution    :   1.055
==============

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

WHAT_CHECK (verification routines from WHAT IF)
    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.