WHAT IF Check report

This file was created 2011-12-16 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 pdb1jdb.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: B and E

All-atom RMS fit for the two chains : 0.512
CA-only RMS fit for the two chains : 0.293

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 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: B and H

All-atom RMS fit for the two chains : 0.470
CA-only RMS fit for the two chains : 0.305

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 H

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: C and F

All-atom RMS fit for the two chains : 0.452
CA-only RMS fit for the two chains : 0.237

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: C and F

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: C and I

All-atom RMS fit for the two chains : 0.473
CA-only RMS fit for the two chains : 0.226

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: C and I

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: C and L

All-atom RMS fit for the two chains : 0.429
CA-only RMS fit for the two chains : 0.211

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: C and L

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.

5776 ADP   (1093-)  B  -
5777 ADP   (1094-)  B  -
5778 ORN   (1095-)  B  -
5779 NET   (1096-)  B  -
5804 ADP   (1095-)  E  -
5805 ADP   (1096-)  E  -
5806 ORN   (1097-)  E  -
5807 NET   (1098-)  E  -
5829 ADP   (1092-)  H  -
5830 ADP   (1093-)  H  -
5831 ORN   (1094-)  H  -
5832 NET   (1095-)  H  -
5857 ADP   (1095-)  K  -
5861 NET   (1098-)  K  -
5862 ORN   (1097-)  K  -
5863 ADP   (1096-)  K  -

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: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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) :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 : 4.439 over 35519 bonds
Average difference in B over a bond : 10.77
RMS difference in B over a bond : 15.33

Note: B-factor plot

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

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Nomenclature related problems

Error: Chain names not unique

The chain names listed below are given for more than one protein/DNA molecule in the structure ('-' represents a chain without chain identifier).

Chain identifier(s): B, E, H, K

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.

 110 GLU   ( 109-)  B      CD   OE1   1.33    4.0
 207 ASP   ( 206-)  B      CG   OD1   1.33    4.4
 208 GLU   ( 207-)  B      CD   OE1   1.34    4.6
 217 GLU   ( 216-)  B      CD   OE2   1.34    5.0
 238 ASP   ( 237-)  B      CG   OD2   1.34    4.6
 430 ASP   ( 429-)  B      CG   OD1   1.33    4.2
 512 GLU   ( 511-)  B      CD   OE1   1.33    4.4
 577 GLU   ( 576-)  B      CD   OE1   1.33    4.3
 592 ASP   ( 591-)  B      CG   OD1   1.33    4.1
 674 ASP   ( 673-)  B      CG   OD1   1.35    5.1
 683 GLU   ( 682-)  B      CD   OE1   1.34    4.8
 939 GLU   ( 954-)  B      CD   OE1   1.33    4.0
 980 GLU   ( 995-)  B      CD   OE2   1.33    4.3
 987 ASP   (1002-)  B      CG   OD1   1.33    4.0
 993 GLU   (1008-)  B      CD   OE1   1.33    4.2
1041 ASP   (1056-)  B      CG   OD1   1.33    4.4
1168 ASP   ( 112-)  C      CG   OD1   1.33    4.0
1290 ASP   ( 234-)  C      CG   OD2   1.33    4.1
1373 ASP   ( 317-)  C      CG   OD1   1.33    4.1
1424 ASP   ( 368-)  C      CG   OD1   1.33    4.1
1493 ASP   (  56-)  E      CG   OD1   1.33    4.4
1622 GLU   ( 185-)  E      CD   OE2   1.33    4.1
1651 GLU   ( 214-)  E      CD   OE1   1.33    4.3
1653 GLU   ( 216-)  E      CD   OE2   1.33    4.2
1655 GLU   ( 218-)  E      CD   OE1   1.34    4.6
And so on for a total of 90 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

 |  1.000960  0.000074  0.000022|
 |  0.000074  0.999374  0.000058|
 |  0.000022  0.000058  0.999876|
Proposed new scale matrix

 |  0.006947  0.000000  0.000000|
 |  0.000000  0.005967  0.000000|
 |  0.000000  0.000000  0.003096|
With corresponding cell

    A    = 143.940  B   = 167.596  C    = 322.957
    Alpha=  90.003  Beta=  90.003  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 143.800  B   = 167.700  C    = 323.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 33.507
(Under-)estimated Z-score: 4.266

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.

   9 SER   (   8-)  B      N    CA   CB  117.64    4.2
  26 PHE   (  25-)  B      CA   CB   CG  107.56   -6.2
  38 ARG   (  37-)  B      CG   CD   NE  117.77    4.3
  38 ARG   (  37-)  B      CD   NE   CZ  128.93    4.0
  43 ARG   (  42-)  B      CG   CD   NE  117.52    4.1
  65 TYR   (  64-)  B      CA   CB   CG  105.88   -4.1
  66 ILE   (  65-)  B      N    CA   CB  117.63    4.2
  68 PRO   (  67-)  B      N    CA   CB  107.64    4.2
  83 PRO   (  82-)  B      N    CA   CB  107.81    4.4
  84 ASP   (  83-)  B      CA   CB   CG  107.03   -5.6
  88 PRO   (  87-)  B      C    CA   CB  100.26   -5.2
  91 GLY   (  90-)  B     -C    N    CA  113.18   -4.4
  93 GLN   (  92-)  B      CB   CG   CD  104.93   -4.5
 101 GLU   ( 100-)  B      CB   CG   CD  119.75    4.2
 118 ALA   ( 117-)  B      N    CA   CB  118.24    5.2
 129 ARG   ( 128-)  B      N    CA   CB  117.59    4.2
 141 LEU   ( 140-)  B      N    CA   CB  117.63    4.2
 144 ALA   ( 143-)  B     -C    N    CA  112.89   -4.9
 161 ASP   ( 160-)  B      CA   CB   CG  118.40    5.8
 182 ALA   ( 181-)  B     -C    N    CA  112.71   -5.0
 188 PHE   ( 187-)  B      N    CA   CB  117.43    4.1
 188 PHE   ( 187-)  B      CA   CB   CG  119.60    5.8
 204 LEU   ( 203-)  B      C    CA   CB  101.23   -4.7
 207 ASP   ( 206-)  B      C    CA   CB  101.46   -4.5
 207 ASP   ( 206-)  B      CA   CB   CG  120.10    7.5
And so on for a total of 762 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.

   9 SER   (   8-)  B      CA    -6.0    23.09    34.32
  88 PRO   (  87-)  B      CA     6.0    46.67    38.15
 118 ALA   ( 117-)  B      CA    -6.2    26.23    34.09
 172 PHE   ( 171-)  B      CA    -6.5    23.54    33.98
 303 ARG   ( 302-)  B      CA     6.4    44.48    33.91
 339 ILE   ( 338-)  B      CA    -8.6    20.29    33.24
 433 ALA   ( 432-)  B      CA     8.6    44.95    34.09
 534 ALA   ( 533-)  B      CA    -6.2    26.27    34.09
 653 ALA   ( 652-)  B      CA    -7.7    24.29    34.09
 721 TYR   ( 728-)  B      CA    -8.4    20.81    34.03
 865 LYS   ( 880-)  B      CA    -6.0    23.92    33.92
 957 ALA   ( 972-)  B      CA    -7.1    25.03    34.09
1061 ALA   (   5-)  C      CA    -6.2    26.22    34.09
1066 GLU   (  10-)  C      CA     6.5    44.68    33.96
1092 MET   (  36-)  C      CA    -7.3    21.06    34.17
1279 THR   ( 223-)  C      CA    -6.0    23.74    33.84
1344 PHE   ( 288-)  C      CA    -6.1    24.20    33.98
1382 ARG   ( 326-)  C      CA    -6.4    23.49    33.91
1462 PHE   (  25-)  E      CA    -6.1    24.28    33.98
1575 ILE   ( 138-)  E      CA    -7.6    21.77    33.24
1775 ILE   ( 338-)  E      CA   -19.9     3.20    33.24
1804 ALA   ( 367-)  E      CA   -10.8    20.37    34.09
1970 ALA   ( 533-)  E      CA    -8.4    23.44    34.09
2112 GLU   ( 675-)  E      CA    -7.2    22.11    33.96
2304 ILE   ( 883-)  E      CA    -6.4    23.53    33.24
And so on for a total of 77 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.

3058 ARG   ( 184-)  H    9.02
1775 ILE   ( 338-)  E    8.13
5007 ILE   ( 697-)  K    7.41
4648 ILE   ( 338-)  K    7.20
 339 ILE   ( 338-)  B    7.11
3212 ILE   ( 338-)  H    6.93
5747 LYS   ( 379-)  L    6.85
1892 THR   ( 455-)  E    6.83
3060 GLU   ( 186-)  H    6.82
4765 THR   ( 455-)  K    6.39
3329 THR   ( 455-)  H    5.94
2213 ALA   ( 792-)  E    5.86
2545 VAL   (  53-)  F    5.85
3192 ILE   ( 318-)  H    5.54
3485 THR   ( 611-)  H    5.46
4144 ARG   ( 215-)  I    5.45
2087 ALA   ( 650-)  E    5.38
 959 HIS   ( 974-)  B    5.28
 543 MET   ( 542-)  B    5.16
4647 ASP   ( 337-)  K    5.15
 651 ALA   ( 650-)  B    5.13
5157 LEU   ( 860-)  K    5.12
3933 SER   (   4-)  I    5.12
5083 VAL   ( 786-)  K    5.11
4852 MET   ( 542-)  K    5.09
And so on for a total of 91 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 : 1.596

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.

1397 HIS   ( 341-)  C    6.10

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.

1524 PRO   (  87-)  E    -3.0
5040 PHE   ( 737-)  K    -3.0
2838 PRO   ( 346-)  F    -3.0
2961 PRO   (  87-)  H    -3.0
4397 PRO   (  87-)  K    -3.0
  88 PRO   (  87-)  B    -2.9
1811 THR   ( 374-)  E    -2.8
3979 ARG   (  50-)  I    -2.8
3832 HIS   ( 974-)  H    -2.8
3519 THR   ( 645-)  H    -2.8
4684 THR   ( 374-)  K    -2.8
5708 ILE   ( 340-)  L    -2.7
5271 HIS   ( 974-)  K    -2.7
3743 PRO   ( 885-)  H    -2.7
4511 LYS   ( 201-)  K    -2.7
2082 THR   ( 645-)  E    -2.7
5418 ARG   (  50-)  L    -2.7
 935 GLU   ( 950-)  B    -2.6
2761 CYS   ( 269-)  F    -2.6
 375 THR   ( 374-)  B    -2.6
5725 SER   ( 357-)  L    -2.6
 959 HIS   ( 974-)  B    -2.6
2542 ARG   (  50-)  F    -2.6
  46 LEU   (  45-)  B    -2.6
2457 LYS   (1036-)  E    -2.6
And so on for a total of 207 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   (  22-)  B  Poor phi/psi
 164 PHE   ( 163-)  B  PRO omega poor
 172 PHE   ( 171-)  B  Poor phi/psi
 226 ASP   ( 225-)  B  Poor phi/psi
 251 ALA   ( 250-)  B  PRO omega poor
 276 GLY   ( 275-)  B  Poor phi/psi
 302 PRO   ( 301-)  B  Poor phi/psi
 375 THR   ( 374-)  B  Poor phi/psi
 403 GLU   ( 402-)  B  Poor phi/psi
 409 PHE   ( 408-)  B  Poor phi/psi
 457 ASN   ( 456-)  B  Poor phi/psi
 530 ASP   ( 529-)  B  Poor phi/psi
 531 THR   ( 530-)  B  Poor phi/psi
 533 ALA   ( 532-)  B  Poor phi/psi
 534 ALA   ( 533-)  B  Poor phi/psi
 686 LYS   ( 685-)  B  Poor phi/psi
 710 TYR   ( 709-)  B  PRO omega poor
 780 LEU   ( 795-)  B  PRO omega poor
 784 THR   ( 799-)  B  Poor phi/psi
 805 GLN   ( 820-)  B  Poor phi/psi
 825 GLU   ( 840-)  B  Poor phi/psi
 828 PRO   ( 843-)  B  Poor phi/psi
 889 PRO   ( 904-)  B  Poor phi/psi
 920 ASN   ( 935-)  B  Poor phi/psi
 959 HIS   ( 974-)  B  Poor phi/psi
And so on for a total of 161 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 : -4.129

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.

4577 SER   ( 267-)  K    0.35
3185 SER   ( 311-)  H    0.35
5467 SER   (  99-)  L    0.36
1156 SER   ( 100-)  C    0.36
 268 SER   ( 267-)  B    0.36
  29 SER   (  28-)  B    0.36
 586 SER   ( 585-)  B    0.36
3141 SER   ( 267-)  H    0.37
1704 SER   ( 267-)  E    0.37
4703 SER   ( 393-)  K    0.37
4029 SER   ( 100-)  I    0.38
5150 SER   ( 853-)  K    0.38
3711 SER   ( 853-)  H    0.38
1155 SER   (  99-)  C    0.39
2022 SER   ( 585-)  E    0.40
2274 SER   ( 853-)  E    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   (   2-)  B      0
   7 ILE   (   6-)  B      0
  17 PRO   (  16-)  B      0
  20 ILE   (  19-)  B      0
  22 GLN   (  21-)  B      0
  23 ALA   (  22-)  B      0
  24 CYS   (  23-)  B      0
  40 GLU   (  39-)  B      0
  49 SER   (  48-)  B      0
  52 ALA   (  51-)  B      0
  60 MET   (  59-)  B      0
  62 ASP   (  61-)  B      0
  63 ALA   (  62-)  B      0
  69 ILE   (  68-)  B      0
  81 GLU   (  80-)  B      0
  82 ARG   (  81-)  B      0
  83 PRO   (  82-)  B      0
  89 THR   (  88-)  B      0
  90 MET   (  89-)  B      0
  93 GLN   (  92-)  B      0
 105 GLN   ( 104-)  B      0
 107 VAL   ( 106-)  B      0
 116 ILE   ( 115-)  B      0
 127 GLU   ( 126-)  B      0
 129 ARG   ( 128-)  B      0
And so on for a total of 2004 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 : 1.644

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!

3440 GLY   ( 566-)  H   3.28   31
 567 GLY   ( 566-)  B   3.26   22
4876 GLY   ( 566-)  K   3.20   35
2003 GLY   ( 566-)  E   3.12   24
 666 PRO   ( 665-)  B   1.53   11

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...

  23 ALA   (  22-)  B   1.69

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   (   1-)  B    0.16 LOW
  17 PRO   (  16-)  B    0.19 LOW
  58 PRO   (  57-)  B    0.06 LOW
  68 PRO   (  67-)  B    0.12 LOW
  83 PRO   (  82-)  B    0.14 LOW
 165 PRO   ( 164-)  B    0.03 LOW
 170 PRO   ( 169-)  B    0.10 LOW
 290 PRO   ( 289-)  B    0.12 LOW
 345 PRO   ( 344-)  B    0.16 LOW
 411 PRO   ( 410-)  B    0.09 LOW
 418 PRO   ( 417-)  B    0.07 LOW
 555 PRO   ( 554-)  B    0.19 LOW
 620 PRO   ( 619-)  B    0.18 LOW
 647 PRO   ( 646-)  B    0.07 LOW
 690 PRO   ( 689-)  B    0.11 LOW
 711 PRO   ( 710-)  B    0.14 LOW
 781 PRO   ( 796-)  B    0.02 LOW
 844 PRO   ( 859-)  B    0.06 LOW
 869 PRO   ( 884-)  B    0.07 LOW
 885 PRO   ( 900-)  B    0.10 LOW
 889 PRO   ( 904-)  B    0.13 LOW
 972 PRO   ( 987-)  B    0.15 LOW
 983 PRO   ( 998-)  B    0.13 LOW
1102 PRO   (  46-)  C    0.18 LOW
1142 PRO   (  86-)  C    0.19 LOW
And so on for a total of 140 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].

  51 PRO   (  50-)  B   -65.9 envelop C-beta (-72 degrees)
  88 PRO   (  87-)  B   -63.3 envelop C-beta (-72 degrees)
 200 PRO   ( 199-)  B   110.3 envelop C-beta (108 degrees)
 302 PRO   ( 301-)  B   -60.6 half-chair C-beta/C-alpha (-54 degrees)
 318 PRO   ( 317-)  B   -22.9 half-chair C-alpha/N (-18 degrees)
 360 PRO   ( 359-)  B     7.0 envelop N (0 degrees)
 635 PRO   ( 634-)  B   -41.2 envelop C-alpha (-36 degrees)
 666 PRO   ( 665-)  B   105.1 envelop C-beta (108 degrees)
 828 PRO   ( 843-)  B    -1.2 envelop N (0 degrees)
1276 PRO   ( 220-)  C  -166.4 half-chair N/C-delta (-162 degrees)
1414 PRO   ( 358-)  C   -31.1 envelop C-alpha (-36 degrees)
1438 PRO   (   1-)  E  -120.0 half-chair C-delta/C-gamma (-126 degrees)
1453 PRO   (  16-)  E   -51.9 half-chair C-beta/C-alpha (-54 degrees)
1524 PRO   (  87-)  E   -48.0 half-chair C-beta/C-alpha (-54 degrees)
1738 PRO   ( 301-)  E   -51.7 half-chair C-beta/C-alpha (-54 degrees)
1754 PRO   ( 317-)  E   -55.3 half-chair C-beta/C-alpha (-54 degrees)
1796 PRO   ( 359-)  E    20.2 half-chair N/C-delta (18 degrees)
2096 PRO   ( 659-)  E   -53.2 half-chair C-beta/C-alpha (-54 degrees)
2102 PRO   ( 665-)  E   107.8 envelop C-beta (108 degrees)
2147 PRO   ( 710-)  E    -8.8 envelop N (0 degrees)
2264 PRO   ( 843-)  E   -40.4 envelop C-alpha (-36 degrees)
2280 PRO   ( 859-)  E   -65.0 envelop C-beta (-72 degrees)
2316 PRO   ( 895-)  E   -62.9 half-chair C-beta/C-alpha (-54 degrees)
2850 PRO   ( 358-)  F   -41.3 envelop C-alpha (-36 degrees)
2875 PRO   (   1-)  H   -36.2 envelop C-alpha (-36 degrees)
And so on for a total of 56 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.

   1 MET   (   0-)  B      N   <->  224 LYS   ( 223-)  B      NZ     0.57    2.28  INTRA BF
2395 HIS   ( 974-)  E      ND1 <-> 3832 HIS   ( 974-)  H      ND1    0.50    2.50  INTRA BL
5107 GLN   ( 810-)  K    A NE2 <-> 5111 LYS   ( 814-)  K      NZ     0.49    2.36  INTRA BF
2424 ARG   (1003-)  E      NE  <-> 5866 HOH   (2092 )  E      O      0.45    2.25  INTRA BF
 723 GLU   ( 730-)  B      OE2 <->  727 ARG   ( 734-)  B      NH2    0.45    2.25  INTRA BF
5446 GLN   (  78-)  L      NE2 <-> 5871 HOH   (4658 )  L      O      0.43    2.27  INTRA BL
4533 LYS   ( 223-)  K      NZ  <-> 5870 HOH   (1138 )  K      O      0.42    2.28  INTRA BF
3801 ARG   ( 943-)  H      NE  <-> 5868 HOH   (1759 )  H      O      0.42    2.28  INTRA BF
1917 ILE   ( 480-)  E      N   <-> 5866 HOH   (1714 )  E      O      0.42    2.28  INTRA
 343 ARG   ( 342-)  B      NH2 <->  539 ASP   ( 538-)  B      OD2    0.41    2.29  INTRA BF
1479 ARG   (  42-)  E      NH1 <-> 5866 HOH   (2039 )  E      O      0.41    2.29  INTRA
5106 ARG   ( 809-)  K      NH2 <-> 5870 HOH   (1952 )  K      O      0.41    2.29  INTRA
5018 GLY   ( 708-)  K      O   <-> 5050 HIS   ( 753-)  K      ND1    0.41    2.29  INTRA BF
3299 ARG   ( 425-)  H      NE  <-> 5868 HOH   (1538 )  H      O      0.41    2.29  INTRA
1566 ARG   ( 129-)  E    A NH2 <-> 5866 HOH   (1375 )  E      O      0.41    2.29  INTRA
2790 LYS   ( 298-)  F      NZ  <-> 2795 ASN   ( 303-)  F      OD1    0.41    2.29  INTRA BF
4144 ARG   ( 215-)  I      NH1 <-> 5869 HOH   (3589 )  I      O      0.41    2.29  INTRA BF
 130 ARG   ( 129-)  B    A NH1 <-> 5864 HOH   (1258 )  B      O      0.41    2.29  INTRA
 959 HIS   ( 974-)  B      ND1 <-> 5271 HIS   ( 974-)  K      ND1    0.41    2.59  INTRA BL
5289 LYS   ( 992-)  K      NZ  <-> 5854 PO4   (1082-)  K      O1     0.41    2.29  INTRA BL
 988 ARG   (1003-)  B      NE  <-> 5864 HOH   (1806 )  B      O      0.41    2.29  INTRA BL
1963 LYS   ( 526-)  E      NZ  <-> 1986 GLU   ( 549-)  E      O      0.41    2.29  INTRA
1278 GLN   ( 222-)  C      NE2 <-> 5865 HOH   ( 508 )  C      O      0.41    2.29  INTRA BF
3811 LYS   ( 953-)  H      NZ  <-> 5827 PO4   (1082-)  H      O4     0.41    2.29  INTRA
 886 GLY   ( 901-)  B      O   <-> 1011 ARG   (1026-)  B      NH2    0.40    2.30  INTRA BF
And so on for a total of 1547 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: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

 343 ARG   ( 342-)  B      -7.72
5294 ARG   ( 997-)  K      -7.55
3216 ARG   ( 342-)  H      -7.51
4652 ARG   ( 342-)  K      -7.43
1779 ARG   ( 342-)  E      -7.41
2418 ARG   ( 997-)  E      -7.15
3855 ARG   ( 997-)  H      -7.05
 982 ARG   ( 997-)  B      -6.74
4492 TYR   ( 182-)  K      -6.56
5218 ARG   ( 921-)  K      -6.37
 183 TYR   ( 182-)  B      -6.36
 174 MET   ( 173-)  B      -6.31
3056 TYR   ( 182-)  H      -6.27
2415 HIS   ( 994-)  E      -6.26
2342 ARG   ( 921-)  E      -6.25
3779 ARG   ( 921-)  H      -6.21
1619 TYR   ( 182-)  E      -6.08
1610 MET   ( 173-)  E      -6.03
 906 ARG   ( 921-)  B      -6.01
4483 MET   ( 173-)  K      -5.89
5180 ILE   ( 883-)  K      -5.87
3047 MET   ( 173-)  H      -5.83
 868 ILE   ( 883-)  B      -5.82
3741 ILE   ( 883-)  H      -5.81
2528 MET   (  36-)  F      -5.78
And so on for a total of 69 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: 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: 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: H

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: I

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: K

Note: Quality value plot

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

Chain identifier: L

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.

3071 LEU   ( 197-)  H   -2.94
4548 ALA   ( 238-)  K   -2.90
  23 ALA   (  22-)  B   -2.85
2934 ALA   (  60-)  H   -2.84
4507 LEU   ( 197-)  K   -2.81
4714 GLY   ( 404-)  K   -2.81
4332 ALA   (  22-)  K   -2.80
 239 ALA   ( 238-)  B   -2.80
2896 ALA   (  22-)  H   -2.80
 877 VAL   ( 892-)  B   -2.73
3750 VAL   ( 892-)  H   -2.69
2493 LYS   (1072-)  E   -2.67
5189 VAL   ( 892-)  K   -2.67
2313 VAL   ( 892-)  E   -2.67
2414 VAL   ( 993-)  E   -2.61
 883 LYS   ( 898-)  B   -2.60
 303 ARG   ( 302-)  B   -2.58
1208 GLY   ( 152-)  C   -2.57
5206 GLU   ( 909-)  K   -2.56
3917 GLU   (1059-)  H   -2.55
1044 GLU   (1059-)  B   -2.51
4081 GLY   ( 152-)  I   -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   ( 574-)  B     -  578 PHE   ( 577-)  B        -1.78
1141 LEU   (  85-)  C     - 1144 ILE   (  88-)  C        -1.88
2011 GLY   ( 574-)  E     - 2014 PHE   ( 577-)  E        -1.80
2577 LEU   (  85-)  F     - 2580 ILE   (  88-)  F        -1.52
3276 GLU   ( 402-)  H     - 3279 ALA   ( 405-)  H        -1.63
3749 GLU   ( 891-)  H     - 3752 LEU   ( 894-)  H        -1.85
4884 GLY   ( 574-)  K     - 4887 PHE   ( 577-)  K        -1.84
5188 GLU   ( 891-)  K     - 5191 LEU   ( 894-)  K        -1.88

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: B

Note: Second generation quality Z-score plot

Chain identifier: C

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: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

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.

5864 HOH   (1213 )  B      O     -2.29   56.68   64.54
5864 HOH   (1959 )  B      O      2.68   52.10   55.81
5864 HOH   (2025 )  B      O     80.61   53.56   59.24
5864 HOH   (2026 )  B      O     81.36   55.50   60.17
5864 HOH   (2034 )  B      O     77.79   56.47   58.12
5864 HOH   (2057 )  B      O     80.76   55.57   63.26
5866 HOH   (1330 )  E      O     81.35  -14.32   76.17
5866 HOH   (1331 )  E      O     33.35   85.25  -75.86
5866 HOH   (1333 )  E      O     35.71   93.25  -67.54
5866 HOH   (1336 )  E      O     35.26   91.09  -70.91
5866 HOH   (1363 )  E      O     70.67  -18.07   86.27
5866 HOH   (1374 )  E      O     75.42  -20.77   85.18
5866 HOH   (1580 )  E      O     40.73  123.42  -61.26
5866 HOH   (2183 )  E      O     93.00   69.47  -82.55
5866 HOH   (2194 )  E      O     92.88   67.14  -81.73
5866 HOH   (2218 )  E      O     48.26  137.26  -64.21
5866 HOH   (2261 )  E      O     48.02   91.53  -77.96
5866 HOH   (2303 )  E      O     46.73   98.68  -75.66
5866 HOH   (2327 )  E      O     74.99  -27.10   73.85
5866 HOH   (2332 )  E      O     69.56  -24.54   86.40
5866 HOH   (2344 )  E      O     10.51   26.33  -54.80
5866 HOH   (2435 )  E      O     69.07  -21.07   88.00
5866 HOH   (2448 )  E      O     68.21  -22.89   85.88
5868 HOH   (1959 )  H      O     59.31  -28.21    0.47
5868 HOH   (1966 )  H      O     66.25  -46.13   29.81
5868 HOH   (1967 )  H      O     67.46  -36.10   15.77
5868 HOH   (2019 )  H      O     70.29    9.51  122.36
5868 HOH   (2020 )  H      O     70.11   11.55  125.13
5870 HOH   (1830 )  K      O     20.43   65.75  -55.38
5870 HOH   (2009 )  K      O     16.77   73.13  -39.17
5870 HOH   (2071 )  K      O     31.16   93.94  -12.39

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.

5864 HOH   (1175 )  B      O
5864 HOH   (1232 )  B      O
5864 HOH   (1436 )  B      O
5864 HOH   (1445 )  B      O
5864 HOH   (1537 )  B      O
5864 HOH   (1622 )  B      O
5864 HOH   (1761 )  B      O
5864 HOH   (1776 )  B      O
5864 HOH   (1796 )  B      O
5864 HOH   (1807 )  B      O
5864 HOH   (1862 )  B      O
5864 HOH   (1885 )  B      O
5864 HOH   (1938 )  B      O
5864 HOH   (1943 )  B      O
5864 HOH   (1950 )  B      O
5864 HOH   (1958 )  B      O
5864 HOH   (1981 )  B      O
5864 HOH   (1987 )  B      O
5864 HOH   (1993 )  B      O
5864 HOH   (1995 )  B      O
5864 HOH   (2006 )  B      O
5864 HOH   (2027 )  B      O
5864 HOH   (2029 )  B      O
5864 HOH   (2030 )  B      O
5864 HOH   (2032 )  B      O
And so on for a total of 137 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.

 243 HIS   ( 242-)  B
 768 GLN   ( 783-)  B
 772 HIS   ( 787-)  B
 971 ASN   ( 986-)  B
 984 HIS   ( 999-)  B
1019 GLN   (1034-)  B
1055 GLN   (1070-)  B
1162 ASN   ( 106-)  C
1260 ASN   ( 204-)  C
1329 GLN   ( 273-)  C
1385 HIS   ( 329-)  C
1407 GLN   ( 351-)  C
1541 GLN   ( 104-)  E
1679 HIS   ( 242-)  E
2115 GLN   ( 678-)  E
2204 GLN   ( 783-)  E
2407 ASN   ( 986-)  E
2420 HIS   ( 999-)  E
2816 ASN   ( 324-)  F
2843 GLN   ( 351-)  F
2978 GLN   ( 104-)  H
3023 HIS   ( 149-)  H
3139 ASN   ( 265-)  H
3641 GLN   ( 783-)  H
3645 HIS   ( 787-)  H
3793 ASN   ( 935-)  H
3824 GLN   ( 966-)  H
3892 GLN   (1034-)  H
3980 GLN   (  51-)  I
4034 HIS   ( 105-)  I
4224 HIS   ( 295-)  I
4414 GLN   ( 104-)  K
4575 ASN   ( 265-)  K
4954 GLN   ( 644-)  K
5080 GLN   ( 783-)  K
5228 GLN   ( 931-)  K
5263 GLN   ( 966-)  K
5296 HIS   ( 999-)  K
5298 GLN   (1001-)  K
5692 ASN   ( 324-)  L
5719 GLN   ( 351-)  L

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.

  16 GLY   (  15-)  B      N
  49 SER   (  48-)  B      OG
 130 ARG   ( 129-)  B    A NE
 131 ARG   ( 130-)  B      NE
 151 THR   ( 150-)  B      N
 173 THR   ( 172-)  B      N
 176 GLY   ( 175-)  B      N
 184 ASN   ( 183-)  B      N
 210 LEU   ( 209-)  B      N
 233 SER   ( 232-)  B      OG
 236 ASN   ( 235-)  B      ND2
 241 GLY   ( 240-)  B      N
 244 THR   ( 243-)  B      N
 249 THR   ( 248-)  B      OG1
 340 THR   ( 339-)  B      OG1
 344 THR   ( 343-)  B      N
 354 TYR   ( 353-)  B      N
 377 GLN   ( 376-)  B      N
 389 ARG   ( 388-)  B      NE
 390 THR   ( 389-)  B      N
 396 GLN   ( 395-)  B      NE2
 501 ARG   ( 500-)  B      N
 547 TYR   ( 546-)  B      OH
 602 ASN   ( 601-)  B      N
 696 THR   ( 695-)  B      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.

 150 HIS   ( 149-)  B      ND1
 391 GLN   ( 390-)  B      OE1
 523 HIS   ( 522-)  B      ND1
 745 GLU   ( 760-)  B      OE2
1409 HIS   ( 353-)  C      NE2
1672 ASN   ( 235-)  E      OD1
1827 GLN   ( 390-)  E      OE1
2109 GLU   ( 672-)  E      OE2
2181 GLU   ( 760-)  E      OE1
2181 GLU   ( 760-)  E      OE2
2201 HIS   ( 780-)  E      ND1
2459 HIS   (1038-)  E      NE2
2845 HIS   ( 353-)  F      NE2
3109 ASN   ( 235-)  H      OD1
3264 GLN   ( 390-)  H      OE1
3396 HIS   ( 522-)  H      NE2
3618 GLU   ( 760-)  H      OE2
3896 HIS   (1038-)  H      NE2
4219 HIS   ( 290-)  I      ND1
4280 GLN   ( 351-)  I      OE1
4341 GLN   (  31-)  K      OE1
4524 GLU   ( 214-)  K      OE2
4545 ASN   ( 235-)  K      OD1
4700 GLN   ( 390-)  K      OE1
4832 HIS   ( 522-)  K      NE2
4869 GLU   ( 559-)  K      OE1
4982 GLU   ( 672-)  K      OE1
5057 GLU   ( 760-)  K      OE1
5057 GLU   ( 760-)  K      OE2
5139 ASN   ( 842-)  K      OD1
5206 GLU   ( 909-)  K      OE2
5721 HIS   ( 353-)  L      NE2

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+.

5757  MN   (1073-)  B   -.-  -.-  Part of ionic cluster
5758  MN   (1074-)  B   -.-  -.-  Part of ionic cluster
5760   K   (1076-)  B   -.-  -.-  Part of ionic cluster
5761   K   (1077-)  B   -.-  -.-  Part of ionic cluster
5761   K   (1077-)  B   -.-  -.-  Too few ligands (3)
5762  MN   (1079-)  B   -.-  -.-  Part of ionic cluster
5763  MN   (1080-)  B   -.-  -.-  Part of ionic cluster
5767   K   (1084-)  B   -.-  -.-  Too few ligands (3)
5782  MN   (1073-)  E   -.-  -.-  Part of ionic cluster
5783  MN   (1074-)  E   -.-  -.-  Part of ionic cluster
5785   K   (1076-)  E   -.-  -.-  Part of ionic cluster
5786   K   (1077-)  E   -.-  -.-  Part of ionic cluster
5788  MN   (1079-)  E   -.-  -.-  Part of ionic cluster
5789  MN   (1080-)  E   -.-  -.-  Part of ionic cluster
5792   K   (1083-)  E   -.-  -.-  Too few ligands (3)
5794   K   (1085-)  E   -.-  -.-  Part of ionic cluster
5794   K   (1085-)  E   -.-  -.-  Too few ligands (3)
5808   K   ( 383-)  F   -.-  -.-  Too few ligands (3)
5810  MN   (1073-)  H   -.-  -.-  Part of ionic cluster
5811  MN   (1074-)  H   -.-  -.-  Part of ionic cluster
5813   K   (1076-)  H   -.-  -.-  Part of ionic cluster
5814   K   (1077-)  H   -.-  -.-  Part of ionic cluster
5814   K   (1077-)  H   -.-  -.-  Too few ligands (3)
5816  MN   (1079-)  H   -.-  -.-  Part of ionic cluster
5817  MN   (1080-)  H   -.-  -.-  Part of ionic cluster
5817  MN   (1080-)  H   -.-  -.-  Too few ligands (3)
5818   K   (1081-)  H     1.79   0.74 Scores about as good as NA
5820   K   (1083-)  H   -.-  -.-  Too few ligands (3)
5835  MN   (1073-)  K   -.-  -.-  Part of ionic cluster
5836  MN   (1074-)  K   -.-  -.-  Part of ionic cluster
5838   K   (1076-)  K   -.-  -.-  Part of ionic cluster
5839   K   (1077-)  K   -.-  -.-  Part of ionic cluster
5841  MN   (1079-)  K   -.-  -.-  Part of ionic cluster
5842  MN   (1080-)  K   -.-  -.-  Part of ionic cluster
5846   K   (1084-)  K   -.-  -.-  Part of ionic cluster
5846   K   (1084-)  K   -.-  -.-  Too few ligands (1)
5847   K   (1085-)  K   -.-  -.-  Too few ligands (3)
5858   K   ( 383-)  L   -.-  -.-  Too few ligands (3)

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.

5864 HOH   (1157 )  B      O  0.89  K  4 *1 and *2
5864 HOH   (1162 )  B      O  0.88 NA  4
5864 HOH   (1291 )  B      O  0.99  K  4 *1 and *2
5864 HOH   (1392 )  B      O  0.87  K  4 *1 and *2
5864 HOH   (1502 )  B      O  1.09  K  4 *1 and *2
5865 HOH   ( 400 )  C      O  0.90  K  4 *1 and *2
5866 HOH   (1510 )  E      O  0.94  K  4 *1 and *2 NCS 1/1
5866 HOH   (1658 )  E      O  1.17  K  4 *1 and *2 NCS 1/1
5868 HOH   (1166 )  H      O  0.93  K  4 *1 and *2 NCS 2/2
5869 HOH   (2872 )  I      O  0.81  K  5 *1 and *2 NCS 2/2
5870 HOH   (1171 )  K      O  0.97  K  4 *1 and *2 NCS 3/3
5870 HOH   (1176 )  K      O  0.87 NA  4 NCS 3/3
5870 HOH   (1528 )  K      O  1.09  K  4 *1 and *2 NCS 3/3
5870 HOH   (1765 )  K      O  0.96  K  4 *1 and *2 ION-B H2O-B
5871 HOH   (4051 )  L      O  1.12  K  5 *1 and *2 NCS 3/3
5871 HOH   (4294 )  L      O  1.20  K  4 *1 and *2 NCS 4/4

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.

 334 GLU   ( 333-)  B   H-bonding suggests Gln
 410 ASP   ( 409-)  B   H-bonding suggests Asn; but Alt-Rotamer
 430 ASP   ( 429-)  B   H-bonding suggests Asn; but Alt-Rotamer
 521 ASP   ( 520-)  B   H-bonding suggests Asn
 683 GLU   ( 682-)  B   H-bonding suggests Gln
 775 ASP   ( 790-)  B   H-bonding suggests Asn
1025 ASP   (1040-)  B   H-bonding suggests Asn; but Alt-Rotamer
1168 ASP   ( 112-)  C   H-bonding suggests Asn
1213 ASP   ( 157-)  C   H-bonding suggests Asn; but Alt-Rotamer
1655 GLU   ( 218-)  E   H-bonding suggests Gln
1770 GLU   ( 333-)  E   H-bonding suggests Gln
1846 ASP   ( 409-)  E   H-bonding suggests Asn; but Alt-Rotamer
1866 ASP   ( 429-)  E   H-bonding suggests Asn; but Alt-Rotamer
2173 ASP   ( 752-)  E   H-bonding suggests Asn
2189 ASP   ( 768-)  E   H-bonding suggests Asn; but Alt-Rotamer
2211 ASP   ( 790-)  E   H-bonding suggests Asn
2227 ASP   ( 806-)  E   H-bonding suggests Asn
2461 ASP   (1040-)  E   H-bonding suggests Asn; Ligand-contact
2576 ASP   (  84-)  F   H-bonding suggests Asn
2604 ASP   ( 112-)  F   H-bonding suggests Asn
2681 GLU   ( 189-)  F   H-bonding suggests Gln; but Alt-Rotamer
2703 ASP   ( 211-)  F   H-bonding suggests Asn
2860 ASP   ( 368-)  F   H-bonding suggests Asn
3092 GLU   ( 218-)  H   H-bonding suggests Gln
3283 ASP   ( 409-)  H   H-bonding suggests Asn; but Alt-Rotamer
3303 ASP   ( 429-)  H   H-bonding suggests Asn
3626 ASP   ( 768-)  H   H-bonding suggests Asn
3648 ASP   ( 790-)  H   H-bonding suggests Asn
3882 ASP   (1024-)  H   H-bonding suggests Asn
4140 ASP   ( 211-)  I   H-bonding suggests Asn
4555 ASP   ( 245-)  K   H-bonding suggests Asn
4643 GLU   ( 333-)  K   H-bonding suggests Gln; but Alt-Rotamer
4719 ASP   ( 409-)  K   H-bonding suggests Asn; but Alt-Rotamer
4739 ASP   ( 429-)  K   H-bonding suggests Asn; but Alt-Rotamer
5087 ASP   ( 790-)  K   H-bonding suggests Asn
5206 GLU   ( 909-)  K   H-bonding suggests Gln
5321 ASP   (1024-)  K   H-bonding suggests Asn
5480 ASP   ( 112-)  L   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 :   0.147
  2nd generation packing quality :  -1.316
  Ramachandran plot appearance   :  -1.379
  chi-1/chi-2 rotamer normality  :  -4.129 (bad)
  Backbone conformation          :   0.242

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.836
  Bond angles                    :   1.434
  Omega angle restraints         :   0.299 (tight)
  Side chain planarity           :   0.651 (tight)
  Improper dihedral distribution :   1.488
  B-factor distribution          :   4.439 (loose)
  Inside/Outside distribution    :   1.014

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 :   0.6
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.836
  Bond angles                    :   1.434
  Omega angle restraints         :   0.299 (tight)
  Side chain planarity           :   0.651 (tight)
  Improper dihedral distribution :   1.488
  B-factor distribution          :   4.439 (loose)
  Inside/Outside distribution    :   1.014
==============

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.