WHAT IF Check report

This file was created 2012-01-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1uwa.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    = 120.983  B   = 177.709  C    = 122.663
    Alpha=  90.000  Beta= 117.700  Gamma=  90.000

Dimensions of a reduced cell

    A    = 120.983  B   = 122.663  C    = 177.709
    Alpha=  90.000  Beta=  90.000  Gamma=  62.300

Dimensions of the conventional cell

    A    = 126.041  B   = 208.518  C    = 177.709
    Alpha=  90.000  Beta=  90.000  Gamma=  90.892

Transformation to conventional cell

 | -1.000000  0.000000 -1.000000|
 | -1.000000  0.000000  1.000000|
 |  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 : 0.064
CA-only RMS fit for the two chains : 0.032

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 E

All-atom RMS fit for the two chains : 0.092
CA-only RMS fit for the two chains : 0.063

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and H

All-atom RMS fit for the two chains : 0.106
CA-only RMS fit for the two chains : 0.058

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 H

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and K

All-atom RMS fit for the two chains : 0.141
CA-only RMS fit for the two chains : 0.064

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 K

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 O

All-atom RMS fit for the two chains : 0.118
CA-only RMS fit for the two chains : 0.063

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 O

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.

4873 CAP   ( 477-)  A  -
4875 CAP   ( 477-)  B  -
4935 CAP   ( 477-)  E  -
4937 CAP   ( 477-)  H  -
4939 CAP   ( 477-)  K  -
4941 CAP   ( 477-)  O  -
4943 CAP   ( 477-)  R  -
4946 CAP   ( 477-)  V  -

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: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

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

Warning: Artificial side chains detected

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

  99 GLU   ( 109-)  A
3121 VAL   (  90-)  O

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'.

1066 ASN   ( 136-)  C      CG
1066 ASN   ( 136-)  C      OD1
1066 ASN   ( 136-)  C      ND2
1067 LYS   ( 137-)  C      CG
1067 LYS   ( 137-)  C      CD
1067 LYS   ( 137-)  C      CE
1067 LYS   ( 137-)  C      NZ
1669 ARG   ( 130-)  F      CD
1669 ARG   ( 130-)  F      NE
1669 ARG   ( 130-)  F      CZ
1669 ARG   ( 130-)  F      NH1
1669 ARG   ( 130-)  F      NH2
1676 LYS   ( 137-)  F      CD
1676 LYS   ( 137-)  F      CE
1676 LYS   ( 137-)  F      NZ
2275 LYS   ( 127-)  I      CG
2275 LYS   ( 127-)  I      CD
2275 LYS   ( 127-)  I      CE
2275 LYS   ( 127-)  I      NZ
2278 ARG   ( 130-)  I      CD
2278 ARG   ( 130-)  I      NE
2278 ARG   ( 130-)  I      CZ
2278 ARG   ( 130-)  I      NH1
2278 ARG   ( 130-)  I      NH2
2284 ASN   ( 136-)  I      CG
And so on for a total of 67 lines.

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 237 CYS   ( 247-)  A    0.75
 702 CYS   ( 247-)  B    0.75
1311 CYS   ( 247-)  E    0.75
1920 CYS   ( 247-)  H    0.75
2372 ARG   (  84-)  J    0.50
2669 CYS   ( 247-)  K    0.75
2981 ARG   (  84-)  M    0.50
3278 CYS   ( 247-)  O    0.75
3883 CYS   ( 247-)  R    0.75
4488 CYS   ( 247-)  V    0.75
4800 ARG   (  84-)  W    0.50

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

Crystal temperature (K) :100.000

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: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 177 ARG   ( 187-)  A
 642 ARG   ( 187-)  B
1068 ARG   ( 138-)  C
1251 ARG   ( 187-)  E
1860 ARG   ( 187-)  H
2609 ARG   ( 187-)  K
3218 ARG   ( 187-)  O
3823 ARG   ( 187-)  R
4428 ARG   ( 187-)  V

Warning: Tyrosine convention problem

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

 273 TYR   ( 283-)  A
 738 TYR   ( 283-)  B
 981 TYR   (  51-)  C
 997 TYR   (  67-)  C
1347 TYR   ( 283-)  E
1590 TYR   (  51-)  F
1606 TYR   (  67-)  F
1643 TYR   ( 104-)  F
2199 TYR   (  51-)  I
2215 TYR   (  67-)  I
2339 TYR   (  51-)  J
2355 TYR   (  67-)  J
2392 TYR   ( 104-)  J
2705 TYR   ( 283-)  K
2948 TYR   (  51-)  M
2964 TYR   (  67-)  M
3314 TYR   ( 283-)  O
3557 TYR   (  51-)  P
3573 TYR   (  67-)  P
3610 TYR   ( 104-)  P
3721 TYR   (  85-)  R
3919 TYR   ( 283-)  R
4162 TYR   (  51-)  T
4178 TYR   (  67-)  T
4215 TYR   ( 104-)  T
4524 TYR   ( 283-)  V
4767 TYR   (  51-)  W
4783 TYR   (  67-)  W

Warning: Phenylalanine convention problem

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

 280 PHE   ( 290-)  A
 392 PHE   ( 402-)  A
 457 PHE   ( 467-)  A
 745 PHE   ( 290-)  B
 857 PHE   ( 402-)  B
 942 PHE   (  12-)  C
 945 PHE   (  15-)  C
 974 PHE   (  44-)  C
 990 PHE   (  60-)  C
1030 PHE   ( 100-)  C
1051 PHE   ( 121-)  C
1354 PHE   ( 290-)  E
1466 PHE   ( 402-)  E
1533 PHE   ( 469-)  E
1551 PHE   (  12-)  F
1554 PHE   (  15-)  F
1583 PHE   (  44-)  F
1599 PHE   (  60-)  F
1639 PHE   ( 100-)  F
1660 PHE   ( 121-)  F
1963 PHE   ( 290-)  H
2075 PHE   ( 402-)  H
2160 PHE   (  12-)  I
2163 PHE   (  15-)  I
2192 PHE   (  44-)  I
And so on for a total of 61 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.

1061 ASP   ( 131-)  C
1670 ASP   ( 131-)  F
2279 ASP   ( 131-)  I
2419 ASP   ( 131-)  J
3028 ASP   ( 131-)  M
3637 ASP   ( 131-)  P
4242 ASP   ( 131-)  T
4847 ASP   ( 131-)  W

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.

  78 GLU   (  88-)  A
 543 GLU   (  88-)  B
 791 GLU   ( 336-)  B
 976 GLU   (  46-)  C
 985 GLU   (  55-)  C
1152 GLU   (  88-)  E
1585 GLU   (  46-)  F
1594 GLU   (  55-)  F
1761 GLU   (  88-)  H
2009 GLU   ( 336-)  H
2194 GLU   (  46-)  I
2203 GLU   (  55-)  I
2334 GLU   (  46-)  J
2343 GLU   (  55-)  J
2510 GLU   (  88-)  K
2943 GLU   (  46-)  M
2952 GLU   (  55-)  M
3119 GLU   (  88-)  O
3290 GLU   ( 259-)  O
3367 GLU   ( 336-)  O
3552 GLU   (  46-)  P
3561 GLU   (  55-)  P
3724 GLU   (  88-)  R
3972 GLU   ( 336-)  R
4157 GLU   (  46-)  T
4166 GLU   (  55-)  T
4329 GLU   (  88-)  V
4577 GLU   ( 336-)  V
4762 GLU   (  46-)  W
4771 GLU   (  55-)  W

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 191 KCX   ( 201-)  A      CH     CX
 191 KCX   ( 201-)  A      OX1    OQ1
 191 KCX   ( 201-)  A      OX2    OQ2
 656 KCX   ( 201-)  B      CH     CX
 656 KCX   ( 201-)  B      OX1    OQ1
 656 KCX   ( 201-)  B      OX2    OQ2
1265 KCX   ( 201-)  E      CH     CX
1265 KCX   ( 201-)  E      OX1    OQ1
1265 KCX   ( 201-)  E      OX2    OQ2
1874 KCX   ( 201-)  H      CH     CX
1874 KCX   ( 201-)  H      OX1    OQ1
1874 KCX   ( 201-)  H      OX2    OQ2
2623 KCX   ( 201-)  K      CH     CX
2623 KCX   ( 201-)  K      OX1    OQ1
2623 KCX   ( 201-)  K      OX2    OQ2
3232 KCX   ( 201-)  O      CH     CX
3232 KCX   ( 201-)  O      OX1    OQ1
3232 KCX   ( 201-)  O      OX2    OQ2
3837 KCX   ( 201-)  R      CH     CX
3837 KCX   ( 201-)  R      OX1    OQ1
3837 KCX   ( 201-)  R      OX2    OQ2
4442 KCX   ( 201-)  V      CH     CX
4442 KCX   ( 201-)  V      OX1    OQ1
4442 KCX   ( 201-)  V      OX2    OQ2

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.

2782 ARG   ( 360-)  K      N   -C     1.82   24.6
2783 GLY   ( 361-)  K      N   -C     2.35   51.3

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

 |  0.995879 -0.000026 -0.000387|
 | -0.000026  0.997641 -0.000012|
 | -0.000387 -0.000012  0.996829|
Proposed new scale matrix

 |  0.008302  0.000000  0.004357|
 |  0.000000  0.005640  0.000000|
 |  0.000004  0.000000  0.009237|
With corresponding cell

    A    = 120.479  B   = 177.295  C    = 122.285
    Alpha=  90.001  Beta= 117.714  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 120.983  B   = 177.709  C    = 122.663
    Alpha=  90.000  Beta= 117.700  Gamma=  90.000

Variance: 1712.136
(Under-)estimated Z-score: 30.495

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.

 317 HIS   ( 327-)  A      CG   ND1  CE1 109.72    4.1
 782 HIS   ( 327-)  B      CG   ND1  CE1 109.60    4.0
1068 ARG   ( 138-)  C      CD   NE   CZ  137.49    8.8
1068 ARG   ( 138-)  C      NE   CZ   NH1 130.50    5.5
1068 ARG   ( 138-)  C      NE   CZ   NH2 109.79   -5.4
1391 HIS   ( 327-)  E      CG   ND1  CE1 109.62    4.0
2720 HIS   ( 298-)  K      CG   ND1  CE1 109.65    4.1
2782 ARG   ( 360-)  K     -O   -C    N   113.59   -5.9
2782 ARG   ( 360-)  K     -CA  -C    N   124.93    4.4
2783 GLY   ( 361-)  K     -O   -C    N    70.29  -32.9
2783 GLY   ( 361-)  K     -CA  -C    N    91.94  -12.1
3903 HIS   ( 267-)  R      CG   ND1  CE1 109.60    4.0
4535 HIS   ( 294-)  V      CG   ND1  CE1 109.77    4.2
4568 HIS   ( 327-)  V      CG   ND1  CE1 109.67    4.1

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.

  78 GLU   (  88-)  A
 177 ARG   ( 187-)  A
 543 GLU   (  88-)  B
 642 ARG   ( 187-)  B
 791 GLU   ( 336-)  B
 976 GLU   (  46-)  C
 985 GLU   (  55-)  C
1061 ASP   ( 131-)  C
1068 ARG   ( 138-)  C
1152 GLU   (  88-)  E
1251 ARG   ( 187-)  E
1585 GLU   (  46-)  F
1594 GLU   (  55-)  F
1670 ASP   ( 131-)  F
1761 GLU   (  88-)  H
1860 ARG   ( 187-)  H
2009 GLU   ( 336-)  H
2194 GLU   (  46-)  I
2203 GLU   (  55-)  I
2279 ASP   ( 131-)  I
2334 GLU   (  46-)  J
2343 GLU   (  55-)  J
2419 ASP   ( 131-)  J
2510 GLU   (  88-)  K
2609 ARG   ( 187-)  K
2943 GLU   (  46-)  M
2952 GLU   (  55-)  M
3028 ASP   ( 131-)  M
3119 GLU   (  88-)  O
3218 ARG   ( 187-)  O
3290 GLU   ( 259-)  O
3367 GLU   ( 336-)  O
3552 GLU   (  46-)  P
3561 GLU   (  55-)  P
3637 ASP   ( 131-)  P
3724 GLU   (  88-)  R
3823 ARG   ( 187-)  R
3972 GLU   ( 336-)  R
4157 GLU   (  46-)  T
4166 GLU   (  55-)  T
4242 ASP   ( 131-)  T
4329 GLU   (  88-)  V
4428 ARG   ( 187-)  V
4577 GLU   ( 336-)  V
4762 GLU   (  46-)  W
4771 GLU   (  55-)  W
4847 ASP   ( 131-)  W

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.

1797 VAL   ( 124-)  H    4.42
2724 ASP   ( 302-)  K    4.19
1366 ASP   ( 302-)  E    4.12

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.

3027 ARG   ( 130-)  M    -2.6
1078 LYS   (  14-)  E    -2.5
3045 LYS   (  14-)  O    -2.4
3650 LYS   (  14-)  R    -2.4
   4 LYS   (  14-)  A    -2.4
4255 LYS   (  14-)  V    -2.4
 469 LYS   (  14-)  B    -2.4
2436 LYS   (  14-)  K    -2.4
4722 PRO   (   6-)  W    -2.4
1687 LYS   (  14-)  H    -2.4
2154 PRO   (   6-)  I    -2.3
4834 ILE   ( 118-)  W    -2.3
3015 ILE   ( 118-)  M    -2.3
1657 ILE   ( 118-)  F    -2.3
1048 ILE   ( 118-)  C    -2.3
4229 ILE   ( 118-)  T    -2.3
2266 ILE   ( 118-)  I    -2.3
3624 ILE   ( 118-)  P    -2.3
2406 ILE   ( 118-)  J    -2.3
4835 MET   ( 119-)  W    -2.3
2903 PRO   (   6-)  M    -2.2
3625 MET   ( 119-)  P    -2.2
3016 MET   ( 119-)  M    -2.2
2337 LYS   (  49-)  J    -2.2
2267 MET   ( 119-)  I    -2.2
And so on for a total of 107 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.

  52 SER   (  62-)  A  Poor phi/psi
  55 THR   (  65-)  A  omega poor
  97 LEU   ( 107-)  A  omega poor
 153 ASN   ( 163-)  A  Poor phi/psi
 165 LYS   ( 175-)  A  PRO omega poor
 189 PHE   ( 199-)  A  omega poor
 197 ASN   ( 207-)  A  Poor phi/psi
 253 PRO   ( 263-)  A  omega poor
 287 MET   ( 297-)  A  Poor phi/psi
 291 ILE   ( 301-)  A  omega poor
 320 THR   ( 330-)  A  omega poor
 321 VAL   ( 331-)  A  Poor phi/psi
 360 SER   ( 370-)  A  Poor phi/psi
 496 ARG   (  41-)  B  omega poor
 517 SER   (  62-)  B  Poor phi/psi
 530 THR   (  75-)  B  Poor phi/psi
 562 LEU   ( 107-)  B  omega poor
 574 SER   ( 119-)  B  omega poor
 618 ASN   ( 163-)  B  Poor phi/psi
 630 LYS   ( 175-)  B  PRO omega poor
 654 PHE   ( 199-)  B  omega poor
 662 ASN   ( 207-)  B  Poor phi/psi
 718 PRO   ( 263-)  B  omega poor
 752 MET   ( 297-)  B  Poor phi/psi
 756 ILE   ( 301-)  B  omega poor
And so on for a total of 177 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.

1343 SER   ( 279-)  E    0.35
 734 SER   ( 279-)  B    0.36
 269 SER   ( 279-)  A    0.36
2701 SER   ( 279-)  K    0.36
1952 SER   ( 279-)  H    0.38
4520 SER   ( 279-)  V    0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   5 ALA   (  15-)  A      0
   8 LYS   (  18-)  A      0
  13 THR   (  23-)  A      0
  14 TYR   (  24-)  A      0
  15 TYR   (  25-)  A      0
  16 THR   (  26-)  A      0
  19 TYR   (  29-)  A      0
  36 PRO   (  46-)  A      0
  51 SER   (  61-)  A      0
  52 SER   (  62-)  A      0
  53 THR   (  63-)  A      0
  56 TRP   (  66-)  A      0
  60 TRP   (  70-)  A      0
  64 LEU   (  74-)  A      0
  65 THR   (  75-)  A      0
  75 TYR   (  85-)  A      0
  76 ASP   (  86-)  A      0
  81 PRO   (  91-)  A      0
  84 ASP   (  94-)  A      0
  85 ASN   (  95-)  A      0
  94 HYP   ( 104-)  A      0
 100 GLU   ( 110-)  A      0
 111 VAL   ( 121-)  A      0
 113 ASN   ( 123-)  A      0
 114 VAL   ( 124-)  A      0
And so on for a total of 1840 lines.

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!

2759 GLY   ( 337-)  K   2.39   12
3973 GLY   ( 337-)  R   2.38   13
1401 GLY   ( 337-)  E   2.37   13
2827 GLY   ( 405-)  K   1.66   80
1469 GLY   ( 405-)  E   1.65   80
 395 GLY   ( 405-)  A   1.64   80
3436 GLY   ( 405-)  O   1.59   80
 860 GLY   ( 405-)  B   1.59   80
2078 GLY   ( 405-)  H   1.57   80
4041 GLY   ( 405-)  R   1.52   80
4646 GLY   ( 405-)  V   1.52   80

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]

  94 HYP   ( 104-)  A    0.05 LOW
 141 HYP   ( 151-)  A    0.09 LOW
 559 HYP   ( 104-)  B    0.06 LOW
 606 HYP   ( 151-)  B    0.10 LOW
 970 PRO   (  40-)  C    0.17 LOW
1168 HYP   ( 104-)  E    0.06 LOW
1215 HYP   ( 151-)  E    0.07 LOW
1579 PRO   (  40-)  F    0.19 LOW
1777 HYP   ( 104-)  H    0.06 LOW
1824 HYP   ( 151-)  H    0.08 LOW
2188 PRO   (  40-)  I    0.17 LOW
2526 HYP   ( 104-)  K    0.06 LOW
2573 HYP   ( 151-)  K    0.09 LOW
2937 PRO   (  40-)  M    0.18 LOW
3135 HYP   ( 104-)  O    0.06 LOW
3182 HYP   ( 151-)  O    0.07 LOW
3740 HYP   ( 104-)  R    0.04 LOW
3787 HYP   ( 151-)  R    0.09 LOW
4345 HYP   ( 104-)  V    0.06 LOW
4392 HYP   ( 151-)  V    0.09 LOW
4756 PRO   (  40-)  W    0.16 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].

  36 PRO   (  46-)  A  -117.4 half-chair C-delta/C-gamma (-126 degrees)
 400 PRO   ( 410-)  A  -112.9 envelop C-gamma (-108 degrees)
 501 PRO   (  46-)  B  -117.6 half-chair C-delta/C-gamma (-126 degrees)
1056 PRO   ( 126-)  C  -116.8 envelop C-gamma (-108 degrees)
1110 PRO   (  46-)  E  -119.1 half-chair C-delta/C-gamma (-126 degrees)
1665 PRO   ( 126-)  F  -113.0 envelop C-gamma (-108 degrees)
1719 PRO   (  46-)  H  -120.0 half-chair C-delta/C-gamma (-126 degrees)
2083 PRO   ( 410-)  H  -113.3 envelop C-gamma (-108 degrees)
2154 PRO   (   6-)  I   -65.0 envelop C-beta (-72 degrees)
2274 PRO   ( 126-)  I  -115.1 envelop C-gamma (-108 degrees)
2328 PRO   (  40-)  J    37.1 envelop C-delta (36 degrees)
2414 PRO   ( 126-)  J  -112.3 envelop C-gamma (-108 degrees)
2468 PRO   (  46-)  K  -119.3 half-chair C-delta/C-gamma (-126 degrees)
2903 PRO   (   6-)  M   -65.4 envelop C-beta (-72 degrees)
3023 PRO   ( 126-)  M  -115.4 envelop C-gamma (-108 degrees)
3077 PRO   (  46-)  O  -120.0 half-chair C-delta/C-gamma (-126 degrees)
3441 PRO   ( 410-)  O  -112.6 envelop C-gamma (-108 degrees)
3546 PRO   (  40-)  P    45.2 half-chair C-delta/C-gamma (54 degrees)
3682 PRO   (  46-)  R  -119.6 half-chair C-delta/C-gamma (-126 degrees)
4151 PRO   (  40-)  T    43.2 envelop C-delta (36 degrees)
4237 PRO   ( 126-)  T  -114.5 envelop C-gamma (-108 degrees)
4287 PRO   (  46-)  V  -120.1 half-chair C-delta/C-gamma (-126 degrees)
4417 PRO   ( 176-)  V  -112.3 envelop C-gamma (-108 degrees)
4722 PRO   (   6-)  W   -64.4 envelop C-beta (-72 degrees)
4842 PRO   ( 126-)  W  -114.8 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

4424 LYS   ( 183-)  V      NZ   <->  4962 HOH   (2078 )  V      O    0.50    2.20  INTRA BF
1765 GLY   (  92-)  H      N    <->  4953 HOH   (2036 )  H      O    0.43    2.27  INTRA BF
 173 LYS   ( 183-)  A      NZ   <->  4947 HOH   (2106 )  A      O    0.40    2.30  INTRA BF
 638 LYS   ( 183-)  B      NZ   <->  4948 HOH   (2106 )  B      O    0.39    2.31  INTRA BF
1677 ARG   ( 138-)  F      NE   <->  4952 HOH   (2047 )  F      O    0.37    2.33  INTRA BF
 753 HIS   ( 298-)  B      ND1  <->   757 ASP   ( 302-)  B      OD2  0.36    2.34  INTRA
1362 HIS   ( 298-)  E      ND1  <->  1366 ASP   ( 302-)  E      OD2  0.32    2.38  INTRA
 288 HIS   ( 298-)  A      ND1  <->   292 ASP   ( 302-)  A      OD2  0.32    2.38  INTRA
 722 HIS   ( 267-)  B      CD2  <->   732 ASN   ( 277-)  B      ND2  0.31    2.79  INTRA BL
4539 HIS   ( 298-)  V      ND1  <->  4543 ASP   ( 302-)  V      OD2  0.30    2.40  INTRA
 794 ARG   ( 339-)  B      NH1  <->  4948 HOH   (2171 )  B      O    0.30    2.40  INTRA BF
 461 THR   ( 471-)  A      OG1  <->  4947 HOH   (2241 )  A      O    0.29    2.11  INTRA
1222 GLU   ( 158-)  E      OE2  <->  1389 HIS   ( 325-)  E      NE2  0.29    2.41  INTRA
3329 HIS   ( 298-)  O      ND1  <->  3333 ASP   ( 302-)  O      OD2  0.29    2.41  INTRA
 257 HIS   ( 267-)  A      CD2  <->   267 ASN   ( 277-)  A      ND2  0.29    2.81  INTRA BL
2454 ARG   (  32-)  K      CZ   <->  4956 HOH   (2027 )  K      O    0.29    2.51  INTRA BF
 466 ALA   (  11-)  B      N    <->  4926 EDO   (  52-)  B      O2   0.29    2.41  INTRA BF
1331 HIS   ( 267-)  E      CD2  <->  1341 ASN   ( 277-)  E      ND2  0.29    2.81  INTRA BL
2580 GLU   ( 158-)  K      OE2  <->  2747 HIS   ( 325-)  K      NE2  0.29    2.41  INTRA
4508 HIS   ( 267-)  V      CD2  <->  4518 ASN   ( 277-)  V      ND2  0.28    2.82  INTRA BL
3903 HIS   ( 267-)  R      CD2  <->  3913 ASN   ( 277-)  R      ND2  0.28    2.82  INTRA BL
3189 GLU   ( 158-)  O      OE2  <->  3356 HIS   ( 325-)  O      NE2  0.28    2.42  INTRA
4099 LYS   ( 463-)  R      NZ   <->  4960 HOH   (2204 )  R      O    0.28    2.42  INTRA BF
2720 HIS   ( 298-)  K      ND1  <->  2724 ASP   ( 302-)  K      OD2  0.28    2.42  INTRA
4399 GLU   ( 158-)  V      OE2  <->  4566 HIS   ( 325-)  V      NE2  0.28    2.42  INTRA
And so on for a total of 371 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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

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.

4800 ARG   (  84-)  W      -7.55
2981 ARG   (  84-)  M      -7.33
2232 ARG   (  84-)  I      -7.03
1014 ARG   (  84-)  C      -7.00
4841 ARG   ( 125-)  W      -6.54
3022 ARG   ( 125-)  M      -6.51
2273 ARG   ( 125-)  I      -6.46
4236 ARG   ( 125-)  T      -6.45
3631 ARG   ( 125-)  P      -6.44
2430 LYS   (   8-)  K      -6.29
4195 ARG   (  84-)  T      -6.25
1681 LYS   (   8-)  H      -6.25
3039 LYS   (   8-)  O      -6.03
1623 ARG   (  84-)  F      -5.93
1072 LYS   (   8-)  E      -5.93
2112 ARG   ( 439-)  H      -5.72
2861 ARG   ( 439-)  K      -5.72
1503 ARG   ( 439-)  E      -5.71
3470 ARG   ( 439-)  O      -5.71
 429 ARG   ( 439-)  A      -5.71
4075 ARG   ( 439-)  R      -5.70
 894 ARG   ( 439-)  B      -5.70
4680 ARG   ( 439-)  V      -5.70
3590 ARG   (  84-)  P      -5.58
4255 LYS   (  14-)  V      -5.55
And so on for a total of 124 lines.

Note: Quality value plot

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

Chain identifier: 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: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: 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: 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: 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: 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: 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: 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: 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: 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

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.

1067 LYS   ( 137-)  C   -3.26
2285 LYS   ( 137-)  I   -3.25
3330 ALA   ( 299-)  O   -2.86
4540 ALA   ( 299-)  V   -2.84
 754 ALA   ( 299-)  B   -2.84
1363 ALA   ( 299-)  E   -2.82
1972 ALA   ( 299-)  H   -2.81
4241 ARG   ( 130-)  T   -2.81
 289 ALA   ( 299-)  A   -2.80
3935 ALA   ( 299-)  R   -2.78
4678 LEU   ( 437-)  V   -2.77
2110 LEU   ( 437-)  H   -2.76
2404 VAL   ( 116-)  J   -2.76
4073 LEU   ( 437-)  R   -2.75
2721 ALA   ( 299-)  K   -2.75
 427 LEU   ( 437-)  A   -2.72
2979 GLY   (  82-)  M   -2.70
 892 LEU   ( 437-)  B   -2.69
1669 ARG   ( 130-)  F   -2.69
2425 LYS   ( 137-)  J   -2.69
3643 LYS   ( 137-)  P   -2.68
3468 LEU   ( 437-)  O   -2.68
1501 LEU   ( 437-)  E   -2.68
3034 LYS   ( 137-)  M   -2.59
2278 ARG   ( 130-)  I   -2.58
3138 LEU   ( 107-)  O   -2.57
1171 LEU   ( 107-)  E   -2.56
1676 LYS   ( 137-)  F   -2.55
  97 LEU   ( 107-)  A   -2.55
1780 LEU   ( 107-)  H   -2.55
3743 LEU   ( 107-)  R   -2.55
4348 LEU   ( 107-)  V   -2.55
4248 LYS   ( 137-)  T   -2.54
2529 LEU   ( 107-)  K   -2.54
 562 LEU   ( 107-)  B   -2.53
2275 LYS   ( 127-)  I   -2.50

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: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

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.

4948 HOH   (2007 )  B      O    -41.75  117.18   36.77

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.

4947 HOH   (2052 )  A      O
4948 HOH   (2011 )  B      O
4950 HOH   (2031 )  D      O
4951 HOH   (2153 )  E      O
4953 HOH   (2179 )  H      O
4960 HOH   (2045 )  R      O
4960 HOH   (2199 )  R      O
4961 HOH   (2031 )  T      O
ERROR. Strange cone in HB2INI
Affected atom 2783 GLY  ( 361-) K      N
Expected ambiguity-2 in FILL1HARR 0 409 5102

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.

 143 HIS   ( 153-)  A
 146 GLN   ( 156-)  A
 219 GLN   ( 229-)  A
 228 HIS   ( 238-)  A
 231 ASN   ( 241-)  A
 257 HIS   ( 267-)  A
 267 ASN   ( 277-)  A
 294 GLN   ( 304-)  A
 391 GLN   ( 401-)  A
 410 ASN   ( 420-)  A
 422 ASN   ( 432-)  A
 608 HIS   ( 153-)  B
 611 GLN   ( 156-)  B
 684 GLN   ( 229-)  B
 693 HIS   ( 238-)  B
 696 ASN   ( 241-)  B
 722 HIS   ( 267-)  B
 732 ASN   ( 277-)  B
 759 GLN   ( 304-)  B
 856 GLN   ( 401-)  B
 875 ASN   ( 420-)  B
 887 ASN   ( 432-)  B
 939 ASN   (   9-)  C
 955 GLN   (  25-)  C
 959 GLN   (  29-)  C
And so on for a total of 133 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.

  55 THR   (  65-)  A      OG1
  57 THR   (  67-)  A      N
  86 GLN   (  96-)  A      N
  90 TYR   ( 100-)  A      OH
 163 THR   ( 173-)  A      N
 163 THR   ( 173-)  A      OG1
 165 LYS   ( 175-)  A      N
 165 LYS   ( 175-)  A      NZ
 168 LEU   ( 178-)  A      N
 169 GLY   ( 179-)  A      N
 201 PHE   ( 211-)  A      N
 207 ARG   ( 217-)  A      NH1
 236 THR   ( 246-)  A      N
 285 ARG   ( 295-)  A      NE
 285 ARG   ( 295-)  A      NH1
 294 GLN   ( 304-)  A      NE2
 356 GLN   ( 366-)  A      NE2
 371 GLY   ( 381-)  A      N
 373 HIS   ( 383-)  A      N
 391 GLN   ( 401-)  A      NE2
 394 GLY   ( 404-)  A      N
 403 ASN   ( 413-)  A      ND2
 520 THR   (  65-)  B      OG1
 522 THR   (  67-)  B      N
 551 GLN   (  96-)  B      N
And so on for a total of 267 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.

 258 ASP   ( 268-)  A      OD1
 258 ASP   ( 268-)  A      OD2
 317 HIS   ( 327-)  A      ND1
 376 HIS   ( 386-)  A      NE2
 723 ASP   ( 268-)  B      OD1
 723 ASP   ( 268-)  B      OD2
 782 HIS   ( 327-)  B      ND1
 841 HIS   ( 386-)  B      NE2
1332 ASP   ( 268-)  E      OD1
1450 HIS   ( 386-)  E      NE2
1941 ASP   ( 268-)  H      OD1
2000 HIS   ( 327-)  H      ND1
2690 ASP   ( 268-)  K      OD1
2690 ASP   ( 268-)  K      OD2
2749 HIS   ( 327-)  K      ND1
2808 HIS   ( 386-)  K      NE2
3290 GLU   ( 259-)  O    A OE1
3299 ASP   ( 268-)  O      OD1
3299 ASP   ( 268-)  O      OD2
3358 HIS   ( 327-)  O      ND1
3904 ASP   ( 268-)  R      OD1
3904 ASP   ( 268-)  R      OD2
3928 HIS   ( 292-)  R      NE2
4022 HIS   ( 386-)  R      NE2
4509 ASP   ( 268-)  V      OD1
4509 ASP   ( 268-)  V      OD2
4568 HIS   ( 327-)  V      ND1

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.

4947 HOH   (2147 )  A      O  0.86  K  4 NCS 7/7
4948 HOH   (2128 )  B      O  1.15  K  4 NCS 4/4
4948 HOH   (2176 )  B      O  1.11  K  4 NCS 4/4
4951 HOH   (2068 )  E      O  0.93  K  5 Ion-B NCS 6/6
4953 HOH   (2094 )  H      O  0.89  K  5 NCS 7/7
4955 HOH   (2019 )  J      O  1.15  K  4 Ion-B NCS 2/2
4955 HOH   (2042 )  J      O  1.10  K  4 Ion-B NCS 4/4
4956 HOH   (2110 )  K      O  1.01  K  5 NCS 7/7
4956 HOH   (2117 )  K      O  1.07  K  4 Ion-B NCS 3/3
4960 HOH   (2100 )  R      O  0.94  K  4 Ion-B NCS 3/3
4960 HOH   (2179 )  R      O  0.89  K  5 Ion-B NCS 2/2
4961 HOH   (2039 )  T      O  0.96  K  4 Ion-B NCS 4/4
4962 HOH   (2121 )  V      O  1.05  K  4 NCS 7/7
4962 HOH   (2169 )  V      O  0.96  K  4 Ion-B NCS 5/5
4963 HOH   (2004 )  W      O  1.03  K  4 NCS 2/2
4963 HOH   (2025 )  W      O  0.87  K  4

Warning: Possible wrong residue type

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

  42 GLU   (  52-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 150 ASP   ( 160-)  A   H-bonding suggests Asn; but Alt-Rotamer
 258 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 463 ASP   ( 473-)  A   H-bonding suggests Asn; Ligand-contact
 507 GLU   (  52-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 615 ASP   ( 160-)  B   H-bonding suggests Asn; but Alt-Rotamer
 723 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 985 GLU   (  55-)  C   H-bonding suggests Gln; Ligand-contact
1116 GLU   (  52-)  E   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1224 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
1332 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1537 ASP   ( 473-)  E   H-bonding suggests Asn; Ligand-contact
1594 GLU   (  55-)  F   H-bonding suggests Gln; Ligand-contact
1725 GLU   (  52-)  H   H-bonding suggests Gln; Ligand-contact
1833 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
1941 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
2146 ASP   ( 473-)  H   H-bonding suggests Asn; Ligand-contact
2203 GLU   (  55-)  I   H-bonding suggests Gln; Ligand-contact
2343 GLU   (  55-)  J   H-bonding suggests Gln; Ligand-contact
2474 GLU   (  52-)  K   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
2582 ASP   ( 160-)  K   H-bonding suggests Asn; but Alt-Rotamer
2690 ASP   ( 268-)  K   H-bonding suggests Asn; but Alt-Rotamer
2952 GLU   (  55-)  M   H-bonding suggests Gln; Ligand-contact
3299 ASP   ( 268-)  O   H-bonding suggests Asn; but Alt-Rotamer
3504 ASP   ( 473-)  O   H-bonding suggests Asn; Ligand-contact
3561 GLU   (  55-)  P   H-bonding suggests Gln; Ligand-contact
3688 GLU   (  52-)  R   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
3904 ASP   ( 268-)  R   H-bonding suggests Asn; but Alt-Rotamer
4109 ASP   ( 473-)  R   H-bonding suggests Asn; Ligand-contact
4293 GLU   (  52-)  V   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
4401 ASP   ( 160-)  V   H-bonding suggests Asn; but Alt-Rotamer
4509 ASP   ( 268-)  V   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 :  -0.752
  2nd generation packing quality :  -0.249
  Ramachandran plot appearance   :  -0.563
  chi-1/chi-2 rotamer normality  :  -1.567
  Backbone conformation          :  -0.624

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.505 (tight)
  Bond angles                    :   0.677
  Omega angle restraints         :   1.085
  Side chain planarity           :   0.422 (tight)
  Improper dihedral distribution :   0.685
  B-factor distribution          :   0.474
  Inside/Outside distribution    :   1.052

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.505 (tight)
  Bond angles                    :   0.677
  Omega angle restraints         :   1.085
  Side chain planarity           :   0.422 (tight)
  Improper dihedral distribution :   0.685
  B-factor distribution          :   0.474
  Inside/Outside distribution    :   1.052
==============

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.