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 pdb1a9x.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 : 0.388
CA-only RMS fit for the two chains : 0.224

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 : 0.452
CA-only RMS fit for the two chains : 0.320

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 : 0.477
CA-only RMS fit for the two chains : 0.358

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 : 0.340
CA-only RMS fit for the two chains : 0.192

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 : 0.357
CA-only RMS fit for the two chains : 0.199

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: 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.

5772 ADP   (1900-)  A  -
5773 ADP   (1910-)  A  -
5774 ORN   (1920-)  A  -
5775 NET   (1950-)  A  -
5798 ADP   (3900-)  C  -
5799 ADP   (3910-)  C  -
5800 ORN   (3920-)  C  -
5801 NET   (3950-)  C  -
5823 ADP   (5900-)  E  -
5824 ADP   (5910-)  E  -
5825 ORN   (5920-)  E  -
5826 NET   (5950-)  E  -
5849 ADP   (7900-)  G  -
5853 NET   (7950-)  G  -
5854 ORN   (7920-)  G  -
5855 ADP   (7910-)  G  -

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: Artificial side chains detected

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

 903 MET   ( 918-)  A
1326 CYG   (1769-)  B
2763 CYG   (3769-)  D
4200 CYG   (5769-)  F
5637 CYG   (7769-)  H

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) :120.000

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 : 3.870 over 35484 bonds
Average difference in B over a bond : 10.23
RMS difference in B over a bond : 14.56

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.

  72 GLU   (  72-)  A      CD   OE2   1.33    4.1
  80 LYS   (  80-)  A      CE   NZ    1.68    6.2
  84 ASP   (  84-)  A      CG   OD1   1.33    4.0
 110 GLU   ( 110-)  A      CD   OE1   1.34    4.8
 121 ASP   ( 121-)  A      CG   OD1   1.33    4.1
 124 ASP   ( 124-)  A      CG   OD1   1.33    4.1
 186 GLU   ( 186-)  A      CD   OE2   1.33    4.0
 207 ASP   ( 207-)  A      CG   OD1   1.34    4.6
 217 GLU   ( 217-)  A      CD   OE2   1.33    4.5
 403 GLU   ( 403-)  A      CD   OE2   1.33    4.1
 441 ASP   ( 441-)  A      CG   OD1   1.33    4.0
 478 GLU   ( 478-)  A      CD   OE1   1.33    4.5
 512 GLU   ( 512-)  A      CD   OE1   1.34    5.0
 539 ASP   ( 539-)  A      CG   OD1   1.33    4.1
 549 GLU   ( 549-)  A      CD   OE2   1.33    4.4
 604 GLU   ( 604-)  A      CD   OE1   1.33    4.0
 655 GLU   ( 655-)  A      CD   OE2   1.34    4.6
 699 GLU   ( 699-)  A      CD   OE1   1.33    4.1
 703 GLU   ( 703-)  A      CD   OE2   1.33    4.4
 726 ASP   ( 733-)  A      CG   OD1   1.33    4.2
 746 GLU   ( 761-)  A      CD   OE1   1.34    4.5
 750 ASP   ( 765-)  A      CG   OD1   1.33    4.0
 756 GLU   ( 771-)  A      CD   OE1   1.34    4.6
 989 ARG   (1004-)  A      NE   CZ    1.39    4.0
1009 GLU   (1024-)  A      CD   OE1   1.33    4.2
And so on for a total of 145 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

 |  1.001336  0.000162  0.000063|
 |  0.000162  1.000428 -0.000391|
 |  0.000063 -0.000391  1.001015|
Proposed new scale matrix

 |  0.006566 -0.000001  0.000000|
 |  0.000000  0.006080  0.000002|
 |  0.000000  0.000001  0.003006|
With corresponding cell

    A    = 152.294  B   = 164.463  C    = 332.674
    Alpha=  90.045  Beta=  90.003  Gamma=  89.992

The CRYST1 cell dimensions

    A    = 152.100  B   = 164.400  C    = 332.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 176.575
(Under-)estimated Z-score: 9.793

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   2 PRO   (   2-)  A      N    CA   CB  108.01    4.6
  26 PHE   (  26-)  A      CA   CB   CG  106.78   -7.0
  27 ASP   (  27-)  A      N    CA   CB  118.48    4.7
  34 CYS   (  34-)  A      N    CA   CB  118.21    4.5
  38 ARG   (  38-)  A      CG   CD   NE  118.35    4.6
  38 ARG   (  38-)  A      CD   NE   CZ  128.99    4.0
  61 ALA   (  61-)  A      C    CA   CB  116.53    4.0
  68 PRO   (  68-)  A      N    CA   CB  107.90    4.5
  88 PRO   (  88-)  A      C    CA   CB  101.92   -4.3
 136 MET   ( 136-)  A      CG   SD   CE  109.97    4.1
 151 THR   ( 151-)  A      C    CA   CB  101.92   -4.3
 161 ASP   ( 161-)  A      CA   CB   CG  116.77    4.2
 164 PHE   ( 164-)  A      CA   CB   CG  107.46   -6.3
 173 THR   ( 173-)  A      N    CA   CB  118.83    4.9
 197 ASP   ( 197-)  A      N    CA   CB  119.43    5.3
 204 LEU   ( 204-)  A      C    CA   CB   96.85   -7.0
 210 LEU   ( 210-)  A      N    CA   CB  117.73    4.3
 219 GLU   ( 219-)  A      C    CA   CB  102.08   -4.2
 225 ASN   ( 225-)  A      CA   CB   CG  107.06   -5.5
 236 ASN   ( 236-)  A     -C    N    CA  114.34   -4.1
 248 ILE   ( 248-)  A      N    CA   C    98.24   -4.6
 266 ASN   ( 266-)  A      CA   CB   CG  117.77    5.2
 278 GLU   ( 278-)  A      C    CA   CB   99.94   -5.3
 279 THR   ( 279-)  A      C    CA   CB  101.79   -4.4
 283 ASN   ( 283-)  A      CA   CB   CG  118.89    6.3
And so on for a total of 634 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.

 435 ARG   ( 435-)  A      CA    -6.8    22.75    33.91
 500 ALA   ( 500-)  A      CA    -6.1    26.33    34.09
 651 ALA   ( 651-)  A      CA    -6.7    25.53    34.09
 675 ARG   ( 675-)  A      CA     6.0    43.82    33.91
 719 GLU   ( 726-)  A      CA   -19.0     2.80    33.96
 939 LYS   ( 954-)  A      CA    -6.7    22.77    33.92
 958 ALA   ( 973-)  A      CA    -6.1    26.37    34.09
 960 HIS   ( 975-)  A      CA    -9.8    16.14    34.11
 984 PRO   ( 999-)  A      N    -10.1   -35.47    -2.48
 984 PRO   ( 999-)  A      CA    -7.6    27.44    38.15
1055 ALA   (1070-)  A      CA    -6.5    25.84    34.09
1115 PRO   (1558-)  B      CA    -6.7    28.66    38.15
1128 GLU   (1571-)  B      CA    -6.3    23.63    33.96
1532 ALA   (2095-)  C      CA    -6.4    26.01    34.09
1776 ILE   (2339-)  C      CA    -9.9    18.25    33.24
2006 PRO   (2569-)  C      N      6.1    17.41    -2.48
2056 GLU   (2619-)  C      CA     6.3    44.36    33.96
2079 TYR   (2642-)  C      CA     6.8    44.71    34.03
2283 LEU   (2861-)  C      CA    -6.5    24.28    34.19
2306 ILE   (2884-)  C      CA   -10.6    17.29    33.24
2328 LEU   (2906-)  C      CA     6.0    43.41    34.19
2421 PRO   (2999-)  C      N     -7.0   -25.32    -2.48
2423 ILE   (3001-)  C      CB   -10.8    18.28    32.31
2436 ILE   (3014-)  C      CA    -7.0    22.68    33.24
2458 TYR   (3036-)  C      CA    -9.6    18.89    34.03
And so on for a total of 58 lines.

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.

4650 ILE   (6339-)  G    7.38
3213 ILE   (4339-)  E    7.09
 543 MET   ( 543-)  A    6.21
 960 HIS   ( 975-)  A    6.20
4962 ALA   (6651-)  G    6.18
2583 ALA   (3589-)  D    6.08
4338 ASP   (6027-)  G    5.81
4630 ILE   (6319-)  G    5.76
4147 LEU   (5716-)  F    5.63
3193 ILE   (4319-)  E    5.55
 196 LEU   ( 196-)  A    5.54
4923 THR   (6612-)  G    5.53
2897 ALA   (4023-)  E    5.27
2397 HIS   (2975-)  C    5.17
2049 THR   (2612-)  C    5.12
 456 THR   ( 456-)  A    4.98
2283 LEU   (2861-)  C    4.95
1893 THR   (2456-)  C    4.93
4020 ALA   (5589-)  F    4.88
1916 VAL   (2479-)  C    4.86
3557 GLU   (4683-)  E    4.83
 651 ALA   ( 651-)  A    4.77
1272 ARG   (1715-)  B    4.72
4145 CYS   (5714-)  F    4.69
5687 ALA   (7819-)  H    4.67
And so on for a total of 81 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 : 1.546

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.

5291 HIS   (6995-)  G    7.92
1828 GLN   (2391-)  C    6.10
4370 GLU   (6059-)  G    5.47
2835 HIS   (3841-)  D    5.20
3544 ASP   (4670-)  E    5.19
2958 ASP   (4084-)  E    4.81
3736 GLN   (4877-)  E    4.51
1738 ASN   (2301-)  C    4.04
4032 TYR   (5601-)  F    4.04
4785 GLU   (6474-)  G    4.03
 667 ASP   ( 667-)  A    4.03

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.

2962 PRO   (4088-)  E    -3.1
  88 PRO   (  88-)  A    -3.0
 375 THR   ( 375-)  A    -3.0
4399 PRO   (6088-)  G    -3.0
1525 PRO   (2088-)  C    -3.0
1812 THR   (2375-)  C    -2.9
2544 ARG   (3550-)  D    -2.9
3981 ARG   (5550-)  F    -2.8
5418 ARG   (7550-)  H    -2.8
4313 PRO   (6002-)  G    -2.8
2222 THR   (2800-)  C    -2.8
1107 ARG   (1550-)  B    -2.7
4513 LYS   (6202-)  G    -2.7
5271 HIS   (6975-)  G    -2.7
3508 LYS   (4634-)  E    -2.7
2852 PRO   (3858-)  D    -2.7
4945 LYS   (6634-)  G    -2.7
2318 PRO   (2896-)  C    -2.7
 960 HIS   ( 975-)  A    -2.7
3834 HIS   (4975-)  E    -2.7
1689 PRO   (2252-)  C    -2.6
1414 SER   (1857-)  B    -2.6
2876 PRO   (4002-)  E    -2.6
3222 PHE   (4348-)  E    -2.6
2851 SER   (3857-)  D    -2.6
And so on for a total of 220 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.

  23 ALA   (  23-)  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
 302 PRO   ( 302-)  A  Poor phi/psi
 303 ARG   ( 303-)  A  Poor phi/psi
 368 ALA   ( 368-)  A  Poor phi/psi
 375 THR   ( 375-)  A  Poor phi/psi
 379 LYS   ( 379-)  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
 531 THR   ( 531-)  A  Poor phi/psi
 534 ALA   ( 534-)  A  Poor phi/psi
 686 LYS   ( 686-)  A  Poor phi/psi
 693 ALA   ( 693-)  A  Poor phi/psi
 710 TYR   ( 710-)  A  PRO omega poor
 781 LEU   ( 796-)  A  PRO omega poor
 785 THR   ( 800-)  A  Poor phi/psi
 820 ASN   ( 835-)  A  Poor phi/psi
 829 PRO   ( 844-)  A  Poor phi/psi
 890 PRO   ( 905-)  A  Poor phi/psi
And so on for a total of 151 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.976

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.

4888 GLU   (6577-)  G    0.35
3142 SER   (4268-)  E    0.36
 312 SER   ( 312-)  A    0.36
1466 SER   (2029-)  C    0.36
4340 SER   (6029-)  G    0.36
4623 SER   (6312-)  G    0.36
4705 SER   (6394-)  G    0.36
5150 SER   (6854-)  G    0.37
1705 SER   (2268-)  C    0.37
 268 SER   ( 268-)  A    0.37
3713 SER   (4854-)  E    0.38
1157 SER   (1600-)  B    0.38
2023 SER   (2586-)  C    0.38
2593 SER   (3599-)  D    0.39
4579 SER   (6268-)  G    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!

   3 LYS   (   3-)  A      0
   7 ILE   (   7-)  A      0
   9 SER   (   9-)  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
  40 GLU   (  40-)  A      0
  52 ALA   (  52-)  A      0
  60 MET   (  60-)  A      0
  62 ASP   (  62-)  A      0
  69 ILE   (  69-)  A      0
  89 THR   (  89-)  A      0
  90 MET   (  90-)  A      0
  93 GLN   (  93-)  A      0
 107 VAL   ( 107-)  A      0
 111 PHE   ( 111-)  A      0
 116 ILE   ( 116-)  A      0
 139 ILE   ( 139-)  A      0
 146 SER   ( 146-)  A      0
 152 MET   ( 152-)  A      0
 162 VAL   ( 162-)  A      0
 164 PHE   ( 164-)  A      0
 166 CYS   ( 166-)  A      0
And so on for a total of 2035 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.866

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!

4878 GLY   (6567-)  G   3.31   25
2004 GLY   (2567-)  C   3.23   34
 567 GLY   ( 567-)  A   3.21   22
3441 GLY   (4567-)  E   3.10   32
5657 GLY   (7789-)  H   1.73   13

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...

2448 SER   (3026-)  C   1.67
3974 LEU   (5543-)  F   1.53

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    0.15 LOW
  58 PRO   (  58-)  A    0.12 LOW
  68 PRO   (  68-)  A    0.08 LOW
 170 PRO   ( 170-)  A    0.19 LOW
 350 PRO   ( 350-)  A    0.13 LOW
 360 PRO   ( 360-)  A    0.15 LOW
 418 PRO   ( 418-)  A    0.12 LOW
 555 PRO   ( 555-)  A    0.12 LOW
 620 PRO   ( 620-)  A    0.14 LOW
 647 PRO   ( 647-)  A    0.12 LOW
 690 PRO   ( 690-)  A    0.17 LOW
 711 PRO   ( 711-)  A    0.15 LOW
 782 PRO   ( 797-)  A    0.13 LOW
 836 PRO   ( 851-)  A    0.18 LOW
 886 PRO   ( 901-)  A    0.13 LOW
 894 PRO   ( 909-)  A    0.13 LOW
1115 PRO   (1558-)  B    0.08 LOW
1195 PRO   (1638-)  B    0.15 LOW
1208 PRO   (1651-)  B    0.07 LOW
1277 PRO   (1720-)  B    0.18 LOW
1304 PRO   (1747-)  B    0.01 LOW
1321 PRO   (1764-)  B    0.19 LOW
1403 PRO   (1846-)  B    0.17 LOW
1411 PRO   (1854-)  B    0.09 LOW
1417 PRO   (1860-)  B    0.13 LOW
And so on for a total of 117 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].

  88 PRO   (  88-)  A   -45.4 half-chair C-beta/C-alpha (-54 degrees)
 165 PRO   ( 165-)  A   -47.1 half-chair C-beta/C-alpha (-54 degrees)
 200 PRO   ( 200-)  A   107.5 envelop C-beta (108 degrees)
 302 PRO   ( 302-)  A   -26.3 half-chair C-alpha/N (-18 degrees)
 318 PRO   ( 318-)  A   -41.4 envelop C-alpha (-36 degrees)
 345 PRO   ( 345-)  A   -61.3 half-chair C-beta/C-alpha (-54 degrees)
 524 PRO   ( 524-)  A   -61.4 half-chair C-beta/C-alpha (-54 degrees)
 635 PRO   ( 635-)  A   -55.0 half-chair C-beta/C-alpha (-54 degrees)
 666 PRO   ( 666-)  A   144.5 envelop C-alpha (144 degrees)
 829 PRO   ( 844-)  A   -28.0 envelop C-alpha (-36 degrees)
 845 PRO   ( 860-)  A   -54.9 half-chair C-beta/C-alpha (-54 degrees)
 881 PRO   ( 896-)  A   -47.0 half-chair C-beta/C-alpha (-54 degrees)
 890 PRO   ( 905-)  A     9.1 half-chair N/C-delta (18 degrees)
 984 PRO   ( 999-)  A   118.8 half-chair C-beta/C-alpha (126 degrees)
1103 PRO   (1546-)  B   103.5 envelop C-beta (108 degrees)
1353 PRO   (1796-)  B   -49.5 half-chair C-beta/C-alpha (-54 degrees)
1415 PRO   (1858-)  B   -58.6 half-chair C-beta/C-alpha (-54 degrees)
1454 PRO   (2017-)  C   -39.3 envelop C-alpha (-36 degrees)
1488 PRO   (2051-)  C   -62.4 half-chair C-beta/C-alpha (-54 degrees)
1525 PRO   (2088-)  C   -61.8 half-chair C-beta/C-alpha (-54 degrees)
1637 PRO   (2200-)  C   110.6 envelop C-beta (108 degrees)
1755 PRO   (2318-)  C   -46.7 half-chair C-beta/C-alpha (-54 degrees)
1787 PRO   (2350-)  C   127.1 half-chair C-beta/C-alpha (126 degrees)
2040 PRO   (2603-)  C   -64.7 envelop C-beta (-72 degrees)
2103 PRO   (2666-)  C   105.3 envelop C-beta (108 degrees)
And so on for a total of 66 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.

2397 HIS   (2975-)  C      ND1 <-> 3834 HIS   (4975-)  E      ND1    0.69    2.31  INTRA BL
 960 HIS   ( 975-)  A      ND1 <-> 5271 HIS   (6975-)  G      ND1    0.63    2.37  INTRA BL
4605 ARG   (6294-)  G      NH1 <-> 5838  CL   (7931-)  G     CL      0.55    2.55  INTRA BF
2210 HIS   (2788-)  C      ND1 <-> 2212 GLY   (2790-)  C      N      0.53    2.47  INTRA BL
3526 ARG   (4652-)  E      NH2 <-> 5860 HOH   (6792 )  E      O      0.49    2.21  INTRA BF
2875 MET   (4001-)  E      N   <-> 5860 HOH   (6621 )  E      O      0.47    2.23  INTRA BF
4153 GLN   (5722-)  F      NE2 <-> 5861 HOH   (3278 )  F      O      0.47    2.23  INTRA BF
4354 ARG   (6043-)  G      NH1 <-> 5862 HOH   ( 838 )  G      O      0.47    2.23  INTRA BF
2875 MET   (4001-)  E      CB  <-> 5860 HOH   (6618 )  E      O      0.46    2.34  INTRA BF
1731 ARG   (2294-)  C      NH1 <-> 5858 HOH   (4151 )  C      O      0.45    2.25  INTRA BF
1758 LYS   (2321-)  C      NZ  <-> 2048 ASP   (2611-)  C      OD2    0.45    2.25  INTRA BF
4068 ASN   (5637-)  F      N   <-> 5861 HOH   (3246 )  F      O      0.44    2.26  INTRA BF
1480 ARG   (2043-)  C      NH2 <-> 1518 GLU   (2081-)  C      OE1    0.43    2.27  INTRA BF
2251 GLN   (2829-)  C      NE2 <-> 5858 HOH   (4825 )  C      O      0.42    2.28  INTRA BF
 715 ARG   ( 715-)  A      NH1 <-> 5856 HOH   (2845 )  A      O      0.42    2.28  INTRA BF
 519 GLN   ( 519-)  A      NE2 <-> 5856 HOH   (2758 )  A      O      0.42    2.28  INTRA BF
2792 LYS   (3798-)  D      NZ  <-> 5859 HOH   (3956 )  D      O      0.41    2.29  INTRA
2113 GLU   (2676-)  C      O   <-> 2117 HIS   (2680-)  C      ND1    0.41    2.29  INTRA BF
4354 ARG   (6043-)  G      NH2 <-> 4392 GLU   (6081-)  G      OE1    0.41    2.29  INTRA BF
5237 LYS   (6941-)  G      NZ  <-> 5352 ALA   (7056-)  G      O      0.41    2.29  INTRA BF
 730 TYR   ( 737-)  A      O   <->  734 ALA   ( 741-)  A      N      0.41    2.29  INTRA BF
3578 LYS   (4704-)  E      NZ  <-> 3581 GLU   (4707-)  E      OE1    0.40    2.30  INTRA BF
1493 THR   (2056-)  C      OG1 <-> 2277 LYS   (2855-)  C      NZ     0.40    2.30  INTRA BL
5647 SER   (7779-)  H      OG  <-> 5710 ARG   (7842-)  H      NH1    0.40    2.30  INTRA BF
3818 ASP   (4959-)  E      OD2 <-> 3822 LYS   (4963-)  E      NZ     0.40    2.30  INTRA BF
And so on for a total of 1648 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.

5294 ARG   (6998-)  G      -7.86
2420 ARG   (2998-)  C      -7.41
3217 ARG   (4343-)  E      -7.33
4654 ARG   (6343-)  G      -7.02
 983 ARG   ( 998-)  A      -7.01
3857 ARG   (4998-)  E      -6.94
 343 ARG   ( 343-)  A      -6.84
1780 ARG   (2343-)  C      -6.64
2344 ARG   (2922-)  C      -6.60
3057 TYR   (4183-)  E      -6.41
3781 ARG   (4922-)  E      -6.39
5291 HIS   (6995-)  G      -6.33
2417 HIS   (2995-)  C      -6.32
3854 HIS   (4995-)  E      -6.31
5218 ARG   (6922-)  G      -6.30
1620 TYR   (2183-)  C      -6.27
4485 MET   (6174-)  G      -6.18
4494 TYR   (6183-)  G      -6.13
 183 TYR   ( 183-)  A      -6.12
 907 ARG   ( 922-)  A      -6.04
1611 MET   (2174-)  C      -6.01
 174 MET   ( 174-)  A      -5.99
3048 MET   (4174-)  E      -5.91
5473 HIS   (7605-)  H      -5.89
2599 HIS   (3605-)  D      -5.89
And so on for a total of 67 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

5491 ARG   (7623-)  H      5493 - LYS   7625- ( H)         -4.43

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.

 198 LEU   ( 198-)  A   -3.07
2934 MET   (4060-)  E   -2.91
4550 ALA   (6239-)  G   -2.90
3072 LEU   (4198-)  E   -2.87
  60 MET   (  60-)  A   -2.85
4334 ALA   (6023-)  G   -2.83
  23 ALA   (  23-)  A   -2.78
2315 VAL   (2893-)  C   -2.77
1842 GLY   (2405-)  C   -2.76
3279 GLY   (4405-)  E   -2.76
 878 VAL   ( 893-)  A   -2.76
1460 ALA   (2023-)  C   -2.74
3752 VAL   (4893-)  E   -2.71
5195 LYS   (6899-)  G   -2.67
5189 VAL   (6893-)  G   -2.65
3758 LYS   (4899-)  E   -2.65
3177 ARG   (4303-)  E   -2.63
1209 GLY   (1652-)  B   -2.54
4083 GLY   (5652-)  F   -2.51
5520 GLY   (7652-)  H   -2.51
2377 GLU   (2955-)  C   -2.50

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        -1.79
 877 GLU   ( 892-)  A     -  880 LEU   ( 895-)  A        -1.91
2012 GLY   (2575-)  C     - 2015 PHE   (2578-)  C        -1.80
2579 LEU   (3585-)  D     - 2582 ILE   (3588-)  D        -1.80
3449 GLY   (4575-)  E     - 3452 PHE   (4578-)  E        -1.79
4016 LEU   (5585-)  F     - 4019 ILE   (5588-)  F        -1.82
4886 GLY   (6575-)  G     - 4889 PHE   (6578-)  G        -1.77
5453 LEU   (7585-)  H     - 5456 ILE   (7588-)  H        -1.87
5730 ASP   (7862-)  H     - 5733 PRO   (7865-)  H        -1.43

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: 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.

5856 HOH   (2481 )  A      O     -1.43  106.29   76.89
5856 HOH   (2621 )  A      O     32.81   -5.84  -77.10
5856 HOH   (2624 )  A      O     32.73   -3.12  -82.76
5856 HOH   (2625 )  A      O     28.45   -5.01  -82.28
5856 HOH   (2636 )  A      O    -10.01   96.53   84.39
5856 HOH   (2638 )  A      O    -10.18   95.17   77.76
5856 HOH   (2650 )  A      O     -0.21   98.22   94.23
5856 HOH   (2653 )  A      O     -6.62  102.39   76.88
5856 HOH   (2662 )  A      O      3.34  106.85   91.40
5856 HOH   (2776 )  A      O    -23.25   18.48  -83.01
5856 HOH   (2838 )  A      O     -1.53   60.45  -52.71
5856 HOH   (2840 )  A      O     -2.31   55.06  -53.02
5858 HOH   (4288 )  C      O    -34.90   68.67   28.93
5858 HOH   (4467 )  C      O     63.16   36.03   46.39
5858 HOH   (4631 )  C      O     76.67   23.85   64.09
5858 HOH   (4657 )  C      O     54.64   42.37   33.62
5858 HOH   (4749 )  C      O    -30.20   74.09   33.35
5858 HOH   (4767 )  C      O    -28.68   68.55   28.35
5858 HOH   (4770 )  C      O    -29.50   74.64   31.26
5858 HOH   (4771 )  C      O    -27.19   75.33   39.42
5859 HOH   (4195 )  D      O     40.32    2.62   84.12
5861 HOH   (2943 )  F      O      7.71   28.99   92.97

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.

5856 HOH   (2042 )  A      O
5856 HOH   (2071 )  A      O
5856 HOH   (2075 )  A      O
5856 HOH   (2136 )  A      O
5856 HOH   (2355 )  A      O
5856 HOH   (2372 )  A      O
5856 HOH   (2432 )  A      O
5856 HOH   (2448 )  A      O
5856 HOH   (2490 )  A      O
5856 HOH   (2506 )  A      O
5856 HOH   (2530 )  A      O
5856 HOH   (2540 )  A      O
5856 HOH   (2595 )  A      O
5856 HOH   (2598 )  A      O
5856 HOH   (2599 )  A      O
5856 HOH   (2617 )  A      O
5856 HOH   (2618 )  A      O
5856 HOH   (2664 )  A      O
5856 HOH   (2668 )  A      O
5856 HOH   (2686 )  A      O
5856 HOH   (2721 )  A      O
5856 HOH   (2776 )  A      O
5856 HOH   (2792 )  A      O
5857 HOH   (1978 )  B      O
5857 HOH   (2051 )  B      O
And so on for a total of 136 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.

 266 ASN   ( 266-)  A
 457 ASN   ( 457-)  A
 799 GLN   ( 814-)  A
 927 HIS   ( 942-)  A
 972 ASN   ( 987-)  A
 985 HIS   (1000-)  A
1040 ASN   (1055-)  A
1116 HIS   (1559-)  B
1279 GLN   (1722-)  B
1408 GLN   (1851-)  B
1542 GLN   (2105-)  C
1680 HIS   (2243-)  C
1720 ASN   (2283-)  C
1960 HIS   (2523-)  C
1991 ASN   (2554-)  C
2007 ASN   (2570-)  C
2206 GLN   (2784-)  C
2236 GLN   (2814-)  C
2257 ASN   (2835-)  C
2397 HIS   (2975-)  C
2409 ASN   (2987-)  C
2422 HIS   (3000-)  C
2457 GLN   (3035-)  C
2545 GLN   (3551-)  D
2588 ASN   (3594-)  D
And so on for a total of 51 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 LYS   (   3-)  A      N
   7 ILE   (   7-)  A      N
  32 GLN   (  32-)  A      NE2
  46 ASN   (  46-)  A      ND2
  49 SER   (  49-)  A      OG
  53 THR   (  53-)  A      N
 173 THR   ( 173-)  A      N
 176 GLY   ( 176-)  A      N
 184 ASN   ( 184-)  A      N
 210 LEU   ( 210-)  A      N
 236 ASN   ( 236-)  A      ND2
 241 GLY   ( 241-)  A      N
 244 THR   ( 244-)  A      N
 279 THR   ( 279-)  A      N
 285 GLN   ( 285-)  A      NE2
 340 THR   ( 340-)  A      N
 377 GLN   ( 377-)  A      N
 389 ARG   ( 389-)  A      NE
 390 THR   ( 390-)  A      N
 396 GLN   ( 396-)  A      NE2
 403 GLU   ( 403-)  A      N
 416 ASP   ( 416-)  A      N
 542 TYR   ( 542-)  A      N
 558 ASP   ( 558-)  A      N
 559 ARG   ( 559-)  A      N
And so on for a total of 284 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.

  46 ASN   (  46-)  A      OD1
 236 ASN   ( 236-)  A      OD1
 391 GLN   ( 391-)  A      OE1
 523 HIS   ( 523-)  A      ND1
 548 GLU   ( 548-)  A      OE1
 604 GLU   ( 604-)  A      OE1
 746 GLU   ( 761-)  A      OE2
 981 GLU   ( 996-)  A      OE2
1330 GLN   (1773-)  B      OE1
1483 ASN   (2046-)  C      OD1
1652 GLU   (2215-)  C      OE2
1656 GLU   (2219-)  C      OE2
1720 ASN   (2283-)  C      OD1
1828 GLN   (2391-)  C      OE1
2183 GLU   (2761-)  C      OE2
2491 HIS   (3069-)  C      ND1
2545 GLN   (3551-)  D      OE1
2767 GLN   (3773-)  D      OE1
2920 ASN   (4046-)  E      OD1
3110 ASN   (4236-)  E      OD1
3265 GLN   (4391-)  E      OE1
3397 HIS   (4523-)  E      ND1
3478 GLU   (4604-)  E      OE1
3612 ASP   (4753-)  E      OD1
3620 GLU   (4761-)  E      OE2
4204 GLN   (5773-)  F      OE1
4317 ASP   (6006-)  G    A OD1
4547 ASN   (6236-)  G      OD1
4645 GLU   (6334-)  G      OE2
4702 GLN   (6391-)  G      OE1
5057 GLU   (6761-)  G      OE2
5473 HIS   (7605-)  H      NE2
5641 GLN   (7773-)  H      OE1

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+.

5758   K   (1904-)  A   -.-  -.-  Part of ionic cluster
5761   K   (1912-)  A   -.-  -.-  Part of ionic cluster
5770   K   (1942-)  A   -.-  -.-  Part of ionic cluster
5770   K   (1942-)  A    0.48  -.-   Poor packing
5771   K   (1943-)  A    0.51  -.-   Poor packing
5781   K   (3904-)  C   -.-  -.-  Part of ionic cluster
5784   K   (3912-)  C   -.-  -.-  Part of ionic cluster
5793   K   (3942-)  C   -.-  -.-  Part of ionic cluster
5793   K   (3942-)  C    0.53  -.-   Poor packing
5807   K   (5904-)  E   -.-  -.-  Part of ionic cluster
5810   K   (5912-)  E   -.-  -.-  Part of ionic cluster
5819   K   (5942-)  E   -.-  -.-  Part of ionic cluster
5832   K   (7904-)  G   -.-  -.-  Part of ionic cluster
5835   K   (7912-)  G   -.-  -.-  Part of ionic cluster
5835   K   (7912-)  G    0.53  -.-   Poor packing
5836   K   (7913-)  G     1.77   0.75 Scores about as good as NA
5844   K   (7942-)  G   -.-  -.-  Part of ionic cluster
5845   K   (7943-)  G    0.60  -.-   Poor packing

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.

5856 HOH   (2004 )  A      O  0.83  K  4 *1 and *2
5856 HOH   (2172 )  A      O  0.86  K  4 *1 and *2
5856 HOH   (2194 )  A      O  0.96  K  6 *1 and *2
5856 HOH   (2223 )  A      O  1.18  K  5 *1 and *2
5856 HOH   (2243 )  A      O  1.19  K  4 *1 and *2
5856 HOH   (2248 )  A      O  1.06  K  4 *1 and *2
5856 HOH   (2258 )  A      O  1.09  K  4 *1 and *2 Ion-B
5856 HOH   (2304 )  A      O  1.01  K  4 *1 and *2
5856 HOH   (2344 )  A      O  1.20  K  4 *1 and *2
5856 HOH   (2413 )  A      O  1.05  K  6 *1 and *2 NCS 1/1
5856 HOH   (2643 )  A      O  0.99  K  4 *1 and *2
5856 HOH   (2726 )  A      O  1.14  K  4 *1 and *2 Ion-B
5856 HOH   (2809 )  A      O  1.19  K  4 *1 and *2 ION-B
5856 HOH   (2810 )  A      O  0.80  K  4 *1 and *2 ION-B
5857 HOH   (1966 )  B      O  0.94  K  4 *1 and *2
5857 HOH   (2099 )  B      O  1.03  K  5 *1 and *2
5858 HOH   (4003 )  C      O  0.97  K  4 *1 and *2 NCS 2/2
5858 HOH   (4170 )  C      O  0.95  K  4 *1 and *2 NCS 2/2
5858 HOH   (4192 )  C      O  0.86  K  6 *1 and *2 NCS 2/2
5858 HOH   (4239 )  C      O  0.99  K  5 *1 and *2 NCS 2/2
5858 HOH   (4244 )  C      O  1.11  K  4 *1 and *2 NCS 1/1
5858 HOH   (4297 )  C      O  1.07  K  6 *1 and *2 NCS 2/2
5858 HOH   (4495 )  C      O  1.15  K  4 *1 and *2 Ion-B NCS 2/2
5858 HOH   (4827 )  C      O  0.97  K  5 *1 and *2
5859 HOH   (4103 )  D      O  1.02  K  4 *1 and *2
5860 HOH   (6006 )  E      O  0.86  K  5 *1 and *2 NCS 2/2
5860 HOH   (6246 )  E      O  0.99  K  4 *1 and *2 NCS 2/2
5860 HOH   (6251 )  E      O  0.95 NA  4 NCS 2/2
5860 HOH   (6307 )  E      O  0.80  K  4 *1 and *2 NCS 2/2
5860 HOH   (6346 )  E      O  1.02  K  4 *1 and *2
5860 HOH   (6432 )  E      O  0.89  K  4 *1 and *2
5860 HOH   (6469 )  E      O  0.83  K  6 *1 and *2 Ion-B NCS 2/2
5861 HOH   (2434 )  F      O  0.78  K  6 *1 and *2 NCS 2/2
5861 HOH   (2465 )  F      O  1.03  K  5 *1 and *2 NCS 2/2
5861 HOH   (2682 )  F      O  1.02 NA  4
5862 HOH   (  20 )  G      O  1.01  K  5 *1 and *2 NCS 3/3
5862 HOH   ( 180 )  G      O  1.02  K  5 *1 and *2 NCS 3/3
5862 HOH   ( 186 )  G      O  0.82  K  4 *1 and *2 NCS 3/3
5862 HOH   ( 192 )  G      O  1.10  K  4 *1 and *2 NCS 3/3
5862 HOH   ( 258 )  G      O  0.96  K  4 *1 and *2 Ion-B NCS 1/1
5862 HOH   ( 280 )  G      O  0.99  K  4 *1 and *2 Ion-B NCS 3/3
5862 HOH   ( 312 )  G      O  1.02  K  5 *1 and *2 NCS 2/2
5862 HOH   ( 341 )  G      O  0.98  K  4 *1 and *2 NCS 3/3
5862 HOH   ( 347 )  G      O  1.03  K  4 *1 and *2 NCS 3/3
5862 HOH   ( 627 )  G      O  0.79  K  5 *1 and *2 NCS 1/1
5862 HOH   ( 860 )  G      O  1.11  K  5 *1 and *2 Ion-B NCS 1/1

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.

  25 GLU   (  25-)  A   H-bonding suggests Gln; but Alt-Rotamer
 187 GLU   ( 187-)  A   H-bonding suggests Gln
 219 GLU   ( 219-)  A   H-bonding suggests Gln
 334 GLU   ( 334-)  A   H-bonding suggests Gln; but Alt-Rotamer
 410 ASP   ( 410-)  A   H-bonding suggests Asn; but Alt-Rotamer
 430 ASP   ( 430-)  A   H-bonding suggests Asn
 738 ASP   ( 753-)  A   H-bonding suggests Asn; but Alt-Rotamer
 754 ASP   ( 769-)  A   H-bonding suggests Asn; but Alt-Rotamer
 776 ASP   ( 791-)  A   H-bonding suggests Asn
 792 ASP   ( 807-)  A   H-bonding suggests Asn
1010 ASP   (1025-)  A   H-bonding suggests Asn
1026 ASP   (1041-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1098 GLU   (1541-)  B   H-bonding suggests Gln
1268 ASP   (1711-)  B   H-bonding suggests Asn; but Alt-Rotamer
1771 GLU   (2334-)  C   H-bonding suggests Gln; but Alt-Rotamer
1847 ASP   (2410-)  C   H-bonding suggests Asn; but Alt-Rotamer
1867 ASP   (2430-)  C   H-bonding suggests Asn
2120 GLU   (2683-)  C   H-bonding suggests Gln
2191 ASP   (2769-)  C   H-bonding suggests Asn; but Alt-Rotamer
2213 ASP   (2791-)  C   H-bonding suggests Asn
2446 GLU   (3024-)  C   H-bonding suggests Gln; but Alt-Rotamer
2447 ASP   (3025-)  C   H-bonding suggests Asn
2463 ASP   (3041-)  C   H-bonding suggests Asn; but Alt-Rotamer
2535 GLU   (3541-)  D   H-bonding suggests Gln; but Alt-Rotamer
2606 ASP   (3612-)  D   H-bonding suggests Asn
2705 ASP   (3711-)  D   H-bonding suggests Asn; but Alt-Rotamer
3208 GLU   (4334-)  E   H-bonding suggests Gln; but Alt-Rotamer
3304 ASP   (4430-)  E   H-bonding suggests Asn; but Alt-Rotamer
3392 ASP   (4518-)  E   H-bonding suggests Asn; but Alt-Rotamer
3628 ASP   (4769-)  E   H-bonding suggests Asn; but Alt-Rotamer
3650 ASP   (4791-)  E   H-bonding suggests Asn
3883 GLU   (5024-)  E   H-bonding suggests Gln; but Alt-Rotamer
3972 GLU   (5541-)  F   H-bonding suggests Gln; but Alt-Rotamer
4043 ASP   (5612-)  F   H-bonding suggests Asn
4142 ASP   (5711-)  F   H-bonding suggests Asn
4498 GLU   (6187-)  G   H-bonding suggests Gln; but Alt-Rotamer
4557 ASP   (6246-)  G   H-bonding suggests Asn
4645 GLU   (6334-)  G   H-bonding suggests Gln; but Alt-Rotamer
4741 ASP   (6430-)  G   H-bonding suggests Asn; but Alt-Rotamer
4829 ASP   (6518-)  G   H-bonding suggests Asn; but Alt-Rotamer
5065 ASP   (6769-)  G   H-bonding suggests Asn; but Alt-Rotamer
5087 ASP   (6791-)  G   H-bonding suggests Asn
5103 ASP   (6807-)  G   H-bonding suggests Asn
5321 ASP   (7025-)  G   H-bonding suggests Asn
5409 GLU   (7541-)  H   H-bonding suggests Gln; but Alt-Rotamer
5464 GLU   (7596-)  H   H-bonding suggests Gln
5480 ASP   (7612-)  H   H-bonding suggests Asn
5579 ASP   (7711-)  H   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.195
  2nd generation packing quality :  -1.216
  Ramachandran plot appearance   :  -1.281
  chi-1/chi-2 rotamer normality  :  -3.976 (poor)
  Backbone conformation          :   0.173

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.928
  Bond angles                    :   1.382
  Omega angle restraints         :   0.339 (tight)
  Side chain planarity           :   1.114
  Improper dihedral distribution :   1.505 (loose)
  B-factor distribution          :   3.870 (loose)
  Inside/Outside distribution    :   1.013

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -3.4 (poor)
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.928
  Bond angles                    :   1.382
  Omega angle restraints         :   0.339 (tight)
  Side chain planarity           :   1.114
  Improper dihedral distribution :   1.505 (loose)
  B-factor distribution          :   3.870 (loose)
  Inside/Outside distribution    :   1.013
==============

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.