WHAT IF Check report

This file was created 2011-12-13 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 pdb1aus.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 157.400  B   = 158.700  C    = 203.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 111.759  B   = 111.759  C    = 203.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.471

Dimensions of the conventional cell

    A    = 111.759  B   = 111.759  C    = 203.000
    Alpha=  90.000  Beta=  90.000  Gamma=  89.529

Transformation to conventional cell

 |  0.500000  0.500000  0.000000|
 | -0.500000  0.500000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: C 2 2 21

Bravais type of conventional cell is: P

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

2255 FMT   ( 477-)  L  -
2257 FMT   ( 477-)  M  -
2259 FMT   ( 477-)  N  -
2260 FMT   ( 477-)  O  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

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

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

 182 LYS   ( 201-)  L  -   NZ  bound to 2255 FMT   ( 477-)  L  -   C
 744 LYS   ( 201-)  M  -   NZ  bound to 2257 FMT   ( 477-)  M  -   C
1306 LYS   ( 201-)  N  -   NZ  bound to 2259 FMT   ( 477-)  N  -   C
1868 LYS   ( 201-)  O  -   NZ  bound to 2260 FMT   ( 477-)  O  -   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: L

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: V

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

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 : 4.04

Note: B-factor plot

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

Chain identifier: L

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: V

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999163  0.000000  0.000013|
 |  0.000000  0.999160  0.000004|
 |  0.000013  0.000004  0.999543|
Proposed new scale matrix

 |  0.006358  0.000000  0.000000|
 |  0.000000  0.006306  0.000000|
 |  0.000000  0.000000  0.004928|
With corresponding cell

    A    = 157.274  B   = 158.572  C    = 202.912
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 157.400  B   = 158.700  C    = 203.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 39.730
(Under-)estimated Z-score: 4.645

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.

  17 ILE   (  36-)  L      N    CA   C    99.31   -4.2
  56 THR   (  75-)  L      C    CA   CB  100.20   -5.2
 105 VAL   ( 124-)  L      C    CA   CB  100.31   -5.2
 244 PRO   ( 263-)  L      N    CA   C   123.51    4.7
 248 HIS   ( 267-)  L      CG   ND1  CE1 109.62    4.0
 263 HIS   ( 282-)  L      CG   ND1  CE1 109.80    4.2
 306 HIS   ( 325-)  L      C    CA   CB  102.47   -4.0
 306 HIS   ( 325-)  L      CG   ND1  CE1 109.95    4.3
 308 HIS   ( 327-)  L      CG   ND1  CE1 109.72    4.1
 438 TRP   ( 462-)  L      N    CA   C   129.73    6.6
 507 THR   (  68-)  S      C    CA   CB  117.90    4.1
 537 PHE   (  98-)  S      N    CA   C    98.49   -4.5
 579 ILE   (  36-)  M      N    CA   C    99.33   -4.2
 618 THR   (  75-)  M      C    CA   CB  100.17   -5.2
 667 VAL   ( 124-)  M      C    CA   CB  100.31   -5.2
 806 PRO   ( 263-)  M      N    CA   C   123.50    4.7
 810 HIS   ( 267-)  M      CG   ND1  CE1 109.63    4.0
 825 HIS   ( 282-)  M      CG   ND1  CE1 109.75    4.1
 868 HIS   ( 325-)  M      C    CA   CB  102.50   -4.0
 868 HIS   ( 325-)  M      CG   ND1  CE1 109.92    4.3
 870 HIS   ( 327-)  M      CG   ND1  CE1 109.77    4.2
1000 TRP   ( 462-)  M      N    CA   C   129.73    6.6
1069 THR   (  68-)  T      C    CA   CB  117.85    4.1
1099 PHE   (  98-)  T      N    CA   C    98.47   -4.5
1141 ILE   (  36-)  N      N    CA   C    99.28   -4.3
1180 THR   (  75-)  N      C    CA   CB  100.21   -5.2
1229 VAL   ( 124-)  N      C    CA   CB  100.27   -5.2
1368 PRO   ( 263-)  N      N    CA   C   123.50    4.7
1372 HIS   ( 267-)  N      CG   ND1  CE1 109.64    4.0
1387 HIS   ( 282-)  N      CG   ND1  CE1 109.76    4.2
1430 HIS   ( 325-)  N      C    CA   CB  102.47   -4.0
1430 HIS   ( 325-)  N      CG   ND1  CE1 109.91    4.3
1432 HIS   ( 327-)  N      CG   ND1  CE1 109.70    4.1
1562 TRP   ( 462-)  N      N    CA   C   129.72    6.6
1631 THR   (  68-)  U      C    CA   CB  117.88    4.1
1661 PHE   (  98-)  U      N    CA   C    98.51   -4.5
1703 ILE   (  36-)  O      N    CA   C    99.31   -4.2
1742 THR   (  75-)  O      C    CA   CB  100.23   -5.2
1791 VAL   ( 124-)  O      C    CA   CB  100.30   -5.2
1930 PRO   ( 263-)  O      N    CA   C   123.50    4.7
1934 HIS   ( 267-)  O      CG   ND1  CE1 109.60    4.0
1949 HIS   ( 282-)  O      CG   ND1  CE1 109.82    4.2
1992 HIS   ( 325-)  O      C    CA   CB  102.45   -4.0
1992 HIS   ( 325-)  O      CG   ND1  CE1 109.90    4.3
1994 HIS   ( 327-)  O      CG   ND1  CE1 109.71    4.1
2124 TRP   ( 462-)  O      N    CA   C   129.73    6.6
2193 THR   (  68-)  V      C    CA   CB  117.88    4.1
2223 PHE   (  98-)  V      N    CA   C    98.51   -4.5

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.

2124 TRP   ( 462-)  O    7.03
1000 TRP   ( 462-)  M    7.03
 438 TRP   ( 462-)  L    7.03
1562 TRP   ( 462-)  N    7.03
1229 VAL   ( 124-)  N    6.54
1791 VAL   ( 124-)  O    6.52
 105 VAL   ( 124-)  L    6.52
 667 VAL   ( 124-)  M    6.51
1969 ASP   ( 302-)  O    6.24
 283 ASP   ( 302-)  L    6.22
1407 ASP   ( 302-)  N    6.21
 845 ASP   ( 302-)  M    6.21
 698 ILE   ( 155-)  M    6.03
1260 ILE   ( 155-)  N    6.01
 136 ILE   ( 155-)  L    6.01
1822 ILE   ( 155-)  O    5.99
2012 ARG   ( 350-)  O    4.98
1450 ARG   ( 350-)  N    4.98
 888 ARG   ( 350-)  M    4.98
 326 ARG   ( 350-)  L    4.98
1691 TYR   (  24-)  O    4.90
   5 TYR   (  24-)  L    4.89
 567 TYR   (  24-)  M    4.89
1129 TYR   (  24-)  N    4.88
1099 PHE   (  98-)  T    4.85
And so on for a total of 68 lines.

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 : 1.705

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.

1686 TYR   ( 123-)  U      OH   4.06
1124 TYR   ( 123-)  T      OH   4.05
 562 TYR   ( 123-)  S      OH   4.05
2248 TYR   ( 123-)  V      OH   4.04
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.897

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

1998 VAL   ( 331-)  O    -2.7
1436 VAL   ( 331-)  N    -2.7
 312 VAL   ( 331-)  L    -2.7
 874 VAL   ( 331-)  M    -2.7
 311 THR   ( 330-)  L    -2.6
1997 THR   ( 330-)  O    -2.6
1435 THR   ( 330-)  N    -2.6
 873 THR   ( 330-)  M    -2.6
 898 ARG   ( 360-)  M    -2.5
1460 ARG   ( 360-)  N    -2.5
2022 ARG   ( 360-)  O    -2.5
 336 ARG   ( 360-)  L    -2.5
2134 LEU   (   9-)  V    -2.4
1010 LEU   (   9-)  T    -2.4
 448 LEU   (   9-)  S    -2.4
1572 LEU   (   9-)  U    -2.4
2031 VAL   ( 369-)  O    -2.4
 907 VAL   ( 369-)  M    -2.4
 345 VAL   ( 369-)  L    -2.4
1469 VAL   ( 369-)  N    -2.4
1742 THR   (  75-)  O    -2.4
1180 THR   (  75-)  N    -2.4
  56 THR   (  75-)  L    -2.4
 618 THR   (  75-)  M    -2.4
1600 LYS   (  37-)  U    -2.3
And so on for a total of 57 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.

   2 LYS   (  21-)  L  Poor phi/psi
  43 SER   (  62-)  L  Poor phi/psi
  44 THR   (  63-)  L  Poor phi/psi
 144 ASN   ( 163-)  L  Poor phi/psi
 156 LYS   ( 175-)  L  PRO omega poor
 188 ASN   ( 207-)  L  Poor phi/psi
 278 MET   ( 297-)  L  Poor phi/psi
 311 THR   ( 330-)  L  Poor phi/psi
 312 VAL   ( 331-)  L  Poor phi/psi
 346 SER   ( 370-)  L  Poor phi/psi
 417 GLY   ( 441-)  L  Poor phi/psi
 438 TRP   ( 462-)  L  Poor phi/psi
 452 GLU   (  13-)  S  Poor phi/psi
 454 LEU   (  15-)  S  Poor phi/psi
 476 LYS   (  37-)  S  Poor phi/psi
 486 ASP   (  47-)  S  Poor phi/psi
 510 LYS   (  71-)  S  Poor phi/psi
 548 GLU   ( 109-)  S  Poor phi/psi
 559 PRO   ( 120-)  S  Poor phi/psi
 560 ALA   ( 121-)  S  Poor phi/psi
 564 LYS   (  21-)  M  Poor phi/psi
 605 SER   (  62-)  M  Poor phi/psi
 606 THR   (  63-)  M  Poor phi/psi
 706 ASN   ( 163-)  M  Poor phi/psi
 718 LYS   ( 175-)  M  PRO omega poor
And so on for a total of 79 lines.

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.

 335 SER   ( 359-)  L    0.39
 897 SER   ( 359-)  M    0.39
1459 SER   ( 359-)  N    0.39
2021 SER   ( 359-)  O    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!

   6 TYR   (  25-)  L      0
   7 THR   (  26-)  L      0
  27 PRO   (  46-)  L      0
  42 SER   (  61-)  L      0
  43 SER   (  62-)  L      0
  44 THR   (  63-)  L      0
  47 TRP   (  66-)  L      0
  51 TRP   (  70-)  L      0
  55 LEU   (  74-)  L      0
  57 ASN   (  76-)  L      0
  58 LEU   (  77-)  L      0
  66 TYR   (  85-)  L      0
  69 GLU   (  88-)  L      0
  72 ALA   (  91-)  L      0
  75 GLU   (  94-)  L      0
  88 LEU   ( 107-)  L      0
  91 GLU   ( 110-)  L      0
 102 VAL   ( 121-)  L      0
 108 PHE   ( 127-)  L      0
 112 ARG   ( 131-)  L      0
 113 ALA   ( 132-)  L      0
 117 GLU   ( 136-)  L      0
 118 ASP   ( 137-)  L      0
 129 PHE   ( 148-)  L      0
 132 PRO   ( 151-)  L      0
And so on for a total of 824 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 : 2.086

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!

 310 GLY   ( 329-)  L   2.23   18
 872 GLY   ( 329-)  M   2.20   17
1996 GLY   ( 329-)  O   2.19   19
1434 GLY   ( 329-)  N   2.15   18
1877 PRO   ( 210-)  O   1.75   11
1315 PRO   ( 210-)  N   1.75   11
 191 PRO   ( 210-)  L   1.75   11
 753 PRO   ( 210-)  M   1.75   11

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].

  25 PRO   (  44-)  L    42.3 envelop C-delta (36 degrees)
  27 PRO   (  46-)  L  -116.3 envelop C-gamma (-108 degrees)
  30 PRO   (  49-)  L    49.7 half-chair C-delta/C-gamma (54 degrees)
 587 PRO   (  44-)  M    42.3 envelop C-delta (36 degrees)
 589 PRO   (  46-)  M  -116.4 envelop C-gamma (-108 degrees)
 592 PRO   (  49-)  M    49.7 half-chair C-delta/C-gamma (54 degrees)
1149 PRO   (  44-)  N    42.2 envelop C-delta (36 degrees)
1151 PRO   (  46-)  N  -116.3 envelop C-gamma (-108 degrees)
1154 PRO   (  49-)  N    49.7 half-chair C-delta/C-gamma (54 degrees)
1711 PRO   (  44-)  O    42.3 envelop C-delta (36 degrees)
1713 PRO   (  46-)  O  -116.3 envelop C-gamma (-108 degrees)
1716 PRO   (  49-)  O    49.7 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.

 715 CYS   ( 172-)  M      SG  <->  735 CYS   ( 192-)  M      SG     0.70    2.75  INTRA
 153 CYS   ( 172-)  L      SG  <->  173 CYS   ( 192-)  L      SG     0.70    2.75  INTRA
1839 CYS   ( 172-)  O      SG  <-> 1859 CYS   ( 192-)  O      SG     0.70    2.75  INTRA
1277 CYS   ( 172-)  N      SG  <-> 1297 CYS   ( 192-)  N      SG     0.70    2.75  INTRA
 873 THR   ( 330-)  M      O   <->  875 VAL   ( 332-)  M      N      0.34    2.36  INTRA
 311 THR   ( 330-)  L      O   <->  313 VAL   ( 332-)  L      N      0.34    2.36  INTRA
1997 THR   ( 330-)  O      O   <-> 1999 VAL   ( 332-)  O      N      0.34    2.36  INTRA
1435 THR   ( 330-)  N      O   <-> 1437 VAL   ( 332-)  N      N      0.34    2.36  INTRA
 160 GLY   ( 179-)  L      O   <-> 2234 GLU   ( 109-)  V      CG     0.31    2.49  INTRA
 137 GLN   ( 156-)  L      NE2 <->  547 ARG   ( 108-)  S      NH2    0.27    2.58  INTRA
 699 GLN   ( 156-)  M      NE2 <-> 1109 ARG   ( 108-)  T      NH2    0.27    2.58  INTRA
1823 GLN   ( 156-)  O      NE2 <-> 2233 ARG   ( 108-)  V      NH2    0.27    2.58  INTRA
1261 GLN   ( 156-)  N      NE2 <-> 1671 ARG   ( 108-)  U      NH2    0.27    2.58  INTRA
1485 TRP   ( 385-)  N      CD1 <-> 1563 LYS   ( 463-)  N      N      0.25    2.85  INTRA
2047 TRP   ( 385-)  O      CD1 <-> 2125 LYS   ( 463-)  O      N      0.25    2.85  INTRA
 361 TRP   ( 385-)  L      CD1 <->  439 LYS   ( 463-)  L      N      0.25    2.85  INTRA
 923 TRP   ( 385-)  M      CD1 <-> 1001 LYS   ( 463-)  M      N      0.25    2.85  INTRA
1672 GLU   ( 109-)  U      CG  <-> 1846 GLY   ( 179-)  O      O      0.25    2.55  INTRA
1110 GLU   ( 109-)  T      CG  <-> 1284 GLY   ( 179-)  N      O      0.24    2.56  INTRA
1998 VAL   ( 331-)  O      CG1 <-> 1999 VAL   ( 332-)  O      N      0.23    2.77  INTRA
 312 VAL   ( 331-)  L      CG1 <->  313 VAL   ( 332-)  L      N      0.23    2.77  INTRA
 874 VAL   ( 331-)  M      CG1 <->  875 VAL   ( 332-)  M      N      0.23    2.77  INTRA
1436 VAL   ( 331-)  N      CG1 <-> 1437 VAL   ( 332-)  N      N      0.23    2.77  INTRA
1243 LEU   ( 138-)  N      O   <-> 1421 LYS   ( 316-)  N      NZ     0.23    2.47  INTRA BL
1805 LEU   ( 138-)  O      O   <-> 1983 LYS   ( 316-)  O      NZ     0.23    2.47  INTRA BL
And so on for a total of 200 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: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

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.

 112 ARG   ( 131-)  L      -6.41
1236 ARG   ( 131-)  N      -6.41
1798 ARG   ( 131-)  O      -6.41
 674 ARG   ( 131-)  M      -6.41
1283 LEU   ( 178-)  N      -6.25
1845 LEU   ( 178-)  O      -6.25
 721 LEU   ( 178-)  M      -6.25
 159 LEU   ( 178-)  L      -6.25
1638 PHE   (  75-)  U      -6.14
 514 PHE   (  75-)  S      -6.14
1076 PHE   (  75-)  T      -6.14
2200 PHE   (  75-)  V      -6.14
 692 GLN   ( 149-)  M      -5.96
1816 GLN   ( 149-)  O      -5.92
1254 GLN   ( 149-)  N      -5.92
 130 GLN   ( 149-)  L      -5.92
 977 ARG   ( 439-)  M      -5.74
2101 ARG   ( 439-)  O      -5.74
1539 ARG   ( 439-)  N      -5.74
 415 ARG   ( 439-)  L      -5.73
 718 LYS   ( 175-)  M      -5.65
 156 LYS   ( 175-)  L      -5.65
1280 LYS   ( 175-)  N      -5.65
1842 LYS   ( 175-)  O      -5.65
  47 TRP   (  66-)  L      -5.40
And so on for a total of 62 lines.

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: L

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: S

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: M

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: T

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: N

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: U

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: O

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: V

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.

 448 LEU   (   9-)  S   -3.06
1404 ALA   ( 299-)  N   -2.68
 280 ALA   ( 299-)  L   -2.68
1966 ALA   ( 299-)  O   -2.64
 549 VAL   ( 110-)  S   -2.63
1673 VAL   ( 110-)  U   -2.63
1111 VAL   ( 110-)  T   -2.63
2235 VAL   ( 110-)  V   -2.62
 842 ALA   ( 299-)  M   -2.60
  88 LEU   ( 107-)  L   -2.59
1212 LEU   ( 107-)  N   -2.57
1774 LEU   ( 107-)  O   -2.54
 650 LEU   ( 107-)  M   -2.54

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: L

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: V

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

2261 HOH   ( 627 )  L      O     24.44   68.23   61.48
2261 HOH   ( 659 )  L      O     17.62   50.22   45.63

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.

2266 HOH   ( 130 )  V      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.

 144 ASN   ( 163-)  L
 165 ASN   ( 184-)  L
 210 GLN   ( 229-)  L
 219 HIS   ( 238-)  L
 222 ASN   ( 241-)  L
 248 HIS   ( 267-)  L
 258 ASN   ( 277-)  L
 263 HIS   ( 282-)  L
 285 GLN   ( 304-)  L
 362 HIS   ( 386-)  L
 396 ASN   ( 420-)  L
 408 ASN   ( 432-)  L
 464 GLN   (  25-)  S
 468 GLN   (  29-)  S
 706 ASN   ( 163-)  M
 727 ASN   ( 184-)  M
 748 ASN   ( 205-)  M
 772 GLN   ( 229-)  M
 781 HIS   ( 238-)  M
 784 ASN   ( 241-)  M
 810 HIS   ( 267-)  M
 820 ASN   ( 277-)  M
 847 GLN   ( 304-)  M
 924 HIS   ( 386-)  M
 958 ASN   ( 420-)  M
And so on for a total of 55 lines.

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 LEU   (  22-)  L      N
   9 GLU   (  28-)  L      N
  32 GLU   (  51-)  L      N
  50 VAL   (  69-)  L      N
  93 SER   ( 112-)  L      OG
 137 GLN   ( 156-)  L      N
 148 ARG   ( 167-)  L      N
 154 THR   ( 173-)  L      N
 156 LYS   ( 175-)  L      N
 159 LEU   ( 178-)  L      N
 162 SER   ( 181-)  L      OG
 178 LEU   ( 197-)  L      N
 188 ASN   ( 207-)  L      ND2
 198 ARG   ( 217-)  L      NH1
 227 THR   ( 246-)  L      N
 252 THR   ( 271-)  L      N
 257 ALA   ( 276-)  L      N
 276 ARG   ( 295-)  L      N
 288 HIS   ( 307-)  L      N
 304 GLY   ( 323-)  L      N
 316 ASP   ( 340-)  L      N
 377 GLN   ( 401-)  L      NE2
 389 ASN   ( 413-)  L      ND2
 441 GLN   (   2-)  S      N
 445 ILE   (   6-)  S      N
And so on for a total of 186 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.

 249 ASP   ( 268-)  L      OD1
 548 GLU   ( 109-)  S      OE1
 701 GLU   ( 158-)  M      OE1
 810 HIS   ( 267-)  M      NE2
 811 ASP   ( 268-)  M      OD1
 825 HIS   ( 282-)  M      ND1
1263 GLU   ( 158-)  N      OE1
1372 HIS   ( 267-)  N      NE2
1373 ASP   ( 268-)  N      OD1
1387 HIS   ( 282-)  N      ND1
1520 ASN   ( 420-)  N      OD1
1672 GLU   ( 109-)  U      OE1
1825 GLU   ( 158-)  O      OE1
1934 HIS   ( 267-)  O      NE2
1935 ASP   ( 268-)  O      OD1
1949 HIS   ( 282-)  O      ND1
2082 ASN   ( 420-)  O      OD1
2234 GLU   ( 109-)  V      OE1

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: 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+.

2253  MG   ( 476-)  L     0.59   0.95 Is perhaps CA
2254  MG   ( 476-)  M     0.51   1.03 Is perhaps NA (Few ligands (4) )
2256  MG   ( 476-)  N     0.51   1.03 Is perhaps NA (Few ligands (4) )
2258  MG   ( 476-)  O     0.51   1.03 Is perhaps NA (Few ligands (4) )

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

2261 HOH   ( 518 )  L      O  0.86  K  5 ION-B
2261 HOH   ( 582 )  L      O  1.04  K  4 Ion-B
2262 HOH   ( 124 )  S      O  0.87  K  5 Ion-B

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.

 141 ASP   ( 160-)  L   H-bonding suggests Asn; but Alt-Rotamer
 249 ASP   ( 268-)  L   H-bonding suggests Asn
 283 ASP   ( 302-)  L   H-bonding suggests Asn
 811 ASP   ( 268-)  M   H-bonding suggests Asn
 845 ASP   ( 302-)  M   H-bonding suggests Asn
1373 ASP   ( 268-)  N   H-bonding suggests Asn
1407 ASP   ( 302-)  N   H-bonding suggests Asn
1935 ASP   ( 268-)  O   H-bonding suggests Asn
1969 ASP   ( 302-)  O   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.938
  2nd generation packing quality :  -0.230
  Ramachandran plot appearance   :  -0.897
  chi-1/chi-2 rotamer normality  :  -2.339
  Backbone conformation          :  -0.552

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.595 (tight)
  Bond angles                    :   0.831
  Omega angle restraints         :   0.379 (tight)
  Side chain planarity           :   0.662 (tight)
  Improper dihedral distribution :   1.073
  B-factor distribution          :   0.531
  Inside/Outside distribution    :   1.073

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.595 (tight)
  Bond angles                    :   0.831
  Omega angle restraints         :   0.379 (tight)
  Side chain planarity           :   0.662 (tight)
  Improper dihedral distribution :   1.073
  B-factor distribution          :   0.531
  Inside/Outside distribution    :   1.073
==============

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.