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 pdb1bxr.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 C

All-atom RMS fit for the two chains : 0.406
CA-only RMS fit for the two chains : 0.264

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 C

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 E

All-atom RMS fit for the two chains : 0.387
CA-only RMS fit for the two chains : 0.274

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 E

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 G

All-atom RMS fit for the two chains : 0.479
CA-only RMS fit for the two chains : 0.318

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 G

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: B and D

All-atom RMS fit for the two chains : 0.325
CA-only RMS fit for the two chains : 0.218

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: B 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: B and F

All-atom RMS fit for the two chains : 0.327
CA-only RMS fit for the two chains : 0.198

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: B and F

Warning: Topology could not be determined for some ligands

Some 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 two or less which PRODRUG also cannot cope with), 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.

5822 ANP   (1083-)  A  -
5823 ANP   (1084-)  A  -
5824 ORN   (1085-)  A  -         OK
5825 NET   (1086-)  A  -         OK
5839 ANP   (1900-)  C  -
5840 ANP   (1910-)  C  -
5841 ORN   (1920-)  C  -         OK
5842 NET   (1950-)  C  -         OK
5855 ANP   (2900-)  E  -
5856 ANP   (2910-)  E  -
5857 ORN   (2920-)  E  -         OK
5858 NET   (2950-)  E  -         OK
5870 ANP   (3900-)  G  -
5872 NET   (3950-)  G  -         OK
5873 ORN   (3920-)  G  -         OK
5874 ORN   (3910-)  G  -         OK

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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:

Crystal temperature (K) :100.000

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 : 4.106 over 33665 bonds
Average difference in B over a bond : 11.77
RMS difference in B over a bond : 16.34

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

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.

  15 ALA   (  15-)  A      C    O     1.13   -5.2
  39 GLU   (  39-)  A      CD   OE1   1.36    5.9
 110 GLU   ( 110-)  A      CD   OE1   1.33    4.1
 190 GLU   ( 190-)  A      CD   OE1   1.33    4.1
 279 THR   ( 279-)  A      C    O     1.10   -6.3
 419 GLU   ( 419-)  A      CD   OE1   1.34    4.8
 577 GLU   ( 577-)  A      CD   OE1   1.33    4.5
 591 GLU   ( 591-)  A      CD   OE1   1.33    4.4
 592 ASP   ( 592-)  A      CG   OD1   1.33    4.2
 625 ASP   ( 625-)  A      CG   OD1   1.34    4.8
 628 GLU   ( 628-)  A      CD   OE1   1.33    4.0
 730 ASP   ( 730-)  A      CG   OD1   1.33    4.4
 804 GLU   ( 804-)  A      CD   OE1   1.34    4.9
 833 LYS   ( 833-)  A      CE   NZ    1.31   -5.9
 910 GLU   ( 910-)  A      CD   OE2   1.33    4.5
 983 GLU   ( 983-)  A      CD   OE1   1.33    4.1
 996 GLU   ( 996-)  A      CD   OE2   1.33    4.2
1561 GLU   ( 109-)  C      CD   OE2   1.34    4.6
1562 GLU   ( 110-)  C      CD   OE1   1.34    5.0
1579 GLU   ( 127-)  C      CD   OE1   1.33    4.2
1642 GLU   ( 190-)  C      CD   OE1   1.33    4.5
1669 GLU   ( 217-)  C      CD   OE2   1.33    4.2
1671 GLU   ( 219-)  C      CD   OE1   1.33    4.3
1730 GLU   ( 278-)  C      CD   OE2   1.33    4.3
1786 GLU   ( 334-)  C      CD   OE2   1.33    4.3
And so on for a total of 83 lines.

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

 |  1.001525  0.000070  0.000021|
 |  0.000070  1.001579 -0.000155|
 |  0.000021 -0.000155  1.001237|
Proposed new scale matrix

 |  0.006573  0.000000  0.000000|
 |  0.000000  0.006069  0.000000|
 |  0.000000  0.000000  0.003003|
With corresponding cell

    A    = 152.138  B   = 164.760  C    = 332.969
    Alpha=  90.003  Beta=  90.003  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 151.900  B   = 164.500  C    = 332.600
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 389.596
(Under-)estimated Z-score: 14.547

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.

  15 ALA   (  15-)  A      CA   C    O   113.02   -4.6
  26 PHE   (  26-)  A      CA   CB   CG  105.41   -8.4
  39 GLU   (  39-)  A      CB   CG   CD  102.95   -5.7
  43 ARG   (  43-)  A     -C    N    CA  113.50   -4.6
  57 ASP   (  57-)  A      CA   CB   CG  104.64   -8.0
  59 GLU   (  59-)  A      CG   CD   OE1 105.06   -5.8
  62 ASP   (  62-)  A      C    CA   CB  118.53    4.4
  81 GLU   (  81-)  A      CG   CD   OE1 108.65   -4.2
 121 ASP   ( 121-)  A     -C    N    CA  113.93   -4.3
 129 ARG   ( 129-)  A      C    CA   CB  117.86    4.1
 133 ASP   ( 133-)  A      CA   CB   CG  108.45   -4.2
 172 PHE   ( 172-)  A      CA   CB   CG  106.09   -7.7
 205 LEU   ( 205-)  A      N    CA   CB  117.67    4.2
 220 VAL   ( 220-)  A      C    CA   CB  101.35   -4.6
 238 ASP   ( 238-)  A      CA   CB   CG  106.37   -6.2
 285 GLN   ( 285-)  A      CB   CG   CD  103.12   -5.6
 331 THR   ( 331-)  A      N    CA   CB  117.31    4.0
 350 PRO   ( 350-)  A      N    CA   CB  108.45    5.0
 360 PRO   ( 360-)  A      N    CA   CB  108.40    4.9
 367 PHE   ( 367-)  A      CA   CB   CG  108.89   -4.9
 403 GLU   ( 403-)  A      CB   CG   CD  104.40   -4.8
 408 GLY   ( 408-)  A     -C    N    CA  127.72    4.2
 422 THR   ( 422-)  A      C    CA   CB  121.19    5.8
 454 ASN   ( 454-)  A      CA   CB   CG  107.97   -4.6
 465 GLN   ( 465-)  A      CA   CB   CG  105.95   -4.1
And so on for a total of 345 lines.

Warning: Chirality deviations detected

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

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

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

  58 PRO   (  58-)  A      N      7.6    22.36    -2.48
  95 ALA   (  95-)  A      CA    -6.6    25.66    34.09
 129 ARG   ( 129-)  A      CA    -9.0    19.22    33.91
 339 ILE   ( 339-)  A      CA    -9.3    19.24    33.24
 435 ARG   ( 435-)  A      CA    -6.2    23.79    33.91
 646 THR   ( 646-)  A      CA    -6.2    23.56    33.84
 728 VAL   ( 728-)  A      CA    -6.3    24.13    33.23
 738 PHE   ( 738-)  A      CA    -8.1    21.03    33.98
 991 VAL   ( 991-)  A      CA    -6.5    23.75    33.23
 996 GLU   ( 996-)  A      CA    -8.0    20.87    33.96
1078 LEU   (   6-)  B      CA    -7.2    23.19    34.19
1455 LYS   (   3-)  C      CA    -6.1    23.82    33.92
1478 PHE   (  26-)  C      CA    -8.7    20.10    33.98
1480 TYR   (  28-)  C      CA    -6.4    23.86    34.03
1591 ILE   ( 139-)  C      CA    -6.1    24.00    33.24
1791 ILE   ( 339-)  C      CA   -13.8    12.46    33.24
2098 THR   ( 646-)  C      CA    -7.9    20.71    33.84
2109 ALA   ( 657-)  C      CA    -7.0    25.26    34.09
2296 PRO   ( 844-)  C      N      7.2    21.07    -2.48
2770 ALA   ( 246-)  D      CA    -6.5    25.89    34.09
3105 THR   ( 201-)  E      CA    -7.1    22.02    33.84
3243 ILE   ( 339-)  E      CA    -9.2    19.30    33.24
3383 VAL   ( 479-)  E      CA    -6.4    23.89    33.23
3463 ARG   ( 559-)  E      CA    -8.2    20.52    33.91
3609 ALA   ( 705-)  E      CA   -13.6    16.85    34.09
3653 PRO   ( 749-)  E      N     -6.5   -23.68    -2.48
3754 VAL   ( 850-)  E      CA    -7.2    22.72    33.23
3976 ILE   (1072-)  E      C      7.0     9.15     0.03
3986 GLU   (  10-)  F      CA     7.3    45.87    33.96
4026 ARG   (  50-)  F      CA   -16.2     7.35    33.91
4382 PHE   (  26-)  G      CA    -6.2    24.04    33.98
4437 GLU   (  81-)  G      CA    -6.1    24.00    33.96
4485 ARG   ( 129-)  G      CA    -6.2    23.69    33.91
4541 ARG   ( 185-)  G      CA    -7.8    21.19    33.91
4676 ALA   ( 320-)  G      CA    -6.2    26.26    34.09
4695 ILE   ( 339-)  G      CA    -7.9    21.25    33.24
4701 PRO   ( 345-)  G      N      6.1    17.38    -2.48
4837 ILE   ( 481-)  G      CA    -7.4    22.07    33.24
5082 GLU   ( 726-)  G      CA     8.5    47.84    33.96
5094 PHE   ( 738-)  G      CA    -6.1    24.23    33.98
5103 ASP   ( 747-)  G      CA    -6.1    21.58    33.73
5298 HIS   ( 942-)  G      C      6.5     9.96     0.15
5307 GLU   ( 951-)  G      CA    -7.6    21.47    33.96
5310 LYS   ( 954-)  G      CA    -7.0    22.29    33.92
5329 ALA   ( 973-)  G      CA    -8.1    23.84    34.09
5364 GLY   (1008-)  G      C     10.7    14.15     0.06
5674 ALA   ( 246-)  H      CA    -6.4    25.97    34.09
The average deviation= 1.637

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.

3903 PRO   ( 999-)  E    9.38
 339 ILE   ( 339-)  A    7.02
4695 ILE   ( 339-)  G    6.03
4511 ALA   ( 155-)  G    5.72
4791 ARG   ( 435-)  G    5.61
4541 ARG   ( 185-)  G    5.36
3609 ALA   ( 705-)  E    5.32
 435 ARG   ( 435-)  A    5.31
  27 ASP   (  27-)  A    5.02
3383 VAL   ( 479-)  E    4.94
 733 ASP   ( 733-)  A    4.93
1938 ALA   ( 486-)  C    4.85
2427 HIS   ( 975-)  C    4.69
3516 THR   ( 612-)  E    4.68
 576 ILE   ( 576-)  A    4.62
3243 ILE   ( 339-)  E    4.61
1771 ILE   ( 319-)  C    4.60
1288 LEU   ( 216-)  B    4.42
4100 GLU   ( 124-)  F    4.40
5384 VAL   (1028-)  G    4.37
5149 ALA   ( 793-)  G    4.31
2403 GLU   ( 951-)  C    4.26
2245 ALA   ( 793-)  C    4.24
3642 PHE   ( 738-)  E    4.21
5206 VAL   ( 850-)  G    4.20
 646 THR   ( 646-)  A    4.18
2098 THR   ( 646-)  C    4.17
1887 ARG   ( 435-)  C    4.15
3858 LYS   ( 954-)  E    4.15
2190 PHE   ( 738-)  C    4.14
4812 THR   ( 456-)  G    4.13
 420 ALA   ( 420-)  A    4.12
1995 MET   ( 543-)  C    4.12
4379 ALA   (  23-)  G    4.11
3223 ILE   ( 319-)  E    4.11
1637 ARG   ( 185-)  C    4.11
2613 ALA   (  89-)  D    4.10
3932 VAL   (1028-)  E    4.09
 951 GLU   ( 951-)  A    4.08
2147 VAL   ( 695-)  C    4.07
 698 ILE   ( 698-)  A    4.06
3360 THR   ( 456-)  E    4.06
3555 ALA   ( 651-)  E    4.05

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.

  59 GLU   (  59-)  A   10.81
2119 ASP   ( 667-)  C    5.29
 699 GLU   ( 699-)  A    5.23
2107 GLU   ( 655-)  C    4.78
3584 HIS   ( 680-)  E    4.39
1835 GLU   ( 383-)  C    4.30
3692 HIS   ( 788-)  E    4.29
 285 GLN   ( 285-)  A    4.04
4238 ASP   ( 262-)  F    4.00

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.

 375 THR   ( 375-)  A    -3.1
3279 THR   ( 375-)  E    -3.1
1418 PRO   ( 346-)  B    -3.1
2992 PRO   (  88-)  E    -3.0
1827 THR   ( 375-)  C    -3.0
  88 PRO   (  88-)  A    -3.0
4438 ARG   (  82-)  G    -3.0
 646 THR   ( 646-)  A    -2.9
2150 ILE   ( 698-)  C    -2.9
1540 PRO   (  88-)  C    -2.9
1454 PRO   (   2-)  C    -2.9
4444 PRO   (  88-)  G    -2.9
1704 PRO   ( 252-)  C    -2.9
4990 LYS   ( 634-)  G    -2.9
5331 HIS   ( 975-)  G    -2.8
4731 THR   ( 375-)  G    -2.8
2023 ARG   ( 571-)  C    -2.8
3800 PRO   ( 896-)  E    -2.8
5008 ARG   ( 652-)  G    -2.8
4358 PRO   (   2-)  G    -2.8
4558 LYS   ( 202-)  G    -2.7
5354 ARG   ( 998-)  G    -2.7
 531 THR   ( 531-)  A    -2.7
3106 LYS   ( 202-)  E    -2.7
2427 HIS   ( 975-)  C    -2.7
And so on for a total of 253 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 PRO   (   2-)  A  Poor phi/psi
  23 ALA   (  23-)  A  Poor phi/psi
  30 GLY   (  30-)  A  Poor phi/psi
 146 SER   ( 146-)  A  Poor phi/psi
 164 PHE   ( 164-)  A  PRO omega poor
 172 PHE   ( 172-)  A  Poor phi/psi
 226 ASP   ( 226-)  A  Poor phi/psi
 251 ALA   ( 251-)  A  PRO omega poor
 299 GLU   ( 299-)  A  Poor phi/psi
 302 PRO   ( 302-)  A  Poor phi/psi
 368 ALA   ( 368-)  A  Poor phi/psi
 369 GLY   ( 369-)  A  Poor phi/psi
 375 THR   ( 375-)  A  Poor phi/psi
 403 GLU   ( 403-)  A  Poor phi/psi
 409 PHE   ( 409-)  A  Poor phi/psi
 457 ASN   ( 457-)  A  Poor phi/psi
 484 LEU   ( 484-)  A  Poor phi/psi
 521 ASP   ( 521-)  A  Poor phi/psi
 530 ASP   ( 530-)  A  Poor phi/psi
 531 THR   ( 531-)  A  Poor phi/psi
 533 ALA   ( 533-)  A  Poor phi/psi
 534 ALA   ( 534-)  A  Poor phi/psi
 548 GLU   ( 548-)  A  Poor phi/psi
 634 LYS   ( 634-)  A  Poor phi/psi
 686 LYS   ( 686-)  A  Poor phi/psi
And so on for a total of 200 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 : -4.671

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.

4260 VAL   ( 284-)  F    0.33
 268 SER   ( 268-)  A    0.35
5528 SER   ( 100-)  H    0.35
4624 SER   ( 268-)  G    0.36
1172 SER   ( 100-)  B    0.36
2624 SER   ( 100-)  D    0.36
5712 VAL   ( 284-)  H    0.36
 394 SER   ( 394-)  A    0.37
3172 SER   ( 268-)  E    0.37
1720 SER   ( 268-)  C    0.37
2195 SER   ( 743-)  C    0.38
4075 SER   (  99-)  F    0.38
3647 SER   ( 743-)  E    0.38
5210 SER   ( 854-)  G    0.38
3298 SER   ( 394-)  E    0.38
1171 SER   (  99-)  B    0.39
4750 SER   ( 394-)  G    0.40

Warning: Unusual backbone conformations

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

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

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

   3 LYS   (   3-)  A      0
   4 ARG   (   4-)  A      0
   7 ILE   (   7-)  A      0
  17 PRO   (  17-)  A      0
  20 ILE   (  20-)  A      0
  22 GLN   (  22-)  A      0
  23 ALA   (  23-)  A      0
  24 CYS   (  24-)  A      0
  60 MET   (  60-)  A      0
  66 ILE   (  66-)  A      0
  69 ILE   (  69-)  A      0
  81 GLU   (  81-)  A      0
  82 ARG   (  82-)  A      0
  89 THR   (  89-)  A      0
  90 MET   (  90-)  A      0
  93 GLN   (  93-)  A      0
 107 VAL   ( 107-)  A      0
 116 ILE   ( 116-)  A      0
 139 ILE   ( 139-)  A      0
 146 SER   ( 146-)  A      0
 162 VAL   ( 162-)  A      0
 164 PHE   ( 164-)  A      0
 166 CYS   ( 166-)  A      0
 171 SER   ( 171-)  A      0
 172 PHE   ( 172-)  A      0
And so on for a total of 2042 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 : 2.200

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!

 567 GLY   ( 567-)  A   3.23   21
2019 GLY   ( 567-)  C   3.17   23
4923 GLY   ( 567-)  G   3.08   21
3471 GLY   ( 567-)  E   3.03   23
2118 PRO   ( 666-)  C   1.78   16

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...

1475 ALA   (  23-)  C   2.01
2927 ALA   (  23-)  E   2.29
5612 ALA   ( 184-)  H   1.60

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]

   2 PRO   (   2-)  A    0.05 LOW
  17 PRO   (  17-)  A    0.10 LOW
  51 PRO   (  51-)  A    0.20 LOW
  68 PRO   (  68-)  A    0.18 LOW
  83 PRO   (  83-)  A    0.02 LOW
 165 PRO   ( 165-)  A    0.09 LOW
 170 PRO   ( 170-)  A    0.11 LOW
 200 PRO   ( 200-)  A    0.14 LOW
 290 PRO   ( 290-)  A    0.13 LOW
 318 PRO   ( 318-)  A    0.12 LOW
 350 PRO   ( 350-)  A    0.16 LOW
 360 PRO   ( 360-)  A    0.15 LOW
 411 PRO   ( 411-)  A    0.10 LOW
 418 PRO   ( 418-)  A    0.06 LOW
 555 PRO   ( 555-)  A    0.03 LOW
 569 PRO   ( 569-)  A    0.15 LOW
 603 PRO   ( 603-)  A    0.18 LOW
 620 PRO   ( 620-)  A    0.18 LOW
 647 PRO   ( 647-)  A    0.01 LOW
 690 PRO   ( 690-)  A    0.14 LOW
 711 PRO   ( 711-)  A    0.14 LOW
 716 PRO   ( 716-)  A    0.07 LOW
 749 PRO   ( 749-)  A    0.04 LOW
 797 PRO   ( 797-)  A    0.07 LOW
 851 PRO   ( 851-)  A    0.17 LOW
And so on for a total of 185 lines.

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].

  58 PRO   (  58-)  A   -17.7 half-chair C-alpha/N (-18 degrees)
  88 PRO   (  88-)  A   -43.1 envelop C-alpha (-36 degrees)
 302 PRO   ( 302-)  A   -37.1 envelop C-alpha (-36 degrees)
 345 PRO   ( 345-)  A   -57.8 half-chair C-beta/C-alpha (-54 degrees)
 524 PRO   ( 524-)  A   -61.0 half-chair C-beta/C-alpha (-54 degrees)
 635 PRO   ( 635-)  A   -40.7 envelop C-alpha (-36 degrees)
 666 PRO   ( 666-)  A   126.0 half-chair C-beta/C-alpha (126 degrees)
 844 PRO   ( 844-)  A   -48.9 half-chair C-beta/C-alpha (-54 degrees)
 860 PRO   ( 860-)  A   -65.9 envelop C-beta (-72 degrees)
1254 PRO   ( 182-)  B   -63.7 envelop C-beta (-72 degrees)
1292 PRO   ( 220-)  B   141.3 envelop C-alpha (144 degrees)
1418 PRO   ( 346-)  B   -29.3 envelop C-alpha (-36 degrees)
1430 PRO   ( 358-)  B   -51.2 half-chair C-beta/C-alpha (-54 degrees)
1503 PRO   (  51-)  C   -64.3 envelop C-beta (-72 degrees)
1540 PRO   (  88-)  C   -62.9 half-chair C-beta/C-alpha (-54 degrees)
1770 PRO   ( 318-)  C   -53.3 half-chair C-beta/C-alpha (-54 degrees)
1802 PRO   ( 350-)  C   100.8 envelop C-beta (108 degrees)
2118 PRO   ( 666-)  C   128.8 half-chair C-beta/C-alpha (126 degrees)
2163 PRO   ( 711-)  C    -1.3 envelop N (0 degrees)
2296 PRO   ( 844-)  C   -30.8 envelop C-alpha (-36 degrees)
2348 PRO   ( 896-)  C   -54.5 half-chair C-beta/C-alpha (-54 degrees)
2744 PRO   ( 220-)  D   127.4 half-chair C-beta/C-alpha (126 degrees)
2820 PRO   ( 296-)  D   -43.3 envelop C-alpha (-36 degrees)
2870 PRO   ( 346-)  D   -34.8 envelop C-alpha (-36 degrees)
2882 PRO   ( 358-)  D   -48.8 half-chair C-beta/C-alpha (-54 degrees)
And so on for a total of 52 lines.

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.

5197 GLU   ( 841-)  G      CG  <-> 5874 ORN   (3910-)  G      NE     0.88    2.22  INTRA BL
5862  MN   (3911-)  G     MN   <-> 5874 ORN   (3910-)  G      CG     0.75    2.45  INTRA BL
 975 HIS   ( 975-)  A      ND1 <-> 5331 HIS   ( 975-)  G      ND1    0.68    2.32  INTRA BF
2026 GLN   ( 574-)  C      NE2 <-> 2097 GLN   ( 645-)  C      N      0.55    2.30  INTRA BF
1413 HIS   ( 341-)  B      ND1 <-> 1414 ARG   ( 342-)  B      N      0.55    2.35  INTRA BF
3465 LYS   ( 561-)  E      N   <-> 5879 HOH   (3185 )  E      O      0.50    2.20  INTRA BL
5197 GLU   ( 841-)  G      CD  <-> 5874 ORN   (3910-)  G      NE     0.50    2.60  INTRA BF
 906 LEU   ( 906-)  A      O   <->  912 ARG   ( 912-)  A    A NH2    0.44    2.26  INTRA BL
 175 GLY   ( 175-)  A      N   <-> 5822 ANP   (1083-)  A      O1G    0.44    2.26  INTRA BF
4399 ARG   (  43-)  G      NH2 <-> 4437 GLU   (  81-)  G      OE1    0.42    2.28  INTRA BF
  43 ARG   (  43-)  A      NH2 <->   81 GLU   (  81-)  A      OE1    0.42    2.28  INTRA BF
1423 GLN   ( 351-)  B      NE2 <-> 5876 HOH   (1119 )  B      O      0.42    2.28  INTRA BF
 559 ARG   ( 559-)  A      NH2 <-> 5875 HOH   (1677 )  A      O      0.42    2.28  INTRA BF
2947 ARG   (  43-)  E      NH2 <-> 2985 GLU   (  81-)  E      OE1    0.42    2.28  INTRA
5357 ILE   (1001-)  G      O   <-> 5361 ILE   (1005-)  G      N      0.41    2.29  INTRA BF
5262 LEU   ( 906-)  G      O   <-> 5268 ARG   ( 912-)  G      NH2    0.41    2.29  INTRA BF
4169 HIS   ( 193-)  F      N   <-> 4210 ASP   ( 234-)  F      OD2    0.41    2.29  INTRA BF
1455 LYS   (   3-)  C      NZ  <-> 5877 HOH   (4567 )  C      O      0.41    2.29  INTRA BF
  51 PRO   (  51-)  A      O   <->  855 LYS   ( 855-)  A      NZ     0.41    2.29  INTRA BL
 321 LYS   ( 321-)  A      NZ  <->  338 ASP   ( 338-)  A      OD2    0.41    2.29  INTRA BF
3217 LYS   ( 313-)  E      NZ  <-> 3507 PRO   ( 603-)  E      O      0.41    2.29  INTRA BL
1495 ARG   (  43-)  C      NH2 <-> 1533 GLU   (  81-)  C      OE1    0.41    2.29  INTRA BF
4507 THR   ( 151-)  G      O   <-> 4511 ALA   ( 155-)  G      N      0.41    2.29  INTRA BF
2358 LEU   ( 906-)  C      O   <-> 2364 ARG   ( 912-)  C      NH2    0.41    2.29  INTRA BF
3626 GLY   ( 722-)  E      N   <-> 5856 ANP   (2910-)  E      O1B    0.41    2.29  INTRA BL
And so on for a total of 1834 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

3902 ARG   ( 998-)  E      -8.15
2450 ARG   ( 998-)  C      -7.81
5354 ARG   ( 998-)  G      -7.68
 998 ARG   ( 998-)  A      -7.66
4699 ARG   ( 343-)  G      -7.15
3247 ARG   ( 343-)  E      -7.08
 343 ARG   ( 343-)  A      -7.01
1795 ARG   ( 343-)  C      -6.88
 922 ARG   ( 922-)  A      -6.61
3826 ARG   ( 922-)  E      -6.51
1635 TYR   ( 183-)  C      -6.39
2181 TYR   ( 729-)  C      -6.35
 729 TYR   ( 729-)  A      -6.31
2374 ARG   ( 922-)  C      -6.30
5278 ARG   ( 922-)  G      -6.27
3633 TYR   ( 729-)  E      -6.18
1626 MET   ( 174-)  C      -6.09
5085 TYR   ( 729-)  G      -6.07
 174 MET   ( 174-)  A      -6.07
 183 TYR   ( 183-)  A      -6.00
2336 ILE   ( 884-)  C      -6.00
4530 MET   ( 174-)  G      -5.95
2560 MET   (  36-)  D      -5.93
3087 TYR   ( 183-)  E      -5.91
 884 ILE   ( 884-)  A      -5.91
And so on for a total of 81 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: 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

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: C

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: F

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: G

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: H

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.

4595 ALA   ( 239-)  G   -2.90
1691 ALA   ( 239-)  C   -2.85
2345 VAL   ( 893-)  C   -2.85
1475 ALA   (  23-)  C   -2.84
4379 ALA   (  23-)  G   -2.84
  23 ALA   (  23-)  A   -2.83
2927 ALA   (  23-)  E   -2.79
3309 GLY   ( 405-)  E   -2.78
 405 GLY   ( 405-)  A   -2.77
5249 VAL   ( 893-)  G   -2.68
3797 VAL   ( 893-)  E   -2.68
4761 GLY   ( 405-)  G   -2.64
 893 VAL   ( 893-)  A   -2.62
5255 LYS   ( 899-)  G   -2.61
2676 GLY   ( 152-)  D   -2.59
  60 MET   (  60-)  A   -2.56
1224 GLY   ( 152-)  B   -2.55
 720 LEU   ( 720-)  A   -2.53

Warning: Abnormal packing Z-score for sequential residues

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

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

 575 GLY   ( 575-)  A     -  578 PHE   ( 578-)  A        -1.88
 892 GLU   ( 892-)  A     -  895 LEU   ( 895-)  A        -1.84
1434 ASP   ( 362-)  B     - 1437 PRO   ( 365-)  B        -1.47
1855 GLU   ( 403-)  C     - 1858 ALA   ( 406-)  C        -1.57
2027 GLY   ( 575-)  C     - 2030 PHE   ( 578-)  C        -1.83
3479 GLY   ( 575-)  E     - 3482 PHE   ( 578-)  E        -1.79
4061 LEU   (  85-)  F     - 4064 ILE   (  88-)  F        -1.87
4931 GLY   ( 575-)  G     - 4934 PHE   ( 578-)  G        -1.89
5513 LEU   (  85-)  H     - 5516 ILE   (  88-)  H        -1.89

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

Note: Second generation quality Z-score plot

Chain identifier: C

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: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

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.

5875 HOH   (1386 )  A      O      1.36  106.07   88.21
5875 HOH   (1390 )  A      O     -6.12  102.24   76.39
5875 HOH   (1401 )  A      O      2.94  104.26   90.01
5875 HOH   (1606 )  A      O    -17.15   37.17  -52.81
5875 HOH   (1641 )  A      O     -0.44   55.81  -57.86
5875 HOH   (1658 )  A      O      3.53   98.33   94.15
5875 HOH   (1667 )  A      O      3.77  108.62   88.32
5875 HOH   (1707 )  A      O    -15.68   22.24  -73.32
5876 HOH   (1145 )  B      O     38.28  -59.13  -47.75
5877 HOH   (4303 )  C      O     62.88   40.42   49.49
5877 HOH   (4570 )  C      O     72.76   20.43   56.60
5882 HOH   (3576 )  H      O    -12.22   20.49 -102.64

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.

5875 HOH   (1364 )  A      O
5875 HOH   (1366 )  A      O
5875 HOH   (1387 )  A      O
5875 HOH   (1413 )  A      O
5875 HOH   (1414 )  A      O
5875 HOH   (1422 )  A      O
5875 HOH   (1445 )  A      O
5875 HOH   (1456 )  A      O
5875 HOH   (1474 )  A      O
5875 HOH   (1487 )  A      O
5875 HOH   (1528 )  A      O
5875 HOH   (1544 )  A      O
5875 HOH   (1564 )  A      O
5875 HOH   (1587 )  A      O
5875 HOH   (1629 )  A      O
5875 HOH   (1650 )  A      O
5875 HOH   (1671 )  A      O
5875 HOH   (1735 )  A      O
5875 HOH   (1751 )  A      O
5875 HOH   (1756 )  A      O
5876 HOH   ( 999 )  B      O
5876 HOH   (1048 )  B      O
5876 HOH   (1064 )  B      O
5876 HOH   (1081 )  B      O
5876 HOH   (1115 )  B      O
And so on for a total of 95 lines.

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.

 523 HIS   ( 523-)  A
 554 ASN   ( 554-)  A
 570 ASN   ( 570-)  A
 574 GLN   ( 574-)  A
 689 GLN   ( 689-)  A
 784 GLN   ( 784-)  A
 812 GLN   ( 812-)  A
 987 ASN   ( 987-)  A
1177 HIS   ( 105-)  B
1396 ASN   ( 324-)  B
1423 GLN   ( 351-)  B
1718 ASN   ( 266-)  C
1737 GLN   ( 285-)  C
2236 GLN   ( 784-)  C
2287 ASN   ( 835-)  C
2439 ASN   ( 987-)  C
2746 GLN   ( 222-)  D
2848 ASN   ( 324-)  D
2875 GLN   ( 351-)  D
2974 HIS   (  70-)  E
3170 ASN   ( 266-)  E
3478 GLN   ( 574-)  E
3593 GLN   ( 689-)  E
3688 GLN   ( 784-)  E
3718 GLN   ( 814-)  E
3739 ASN   ( 835-)  E
3896 ASN   ( 992-)  E
4027 GLN   (  51-)  F
4232 GLN   ( 256-)  F
4300 ASN   ( 324-)  F
4327 GLN   ( 351-)  F
4622 ASN   ( 266-)  G
4930 GLN   ( 574-)  G
5045 GLN   ( 689-)  G
5140 GLN   ( 784-)  G
5191 ASN   ( 835-)  G
5533 HIS   ( 105-)  H
5660 ASN   ( 232-)  H
5684 GLN   ( 256-)  H
5752 ASN   ( 324-)  H
5779 GLN   ( 351-)  H

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 LYS   (   3-)  A      N
   7 ILE   (   7-)  A      N
  61 ALA   (  61-)  A      N
  92 GLY   (  92-)  A      N
  93 GLN   (  93-)  A      NE2
 119 THR   ( 119-)  A      N
 161 ASP   ( 161-)  A      N
 173 THR   ( 173-)  A      N
 175 GLY   ( 175-)  A      N
 176 GLY   ( 176-)  A      N
 184 ASN   ( 184-)  A      N
 210 LEU   ( 210-)  A      N
 225 ASN   ( 225-)  A      N
 227 ASN   ( 227-)  A      ND2
 236 ASN   ( 236-)  A      ND2
 241 GLY   ( 241-)  A      N
 243 HIS   ( 243-)  A      NE2
 279 THR   ( 279-)  A      N
 282 SER   ( 282-)  A      OG
 285 GLN   ( 285-)  A      NE2
 303 ARG   ( 303-)  A      NE
 303 ARG   ( 303-)  A      NH2
 309 ALA   ( 309-)  A      N
 331 THR   ( 331-)  A      N
 339 ILE   ( 339-)  A      N
And so on for a total of 390 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.

 215 GLU   ( 215-)  A      OE1
 334 GLU   ( 334-)  A      OE1
 383 GLU   ( 383-)  A      OE2
 391 GLN   ( 391-)  A      OE1
 548 GLU   ( 548-)  A      OE1
 645 GLN   ( 645-)  A      OE1
 761 GLU   ( 761-)  A      OE2
1101 GLU   (  29-)  B      OE2
1425 HIS   ( 353-)  B      NE2
1545 GLN   (  93-)  C      OE1
1667 GLU   ( 215-)  C      OE2
1688 ASN   ( 236-)  C      OD1
1737 GLN   ( 285-)  C      OE1
1843 GLN   ( 391-)  C      OE1
2036 HIS   ( 584-)  C      ND1
2097 GLN   ( 645-)  C      OE1
2185 ASP   ( 733-)  C      OD1
2213 GLU   ( 761-)  C      OE1
2213 GLU   ( 761-)  C      OE2
2877 HIS   ( 353-)  D      NE2
2997 GLN   (  93-)  E      OE1
3119 GLU   ( 215-)  E      OE2
3140 ASN   ( 236-)  E      OD1
3287 GLU   ( 383-)  E      OE2
3295 GLN   ( 391-)  E      OE1
3307 GLU   ( 403-)  E      OE2
3427 HIS   ( 523-)  E      ND1
3452 GLU   ( 548-)  E      OE1
3488 HIS   ( 584-)  E      ND1
3508 GLU   ( 604-)  E      OE1
3549 GLN   ( 645-)  E      OE1
3637 ASP   ( 733-)  E      OD2
3665 GLU   ( 761-)  E      OE1
3665 GLU   ( 761-)  E      OE2
4329 HIS   ( 353-)  F      NE2
4449 GLN   (  93-)  G      OE1
4571 GLU   ( 215-)  G      OE2
4592 ASN   ( 236-)  G      OD1
4747 GLN   ( 391-)  G      OE1
4940 HIS   ( 584-)  G      ND1
4960 GLU   ( 604-)  G      OE1
5001 GLN   ( 645-)  G      OE1
5117 GLU   ( 761-)  G      OE2
5425 HIS   (1069-)  G      ND1
5700 HIS   ( 272-)  H      ND1
5740 HIS   ( 312-)  H      ND1

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+.

5815   K   (1076-)  A   -.-  -.-  Part of ionic cluster
5815   K   (1076-)  A     2.26   0.68 Is perhaps NA
5830   K   (1904-)  C   -.-  -.-  Part of ionic cluster
5830   K   (1904-)  C    0.67  -.-   Poor packing
5846   K   (2903-)  E     1.60   0.74 Scores about as good as NA
5847   K   (2904-)  E   -.-  -.-  Part of ionic cluster
5853   K   (2982-)  E   -.-  -.-  Too few ligands (1)
5860   K   (3903-)  G    1.57  -.-   Poor packing
5861   K   (3904-)  G   -.-  -.-  Part of ionic cluster

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.

5875 HOH   (1151 )  A      O  0.91  K  5 *1
5875 HOH   (1154 )  A      O  0.95  K  4 *1
5875 HOH   (1160 )  A      O  1.00  K  4 *1
5875 HOH   (1173 )  A      O  0.92 NA  4
5875 HOH   (1310 )  A      O  0.90  K  6 *1
5877 HOH   (4059 )  C      O  1.14  K  4 *1 NCS 1/1
5877 HOH   (4111 )  C      O  1.05  K  4 *1 NCS 1/1
5877 HOH   (4144 )  C      O  1.00  K  4 *1 NCS 1/1
5877 HOH   (4154 )  C      O  1.11  K  4 *1 ION-B
5878 HOH   (1090 )  D      O  0.90  K  4 *1 NCS 1/1
5879 HOH   (3060 )  E      O  1.04  K  4 *1 NCS 2/2
5879 HOH   (3191 )  E      O  0.92  K  4 *1 NCS 2/2
5880 HOH   (2326 )  F      O  1.13  K  4 *1 Ion-B
5881 HOH   (4013 )  G      O  0.99  K  4 *1 NCS 3/3
5881 HOH   (4066 )  G      O  1.05  K  4 *1 NCS 3/3
5881 HOH   (4148 )  G      O  0.93  K  4 *1 NCS 2/2
5881 HOH   (4152 )  G      O  0.96  K  4 *1 Ion-B
5881 HOH   (4248 )  G      O  0.85  K  4 *1 NCS 2/2
5881 HOH   (4370 )  G      O  0.89  K  4 *1 ION-B H2O-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.

 187 GLU   ( 187-)  A   H-bonding suggests Gln; but Alt-Rotamer
 246 ASP   ( 246-)  A   H-bonding suggests Asn
 410 ASP   ( 410-)  A   H-bonding suggests Asn; but Alt-Rotamer
 430 ASP   ( 430-)  A   H-bonding suggests Asn; but Alt-Rotamer
 707 GLU   ( 707-)  A   H-bonding suggests Gln
 769 ASP   ( 769-)  A   H-bonding suggests Asn; but Alt-Rotamer
 791 ASP   ( 791-)  A   H-bonding suggests Asn
1025 ASP   (1025-)  A   H-bonding suggests Asn
1041 ASP   (1041-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1283 ASP   ( 211-)  B   H-bonding suggests Asn
1786 GLU   ( 334-)  C   H-bonding suggests Gln
1862 ASP   ( 410-)  C   H-bonding suggests Asn
1882 ASP   ( 430-)  C   H-bonding suggests Asn
1970 ASP   ( 518-)  C   H-bonding suggests Asn; but Alt-Rotamer
2259 ASP   ( 807-)  C   H-bonding suggests Asn
2636 ASP   ( 112-)  D   H-bonding suggests Asn
2735 ASP   ( 211-)  D   H-bonding suggests Asn
3314 ASP   ( 410-)  E   H-bonding suggests Asn
3673 ASP   ( 769-)  E   H-bonding suggests Asn; but Alt-Rotamer
3695 ASP   ( 791-)  E   H-bonding suggests Asn
3711 ASP   ( 807-)  E   H-bonding suggests Asn; but Alt-Rotamer
3945 ASP   (1041-)  E   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
4088 ASP   ( 112-)  F   H-bonding suggests Asn
4187 ASP   ( 211-)  F   H-bonding suggests Asn
4543 GLU   ( 187-)  G   H-bonding suggests Gln
4602 ASP   ( 246-)  G   H-bonding suggests Asn
4690 GLU   ( 334-)  G   H-bonding suggests Gln; but Alt-Rotamer
4759 GLU   ( 403-)  G   H-bonding suggests Gln
4786 ASP   ( 430-)  G   H-bonding suggests Asn
5082 GLU   ( 726-)  G   H-bonding suggests Gln; but Alt-Rotamer
5125 ASP   ( 769-)  G   H-bonding suggests Asn; but Alt-Rotamer
5163 ASP   ( 807-)  G   H-bonding suggests Asn
5381 ASP   (1025-)  G   H-bonding suggests Asn
5469 GLU   (  41-)  H   H-bonding suggests Gln; but Alt-Rotamer
5540 ASP   ( 112-)  H   H-bonding suggests Asn
5639 ASP   ( 211-)  H   H-bonding suggests Asn
5662 ASP   ( 234-)  H   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 :  -0.023
  2nd generation packing quality :  -1.393
  Ramachandran plot appearance   :  -1.839
  chi-1/chi-2 rotamer normality  :  -4.671 (bad)
  Backbone conformation          :   0.094

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.825
  Bond angles                    :   1.217
  Omega angle restraints         :   0.400 (tight)
  Side chain planarity           :   0.957
  Improper dihedral distribution :   1.421
  B-factor distribution          :   4.106 (loose)
  Inside/Outside distribution    :   1.020

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -3.1 (poor)
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.825
  Bond angles                    :   1.217
  Omega angle restraints         :   0.400 (tight)
  Side chain planarity           :   0.957
  Improper dihedral distribution :   1.421
  B-factor distribution          :   4.106 (loose)
  Inside/Outside distribution    :   1.020
==============

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.