WHAT IF Check report

This file was created 2012-01-30 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 pdb3hkz.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: C and M

All-atom RMS fit for the two chains : 0.946
CA-only RMS fit for the two chains : 0.608

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 M

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: E and Q

All-atom RMS fit for the two chains : 0.923
CA-only RMS fit for the two chains : 0.600

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: E and Q

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

6687 F3S   (1001-)  D  -         Atom types
6694 F3S   (1001-)  O  -         Atom types

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: C

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Z

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

2879 ILE   (  58-)  G      CG1
2879 ILE   (  58-)  G      CG2
2879 ILE   (  58-)  G      CD1
6217 ILE   (  58-)  S      CG1
6217 ILE   (  58-)  S      CG2
6217 ILE   (  58-)  S      CD1

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 LYS   (   4-)  A    High
   7 LYS   (  10-)  A    High
  23 ALA   (  26-)  A    High
  24 ILE   (  27-)  A    High
  25 ILE   (  28-)  A    High
  26 THR   (  29-)  A    High
  27 PRO   (  30-)  A    High
  28 MET   (  45-)  A    High
  29 ASP   (  46-)  A    High
  30 PRO   (  47-)  A    High
  31 ARG   (  48-)  A    High
  32 LEU   (  49-)  A    High
  33 GLY   (  50-)  A    High
  42 PRO   (  59-)  A    High
  43 THR   (  60-)  A    High
  44 CYS   (  61-)  A    High
  45 GLY   (  62-)  A    High
  46 ASN   (  63-)  A    High
  55 PHE   (  72-)  A    High
  91 GLU   ( 108-)  A    High
  92 ASP   ( 109-)  A    High
  93 GLU   ( 110-)  A    High
  94 ILE   ( 111-)  A    High
  95 GLU   ( 112-)  A    High
  96 LYS   ( 113-)  A    High
And so on for a total of 1575 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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: C

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Z

Nomenclature related problems

Warning: Tyrosine convention problem

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

 101 TYR   ( 118-)  A
 163 TYR   ( 197-)  A
 228 TYR   ( 271-)  A
 410 TYR   ( 453-)  A
 448 TYR   ( 491-)  A
 464 TYR   ( 507-)  A
 502 TYR   ( 545-)  A
 576 TYR   ( 619-)  A
 619 TYR   ( 662-)  A
 656 TYR   ( 699-)  A
 683 TYR   ( 726-)  A
 729 TYR   ( 772-)  A
 740 TYR   ( 783-)  A
 816 TYR   ( 859-)  A
 838 TYR   (  12-)  C
 936 TYR   ( 125-)  C
 941 TYR   ( 130-)  C
 957 TYR   ( 146-)  C
1294 TYR   (  92-)  B
1353 TYR   ( 151-)  B
1515 TYR   ( 313-)  B
1516 TYR   ( 314-)  B
1519 TYR   ( 317-)  B
1528 TYR   ( 326-)  B
1540 TYR   ( 338-)  B
And so on for a total of 123 lines.

Warning: Phenylalanine convention problem

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

  55 PHE   (  72-)  A
  76 PHE   (  93-)  A
 266 PHE   ( 309-)  A
 277 PHE   ( 320-)  A
 321 PHE   ( 364-)  A
 400 PHE   ( 443-)  A
 414 PHE   ( 457-)  A
 555 PHE   ( 598-)  A
 592 PHE   ( 635-)  A
 601 PHE   ( 644-)  A
 681 PHE   ( 724-)  A
 726 PHE   ( 769-)  A
 738 PHE   ( 781-)  A
 743 PHE   ( 786-)  A
 754 PHE   ( 797-)  A
 813 PHE   ( 856-)  A
 878 PHE   (  52-)  C
1021 PHE   ( 210-)  C
1031 PHE   ( 220-)  C
1236 PHE   (  34-)  B
1354 PHE   ( 152-)  B
1499 PHE   ( 297-)  B
1552 PHE   ( 350-)  B
1560 PHE   ( 358-)  B
1563 PHE   ( 361-)  B
And so on for a total of 78 lines.

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.

 145 ASP   ( 179-)  A
 155 ASP   ( 189-)  A
 157 ASP   ( 191-)  A
 164 ASP   ( 198-)  A
 190 ASP   ( 233-)  A
 221 ASP   ( 264-)  A
 286 ASP   ( 329-)  A
 344 ASP   ( 387-)  A
 350 ASP   ( 393-)  A
 370 ASP   ( 413-)  A
 458 ASP   ( 501-)  A
 486 ASP   ( 529-)  A
 623 ASP   ( 666-)  A
 677 ASP   ( 720-)  A
 939 ASP   ( 128-)  C
 946 ASP   ( 135-)  C
 970 ASP   ( 159-)  C
 994 ASP   ( 183-)  C
1118 ASP   ( 307-)  C
1120 ASP   ( 309-)  C
1129 ASP   ( 318-)  C
1210 ASP   (   8-)  B
1246 ASP   (  44-)  B
1330 ASP   ( 128-)  B
1346 ASP   ( 144-)  B
And so on for a total of 110 lines.

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.

 148 GLU   ( 182-)  A
 220 GLU   ( 263-)  A
 237 GLU   ( 280-)  A
 298 GLU   ( 341-)  A
 365 GLU   ( 408-)  A
 432 GLU   ( 475-)  A
 501 GLU   ( 544-)  A
 535 GLU   ( 578-)  A
 575 GLU   ( 618-)  A
 606 GLU   ( 649-)  A
 621 GLU   ( 664-)  A
 628 GLU   ( 671-)  A
 734 GLU   ( 777-)  A
 840 GLU   (  14-)  C
 884 GLU   (  58-)  C
 940 GLU   ( 129-)  C
 956 GLU   ( 145-)  C
 961 GLU   ( 150-)  C
1013 GLU   ( 202-)  C
1114 GLU   ( 303-)  C
1198 GLU   ( 387-)  C
1211 GLU   (   9-)  B
1310 GLU   ( 108-)  B
1314 GLU   ( 112-)  B
1315 GLU   ( 113-)  B
And so on for a total of 122 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.

 854 ILE   (  28-)  C      CA   CB    1.64    5.3
3053 ILE   (  51-)  K      CA   CB    1.62    4.3
6391 ILE   (  51-)  U      CA   CB    1.62    4.7
6402 ILE   (  62-)  U      CA   CB    1.62    4.7

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

 |  0.996519 -0.000050  0.000018|
 | -0.000050  0.996354 -0.000028|
 |  0.000018 -0.000028  0.996615|
Proposed new scale matrix

 |  0.007976  0.000000  0.001538|
 |  0.000000  0.004987  0.000000|
 |  0.000000  0.000000  0.005213|
With corresponding cell

    A    = 125.381  B   = 200.514  C    = 195.377
    Alpha=  90.002  Beta= 100.916  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 125.820  B   = 201.235  C    = 196.050
    Alpha=  90.000  Beta= 100.920  Gamma=  90.000

Variance: 2689.642
(Under-)estimated Z-score: 38.222

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.

 421 LEU   ( 464-)  A      CA   CB   CG  131.05    4.2
 422 HIS   ( 465-)  A      CG   ND1  CE1 109.73    4.1
 819 HIS   ( 862-)  A      CG   ND1  CE1 109.75    4.2
 822 THR   ( 865-)  A      N    CA   CB  117.49    4.1
1320 ASP   ( 118-)  B      N    CA   C    99.65   -4.1
1627 HIS   ( 425-)  B      CG   ND1  CE1 109.64    4.0
1638 GLY   ( 436-)  B      N    CA   C    99.52   -4.5
1760 ASP   ( 571-)  B     -C    N    CA  129.49    4.3
1760 ASP   ( 571-)  B      N    CA   C   126.86    5.6
1791 ILE   ( 602-)  B      C    CA   CB  117.84    4.1
2123 TYR   ( 946-)  B      N    CA   C   123.18    4.3
3534 LEU   ( 239-)  I      CA   CB   CG  130.36    4.0
3778 HIS   ( 483-)  I      CG   ND1  CE1 109.84    4.2
4658 ASP   ( 118-)  J      N    CA   C    99.83   -4.1
4965 HIS   ( 425-)  J      CG   ND1  CE1 109.66    4.1
5098 ASP   ( 571-)  J     -C    N    CA  129.65    4.4
5098 ASP   ( 571-)  J      N    CA   C   126.77    5.6
5129 ILE   ( 602-)  J      C    CA   CB  118.13    4.2
5187 HIS   ( 660-)  J      CG   ND1  CE1 109.64    4.0
5214 ARG   ( 687-)  J      CG   CD   NE  118.17    4.5
6366 ARG   (  26-)  U      N    CA   C   123.45    4.4
6400 ASP   (  60-)  U      N    CA   C   124.69    4.8
6548 ARG   (  24-)  W      CB   CG   CD  105.23   -4.4
6676 ARG   (  82-)  Z     -C    N    CA  129.29    4.2

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.

 145 ASP   ( 179-)  A
 148 GLU   ( 182-)  A
 155 ASP   ( 189-)  A
 157 ASP   ( 191-)  A
 164 ASP   ( 198-)  A
 190 ASP   ( 233-)  A
 220 GLU   ( 263-)  A
 221 ASP   ( 264-)  A
 237 GLU   ( 280-)  A
 286 ASP   ( 329-)  A
 298 GLU   ( 341-)  A
 344 ASP   ( 387-)  A
 350 ASP   ( 393-)  A
 365 GLU   ( 408-)  A
 370 ASP   ( 413-)  A
 432 GLU   ( 475-)  A
 458 ASP   ( 501-)  A
 486 ASP   ( 529-)  A
 501 GLU   ( 544-)  A
 535 GLU   ( 578-)  A
 575 GLU   ( 618-)  A
 606 GLU   ( 649-)  A
 621 GLU   ( 664-)  A
 623 ASP   ( 666-)  A
 628 GLU   ( 671-)  A
And so on for a total of 232 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.

 892 PRO   (  66-)  C      N     -6.4   -23.41    -2.48
4230 PRO   (  66-)  M      N     -6.0   -22.19    -2.48
The average deviation= 0.929

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.

4711 ARG   ( 171-)  J    5.98
 465 LEU   ( 508-)  A    5.57
1373 ARG   ( 171-)  B    5.57
1760 ASP   ( 571-)  B    5.28
5098 ASP   ( 571-)  J    5.25
5901 LYS   (   3-)  Q    5.23
 560 ILE   ( 603-)  A    5.17
4446 ILE   ( 297-)  M    5.07
2900 THR   (  79-)  G    5.06
1638 GLY   ( 436-)  B    5.04
6293 ILE   (  25-)  T    5.02
 850 LEU   (  24-)  C    4.96
3803 LEU   ( 508-)  I    4.95
6106 ASN   (  32-)  R    4.90
4437 ALA   ( 288-)  M    4.84
2367 ALA   (  72-)  D    4.79
1517 LEU   ( 315-)  B    4.78
 880 LEU   (  54-)  C    4.70
4890 PHE   ( 350-)  J    4.67
2123 TYR   ( 946-)  B    4.56
6465 ARG   (  33-)  V    4.55
6366 ARG   (  26-)  U    4.55
6400 ASP   (  60-)  U    4.54
1232 SER   (  30-)  B    4.53
 918 LEU   ( 107-)  C    4.50
And so on for a total of 53 lines.

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 : -5.702

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.

2122 PHE   ( 945-)  B    -3.7
4276 THR   ( 127-)  M    -3.7
 930 THR   ( 119-)  C    -3.7
5460 PHE   ( 945-)  J    -3.7
4733 THR   ( 193-)  J    -3.6
1395 THR   ( 193-)  B    -3.5
4208 THR   (  44-)  M    -3.5
3381 THR   (  60-)  I    -3.5
  43 THR   (  60-)  A    -3.4
1253 THR   (  51-)  B    -3.4
4591 THR   (  51-)  J    -3.4
1040 THR   ( 229-)  C    -3.4
 602 THR   ( 645-)  A    -3.3
3940 THR   ( 645-)  I    -3.3
2945 TYR   (  15-)  H    -3.3
6476 TYR   (  44-)  V    -3.3
2125 THR   ( 948-)  B    -3.2
2626 THR   (  66-)  E    -3.2
4538 THR   ( 389-)  M    -3.2
5463 THR   ( 948-)  J    -3.2
5768 THR   ( 135-)  O    -3.2
1200 THR   ( 389-)  C    -3.2
1134 THR   ( 323-)  C    -3.2
 938 THR   ( 127-)  C    -3.2
2430 THR   ( 135-)  D    -3.1
And so on for a total of 870 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.

  36 GLU   (  53-)  A  Poor phi/psi
  39 GLN   (  56-)  A  Poor phi/psi
  41 CYS   (  58-)  A  Poor phi/psi
  43 THR   (  60-)  A  Poor phi/psi
  45 GLY   (  62-)  A  omega poor
  47 THR   (  64-)  A  Poor phi/psi
  54 HIS   (  71-)  A  omega poor
  59 GLU   (  76-)  A  Poor phi/psi
  61 VAL   (  78-)  A  omega poor
  78 LYS   (  95-)  A  omega poor
  79 ALA   (  96-)  A  Poor phi/psi
  80 THR   (  97-)  A  Poor phi/psi
  82 ARG   (  99-)  A  Poor phi/psi
  83 ARG   ( 100-)  A  Poor phi/psi
  84 CYS   ( 101-)  A  Poor phi/psi
  86 ARG   ( 103-)  A  Poor phi/psi
  87 VAL   ( 104-)  A  Poor phi/psi
  88 LYS   ( 105-)  A  Poor phi/psi
  89 ILE   ( 106-)  A  Poor phi/psi
  91 GLU   ( 108-)  A  omega poor
 101 TYR   ( 118-)  A  Poor phi/psi
 104 ILE   ( 121-)  A  Poor phi/psi
 125 LYS   ( 142-)  A  Poor phi/psi
 126 ALA   ( 143-)  A  Poor phi/psi
 131 HIS   ( 148-)  A  Poor phi/psi
And so on for a total of 1178 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 : -6.248

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.

4408 SER   ( 259-)  M    0.34
1933 SER   ( 744-)  B    0.35
5271 SER   ( 744-)  J    0.36
 461 SER   ( 504-)  A    0.36
4447 SER   ( 298-)  M    0.37
2356 ARG   (  61-)  D    0.38
2752 VAL   (  16-)  F    0.38
4299 GLU   ( 150-)  M    0.38
5119 GLU   ( 592-)  J    0.38

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!

   4 LYS   (   7-)  A      0
   8 PHE   (  11-)  A      0
  20 SER   (  23-)  A      0
  21 VAL   (  24-)  A      0
  22 THR   (  25-)  A      0
  23 ALA   (  26-)  A      0
  24 ILE   (  27-)  A      0
  25 ILE   (  28-)  A      0
  26 THR   (  29-)  A      0
  27 PRO   (  30-)  A      0
  28 MET   (  45-)  A      0
  29 ASP   (  46-)  A      0
  30 PRO   (  47-)  A      0
  31 ARG   (  48-)  A      0
  32 LEU   (  49-)  A      0
  35 ILE   (  52-)  A      0
  36 GLU   (  53-)  A      0
  37 PRO   (  54-)  A      0
  39 GLN   (  56-)  A      0
  41 CYS   (  58-)  A      0
  42 PRO   (  59-)  A      0
  43 THR   (  60-)  A      0
  44 CYS   (  61-)  A      0
  47 THR   (  64-)  A      0
  48 LEU   (  65-)  A      0
And so on for a total of 3354 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.889

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!

4485 GLY   ( 336-)  M   3.17   31
6386 GLY   (  46-)  U   3.05   80
 705 GLY   ( 748-)  A   3.00   15
6552 GLY   (  28-)  W   2.99   80
3214 GLY   (  28-)  N   2.95   80
4043 GLY   ( 748-)  I   2.89   17
6259 GLY   ( 100-)  S   2.51   12
2647 GLY   (  87-)  E   2.46   17
2622 GLY   (  62-)  E   2.46   12
2921 GLY   ( 100-)  G   2.42   12
 746 GLY   ( 789-)  A   2.40   10
5767 GLY   ( 134-)  O   2.40   17
2429 GLY   ( 134-)  D   2.32   14
3048 GLY   (  46-)  K   2.30   80
4084 GLY   ( 789-)  I   2.29   11
2765 GLY   (  29-)  F   2.22   14
1530 GLY   ( 328-)  B   2.13   57
5539 GLY   (1024-)  J   2.11   23
2201 GLY   (1024-)  B   2.06   23
4868 GLY   ( 328-)  J   2.03   48
3602 GLY   ( 307-)  I   1.95   22
 264 GLY   ( 307-)  A   1.89   20
 689 GLY   ( 732-)  A   1.88   68
1859 SER   ( 670-)  B   1.84   11
4027 GLY   ( 732-)  I   1.79   63
4327 GLY   ( 178-)  M   1.78   41
 162 GLY   ( 196-)  A   1.72   28
5652 GLY   (  19-)  O   1.71   80
3500 GLY   ( 196-)  I   1.68   37
3530 LEU   ( 235-)  I   1.67   62
 192 LEU   ( 235-)  A   1.66   53
4595 GLY   (  55-)  J   1.66   74
1257 GLY   (  55-)  B   1.65   75
4601 GLY   (  61-)  J   1.64   12
2318 GLU   (  23-)  D   1.64   76
6027 GLY   ( 129-)  Q   1.63   27
1263 GLY   (  61-)  B   1.63   12
 733 PRO   ( 776-)  A   1.62   14
4071 PRO   ( 776-)  I   1.61   19
6613 GLY   (  30-)  X   1.61   23
5112 GLY   ( 585-)  J   1.61   10
2314 GLY   (  19-)  D   1.58   80
3074 GLY   (  72-)  K   1.55   54
4506 ALA   ( 357-)  M   1.54   14
5656 GLU   (  23-)  O   1.54   13
2689 GLY   ( 129-)  E   1.54   21
3275 GLY   (  30-)  P   1.54   24
5994 GLY   (  96-)  Q   1.52   19
6378 ALA   (  38-)  U   1.51   12
3131 GLY   (  37-)  L   1.51   10

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...

1200 THR   ( 389-)  C   1.57

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]

1589 PRO   ( 387-)  B    0.13 LOW
2070 PRO   ( 893-)  B    0.14 LOW
4927 PRO   ( 387-)  J    0.15 LOW
5408 PRO   ( 893-)  J    0.18 LOW
5421 PRO   ( 906-)  J    0.19 LOW

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].

  13 PRO   (  16-)  A   -60.3 half-chair C-beta/C-alpha (-54 degrees)
  27 PRO   (  30-)  A    14.1 half-chair N/C-delta (18 degrees)
  30 PRO   (  47-)  A    -5.9 envelop N (0 degrees)
  42 PRO   (  59-)  A   -38.6 envelop C-alpha (-36 degrees)
  52 PRO   (  69-)  A  -121.5 half-chair C-delta/C-gamma (-126 degrees)
  63 PRO   (  80-)  A   119.3 half-chair C-beta/C-alpha (126 degrees)
 109 PRO   ( 126-)  A   120.4 half-chair C-beta/C-alpha (126 degrees)
 130 PRO   ( 147-)  A     7.0 envelop N (0 degrees)
 182 PRO   ( 216-)  A  -117.1 half-chair C-delta/C-gamma (-126 degrees)
 187 PRO   ( 221-)  A   -25.4 half-chair C-alpha/N (-18 degrees)
 215 PRO   ( 258-)  A    42.5 envelop C-delta (36 degrees)
 239 PRO   ( 282-)  A    37.0 envelop C-delta (36 degrees)
 242 PRO   ( 285-)  A  -173.7 envelop N (180 degrees)
 243 PRO   ( 286-)  A   -25.8 half-chair C-alpha/N (-18 degrees)
 312 PRO   ( 355-)  A  -143.5 envelop C-delta (-144 degrees)
 326 PRO   ( 369-)  A   -41.3 envelop C-alpha (-36 degrees)
 360 PRO   ( 403-)  A   152.7 envelop C-alpha (144 degrees)
 409 PRO   ( 452-)  A  -126.0 half-chair C-delta/C-gamma (-126 degrees)
 494 PRO   ( 537-)  A   114.2 envelop C-beta (108 degrees)
 538 PRO   ( 581-)  A  -176.0 envelop N (180 degrees)
 565 PRO   ( 608-)  A   155.3 half-chair C-alpha/N (162 degrees)
 643 PRO   ( 686-)  A   -55.9 half-chair C-beta/C-alpha (-54 degrees)
 645 PRO   ( 688-)  A  -121.2 half-chair C-delta/C-gamma (-126 degrees)
 678 PRO   ( 721-)  A   103.1 envelop C-beta (108 degrees)
 728 PRO   ( 771-)  A  -119.6 half-chair C-delta/C-gamma (-126 degrees)
And so on for a total of 154 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.

  51 CYS   (  68-)  A      SG  <->   54 HIS   (  71-)  A      NE2    1.04    2.26  INTRA BF
3389 CYS   (  68-)  I      SG  <-> 3392 HIS   (  71-)  I      NE2    1.02    2.28  INTRA BF
3870 CYS   ( 575-)  I      SG  <-> 3875 CYS   ( 580-)  I      SG     0.92    2.53  INTRA BL
2498 CYS   ( 203-)  D      SG  <-> 6687 F3S   (1001-)  D      S3     0.79    2.81  INTRA BF
2210 ARG   (1033-)  B      NH1 <-> 2211 ASP   (1034-)  B      OD1    0.78    1.92  INTRA BL
 532 CYS   ( 575-)  A      SG  <->  537 CYS   ( 580-)  A      SG     0.71    2.74  INTRA BL
5548 ARG   (1033-)  J      NH1 <-> 5549 ASP   (1034-)  J      OD1    0.70    2.00  INTRA BL
5013 MET   ( 473-)  J      SD  <-> 5015 GLN   ( 475-)  J      N      0.69    2.61  INTRA BL
2047 ARG   ( 870-)  B      CZ  <-> 2173 MET   ( 996-)  B      SD     0.65    2.75  INTRA BL
5836 CYS   ( 203-)  O      SG  <-> 6694 F3S   (1001-)  O      S3     0.64    2.96  INTRA BF
 834 GLY   ( 877-)  A      C   <-> 4917 ARG   ( 377-)  J      NH1    0.63    2.47  INTRA BL
4170 VAL   ( 875-)  I      O   <-> 4172 GLY   ( 877-)  I      N      0.62    2.08  INTRA BL
5013 MET   ( 473-)  J      SD  <-> 5014 ALA   ( 474-)  J      N      0.62    2.58  INTRA BL
5816 CYS   ( 183-)  O      SG  <-> 6694 F3S   (1001-)  O      S1     0.60    3.00  INTRA BF
 798 LEU   ( 841-)  A      O   <->  800 GLY   ( 843-)  A      N      0.60    2.10  INTRA BL
 832 VAL   ( 875-)  A      O   <->  834 GLY   ( 877-)  A      N      0.60    2.10  INTRA BL
  51 CYS   (  68-)  A      SG  <->   54 HIS   (  71-)  A      CE1    0.58    2.82  INTRA BF
 498 ALA   ( 541-)  A      CB  <->  499 PRO   ( 542-)  A      CD     0.58    2.52  INTRA BL
1675 MET   ( 473-)  B      SD  <-> 1677 GLN   ( 475-)  B      N      0.58    2.72  INTRA BL
 547 ASN   ( 590-)  A      ND2 <-> 4917 ARG   ( 377-)  J      CB     0.57    2.53  INTRA BF
4263 LYS   ( 114-)  M      O   <-> 4265 VAL   ( 116-)  M      N      0.57    2.13  INTRA BF
5327 PRO   ( 800-)  J      O   <-> 5329 VAL   ( 802-)  J      N      0.56    2.14  INTRA BL
2959 TYR   (  29-)  H      OH  <-> 3323 LEU   (  67-)  Y      CD2    0.55    2.25  INTRA BF
2504 CYS   ( 209-)  D      SG  <-> 6687 F3S   (1001-)  D      S1     0.54    3.06  INTRA BF
5842 CYS   ( 209-)  O      SG  <-> 6694 F3S   (1001-)  O      S2     0.54    3.06  INTRA BF
And so on for a total of 2413 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: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

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.

6611 TYR   (  28-)  X      -8.92
 838 TYR   (  12-)  C      -8.81
4176 TYR   (  12-)  M      -8.62
3273 TYR   (  28-)  P      -8.56
3585 ARG   ( 290-)  I      -8.48
 247 ARG   ( 290-)  A      -8.46
6675 ARG   (  81-)  Z      -8.28
4615 ARG   (  75-)  J      -7.98
1277 ARG   (  75-)  B      -7.94
 137 TYR   ( 154-)  A      -7.91
1579 ARG   ( 377-)  B      -7.81
3475 TYR   ( 154-)  I      -7.66
6258 TYR   (  99-)  S      -7.55
6366 ARG   (  26-)  U      -7.49
2183 ARG   (1006-)  B      -7.46
 241 LEU   ( 284-)  A      -7.45
3579 LEU   ( 284-)  I      -7.45
  83 ARG   ( 100-)  A      -7.45
3421 ARG   ( 100-)  I      -7.41
3028 ARG   (  26-)  K      -7.37
6672 ARG   (  78-)  Z      -7.36
4737 ARG   ( 197-)  J      -7.35
4067 TYR   ( 772-)  I      -7.34
5521 ARG   (1006-)  J      -7.32
2920 TYR   (  99-)  G      -7.28
And so on for a total of 317 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.

  34 VAL   (  51-)  A        36 - GLU     53- ( A)         -4.97
 133 ASN   ( 150-)  A       138 - LYS    155- ( A)         -5.94
 267 ARG   ( 310-)  A       269 - ASN    312- ( A)         -4.54
 529 PRO   ( 572-)  A       531 - LEU    574- ( A)         -4.90
 910 GLN   (  84-)  C       912 - THR     86- ( C)         -5.14
 999 ILE   ( 188-)  C      1004 - LEU    193- ( C)         -5.00
1574 SER   ( 372-)  B      1579 - ARG    377- ( B)         -5.29
1637 ARG   ( 435-)  B      1639 - GLN    437- ( B)         -4.91
1953 LYS   ( 764-)  B      1955 - PRO    766- ( B)         -5.04
2122 PHE   ( 945-)  B      2124 - LYS    947- ( B)         -5.77
2250 ASN   (1073-)  B      2252 - ASN   1075- ( B)         -4.36
3331 TYR   (  75-)  Y      3335 - ASP     79- ( Y)         -5.28
3372 VAL   (  51-)  I      3374 - GLU     53- ( I)         -4.95
3471 ASN   ( 150-)  I      3476 - LYS    155- ( I)         -5.89
3605 ARG   ( 310-)  I      3607 - ASN    312- ( I)         -4.51
3867 PRO   ( 572-)  I      3869 - LEU    574- ( I)         -4.91
4248 GLN   (  84-)  M      4250 - THR     86- ( M)         -4.64
4337 ILE   ( 188-)  M      4342 - LEU    193- ( M)         -5.41
4869 ARG   ( 329-)  J      4871 - GLU    331- ( J)         -4.78
4912 SER   ( 372-)  J      4915 - ARG    375- ( J)         -4.89
4975 ARG   ( 435-)  J      4977 - GLN    437- ( J)         -4.86
5291 LYS   ( 764-)  J      5293 - PRO    766- ( J)         -5.08
5460 PHE   ( 945-)  J      5462 - LYS    947- ( J)         -5.86
5588 ASN   (1073-)  J      5590 - ASN   1075- ( J)         -4.37
6256 SER   (  97-)  S      6258 - TYR     99- ( S)         -6.13

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 6676 : -1.699

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: 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: 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: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

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

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: P

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: Y

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: M

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: Q

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: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

Note: Quality value plot

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

Chain identifier: V

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: W

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: X

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: Z

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.

4534 MET   ( 385-)  M   -3.17
1196 MET   ( 385-)  C   -3.13
4913 LYS   ( 373-)  J   -3.12
1575 LYS   ( 373-)  B   -3.09
4816 VAL   ( 276-)  J   -2.95
5116 VAL   ( 589-)  J   -2.90
5213 LEU   ( 686-)  J   -2.89
1778 VAL   ( 589-)  B   -2.89
1875 LEU   ( 686-)  B   -2.89
 185 ILE   ( 219-)  A   -2.62
3246 ILE   (  60-)  N   -2.59
5788 LYS   ( 155-)  O   -2.59
2450 LYS   ( 155-)  D   -2.58
3417 ALA   (  96-)  I   -2.55
1822 LEU   ( 633-)  B   -2.54
5600 LYS   (1085-)  J   -2.53
5160 LEU   ( 633-)  J   -2.53
  79 ALA   (  96-)  A   -2.52
2227 LEU   (1050-)  B   -2.51
 395 LEU   ( 438-)  A   -2.51

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.

 816 TYR   ( 859-)  A     -  819 HIS   ( 862-)  A        -1.77
1813 ALA   ( 624-)  B     - 1817 LEU   ( 628-)  B        -1.59
4970 ILE   ( 430-)  J     - 4973 LEU   ( 433-)  J        -1.74
5151 ALA   ( 624-)  J     - 5155 LEU   ( 628-)  J        -1.62

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: C

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Z

Water, ion, and hydrogenbond related checks

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.

   2 ASN   (   5-)  A
 194 HIS   ( 237-)  A
 229 HIS   ( 272-)  A
 269 ASN   ( 312-)  A
 320 GLN   ( 363-)  A
 379 GLN   ( 422-)  A
 403 ASN   ( 446-)  A
 422 HIS   ( 465-)  A
 442 ASN   ( 485-)  A
 479 GLN   ( 522-)  A
 518 ASN   ( 561-)  A
 680 ASN   ( 723-)  A
 725 HIS   ( 768-)  A
 902 GLN   (  76-)  C
 910 GLN   (  84-)  C
1123 HIS   ( 312-)  C
1308 ASN   ( 106-)  B
1334 GLN   ( 132-)  B
1451 GLN   ( 249-)  B
1492 GLN   ( 290-)  B
1493 GLN   ( 291-)  B
1502 HIS   ( 300-)  B
1570 GLN   ( 368-)  B
1648 HIS   ( 446-)  B
1651 GLN   ( 449-)  B
And so on for a total of 96 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.

   4 LYS   (   7-)  A      N
   5 GLY   (   8-)  A      N
   9 GLY   (  12-)  A      N
  11 LEU   (  14-)  A      N
  15 GLU   (  18-)  A      N
  31 ARG   (  48-)  A      N
  32 LEU   (  49-)  A      N
  33 GLY   (  50-)  A      N
  34 VAL   (  51-)  A      N
  41 CYS   (  58-)  A      N
  44 CYS   (  61-)  A      N
  45 GLY   (  62-)  A      N
  46 ASN   (  63-)  A      N
  46 ASN   (  63-)  A      ND2
  50 ASN   (  67-)  A      N
  51 CYS   (  68-)  A      N
  53 GLY   (  70-)  A      N
  54 HIS   (  71-)  A      N
  54 HIS   (  71-)  A      ND1
  59 GLU   (  76-)  A      N
  62 ARG   (  79-)  A      N
  65 ILE   (  82-)  A      N
  67 VAL   (  84-)  A      N
  80 THR   (  97-)  A      N
  82 ARG   (  99-)  A      N
And so on for a total of 1568 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.

 171 GLU   ( 205-)  A      OE2
 367 HIS   ( 410-)  A      ND1
 383 HIS   ( 426-)  A      NE2
 425 GLN   ( 468-)  A      OE1
 507 GLN   ( 550-)  A      OE1
 556 ASP   ( 599-)  A      OD1
 562 ASN   ( 605-)  A      OD1
 570 HIS   ( 613-)  A      ND1
 621 GLU   ( 664-)  A      OE2
 824 ASP   ( 867-)  A      OD1
 856 ASP   (  30-)  C      OD1
 866 GLU   (  40-)  C      OE1
 873 GLU   (  47-)  C      OE1
1025 ASP   ( 214-)  C      OD1
1087 ASN   ( 276-)  C      OD1
1098 GLU   ( 287-)  C      OE2
1102 GLU   ( 291-)  C      OE1
1120 ASP   ( 309-)  C      OD2
1183 ASN   ( 372-)  C      OD1
1228 GLN   (  26-)  B      OE1
1229 HIS   (  27-)  B      ND1
1250 GLU   (  48-)  B      OE1
1345 GLU   ( 143-)  B      OE1
1366 GLN   ( 164-)  B      OE1
1405 GLU   ( 203-)  B      OE1
And so on for a total of 125 lines.

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+.

6685  MG   (1003-)  A     0.39   0.78 Is perhaps NA
6692  MG   (1003-)  I     0.39   0.79 Is perhaps NA
Since there are no waters, the water check has been skipped.

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.

  92 ASP   ( 109-)  A   H-bonding suggests Asn; but Alt-Rotamer
 134 GLU   ( 151-)  A   H-bonding suggests Gln
 171 GLU   ( 205-)  A   H-bonding suggests Gln; but Alt-Rotamer
 204 GLU   ( 247-)  A   H-bonding suggests Gln
 211 ASP   ( 254-)  A   H-bonding suggests Asn
 224 ASP   ( 267-)  A   H-bonding suggests Asn
 286 ASP   ( 329-)  A   H-bonding suggests Asn; but Alt-Rotamer
 316 GLU   ( 359-)  A   H-bonding suggests Gln
 552 GLU   ( 595-)  A   H-bonding suggests Gln
 579 GLU   ( 622-)  A   H-bonding suggests Gln
 586 ASP   ( 629-)  A   H-bonding suggests Asn
 623 ASP   ( 666-)  A   H-bonding suggests Asn
 659 ASP   ( 702-)  A   H-bonding suggests Asn
 761 GLU   ( 804-)  A   H-bonding suggests Gln; but Alt-Rotamer
 810 ASP   ( 853-)  A   H-bonding suggests Asn
 840 GLU   (  14-)  C   H-bonding suggests Gln; but Alt-Rotamer
 872 ASP   (  46-)  C   H-bonding suggests Asn; but Alt-Rotamer
 873 GLU   (  47-)  C   H-bonding suggests Gln; but Alt-Rotamer
 970 ASP   ( 159-)  C   H-bonding suggests Asn; but Alt-Rotamer
 987 ASP   ( 176-)  C   H-bonding suggests Asn; but Alt-Rotamer
1006 ASP   ( 195-)  C   H-bonding suggests Asn; but Alt-Rotamer
1025 ASP   ( 214-)  C   H-bonding suggests Asn
1093 GLU   ( 282-)  C   H-bonding suggests Gln
1120 ASP   ( 309-)  C   H-bonding suggests Asn
1148 GLU   ( 337-)  C   H-bonding suggests Gln
And so on for a total of 128 lines.

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 :  -2.999
  2nd generation packing quality :  -3.223 (poor)
  Ramachandran plot appearance   :  -5.702 (bad)
  chi-1/chi-2 rotamer normality  :  -6.248 (bad)
  Backbone conformation          :  -1.664

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.593 (tight)
  Bond angles                    :   0.782
  Omega angle restraints         :   1.434 (loose)
  Side chain planarity           :   0.408 (tight)
  Improper dihedral distribution :   0.814
  B-factor distribution          :   0.398
  Inside/Outside distribution    :   1.096

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 : 3.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.5
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -2.6
  chi-1/chi-2 rotamer normality  :  -3.6 (poor)
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.593 (tight)
  Bond angles                    :   0.782
  Omega angle restraints         :   1.434 (loose)
  Side chain planarity           :   0.408 (tight)
  Improper dihedral distribution :   0.814
  B-factor distribution          :   0.398
  Inside/Outside distribution    :   1.096
==============

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.