WHAT IF Check report

This file was created 2012-01-13 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 pdb1s0v.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.043
CA-only RMS fit for the two chains : 0.767

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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 : 0.839
CA-only RMS fit for the two chains : 0.517

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 D

All-atom RMS fit for the two chains : 0.947
CA-only RMS fit for the two chains : 0.656

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 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 C

All-atom RMS fit for the two chains : 1.063
CA-only RMS fit for the two chains : 0.815

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 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: B and D

All-atom RMS fit for the two chains : 1.286
CA-only RMS fit for the two chains : 1.090

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

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.

3571 APC   (2000-)  A  -
3574 APC   (2001-)  B  -
3577 APC   (2002-)  C  -
3580 APC   (2003-)  D  -

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

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 DGUA  (   2-)  E    High
   2 DGUA  (   3-)  E    High
   3 DADE  (   4-)  E    High
   4 DADE  (   5-)  E    High
   5 DTHY  (   6-)  E    High
   6 DCYT  (   7-)  E    High
   7 DGUA  (   8-)  E    High
   8 DADE  (   9-)  E    High
  26 DGUA  (   1-)  G    High
  27 DTHY  (   2-)  G    High
  28 DCYT  (   3-)  G    High
  29 DGUA  (   4-)  G    High
  30 DADE  (   5-)  G    High
  31 DTHY  (   6-)  G    High
  32 DTHY  (   7-)  G    High
  33 DCYT  (   8-)  G    High
  34 DCYT  (   9-)  G    High
  35 DGUA  (   2-)  H    High
  36 DGUA  (   3-)  H    High
  37 DADE  (   4-)  H    High
  38 DADE  (   5-)  H    High
  39 DTHY  (   6-)  H    High
  40 DCYT  (   7-)  H    High
  41 DGUA  (   8-)  H    High
  51 DCYT  (  18-)  H    High
And so on for a total of 1438 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

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

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

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 187 ARG   (  52-)  A
1044 ARG   (  52-)  B
1901 ARG   (  52-)  C
2758 ARG   (  52-)  D

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

 163 TYR   (  28-)  A
 179 TYR   (  44-)  A
 385 TYR   ( 250-)  A
 421 TYR   ( 286-)  A
 443 TYR   ( 308-)  A
 504 TYR   ( 385-)  A
 576 TYR   ( 457-)  A
 912 TYR   ( 802-)  A
1020 TYR   (  28-)  B
1108 TYR   ( 116-)  B
1170 TYR   ( 178-)  B
1242 TYR   ( 250-)  B
1300 TYR   ( 308-)  B
1361 TYR   ( 385-)  B
1394 TYR   ( 418-)  B
1434 TYR   ( 458-)  B
1494 TYR   ( 518-)  B
1715 TYR   ( 739-)  B
1803 TYR   ( 836-)  B
1877 TYR   (  28-)  C
2027 TYR   ( 178-)  C
2099 TYR   ( 250-)  C
2157 TYR   ( 308-)  C
2166 TYR   ( 317-)  C
2218 TYR   ( 385-)  C
2660 TYR   ( 836-)  C
2734 TYR   (  28-)  D
2822 TYR   ( 116-)  D
2884 TYR   ( 178-)  D
2956 TYR   ( 250-)  D
3014 TYR   ( 308-)  D
3075 TYR   ( 385-)  D
3148 TYR   ( 458-)  D
3208 TYR   ( 518-)  D
3261 TYR   ( 571-)  D
3517 TYR   ( 836-)  D
3527 TYR   ( 846-)  D

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

 240 PHE   ( 105-)  A
 297 PHE   ( 162-)  A
 519 PHE   ( 400-)  A
 594 PHE   ( 475-)  A
 600 PHE   ( 481-)  A
 630 PHE   ( 511-)  A
 763 PHE   ( 644-)  A
 852 PHE   ( 733-)  A
 870 PHE   ( 751-)  A
1043 PHE   (  51-)  B
1047 PHE   (  55-)  B
1097 PHE   ( 105-)  B
1154 PHE   ( 162-)  B
1174 PHE   ( 182-)  B
1384 PHE   ( 408-)  B
1392 PHE   ( 416-)  B
1408 PHE   ( 432-)  B
1620 PHE   ( 644-)  B
1643 PHE   ( 667-)  B
1952 PHE   ( 103-)  C
1954 PHE   ( 105-)  C
2011 PHE   ( 162-)  C
2233 PHE   ( 400-)  C
2249 PHE   ( 416-)  C
2342 PHE   ( 509-)  C
2566 PHE   ( 733-)  C
2649 PHE   ( 825-)  C
2673 PHE   ( 849-)  C
2757 PHE   (  51-)  D
2811 PHE   ( 105-)  D
2868 PHE   ( 162-)  D
3106 PHE   ( 416-)  D
3204 PHE   ( 514-)  D
3423 PHE   ( 733-)  D

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 201 ASP   (  66-)  A
 324 ASP   ( 189-)  A
 343 ASP   ( 208-)  A
 486 ASP   ( 351-)  A
 625 ASP   ( 506-)  A
 671 ASP   ( 552-)  A
1181 ASP   ( 189-)  B
1200 ASP   ( 208-)  B
1232 ASP   ( 240-)  B
1482 ASP   ( 506-)  B
1567 ASP   ( 591-)  B
1575 ASP   ( 599-)  B
1875 ASP   (  26-)  C
1915 ASP   (  66-)  C
2038 ASP   ( 189-)  C
2057 ASP   ( 208-)  C
2200 ASP   ( 351-)  C
2339 ASP   ( 506-)  C
2590 ASP   ( 766-)  C
2772 ASP   (  66-)  D
2895 ASP   ( 189-)  D
2914 ASP   ( 208-)  D
3057 ASP   ( 351-)  D
3196 ASP   ( 506-)  D
3281 ASP   ( 591-)  D
3540 ASP   ( 859-)  D

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 170 GLU   (  35-)  A
 180 GLU   (  45-)  A
 293 GLU   ( 158-)  A
 334 GLU   ( 199-)  A
 353 GLU   ( 218-)  A
 518 GLU   ( 399-)  A
 602 GLU   ( 483-)  A
 603 GLU   ( 484-)  A
 617 GLU   ( 498-)  A
 623 GLU   ( 504-)  A
 699 GLU   ( 580-)  A
 719 GLU   ( 600-)  A
 723 GLU   ( 604-)  A
 802 GLU   ( 683-)  A
 836 GLU   ( 717-)  A
 857 GLU   ( 738-)  A
 878 GLU   ( 768-)  A
 987 GLU   ( 877-)  A
1027 GLU   (  35-)  B
1048 GLU   (  56-)  B
1100 GLU   ( 108-)  B
1150 GLU   ( 158-)  B
1159 GLU   ( 167-)  B
1191 GLU   ( 199-)  B
1210 GLU   ( 218-)  B
And so on for a total of 75 lines.

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.

   9 DTHY  (  10-)  E      N1   C2    1.33   -5.6
  10 DADE  (  11-)  E      C3'  O3'   1.37   -4.7
  10 DADE  (  11-)  E      N9   C4    1.33   -6.8
  10 DADE  (  11-)  E      N7   C5    1.36   -5.0
  10 DADE  (  11-)  E      N3   C4    1.32   -4.0
  10 DADE  (  11-)  E      C5   C6    1.33   -8.4
  11 DTHY  (  12-)  E      C3'  O3'   1.37   -4.8
  11 DTHY  (  12-)  E      N1   C2    1.32   -6.7
  11 DTHY  (  12-)  E      C5   C4    1.39   -5.6
  12 DCYT  (  13-)  E      N3   C2    1.32   -4.3
  12 DCYT  (  13-)  E      C4   N4    1.28   -5.8
  13 DGUA  (  14-)  E      N3   C4    1.31   -5.2
  14 DCYT  (  15-)  E      C1'  N1    1.41   -5.0
  14 DCYT  (  15-)  E      N1   C2    1.35   -4.6
  14 DCYT  (  15-)  E      C4   N3    1.30   -4.4
  16 DGUA  (  17-)  E      C5   C6    1.38   -4.2
  18 OGUA  (   1-)  F      C3'  O3'   1.48    4.1
  18 OGUA  (   1-)  F      N9   C4    1.41    4.5
  18 OGUA  (   1-)  F      C2   N3    1.36    4.5
  18 OGUA  (   1-)  F      C5   C6    1.48    6.0
  21 OGUA  (   4-)  F      C6   O6    1.27    4.0
  22 OCYT  (   5-)  F      N1   C2    1.32   -7.6
  22 OCYT  (   5-)  F      C5   C4    1.39   -4.6
  23 OGUA  (   6-)  F      C5   C6    1.49    7.1
  23 OGUA  (   6-)  F      C6   N1    1.34   -7.1
And so on for a total of 160 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

 |  0.999292  0.000448 -0.000022|
 |  0.000448  0.997964  0.000902|
 | -0.000022  0.000902  0.999116|
Proposed new scale matrix

 |  0.012332  0.004652  0.000414|
 | -0.000005  0.012210  0.000510|
 |  0.000000 -0.000004  0.004851|
With corresponding cell

    A    =  81.078  B   =  87.513  C    = 206.336
    Alpha=  91.830  Beta=  91.023  Gamma= 110.643

The CRYST1 cell dimensions

    A    =  81.133  B   =  87.703  C    = 206.531
    Alpha=  91.930  Beta=  91.020  Gamma= 110.660

Variance: 333.313
(Under-)estimated Z-score: 13.455

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.

   1 DGUA  (   2-)  E      O5'  C5'  C4' 116.30    4.4
   1 DGUA  (   2-)  E      N9   C8   N7  113.14    4.1
   2 DGUA  (   3-)  E      N9   C8   N7  113.27    4.3
   7 DGUA  (   8-)  E      N9   C8   N7  113.11    4.0
  10 DADE  (  11-)  E      C3'  C4'  C5' 107.30   -4.9
  10 DADE  (  11-)  E      C2'  C1'  N9  106.01   -5.1
  11 DTHY  (  12-)  E      O4'  C1'  N1  111.45    4.6
  11 DTHY  (  12-)  E      C1'  N1   C6  128.03    5.1
  11 DTHY  (  12-)  E      C1'  N1   C2  111.71   -4.1
  12 DCYT  (  13-)  E      C5'  C4'  O4'  93.67   -9.8
  12 DCYT  (  13-)  E      C2'  C1'  N1  107.68   -4.1
  13 DGUA  (  14-)  E      P    O5'  C5' 114.42   -4.0
  13 DGUA  (  14-)  E      C2'  C1'  N9  104.40   -6.1
  13 DGUA  (  14-)  E      C5   C6   O6  125.94   -4.4
  13 DGUA  (  14-)  E      O6   C6   N1  122.33    4.0
  14 DCYT  (  15-)  E      C2'  C1'  N1  103.04   -7.0
  15 DCYT  (  16-)  E      C3'  C4'  C5' 105.76   -6.0
  15 DCYT  (  16-)  E      C2'  C1'  N1  102.11   -7.6
  16 DGUA  (  17-)  E      C3'  C4'  C5' 103.43   -7.5
  16 DGUA  (  17-)  E      C2'  C1'  N9  104.93   -5.8
  16 DGUA  (  17-)  E      N9   C8   N7  113.25    4.3
  17 DCYT  (  18-)  E      O3'  C3'  C2'  93.80   -6.2
  18 OGUA  (   1-)  F      N9   C8   N7  113.27    4.3
  19 OCYT  (   2-)  F      C3'  C4'  C5' 121.64    4.1
  20 OGUA  (   3-)  F      C3'  C4'  C5' 123.73    5.5
And so on for a total of 260 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

 170 GLU   (  35-)  A
 180 GLU   (  45-)  A
 187 ARG   (  52-)  A
 201 ASP   (  66-)  A
 293 GLU   ( 158-)  A
 324 ASP   ( 189-)  A
 334 GLU   ( 199-)  A
 343 ASP   ( 208-)  A
 353 GLU   ( 218-)  A
 486 ASP   ( 351-)  A
 518 GLU   ( 399-)  A
 602 GLU   ( 483-)  A
 603 GLU   ( 484-)  A
 617 GLU   ( 498-)  A
 623 GLU   ( 504-)  A
 625 ASP   ( 506-)  A
 671 ASP   ( 552-)  A
 699 GLU   ( 580-)  A
 719 GLU   ( 600-)  A
 723 GLU   ( 604-)  A
 802 GLU   ( 683-)  A
 836 GLU   ( 717-)  A
 857 GLU   ( 738-)  A
 878 GLU   ( 768-)  A
 987 GLU   ( 877-)  A
And so on for a total of 105 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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 515 ILE   ( 396-)  A      CB     7.6    42.21    32.31
 536 PRO   ( 417-)  A      N     -6.4   -23.40    -2.48
 570 PRO   ( 451-)  A      N     -7.6   -27.33    -2.48
 627 PRO   ( 508-)  A      N     10.8    33.07    -2.48
 928 PRO   ( 818-)  A      N      9.4    28.34    -2.48
1777 ILE   ( 810-)  B      CB     6.7    40.98    32.31
2119 PRO   ( 270-)  C      N     -6.4   -23.61    -2.48
The average deviation= 0.905

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.

 579 LEU   ( 460-)  A    5.64
1552 LYS   ( 576-)  B    4.54
1556 GLU   ( 580-)  B    4.49
 895 SER   ( 785-)  A    4.03

Error: Connections to aromatic rings out of plane

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

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

 946 TYR   ( 836-)  A      CB   4.25
 633 PHE   ( 514-)  A      CB   4.14

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

  93 OURA  (   8-)  L    0.20
  25 OURA  (   8-)  F    0.20
  46 DCYT  (  13-)  H    0.17
  12 DCYT  (  13-)  E    0.16
  82 DCYT  (  15-)  K    0.15
  50 DGUA  (  17-)  H    0.14
  23 OGUA  (   6-)  F    0.13
  43 DTHY  (  10-)  H    0.12
  56 OCYT  (   5-)  I    0.12
 115 DGUA  (  14-)  N    0.12
  11 DTHY  (  12-)  E    0.11
  13 DGUA  (  14-)  E    0.10
  49 DCYT  (  16-)  H    0.10
  45 DTHY  (  12-)  H    0.10
 Ramachandran Z-score : -6.314

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -6.314

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.

2706 PHE   ( 882-)  C    -3.8
 926 THR   ( 816-)  A    -3.2
2828 THR   ( 122-)  D    -3.1
 627 PRO   ( 508-)  A    -3.1
 789 PRO   ( 670-)  A    -3.1
 488 PRO   ( 353-)  A    -3.0
2824 THR   ( 118-)  D    -3.0
 405 PRO   ( 270-)  A    -3.0
 992 PHE   ( 882-)  A    -3.0
2341 PRO   ( 508-)  C    -3.0
1428 ILE   ( 452-)  B    -2.9
3198 PRO   ( 508-)  D    -2.9
3166 PRO   ( 476-)  D    -2.9
3142 ILE   ( 452-)  D    -2.9
1042 ARG   (  50-)  B    -2.9
1849 PHE   ( 882-)  B    -2.9
1785 PRO   ( 818-)  B    -2.9
3563 PHE   ( 882-)  D    -2.9
1722 ARG   ( 746-)  B    -2.9
2635 HIS   ( 811-)  C    -2.8
1527 ARG   ( 551-)  B    -2.8
 766 ARG   ( 647-)  A    -2.8
2725 ILE   (  19-)  D    -2.8
 870 PHE   ( 751-)  A    -2.8
1421 THR   ( 445-)  B    -2.7
And so on for a total of 293 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.

 142 ALA   (   7-)  A  Poor phi/psi
 143 LYS   (   8-)  A  Poor phi/psi
 152 ALA   (  17-)  A  Poor phi/psi
 155 PRO   (  20-)  A  Poor phi/psi
 163 TYR   (  28-)  A  Poor phi/psi
 195 LYS   (  60-)  A  Poor phi/psi
 241 LEU   ( 106-)  A  Poor phi/psi
 302 GLU   ( 167-)  A  Poor phi/psi
 312 VAL   ( 177-)  A  Poor phi/psi
 329 GLY   ( 194-)  A  Poor phi/psi
 334 GLU   ( 199-)  A  Poor phi/psi
 335 ALA   ( 200-)  A  Poor phi/psi
 368 ASN   ( 233-)  A  Poor phi/psi
 370 GLY   ( 235-)  A  Poor phi/psi
 374 GLN   ( 239-)  A  Poor phi/psi
 412 PRO   ( 277-)  A  Poor phi/psi
 416 ILE   ( 281-)  A  Poor phi/psi
 423 ALA   ( 288-)  A  Poor phi/psi
 426 ARG   ( 291-)  A  Poor phi/psi
 444 GLU   ( 309-)  A  Poor phi/psi
 448 MET   ( 313-)  A  Poor phi/psi
 467 LYS   ( 332-)  A  Poor phi/psi
 480 LYS   ( 345-)  A  Poor phi/psi
 483 PRO   ( 348-)  A  Poor phi/psi
 488 PRO   ( 353-)  A  Poor phi/psi
And so on for a total of 281 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 : -6.146

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.

 178 SER   (  43-)  A    0.35
2380 SER   ( 547-)  C    0.38
1743 SER   ( 776-)  B    0.38
2915 SER   ( 209-)  D    0.38
1523 SER   ( 547-)  B    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 DADE  (   4-)  E      0
   4 DADE  (   5-)  E      0
   5 DTHY  (   6-)  E      0
   6 DCYT  (   7-)  E      0
   7 DGUA  (   8-)  E      0
   8 DADE  (   9-)  E      0
   9 DTHY  (  10-)  E      0
  10 DADE  (  11-)  E      0
  11 DTHY  (  12-)  E      0
  12 DCYT  (  13-)  E      0
  13 DGUA  (  14-)  E      0
  14 DCYT  (  15-)  E      0
  15 DCYT  (  16-)  E      0
  16 DGUA  (  17-)  E      0
  17 DCYT  (  18-)  E      0
  18 OGUA  (   1-)  F      0
  19 OCYT  (   2-)  F      0
  20 OGUA  (   3-)  F      0
  21 OGUA  (   4-)  F      0
  22 OCYT  (   5-)  F      0
  23 OGUA  (   6-)  F      0
  24 OADE  (   7-)  F      0
  25 OURA  (   8-)  F      0
  26 DGUA  (   1-)  G      0
  27 DTHY  (   2-)  G      0
And so on for a total of 1254 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 2.211

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!

2047 GLY   ( 198-)  C   2.63   14
1190 GLY   ( 198-)  B   2.45   10
1600 GLY   ( 624-)  B   2.07   10
 543 GLY   ( 424-)  A   1.95   80
1946 GLY   (  97-)  C   1.76   15
 195 LYS   (  60-)  A   1.73   19
2457 GLY   ( 624-)  C   1.72   10
1616 GLY   ( 640-)  B   1.66   80
 759 GLY   ( 640-)  A   1.62   80
 494 THR   ( 375-)  A   1.61   70
1621 GLY   ( 645-)  B   1.60   80
1638 GLY   ( 662-)  B   1.59   16
 555 GLY   ( 436-)  A   1.56   19
2692 GLY   ( 868-)  C   1.53   15
1425 GLY   ( 449-)  B   1.50   64

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]

 570 PRO   ( 451-)  A    0.49 HIGH
 593 PRO   ( 474-)  A    0.46 HIGH
 789 PRO   ( 670-)  A    0.50 HIGH
 849 PRO   ( 730-)  A    0.46 HIGH
 853 PRO   ( 734-)  A    0.48 HIGH
1071 PRO   (  79-)  B    0.46 HIGH
1269 PRO   ( 277-)  B    0.47 HIGH
1306 PRO   ( 314-)  B    0.47 HIGH
1345 PRO   ( 353-)  B    0.47 HIGH
1450 PRO   ( 474-)  B    0.45 HIGH
1452 PRO   ( 476-)  B    0.45 HIGH
1484 PRO   ( 508-)  B    0.45 HIGH
1539 PRO   ( 563-)  B    0.49 HIGH
1710 PRO   ( 734-)  B    0.47 HIGH
1747 PRO   ( 780-)  B    0.47 HIGH
2119 PRO   ( 270-)  C    0.50 HIGH
2284 PRO   ( 451-)  C    0.45 HIGH
2309 PRO   ( 476-)  C    0.46 HIGH
2490 PRO   ( 657-)  C    0.47 HIGH
2686 PRO   ( 862-)  C    0.46 HIGH
2689 PRO   ( 865-)  C    0.46 HIGH
2976 PRO   ( 270-)  D    0.46 HIGH
3054 PRO   ( 348-)  D    0.47 HIGH
3360 PRO   ( 670-)  D    0.45 HIGH
3424 PRO   ( 734-)  D    0.52 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 235 PRO   ( 100-)  A  -114.9 envelop C-gamma (-108 degrees)
 246 PRO   ( 111-)  A  -114.1 envelop C-gamma (-108 degrees)
 412 PRO   ( 277-)  A   102.1 envelop C-beta (108 degrees)
 428 PRO   ( 293-)  A   102.5 envelop C-beta (108 degrees)
 449 PRO   ( 314-)  A     2.5 envelop N (0 degrees)
 488 PRO   ( 353-)  A  -135.3 envelop C-delta (-144 degrees)
 536 PRO   ( 417-)  A  -140.3 envelop C-delta (-144 degrees)
 553 PRO   ( 434-)  A   127.6 half-chair C-beta/C-alpha (126 degrees)
 570 PRO   ( 451-)  A   100.0 envelop C-beta (108 degrees)
 593 PRO   ( 474-)  A  -134.6 half-chair C-delta/C-gamma (-126 degrees)
 615 PRO   ( 496-)  A   -62.3 half-chair C-beta/C-alpha (-54 degrees)
 652 PRO   ( 533-)  A  -116.8 envelop C-gamma (-108 degrees)
 849 PRO   ( 730-)  A   120.3 half-chair C-beta/C-alpha (126 degrees)
 928 PRO   ( 818-)  A    51.6 half-chair C-delta/C-gamma (54 degrees)
 972 PRO   ( 862-)  A  -121.0 half-chair C-delta/C-gamma (-126 degrees)
1258 PRO   ( 266-)  B   -49.2 half-chair C-beta/C-alpha (-54 degrees)
1262 PRO   ( 270-)  B    51.9 half-chair C-delta/C-gamma (54 degrees)
1267 PRO   ( 275-)  B    51.1 half-chair C-delta/C-gamma (54 degrees)
1269 PRO   ( 277-)  B   110.8 envelop C-beta (108 degrees)
1345 PRO   ( 353-)  B  -115.1 envelop C-gamma (-108 degrees)
1410 PRO   ( 434-)  B    24.1 half-chair N/C-delta (18 degrees)
1452 PRO   ( 476-)  B  -123.9 half-chair C-delta/C-gamma (-126 degrees)
1472 PRO   ( 496-)  B  -165.7 half-chair N/C-delta (-162 degrees)
1484 PRO   ( 508-)  B  -117.4 half-chair C-delta/C-gamma (-126 degrees)
1706 PRO   ( 730-)  B   103.5 envelop C-beta (108 degrees)
1747 PRO   ( 780-)  B   -40.5 envelop C-alpha (-36 degrees)
1785 PRO   ( 818-)  B   103.7 envelop C-beta (108 degrees)
1829 PRO   ( 862-)  B  -132.3 half-chair C-delta/C-gamma (-126 degrees)
1832 PRO   ( 865-)  B  -138.7 envelop C-delta (-144 degrees)
1949 PRO   ( 100-)  C  -115.7 envelop C-gamma (-108 degrees)
2115 PRO   ( 266-)  C   -48.9 half-chair C-beta/C-alpha (-54 degrees)
2163 PRO   ( 314-)  C    35.1 envelop C-delta (36 degrees)
2202 PRO   ( 353-)  C   125.9 half-chair C-beta/C-alpha (126 degrees)
2250 PRO   ( 417-)  C  -113.1 envelop C-gamma (-108 degrees)
2267 PRO   ( 434-)  C   118.0 half-chair C-beta/C-alpha (126 degrees)
2307 PRO   ( 474-)  C  -149.0 envelop C-delta (-144 degrees)
2341 PRO   ( 508-)  C   175.0 envelop N (180 degrees)
2366 PRO   ( 533-)  C  -113.4 envelop C-gamma (-108 degrees)
2575 PRO   ( 742-)  C    16.2 half-chair N/C-delta (18 degrees)
2817 PRO   ( 111-)  D  -117.1 half-chair C-delta/C-gamma (-126 degrees)
3020 PRO   ( 314-)  D    50.1 half-chair C-delta/C-gamma (54 degrees)
3054 PRO   ( 348-)  D   100.4 envelop C-beta (108 degrees)
3059 PRO   ( 353-)  D   169.0 half-chair C-alpha/N (162 degrees)
3107 PRO   ( 417-)  D  -126.0 half-chair C-delta/C-gamma (-126 degrees)
3164 PRO   ( 474-)  D  -148.3 envelop C-delta (-144 degrees)
3198 PRO   ( 508-)  D  -126.9 half-chair C-delta/C-gamma (-126 degrees)
3223 PRO   ( 533-)  D  -116.3 envelop C-gamma (-108 degrees)
3420 PRO   ( 730-)  D   104.1 envelop C-beta (108 degrees)
3546 PRO   ( 865-)  D  -118.6 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 542 ARG   ( 423-)  A      NH2 <->  894 HIS   ( 784-)  A      ND1    0.82    2.18  INTRA BL
 935 PHE   ( 825-)  A      CE1 <->  939 ARG   ( 829-)  A      NH1    0.71    2.39  INTRA BL
1428 ILE   ( 452-)  B      CG2 <-> 1429 GLY   ( 453-)  B      N      0.67    2.33  INTRA BL
 415 GLY   ( 280-)  A      O   <->  417 THR   ( 282-)  A      N      0.66    2.04  INTRA BL
2464 LYS   ( 631-)  C      NZ  <-> 3577 APC   (2002-)  C      C3A    0.65    2.45  INTRA BL
2254 ASP   ( 421-)  C      O   <-> 2256 ARG   ( 423-)  C      N      0.63    2.07  INTRA BL
2256 ARG   ( 423-)  C      NH2 <-> 2608 HIS   ( 784-)  C      ND1    0.63    2.37  INTRA BL
2166 TYR   ( 317-)  C      O   <-> 2170 ASN   ( 321-)  C      ND2    0.63    2.07  INTRA BL
 502 ALA   ( 383-)  A      O   <->  504 TYR   ( 385-)  A      N      0.62    2.08  INTRA BL
 750 LYS   ( 631-)  A      NZ  <-> 3571 APC   (2000-)  A      C3A    0.62    2.48  INTRA BL
 505 ARG   ( 386-)  A      O   <->  508 LYS   ( 389-)  A      N      0.61    2.09  INTRA BL
2187 ALA   ( 338-)  C      O   <-> 2189 VAL   ( 340-)  C      N      0.60    2.10  INTRA BL
 624 GLN   ( 505-)  A      O   <->  626 SER   ( 507-)  A      N      0.60    2.10  INTRA BL
  42 DADE  (   9-)  H      N6  <->   60 DGUA  (   1-)  J      N2     0.59    2.26  INTRA BF
3242 ASP   ( 552-)  D      OD1 <-> 3245 GLY   ( 555-)  D      N      0.59    2.11  INTRA BF
 850 ASP   ( 731-)  A      OD1 <->  902 ARG   ( 792-)  A      NH2    0.59    2.11  INTRA BL
 935 PHE   ( 825-)  A      CZ  <->  939 ARG   ( 829-)  A      NH2    0.58    2.52  INTRA BL
2166 TYR   ( 317-)  C      C   <-> 2170 ASN   ( 321-)  C      ND2    0.58    2.52  INTRA BL
 665 PHE   ( 546-)  A      CE1 <->  893 VAL   ( 783-)  A      CG2    0.57    2.63  INTRA BL
 912 TYR   ( 802-)  A      O   <->  914 ILE   ( 804-)  A      N      0.57    2.13  INTRA BL
1399 ARG   ( 423-)  B      CG  <-> 1748 ASN   ( 781-)  B      ND2    0.57    2.53  INTRA BL
3521 ASP   ( 840-)  D      O   <-> 3523 LEU   ( 842-)  D      N      0.56    2.14  INTRA BF
1796 ARG   ( 829-)  B      NH2 <-> 1849 PHE   ( 882-)  B      CA     0.56    2.54  INTRA BL
 520 MET   ( 401-)  A      O   <->  522 GLU   ( 403-)  A      N      0.56    2.14  INTRA BL
2612 GLY   ( 788-)  C      C   <-> 2616 ARG   ( 792-)  C      NH1    0.56    2.54  INTRA BL
And so on for a total of 3421 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

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.

 231 ARG   (  96-)  A      -8.49
1088 ARG   (  96-)  B      -8.46
1945 ARG   (  96-)  C      -8.20
2802 ARG   (  96-)  D      -8.11
2140 ARG   ( 291-)  C      -7.40
1283 ARG   ( 291-)  B      -7.33
1304 TYR   ( 312-)  B      -6.96
2998 ARG   ( 292-)  D      -6.75
2804 LYS   (  98-)  D      -6.73
1090 LYS   (  98-)  B      -6.73
1947 LYS   (  98-)  C      -6.57
 233 LYS   (  98-)  A      -6.47
 426 ARG   ( 291-)  A      -6.39
2997 ARG   ( 291-)  D      -6.38
2193 TRP   ( 344-)  C      -6.35
1876 HIS   (  27-)  C      -6.34
 643 HIS   ( 524-)  A      -6.32
1500 HIS   ( 524-)  B      -6.32
 447 TYR   ( 312-)  A      -6.31
1019 HIS   (  27-)  B      -6.26
 479 TRP   ( 344-)  A      -6.25
 162 HIS   (  27-)  A      -6.20
2577 GLN   ( 744-)  C      -6.19
1336 TRP   ( 344-)  B      -6.19
2733 HIS   (  27-)  D      -6.19
And so on for a total of 93 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.

 307 LYS   ( 172-)  A       309 - VAL    174- ( A)         -4.65
 862 ILE   ( 743-)  A       866 - LEU    747- ( A)         -5.13
1343 ASP   ( 351-)  B      1346 - ALA    354- ( B)         -4.15
1719 ILE   ( 743-)  B      1723 - LEU    747- ( B)         -5.16
3433 ILE   ( 743-)  D      3435 - THR    745- ( D)         -4.84

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

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.

3286 THR   ( 596-)  D   -3.35
3329 TYR   ( 639-)  D   -2.79
2429 THR   ( 596-)  C   -2.78
 867 ASN   ( 748-)  A   -2.77
1615 TYR   ( 639-)  B   -2.73
 758 TYR   ( 639-)  A   -2.70
1777 ILE   ( 810-)  B   -2.69
2472 TYR   ( 639-)  C   -2.69
 871 LEU   ( 752-)  A   -2.68
 754 MET   ( 635-)  A   -2.66
3125 GLN   ( 435-)  D   -2.60
 554 GLN   ( 435-)  A   -2.60
3325 MET   ( 635-)  D   -2.57
 485 GLU   ( 350-)  A   -2.53
2696 LEU   ( 872-)  C   -2.53
1342 GLU   ( 350-)  B   -2.51
2268 GLN   ( 435-)  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.

 422 TRP   ( 287-)  A     -  425 GLY   ( 290-)  A        -1.27
1612 THR   ( 636-)  B     - 1615 TYR   ( 639-)  B        -1.87
1723 LEU   ( 747-)  B     - 1726 MET   ( 750-)  B        -1.83
3326 THR   ( 636-)  D     - 3329 TYR   ( 639-)  D        -1.83
3480 HIS   ( 799-)  D     - 3483 TYR   ( 802-)  D        -1.51

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

3586 HOH   ( 999 )  J      O    -21.78  -23.54   65.52
3593 HOH   (3129 )  A      O    -10.88  -27.41  -32.57
3593 HOH   (3161 )  A      O     44.71   15.11   -8.61
3593 HOH   (3175 )  A      O     44.21   21.58  -15.48
3593 HOH   (3181 )  A      O     42.78   18.65  -14.26
3593 HOH   (3187 )  A      O     -8.97  -27.67  -35.36
3594 HOH   (3143 )  B      O    -11.68  -55.32   51.51
3594 HOH   (3156 )  B      O     66.70  -48.89   56.84
3594 HOH   (3196 )  B      O      8.19   21.07   28.08
3594 HOH   (3201 )  B      O     12.82   24.67   26.56
3594 HOH   (3209 )  B      O     12.23   -9.30   58.77
3595 HOH   (3153 )  C      O    -26.17    1.15  103.79
3596 HOH   (3142 )  D      O     -5.21  -27.96  114.73
3596 HOH   (3164 )  D      O     -2.83  -28.97  116.91
3596 HOH   (3167 )  D      O     -4.57  -29.03  112.35

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.

3581 HOH   (  25 )  E      O
3581 HOH   (  39 )  E      O
3584 HOH   ( 484 )  H      O
3584 HOH   ( 747 )  H      O
3584 HOH   (1027 )  H      O
3585 HOH   ( 945 )  I      O
3586 HOH   ( 453 )  J      O
3587 HOH   ( 962 )  K      O
3587 HOH   ( 976 )  K      O
3589 HOH   ( 542 )  M      O
3589 HOH   (1097 )  M      O
3589 HOH   (1125 )  M      O
3590 HOH   ( 311 )  N      O
3590 HOH   ( 718 )  N      O
3590 HOH   ( 930 )  N      O
3591 HOH   ( 769 )  O      O
3592 HOH   ( 284 )  P      O
3593 HOH   (3008 )  A      O
3593 HOH   (3014 )  A      O
3593 HOH   (3034 )  A      O
3593 HOH   (3042 )  A      O
3593 HOH   (3046 )  A      O
3593 HOH   (3049 )  A      O
3593 HOH   (3052 )  A      O
3593 HOH   (3057 )  A      O
And so on for a total of 153 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.

 270 GLN   ( 135-)  A
 304 GLN   ( 169-)  A
 368 ASN   ( 233-)  A
 404 GLN   ( 269-)  A
 435 HIS   ( 300-)  A
 554 GLN   ( 435-)  A
 582 HIS   ( 463-)  A
 605 HIS   ( 486-)  A
 607 ASN   ( 488-)  A
 738 GLN   ( 619-)  A
 867 ASN   ( 748-)  A
 891 ASN   ( 781-)  A
 964 HIS   ( 854-)  A
 967 GLN   ( 857-)  A
1153 HIS   ( 161-)  B
1197 HIS   ( 205-)  B
1224 GLN   ( 232-)  B
1261 GLN   ( 269-)  B
1292 HIS   ( 300-)  B
1411 GLN   ( 435-)  B
1413 ASN   ( 437-)  B
1595 GLN   ( 619-)  B
1724 ASN   ( 748-)  B
1730 GLN   ( 754-)  B
1748 ASN   ( 781-)  B
And so on for a total of 52 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.

  59 OURA  (   8-)  I      O2'
 142 ALA   (   7-)  A      N
 151 LEU   (  16-)  A      N
 152 ALA   (  17-)  A      N
 153 ALA   (  18-)  A      N
 157 ASN   (  22-)  A      N
 171 GLN   (  36-)  A      NE2
 193 GLN   (  58-)  A      N
 196 ALA   (  61-)  A      N
 200 ALA   (  65-)  A      N
 202 ASN   (  67-)  A      N
 208 LEU   (  73-)  A      N
 210 THR   (  75-)  A      N
 213 LEU   (  78-)  A      N
 238 PHE   ( 103-)  A      N
 239 GLN   ( 104-)  A      N
 242 GLN   ( 107-)  A      N
 244 ILE   ( 109-)  A      N
 247 GLU   ( 112-)  A      N
 268 THR   ( 133-)  A      N
 288 ARG   ( 153-)  A      N
 289 ILE   ( 154-)  A      N
 336 TRP   ( 201-)  A      NE1
 339 TRP   ( 204-)  A      N
 342 GLU   ( 207-)  A      N
And so on for a total of 477 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.

 176 HIS   (  41-)  A      ND1
 191 GLU   (  56-)  A      OE1
 459 GLN   ( 324-)  A      OE1
 540 ASP   ( 421-)  A      OD2
 648 ASN   ( 529-)  A      OD1
 768 GLN   ( 649-)  A      OE1
 856 GLN   ( 737-)  A      OE1
 857 GLU   ( 738-)  A      OE2
 896 GLN   ( 786-)  A      OE1
 921 HIS   ( 811-)  A      NE2
1058 ASP   (  66-)  B      OD1
1096 GLN   ( 104-)  B      OE1
1380 GLN   ( 404-)  B      OE1
1397 ASP   ( 421-)  B      OD2
1439 HIS   ( 463-)  B      ND1
1442 ASN   ( 466-)  B      OD1
1459 GLU   ( 483-)  B      OE2
1462 HIS   ( 486-)  B      ND1
1500 HIS   ( 524-)  B      ND1
1520 GLN   ( 544-)  B      OE1
1625 GLN   ( 649-)  B      OE1
1713 GLN   ( 737-)  B      OE1
1778 HIS   ( 811-)  B      NE2
1915 ASP   (  66-)  C      OD1
2296 HIS   ( 463-)  C      ND1
2319 HIS   ( 486-)  C      NE2
2357 HIS   ( 524-)  C      ND1
2482 GLN   ( 649-)  C      OE1
2564 ASP   ( 731-)  C      OD2
2570 GLN   ( 737-)  C      OE1
2893 GLU   ( 187-)  D      OE1
2975 GLN   ( 269-)  D      OE1
3045 ASN   ( 339-)  D      OD1
3153 HIS   ( 463-)  D      ND1
3219 ASN   ( 529-)  D      OD1
3234 GLN   ( 544-)  D      OE1
3242 ASP   ( 552-)  D      OD1
3309 GLN   ( 619-)  D      OE1
3427 GLN   ( 737-)  D      OE1
3467 GLN   ( 786-)  D      OE1
3468 ASP   ( 787-)  D      OD1
3492 HIS   ( 811-)  D      NE2

Warning: No crystallisation information

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

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

3569  MG   (3005-)  A     0.64   1.04 Is perhaps CA (Few ligands (4) )
3570  MG   (3001-)  A     0.51   1.03 Is perhaps NA
3572  MG   (3002-)  B     0.39   0.77 Is perhaps NA (Few ligands (4) )
3573  MG   (3006-)  B     0.51   1.02 Is perhaps NA (Few ligands (4) )
3575  MG   (3003-)  C     0.46   0.92 Is perhaps NA
3576  MG   (3007-)  C   -.-  -.-  Too few ligands (3)
3578  MG   (3004-)  D     0.28   1.37 Could be  K
3579  MG   (3008-)  D   -.-  -.-  Too few ligands (2)

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.

3595 HOH   (3113 )  C      O  1.06  K  4 Ion-B

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 243 GLU   ( 108-)  A   H-bonding suggests Gln; but Alt-Rotamer
 265 ASP   ( 130-)  A   H-bonding suggests Asn; but Alt-Rotamer
 282 ASP   ( 147-)  A   H-bonding suggests Asn; but Alt-Rotamer
 303 GLU   ( 168-)  A   H-bonding suggests Gln
 343 ASP   ( 208-)  A   H-bonding suggests Asn
 557 ASP   ( 438-)  A   H-bonding suggests Asn; but Alt-Rotamer
 623 GLU   ( 504-)  A   H-bonding suggests Gln; but Alt-Rotamer
 636 GLU   ( 517-)  A   H-bonding suggests Gln; but Alt-Rotamer
 771 GLU   ( 652-)  A   H-bonding suggests Gln
 922 ASP   ( 812-)  A   H-bonding suggests Asn; but Alt-Rotamer
 954 ASP   ( 844-)  A   H-bonding suggests Asn
 984 ASP   ( 874-)  A   H-bonding suggests Asn
1005 ASP   (  13-)  B   H-bonding suggests Asn
1007 GLU   (  15-)  B   H-bonding suggests Gln
1079 ASP   (  87-)  B   H-bonding suggests Asn
1083 GLU   (  91-)  B   H-bonding suggests Gln
1122 ASP   ( 130-)  B   H-bonding suggests Asn; but Alt-Rotamer
1139 ASP   ( 147-)  B   H-bonding suggests Asn
1200 ASP   ( 208-)  B   H-bonding suggests Asn
1482 ASP   ( 506-)  B   H-bonding suggests Asn
1629 ASP   ( 653-)  B   H-bonding suggests Asn
1636 ASP   ( 660-)  B   H-bonding suggests Asn
1818 ASP   ( 851-)  B   H-bonding suggests Asn; but Alt-Rotamer
1826 ASP   ( 859-)  B   H-bonding suggests Asn
1841 ASP   ( 874-)  B   H-bonding suggests Asn; but Alt-Rotamer
1862 ASP   (  13-)  C   H-bonding suggests Asn; but Alt-Rotamer
1905 GLU   (  56-)  C   H-bonding suggests Gln
1915 ASP   (  66-)  C   H-bonding suggests Asn; but Alt-Rotamer
1940 GLU   (  91-)  C   H-bonding suggests Gln
1996 ASP   ( 147-)  C   H-bonding suggests Asn
2017 GLU   ( 168-)  C   H-bonding suggests Gln
2159 ASP   ( 310-)  C   H-bonding suggests Asn
2200 ASP   ( 351-)  C   H-bonding suggests Asn; but Alt-Rotamer
2337 GLU   ( 504-)  C   H-bonding suggests Gln
2418 ASP   ( 585-)  C   H-bonding suggests Asn; but Alt-Rotamer
2683 ASP   ( 859-)  C   H-bonding suggests Asn; but Alt-Rotamer
2698 ASP   ( 874-)  C   H-bonding suggests Asn
2719 ASP   (  13-)  D   H-bonding suggests Asn; but Alt-Rotamer
2853 ASP   ( 147-)  D   H-bonding suggests Asn; but Alt-Rotamer
2862 ASP   ( 156-)  D   H-bonding suggests Asn
2924 GLU   ( 218-)  D   H-bonding suggests Gln
3016 ASP   ( 310-)  D   H-bonding suggests Asn; but Alt-Rotamer
3161 ASP   ( 471-)  D   H-bonding suggests Asn; but Alt-Rotamer
3173 GLU   ( 483-)  D   H-bonding suggests Gln
3194 GLU   ( 504-)  D   H-bonding suggests Gln
3275 ASP   ( 585-)  D   H-bonding suggests Asn
3342 GLU   ( 652-)  D   H-bonding suggests Gln
3350 ASP   ( 660-)  D   H-bonding suggests Asn
3532 ASP   ( 851-)  D   H-bonding suggests Asn; but Alt-Rotamer
3555 ASP   ( 874-)  D   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 :  -2.230
  2nd generation packing quality :  -3.246 (poor)
  Ramachandran plot appearance   :  -6.314 (bad)
  chi-1/chi-2 rotamer normality  :  -6.146 (bad)
  Backbone conformation          :  -0.640

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.049
  Bond angles                    :   1.108
  Omega angle restraints         :   0.402 (tight)
  Side chain planarity           :   0.259 (tight)
  Improper dihedral distribution :   0.848
  B-factor distribution          :   0.470
  Inside/Outside distribution    :   1.020

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -3.2 (poor)
  chi-1/chi-2 rotamer normality  :  -3.6 (poor)
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.049
  Bond angles                    :   1.108
  Omega angle restraints         :   0.402 (tight)
  Side chain planarity           :   0.259 (tight)
  Improper dihedral distribution :   0.848
  B-factor distribution          :   0.470
  Inside/Outside distribution    :   1.020
==============

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

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.