WHAT IF Check report

This file was created 2013-12-09 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 pdb3rik.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 107.980  B   =  91.553  C    = 152.213
    Alpha=  90.000  Beta= 110.700  Gamma=  90.000

Dimensions of a reduced cell

    A    =  91.553  B   = 107.980  C    = 152.213
    Alpha= 110.700  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 107.980  B   = 284.774  C    =  91.553
    Alpha=  90.000  Beta=  90.000  Gamma=  89.925

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 |  1.000000  0.000000  2.000000|
 |  0.000000 -1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: 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 B

All-atom RMS fit for the two chains : 1.265
CA-only RMS fit for the two chains : 0.894

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 : 0.418
CA-only RMS fit for the two chains : 0.185

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 : 1.295
CA-only RMS fit for the two chains : 0.903

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 : 1.258
CA-only RMS fit for the two chains : 0.874

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 : 0.402
CA-only RMS fit for the two chains : 0.209

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: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

2003 3RI   ( 501-)  B  -
2028 3RI   ( 501-)  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.

 815 ALA   ( 318-)  B    High
1808 LEU   ( 317-)  D    High
1809 ALA   ( 318-)  D    High

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: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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

  11 TYR   (  11-)  A
  22 TYR   (  22-)  A
 108 TYR   ( 108-)  A
 116 TYR   ( 116-)  A
 135 TYR   ( 135-)  A
 205 TYR   ( 205-)  A
 212 TYR   ( 212-)  A
 304 TYR   ( 304-)  A
 373 TYR   ( 373-)  A
 412 TYR   ( 412-)  A
 487 TYR   ( 487-)  A
 508 TYR   (  11-)  B
 519 TYR   (  22-)  B
 605 TYR   ( 108-)  B
 613 TYR   ( 116-)  B
 632 TYR   ( 135-)  B
 709 TYR   ( 212-)  B
 801 TYR   ( 304-)  B
 810 TYR   ( 313-)  B
 870 TYR   ( 373-)  B
 909 TYR   ( 412-)  B
 915 TYR   ( 418-)  B
 984 TYR   ( 487-)  B
 989 TYR   ( 492-)  B
1005 TYR   (  11-)  C
1016 TYR   (  22-)  C
1102 TYR   ( 108-)  C
1110 TYR   ( 116-)  C
1127 TYR   ( 133-)  C
1129 TYR   ( 135-)  C
1199 TYR   ( 205-)  C
1206 TYR   ( 212-)  C
1298 TYR   ( 304-)  C
1367 TYR   ( 373-)  C
1406 TYR   ( 412-)  C
1481 TYR   ( 487-)  C
1502 TYR   (  11-)  D
1513 TYR   (  22-)  D
1599 TYR   ( 108-)  D
1607 TYR   ( 116-)  D
1626 TYR   ( 135-)  D
1696 TYR   ( 205-)  D
1703 TYR   ( 212-)  D
1795 TYR   ( 304-)  D
1804 TYR   ( 313-)  D
1864 TYR   ( 373-)  D
1903 TYR   ( 412-)  D
1909 TYR   ( 418-)  D
1978 TYR   ( 487-)  D
1983 TYR   ( 492-)  D

Warning: Phenylalanine convention problem

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

  26 PHE   (  26-)  A
  75 PHE   (  75-)  A
 109 PHE   ( 109-)  A
 142 PHE   ( 142-)  A
 147 PHE   ( 147-)  A
 246 PHE   ( 246-)  A
 331 PHE   ( 331-)  A
 337 PHE   ( 337-)  A
 411 PHE   ( 411-)  A
 417 PHE   ( 417-)  A
 426 PHE   ( 426-)  A
 523 PHE   (  26-)  B
 572 PHE   (  75-)  B
 606 PHE   ( 109-)  B
 625 PHE   ( 128-)  B
 639 PHE   ( 142-)  B
 644 PHE   ( 147-)  B
 724 PHE   ( 227-)  B
 748 PHE   ( 251-)  B
 813 PHE   ( 316-)  B
 828 PHE   ( 331-)  B
 908 PHE   ( 411-)  B
 914 PHE   ( 417-)  B
 920 PHE   ( 423-)  B
 923 PHE   ( 426-)  B
And so on for a total of 54 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.

 315 ASP   ( 315-)  A
 812 ASP   ( 315-)  B
1147 ASP   ( 153-)  C
1644 ASP   ( 153-)  D
1806 ASP   ( 315-)  D
1849 ASP   ( 358-)  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.

  50 GLU   (  50-)  A
  72 GLU   (  72-)  A
 151 GLU   ( 151-)  A
 648 GLU   ( 151-)  B
 797 GLU   ( 300-)  B
 823 GLU   ( 326-)  B
1044 GLU   (  50-)  C
1066 GLU   (  72-)  C
1145 GLU   ( 151-)  C
1382 GLU   ( 388-)  C
1642 GLU   ( 151-)  D
1791 GLU   ( 300-)  D
1817 GLU   ( 326-)  D
1831 GLU   ( 340-)  D
1840 GLU   ( 349-)  D

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.

  60 HIS   (  60-)  A      CG   CD2   1.40    4.4
 184 TRP   ( 184-)  A      CD2  CE2   1.49    4.7
 206 HIS   ( 206-)  A      CG   CD2   1.41    4.5
 255 HIS   ( 255-)  A      CG   CD2   1.41    4.7
 273 HIS   ( 273-)  A      CG   CD2   1.40    4.1
 290 HIS   ( 290-)  A      CG   CD2   1.41    4.8
 291 TRP   ( 291-)  A      CD2  CE2   1.49    4.8
 381 TRP   ( 381-)  A      CD2  CE2   1.48    4.3
 419 HIS   ( 419-)  A      CG   CD2   1.41    4.5
 451 HIS   ( 451-)  A      CG   CD2   1.40    4.0
 495 HIS   ( 495-)  A      CG   CD2   1.41    4.7
 642 HIS   ( 145-)  B      CG   CD2   1.43    6.5
 659 HIS   ( 162-)  B      CG   CD2   1.41    4.7
 681 TRP   ( 184-)  B      CD2  CE2   1.50    5.1
 703 HIS   ( 206-)  B      CG   CD2   1.42    5.6
 770 HIS   ( 273-)  B      CG   CD2   1.41    4.9
 771 HIS   ( 274-)  B      CG   CD2   1.40    4.4
 788 TRP   ( 291-)  B      CD2  CE2   1.49    5.0
 808 HIS   ( 311-)  B      CG   CD2   1.41    5.3
 825 HIS   ( 328-)  B      CG   CD2   1.42    5.6
 825 HIS   ( 328-)  B      ND1  CE1   1.37    4.0
 845 TRP   ( 348-)  B      CD2  CE2   1.49    4.5
 871 HIS   ( 374-)  B      CG   CD2   1.40    4.0
 875 TRP   ( 378-)  B      CD2  CE2   1.49    4.5
 890 TRP   ( 393-)  B      CD2  CE2   1.48    4.5
And so on for a total of 65 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

 |  0.997898  0.000153  0.000064|
 |  0.000153  0.998520 -0.000043|
 |  0.000064 -0.000043  0.998440|
Proposed new scale matrix

 |  0.009280 -0.000001  0.003504|
 | -0.000002  0.010939  0.000000|
 |  0.000000  0.000000  0.007034|
With corresponding cell

    A    = 107.756  B   =  91.414  C    = 151.964
    Alpha=  90.007  Beta= 110.685  Gamma=  89.983

The CRYST1 cell dimensions

    A    = 107.980  B   =  91.553  C    = 152.213
    Alpha=  90.000  Beta= 110.700  Gamma=  90.000

Variance: 200.585
(Under-)estimated Z-score: 10.438

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.

  44 ARG   (  44-)  A      CB   CG   CD  103.84   -5.1
  47 ARG   (  47-)  A      CB   CG   CD  105.61   -4.2
  60 HIS   (  60-)  A      CG   ND1  CE1 109.66    4.1
  73 GLN   (  73-)  A      CA   CB   CG  123.50    4.7
 145 HIS   ( 145-)  A      CG   ND1  CE1 109.76    4.2
 318 ALA   ( 318-)  A     -C    N    CA  129.03    4.1
 343 VAL   ( 343-)  A     -C    N    CA  129.28    4.2
 343 VAL   ( 343-)  A      N    CA   C    99.31   -4.2
 343 VAL   ( 343-)  A      N    CA   CB  117.90    4.4
 345 SER   ( 345-)  A     -C    N    CA  130.31    4.8
 350 GLN   ( 350-)  A      CB   CG   CD  121.13    5.0
 422 HIS   ( 422-)  A      CG   ND1  CE1 109.99    4.4
 433 ARG   ( 433-)  A      CG   CD   NE  101.34   -5.4
 502 ILE   (   5-)  B      CG2  CB   CG1  96.56   -4.7
 541 ARG   (  44-)  B      CB   CG   CD  101.45   -6.3
 787 HIS   ( 290-)  B      CG   ND1  CE1 109.75    4.1
 815 ALA   ( 318-)  B     -C    N    CA  129.06    4.1
 816 PRO   ( 319-)  B     -C    N    CA  146.75    4.8
 816 PRO   ( 319-)  B     -C    N    CD  105.24   -4.8
 816 PRO   ( 319-)  B      N    CA   C   122.82    4.4
 844 PHE   ( 347-)  B      N    CA   C   123.52    4.4
 845 TRP   ( 348-)  B     -C    N    CA  131.87    5.6
 845 TRP   ( 348-)  B      C    CA   CB  118.63    4.5
 862 HIS   ( 365-)  B      CG   ND1  CE1 109.73    4.1
 891 VAL   ( 394-)  B      C    CA   CB  119.23    4.8
 916 HIS   ( 419-)  B      CG   ND1  CE1 109.81    4.2
 948 HIS   ( 451-)  B      CG   ND1  CE1 109.65    4.0
1038 ARG   (  44-)  C      CB   CG   CD  105.36   -4.4
1054 HIS   (  60-)  C      CG   ND1  CE1 109.80    4.2
1114 ARG   ( 120-)  C      CB   CG   CD  104.13   -5.0
1139 HIS   ( 145-)  C      CG   ND1  CE1 109.64    4.0
1156 HIS   ( 162-)  C      CG   ND1  CE1 110.01    4.4
1217 HIS   ( 223-)  C      CG   ND1  CE1 109.67    4.1
1322 HIS   ( 328-)  C      CG   ND1  CE1 109.65    4.0
1337 VAL   ( 343-)  C      N    CA   CB  117.81    4.3
1344 GLN   ( 350-)  C      CB   CG   CD  120.11    4.4
1359 HIS   ( 365-)  C      CG   ND1  CE1 109.95    4.4
1416 HIS   ( 422-)  C      CG   ND1  CE1 109.99    4.4
1427 ARG   ( 433-)  C      CG   CD   NE  101.57   -5.3
1781 HIS   ( 290-)  D      CG   ND1  CE1 109.72    4.1
1802 HIS   ( 311-)  D      CG   ND1  CE1 109.60    4.0
1885 VAL   ( 394-)  D      C    CA   CB  119.09    4.7
1942 HIS   ( 451-)  D      N    CA   CB  102.64   -4.6

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.

  50 GLU   (  50-)  A
  72 GLU   (  72-)  A
 151 GLU   ( 151-)  A
 315 ASP   ( 315-)  A
 648 GLU   ( 151-)  B
 797 GLU   ( 300-)  B
 812 ASP   ( 315-)  B
 823 GLU   ( 326-)  B
1044 GLU   (  50-)  C
1066 GLU   (  72-)  C
1145 GLU   ( 151-)  C
1147 ASP   ( 153-)  C
1382 GLU   ( 388-)  C
1642 GLU   ( 151-)  D
1644 ASP   ( 153-)  D
1791 GLU   ( 300-)  D
1806 ASP   ( 315-)  D
1817 GLU   ( 326-)  D
1831 GLU   ( 340-)  D
1840 GLU   ( 349-)  D
1849 ASP   ( 358-)  D

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.

 502 ILE   (   5-)  B      CB     7.6    42.18    32.31
 844 PHE   ( 347-)  B      CA    -7.2    22.46    33.98
The average deviation= 1.171

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.

 844 PHE   ( 347-)  B    4.73
1600 PHE   ( 109-)  D    4.66
 606 PHE   ( 109-)  B    4.47
1311 LEU   ( 317-)  C    4.46
1760 ALA   ( 269-)  D    4.15
 343 VAL   ( 343-)  A    4.14
 499 ARG   (   2-)  B    4.06

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

1307 TYR   ( 313-)  C    -3.0
 319 PRO   ( 319-)  A    -2.9
1973 THR   ( 482-)  D    -2.8
 979 THR   ( 482-)  B    -2.8
1476 THR   ( 482-)  C    -2.7
 842 SER   ( 345-)  B    -2.7
 482 THR   ( 482-)  A    -2.7
1961 LEU   ( 470-)  D    -2.6
 967 LEU   ( 470-)  B    -2.6
 558 THR   (  61-)  B    -2.5
1780 PRO   ( 289-)  D    -2.5
 502 ILE   (   5-)  B    -2.4
 786 PRO   ( 289-)  B    -2.4
 130 ILE   ( 130-)  A    -2.3
 499 ARG   (   2-)  B    -2.3
 560 THR   (  63-)  B    -2.3
 397 PHE   ( 397-)  A    -2.3
1283 PRO   ( 289-)  C    -2.3
 627 ILE   ( 130-)  B    -2.2
1932 LYS   ( 441-)  D    -2.2
1218 LYS   ( 224-)  C    -2.2
 289 PRO   ( 289-)  A    -2.2
 732 GLU   ( 235-)  B    -2.2
1726 GLU   ( 235-)  D    -2.2
1391 PHE   ( 397-)  C    -2.1
 487 TYR   ( 487-)  A    -2.1
 778 LEU   ( 281-)  B    -2.1
1940 LEU   ( 449-)  D    -2.1
 845 TRP   ( 348-)  B    -2.1
 342 CYS   ( 342-)  A    -2.1
 470 LEU   ( 470-)  A    -2.1
 743 PHE   ( 246-)  B    -2.0
 996 ARG   (   2-)  C    -2.0
 285 ARG   ( 285-)  A    -2.0
 345 SER   ( 345-)  A    -2.0
1110 TYR   ( 116-)  C    -2.0

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.

  19 ASN   (  19-)  A  Poor phi/psi
  22 TYR   (  22-)  A  omega poor
  41 GLU   (  41-)  A  omega poor
  55 PRO   (  55-)  A  omega poor
  75 PHE   (  75-)  A  Poor phi/psi
 108 TYR   ( 108-)  A  omega poor
 124 ALA   ( 124-)  A  Poor phi/psi
 168 ALA   ( 168-)  A  omega poor
 169 GLN   ( 169-)  A  omega poor
 182 PRO   ( 182-)  A  omega poor
 192 ASN   ( 192-)  A  Poor phi/psi
 196 SER   ( 196-)  A  omega poor
 224 LYS   ( 224-)  A  Poor phi/psi
 233 GLU   ( 233-)  A  Poor phi/psi
 262 ARG   ( 262-)  A  omega poor
 281 LEU   ( 281-)  A  Poor phi/psi
 288 LEU   ( 288-)  A  PRO omega poor
 318 ALA   ( 318-)  A  Poor phi/psi, PRO omega poor
 323 THR   ( 323-)  A  Poor phi/psi
 342 CYS   ( 342-)  A  omega poor
 343 VAL   ( 343-)  A  Poor phi/psi
 344 GLY   ( 344-)  A  omega poor
 345 SER   ( 345-)  A  Poor phi/psi, omega poor
 346 LYS   ( 346-)  A  omega poor
 373 TYR   ( 373-)  A  omega poor
And so on for a total of 128 lines.

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.

1360 SER   ( 366-)  C    0.36
 727 VAL   ( 230-)  B    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!

   6 PRO   (   6-)  A      0
   9 PHE   (   9-)  A      0
  11 TYR   (  11-)  A      0
  12 SER   (  12-)  A      0
  18 CYS   (  18-)  A      0
  19 ASN   (  19-)  A      0
  21 THR   (  21-)  A      0
  22 TYR   (  22-)  A      0
  23 CYS   (  23-)  A      0
  24 ASP   (  24-)  A      0
  26 PHE   (  26-)  A      0
  34 LEU   (  34-)  A      0
  45 SER   (  45-)  A      0
  48 ARG   (  48-)  A      0
  49 MET   (  49-)  A      0
  57 GLN   (  57-)  A      0
  59 ASN   (  59-)  A      0
  60 HIS   (  60-)  A      0
  65 LEU   (  65-)  A      0
  70 GLN   (  70-)  A      0
  73 GLN   (  73-)  A      0
  75 PHE   (  75-)  A      0
  79 LYS   (  79-)  A      0
  81 PHE   (  81-)  A      0
  85 MET   (  85-)  A      0
And so on for a total of 848 lines.

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]

 898 PRO   ( 401-)  B    0.46 HIGH
1463 PRO   ( 469-)  C    0.18 LOW
1562 PRO   (  71-)  D    0.20 LOW
1669 PRO   ( 178-)  D    0.20 LOW
1966 PRO   ( 475-)  D    0.17 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].

 236 PRO   ( 236-)  A  -116.5 envelop C-gamma (-108 degrees)
 253 PRO   ( 253-)  A  -113.9 envelop C-gamma (-108 degrees)
 299 PRO   ( 299-)  A    32.5 envelop C-delta (36 degrees)
 319 PRO   ( 319-)  A   -49.6 half-chair C-beta/C-alpha (-54 degrees)
 415 PRO   ( 415-)  A   103.6 envelop C-beta (108 degrees)
 503 PRO   (   6-)  B    28.8 envelop C-delta (36 degrees)
 526 PRO   (  29-)  B   -22.0 half-chair C-alpha/N (-18 degrees)
 552 PRO   (  55-)  B   -52.7 half-chair C-beta/C-alpha (-54 degrees)
 675 PRO   ( 178-)  B   -64.5 envelop C-beta (-72 degrees)
 679 PRO   ( 182-)  B   131.7 half-chair C-beta/C-alpha (126 degrees)
 750 PRO   ( 253-)  B  -124.8 half-chair C-delta/C-gamma (-126 degrees)
 786 PRO   ( 289-)  B   -64.0 envelop C-beta (-72 degrees)
 816 PRO   ( 319-)  B   144.1 envelop C-alpha (144 degrees)
 912 PRO   ( 415-)  B   118.8 half-chair C-beta/C-alpha (126 degrees)
 949 PRO   ( 452-)  B    99.3 envelop C-beta (108 degrees)
 966 PRO   ( 469-)  B    17.4 half-chair N/C-delta (18 degrees)
 972 PRO   ( 475-)  B  -130.9 half-chair C-delta/C-gamma (-126 degrees)
1049 PRO   (  55-)  C   -62.5 half-chair C-beta/C-alpha (-54 degrees)
1172 PRO   ( 178-)  C   -35.1 envelop C-alpha (-36 degrees)
1176 PRO   ( 182-)  C   108.3 envelop C-beta (108 degrees)
1195 PRO   ( 201-)  C   102.8 envelop C-beta (108 degrees)
1230 PRO   ( 236-)  C  -112.8 envelop C-gamma (-108 degrees)
1409 PRO   ( 415-)  C   112.4 envelop C-beta (108 degrees)
1519 PRO   (  28-)  D  -152.2 envelop C-delta (-144 degrees)
1520 PRO   (  29-)  D  -114.5 envelop C-gamma (-108 degrees)
1546 PRO   (  55-)  D   -55.6 half-chair C-beta/C-alpha (-54 degrees)
1589 PRO   (  98-)  D    99.4 envelop C-beta (108 degrees)
1590 PRO   (  99-)  D    44.8 envelop C-delta (36 degrees)
1630 PRO   ( 139-)  D    99.1 envelop C-beta (108 degrees)
1641 PRO   ( 150-)  D   -52.8 half-chair C-beta/C-alpha (-54 degrees)
1673 PRO   ( 182-)  D    99.5 envelop C-beta (108 degrees)
1810 PRO   ( 319-)  D   126.8 half-chair C-beta/C-alpha (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.

 516 ASN   (  19-)  B      ND2 <-> 1990 NAG   ( 510-)  B      C1     1.24    1.86  INTRA
1510 ASN   (  19-)  D      ND2 <-> 1992 NAG   ( 509-)  D      C1     1.16    1.94  INTRA
1013 ASN   (  19-)  C      ND2 <-> 1991 NAG   ( 510-)  C      C1     0.98    2.12  INTRA
 782 ARG   ( 285-)  B      NH2 <->  815 ALA   ( 318-)  B      CB     0.46    2.64  INTRA BF
 544 ARG   (  47-)  B      NH1 <-> 2030 HOH   ( 713 )  B      O      0.42    2.28  INTRA BF
1697 HIS   ( 206-)  D      NE2 <-> 1746 HIS   ( 255-)  D      NE2    0.40    2.60  INTRA BL
 270 ASN   ( 270-)  A      ND2 <-> 2029 HOH   ( 687 )  A      O      0.40    2.30  INTRA BF
1437 ASP   ( 443-)  C      N   <-> 2031 HOH   ( 659 )  C      O      0.39    2.31  INTRA
 516 ASN   (  19-)  B      ND2 <-> 1990 NAG   ( 510-)  B      C2     0.39    2.71  INTRA
1510 ASN   (  19-)  D      CG  <-> 1992 NAG   ( 509-)  D      C1     0.34    2.86  INTRA
 342 CYS   ( 342-)  A      SG  <->  343 VAL   ( 343-)  A      N      0.34    2.86  INTRA BF
 516 ASN   (  19-)  B      CG  <-> 1990 NAG   ( 510-)  B      C1     0.34    2.86  INTRA
 703 HIS   ( 206-)  B      NE2 <->  752 HIS   ( 255-)  B      NE2    0.33    2.67  INTRA BL
1267 HIS   ( 273-)  C      ND1 <-> 2031 HOH   ( 739 )  C      O      0.31    2.39  INTRA
1013 ASN   (  19-)  C      ND2 <-> 1991 NAG   ( 510-)  C      C2     0.31    2.79  INTRA
 527 THR   (  30-)  B      CG2 <-> 2030 HOH   ( 784 )  B      O      0.30    2.50  INTRA BF
1565 LYS   (  74-)  D      NZ  <-> 2032 HOH   ( 643 )  D      O      0.30    2.40  INTRA BF
1510 ASN   (  19-)  D      ND2 <-> 1992 NAG   ( 509-)  D      C2     0.29    2.81  INTRA
 207 GLN   ( 207-)  A      NE2 <->  263 ASP   ( 263-)  A      OD1    0.29    2.41  INTRA
 318 ALA   ( 318-)  A      CB  <->  319 PRO   ( 319-)  A      CA     0.29    2.71  INTRA BF
 169 GLN   ( 169-)  A      NE2 <-> 2029 HOH   ( 641 )  A      O      0.29    2.41  INTRA
 285 ARG   ( 285-)  A      NH1 <->  318 ALA   ( 318-)  A      CB     0.29    2.81  INTRA
2031 HOH   ( 805 )  C      O   <-> 2031 HOH   ( 813 )  C      O      0.28    1.92  INTRA
1013 ASN   (  19-)  C      CG  <-> 1991 NAG   ( 510-)  C      C1     0.28    2.92  INTRA
1776 ARG   ( 285-)  D      NH2 <-> 1809 ALA   ( 318-)  D      O      0.28    2.42  INTRA BF
And so on for a total of 283 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.

1660 GLN   ( 169-)  D      -6.88
 938 LYS   ( 441-)  B      -6.65
 666 GLN   ( 169-)  B      -6.65
 441 LYS   ( 441-)  A      -6.55
1932 LYS   ( 441-)  D      -6.52
1435 LYS   ( 441-)  C      -6.51
1808 LEU   ( 317-)  D      -6.39
 169 GLN   ( 169-)  A      -6.39
 697 GLN   ( 200-)  B      -6.37
1691 GLN   ( 200-)  D      -6.23
1163 GLN   ( 169-)  C      -6.07
1194 GLN   ( 200-)  C      -6.04
  31 PHE   (  31-)  A      -5.90
1025 PHE   (  31-)  C      -5.84
 200 GLN   ( 200-)  A      -5.77
 814 LEU   ( 317-)  B      -5.57
1341 PHE   ( 347-)  C      -5.54
1753 ARG   ( 262-)  D      -5.53
1987 ARG   ( 496-)  D      -5.48
 262 ARG   ( 262-)  A      -5.48
1256 ARG   ( 262-)  C      -5.47
 759 ARG   ( 262-)  B      -5.41
1188 LYS   ( 194-)  C      -5.35
 993 ARG   ( 496-)  B      -5.33
 194 LYS   ( 194-)  A      -5.25
1551 HIS   (  60-)  D      -5.18
 528 PHE   (  31-)  B      -5.14
1490 ARG   ( 496-)  C      -5.13
 541 ARG   (  44-)  B      -5.11
  44 ARG   (  44-)  A      -5.10
 496 ARG   ( 496-)  A      -5.10
 347 PHE   ( 347-)  A      -5.06
1038 ARG   (  44-)  C      -5.04
 123 MET   ( 123-)  A      -5.01

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.

 557 HIS   (  60-)  B       560 - THR     63- ( B)         -4.40
1551 HIS   (  60-)  D      1554 - THR     63- ( D)         -4.57

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.

 559 GLY   (  62-)  B   -2.91
  62 GLY   (  62-)  A   -2.81
1164 ARG   ( 170-)  C   -2.68
 126 CYS   ( 126-)  A   -2.60
1120 CYS   ( 126-)  C   -2.58
 170 ARG   ( 170-)  A   -2.56

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.

2029 HOH   ( 770 )  A      O    -26.23  -54.59   64.86

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.

2029 HOH   ( 678 )  A      O
2029 HOH   ( 824 )  A      O
2030 HOH   ( 767 )  B      O
2030 HOH   ( 803 )  B      O
2030 HOH   ( 826 )  B      O
2031 HOH   ( 711 )  C      O
2031 HOH   ( 714 )  C      O
2031 HOH   ( 808 )  C      O
2032 HOH   ( 799 )  D      O
Bound group on Asn; dont flip   19 ASN  (  19-) A
Bound to: 1989 NAG  ( 511-) A

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.

  57 GLN   (  57-)  A
 284 GLN   ( 284-)  A
 567 GLN   (  70-)  B
 659 HIS   ( 162-)  B
 781 GLN   ( 284-)  B
 859 GLN   ( 362-)  B
 893 ASN   ( 396-)  B
1163 GLN   ( 169-)  C
1268 HIS   ( 274-)  C
1278 GLN   ( 284-)  C
1322 HIS   ( 328-)  C
1491 GLN   ( 497-)  C
1551 HIS   (  60-)  D
1636 HIS   ( 145-)  D
1714 HIS   ( 223-)  D
1761 ASN   ( 270-)  D
1775 GLN   ( 284-)  D
1942 HIS   ( 451-)  D

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.

  23 CYS   (  23-)  A      N
  43 THR   (  43-)  A      OG1
  57 GLN   (  57-)  A      NE2
  72 GLU   (  72-)  A      N
 131 ARG   ( 131-)  A      N
 141 ASP   ( 141-)  A      N
 147 PHE   ( 147-)  A      N
 184 TRP   ( 184-)  A      N
 191 VAL   ( 191-)  A      N
 239 GLY   ( 239-)  A      N
 246 PHE   ( 246-)  A      N
 286 LEU   ( 286-)  A      N
 343 VAL   ( 343-)  A      N
 344 GLY   ( 344-)  A      N
 348 TRP   ( 348-)  A      N
 357 TRP   ( 357-)  A      NE1
 364 SER   ( 364-)  A      OG
 377 GLY   ( 377-)  A      N
 379 THR   ( 379-)  A      OG1
 382 ASN   ( 382-)  A      ND2
 384 ALA   ( 384-)  A      N
 396 ASN   ( 396-)  A      N
 399 ASP   ( 399-)  A      N
 406 ILE   ( 406-)  A      N
 407 THR   ( 407-)  A      N
And so on for a total of 109 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.

  60 HIS   (  60-)  A      ND1
  87 ASP   (  87-)  A      OD1
 419 HIS   ( 419-)  A      NE2
 584 ASP   (  87-)  B      OD1
 642 HIS   ( 145-)  B      NE2
 837 GLU   ( 340-)  B      OE2
 916 HIS   ( 419-)  B      NE2
1054 HIS   (  60-)  C      ND1
1227 GLU   ( 233-)  C      OE1
1642 GLU   ( 151-)  D      OE1
1802 HIS   ( 311-)  D      ND1
1831 GLU   ( 340-)  D      OE1
1853 GLN   ( 362-)  D      OE1

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.

2029 HOH   ( 782 )  A      O  0.99  K  5 Ion-B
2031 HOH   ( 754 )  C      O  0.99  K  5 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.

 203 ASP   ( 203-)  A   H-bonding suggests Asn
 218 ASP   ( 218-)  A   H-bonding suggests Asn
 233 GLU   ( 233-)  A   H-bonding suggests Gln
 380 ASP   ( 380-)  A   H-bonding suggests Asn; but Alt-Rotamer
 634 ASP   ( 137-)  B   H-bonding suggests Asn
 700 ASP   ( 203-)  B   H-bonding suggests Asn
 715 ASP   ( 218-)  B   H-bonding suggests Asn
 730 GLU   ( 233-)  B   H-bonding suggests Gln
 823 GLU   ( 326-)  B   H-bonding suggests Gln
 877 ASP   ( 380-)  B   H-bonding suggests Asn
 896 ASP   ( 399-)  B   H-bonding suggests Asn
1197 ASP   ( 203-)  C   H-bonding suggests Asn
1212 ASP   ( 218-)  C   H-bonding suggests Asn; but Alt-Rotamer
1227 GLU   ( 233-)  C   H-bonding suggests Gln; but Alt-Rotamer
1374 ASP   ( 380-)  C   H-bonding suggests Asn; but Alt-Rotamer
1694 ASP   ( 203-)  D   H-bonding suggests Asn
1709 ASP   ( 218-)  D   H-bonding suggests Asn; but Alt-Rotamer
1724 GLU   ( 233-)  D   H-bonding suggests Gln
1871 ASP   ( 380-)  D   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.281
  2nd generation packing quality :  -1.444
  Ramachandran plot appearance   :  -1.260
  chi-1/chi-2 rotamer normality  :  -2.760
  Backbone conformation          :  -0.495

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.849
  Bond angles                    :   0.889
  Omega angle restraints         :   1.236
  Side chain planarity           :   0.793
  Improper dihedral distribution :   0.941
  B-factor distribution          :   0.599
  Inside/Outside distribution    :   1.026

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.48


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.849
  Bond angles                    :   0.889
  Omega angle restraints         :   1.236
  Side chain planarity           :   0.793
  Improper dihedral distribution :   0.941
  B-factor distribution          :   0.599
  Inside/Outside distribution    :   1.026
==============

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.