WHAT IF Check report

This file was created 2012-01-25 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 pdb2ian.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.533
CA-only RMS fit for the two chains : 0.302

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 F

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and K

All-atom RMS fit for the two chains : 0.587
CA-only RMS fit for the two chains : 0.370

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 P

All-atom RMS fit for the two chains : 0.647
CA-only RMS fit for the two chains : 0.407

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 P

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 G

All-atom RMS fit for the two chains : 0.463
CA-only RMS fit for the two chains : 0.228

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 G

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: C and H

All-atom RMS fit for the two chains : 0.575
CA-only RMS fit for the two chains : 0.294

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: C and H

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

2441 ASP   ( 240-)  O  -

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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

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

Warning: Missing atoms

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

2441 ASP   ( 240-)  O      O

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

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 2.07

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

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

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

 223 TYR   (  47-)  B
 278 TYR   ( 102-)  B
 292 TYR   ( 123-)  B
 442 TYR   (  68-)  D
 458 TYR   (  84-)  D
 605 TYR   (  35-)  E
 634 TYR   (  64-)  E
 670 TYR   ( 100-)  E
 754 TYR   ( 184-)  E
 969 TYR   ( 161-)  F
1035 TYR   (  47-)  G
1071 TYR   (  83-)  G
1090 TYR   ( 102-)  G
1104 TYR   ( 123-)  G
1254 TYR   (  68-)  I
1258 TYR   (  72-)  I
1270 TYR   (  84-)  I
1418 TYR   (  35-)  J
1447 TYR   (  64-)  J
1483 TYR   ( 100-)  J
1594 TYR   ( 211-)  J
1847 TYR   (  47-)  L
1923 TYR   ( 123-)  L
2073 TYR   (  68-)  N
2089 TYR   (  84-)  N
2265 TYR   (  64-)  O
2301 TYR   ( 100-)  O
2452 TYR   (  13-)  P
2518 TYR   (  79-)  P
2665 TYR   (  47-)  Q
2741 TYR   ( 123-)  Q
2789 TYR   ( 171-)  Q
2891 TYR   (  68-)  S
2895 TYR   (  72-)  S
2907 TYR   (  84-)  S
3052 TYR   (  33-)  T
3054 TYR   (  35-)  T
3083 TYR   (  64-)  T
3119 TYR   ( 100-)  T
3203 TYR   ( 184-)  T

Warning: Phenylalanine convention problem

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

  23 PHE   (  26-)  A
  29 PHE   (  32-)  A
 134 PHE   ( 137-)  A
 183 PHE   (   7-)  B
 193 PHE   (  17-)  B
 398 PHE   (  24-)  D
 408 PHE   (  34-)  D
 510 PHE   ( 136-)  D
 671 PHE   ( 101-)  E
 766 PHE   ( 196-)  E
 774 PHE   ( 204-)  E
 834 PHE   (  26-)  F
 840 PHE   (  32-)  F
 945 PHE   ( 137-)  F
 953 PHE   ( 145-)  F
 995 PHE   (   7-)  G
1005 PHE   (  17-)  G
1113 PHE   ( 132-)  G
1210 PHE   (  24-)  I
1220 PHE   (  34-)  I
1322 PHE   ( 136-)  I
1371 PHE   ( 185-)  I
1500 PHE   ( 117-)  J
1579 PHE   ( 196-)  J
1643 PHE   (  22-)  K
And so on for a total of 51 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.

 156 ASP   ( 159-)  A
 178 ASP   ( 181-)  A
 374 ASP   (  37-)  C
 521 ASP   ( 147-)  D
 528 ASP   ( 154-)  D
 567 ASP   ( 193-)  D
 608 ASP   (  38-)  E
 751 ASP   ( 181-)  E
 967 ASP   ( 159-)  F
1186 ASP   (  37-)  H
1333 ASP   ( 147-)  I
1421 ASP   (  38-)  J
1495 ASP   ( 112-)  J
1564 ASP   ( 181-)  J
1780 ASP   ( 159-)  K
1802 ASP   ( 181-)  K
2005 ASP   (  37-)  M
2239 ASP   (  38-)  O
2382 ASP   ( 181-)  O
2598 ASP   ( 159-)  P
2620 ASP   ( 181-)  P
2823 ASP   (  37-)  R
2832 ASP   (   9-)  S
2970 ASP   ( 147-)  S
2972 ASP   ( 149-)  S
2977 ASP   ( 154-)  S
3057 ASP   (  38-)  T
3200 ASP   ( 181-)  T

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.

  18 GLU   (  21-)  A
  43 GLU   (  46-)  A
  44 GLU   (  47-)  A
  68 GLU   (  71-)  A
 131 GLU   ( 134-)  A
 163 GLU   ( 166-)  A
 169 GLU   ( 172-)  A
 176 GLU   ( 179-)  A
 198 GLU   (  22-)  B
 228 GLU   (  52-)  B
 272 GLU   (  96-)  B
 297 GLU   ( 128-)  B
 306 GLU   ( 137-)  B
 331 GLU   ( 162-)  B
 338 GLU   ( 169-)  B
 356 GLU   ( 187-)  B
 361 GLU   (  24-)  C
 388 GLU   (  14-)  D
 812 GLU   (   4-)  F
 829 GLU   (  21-)  F
 854 GLU   (  46-)  F
 855 GLU   (  47-)  F
 896 GLU   (  88-)  F
 942 GLU   ( 134-)  F
 974 GLU   ( 166-)  F
And so on for a total of 76 lines.

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

1187 ILE   (   1-)  I      CA   CB    1.62    4.4
1221 HIS   (  35-)  I      C    O     1.13   -4.8
1222 GLN   (  36-)  I      N    CA    1.55    4.7

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.997671  0.000050 -0.000053|
 |  0.000050  0.998272 -0.000157|
 | -0.000053 -0.000157  0.997964|
Proposed new scale matrix

 |  0.010723  0.000000  0.004183|
 |  0.000000  0.004124  0.000000|
 |  0.000000  0.000002  0.010223|
With corresponding cell

    A    =  93.256  B   = 242.476  C    = 105.000
    Alpha=  90.010  Beta= 111.311  Gamma=  89.998

The CRYST1 cell dimensions

    A    =  93.474  B   = 242.866  C    = 105.222
    Alpha=  90.000  Beta= 111.320  Gamma=  90.000

Variance: 461.210
(Under-)estimated Z-score: 15.828

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.

  30 HIS   (  33-)  A      CG   ND1  CE1 109.63    4.0
 120 ARG   ( 123-)  A      CB   CG   CD  105.97   -4.1
 293 PRO   ( 124-)  B      N    CA   C   101.24   -4.2
 405 LEU   (  31-)  D      CA   CB   CG  100.56   -4.5
 409 HIS   (  35-)  D      CG   ND1  CE1 109.74    4.1
 575 THR   (   5-)  E      C    CA   CB  117.79    4.0
 578 PRO   (   8-)  E      CD   N    CA  106.31   -4.1
 666 HIS   (  96-)  E      CG   ND1  CE1 109.86    4.3
 841 HIS   (  33-)  F      CG   ND1  CE1 109.81    4.2
1017 ARG   (  29-)  G      CB   CG   CD  103.04   -5.5
1063 VAL   (  75-)  G      C    CA   CB  118.91    4.6
1105 PRO   ( 124-)  G      N    CA   C   100.49   -4.5
1144 THR   ( 163-)  G      C    CA   CB  101.83   -4.4
1222 GLN   (  36-)  I     -O   -C    N   114.66   -5.2
1222 GLN   (  36-)  I     -CA  -C    N   129.37    6.6
1222 GLN   (  36-)  I      N    CA   CB  118.67    4.8
1223 ASN   (  37-)  I      N    CA   C    98.73   -4.5
1280 GLN   (  94-)  I     -C    N    CA  112.92   -4.9
1344 LEU   ( 158-)  I      CA   CB   CG  130.84    4.2
1386 GLY   (   3-)  J      N    CA   C   124.18    4.0
1477 THR   (  94-)  J      C    CA   CB   99.06   -5.8
1637 PRO   (  16-)  K     -C    N    CD  105.64   -4.7
1734 THR   ( 113-)  K      C    CA   CB  118.08    4.2
1924 PRO   ( 124-)  L      N    CA   C   101.13   -4.3
1967 SER   ( 167-)  L     -CA  -C    N   125.03    4.4
2295 THR   (  94-)  O      C    CA   CB  102.16   -4.2
2349 PRO   ( 148-)  O     -C    N    CD  106.00   -4.6
2349 PRO   ( 148-)  O      CD   N    CA  105.07   -4.9
2552 THR   ( 113-)  P      C    CA   CB  117.72    4.0
2562 ARG   ( 123-)  P      CB   CG   CD  106.06   -4.0
2647 ARG   (  29-)  Q      CB   CG   CD  104.36   -4.9
2647 ARG   (  29-)  Q      CG   CD   NE  117.67    4.2
2742 PRO   ( 124-)  Q     -C    N    CD  108.05   -4.1
3115 HIS   (  96-)  T      CG   ND1  CE1 109.72    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.

  18 GLU   (  21-)  A
  43 GLU   (  46-)  A
  44 GLU   (  47-)  A
  68 GLU   (  71-)  A
 131 GLU   ( 134-)  A
 156 ASP   ( 159-)  A
 163 GLU   ( 166-)  A
 169 GLU   ( 172-)  A
 176 GLU   ( 179-)  A
 178 ASP   ( 181-)  A
 198 GLU   (  22-)  B
 228 GLU   (  52-)  B
 272 GLU   (  96-)  B
 297 GLU   ( 128-)  B
 306 GLU   ( 137-)  B
 331 GLU   ( 162-)  B
 338 GLU   ( 169-)  B
 356 GLU   ( 187-)  B
 361 GLU   (  24-)  C
 374 ASP   (  37-)  C
 388 GLU   (  14-)  D
 521 ASP   ( 147-)  D
 528 ASP   ( 154-)  D
 567 ASP   ( 193-)  D
 608 ASP   (  38-)  E
And so on for a total of 104 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

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

 111 PRO   ( 114-)  A      N      7.7    22.88    -2.48
 292 TYR   ( 123-)  B      C     -6.1    -9.16     0.33
 381 PRO   (   7-)  D      N      6.4    18.41    -2.48
 718 PRO   ( 148-)  E      N      7.3    21.61    -2.48
 922 PRO   ( 114-)  F      N      7.7    22.68    -2.48
1104 TYR   ( 123-)  G      C     -6.2    -9.34     0.33
1193 PRO   (   7-)  I      N      6.4    18.36    -2.48
1391 PRO   (   8-)  J      N      7.0    20.50    -2.48
1531 PRO   ( 148-)  J      N      6.9    20.26    -2.48
1636 ASN   (  15-)  K      C     -6.2    -9.49     0.27
1637 PRO   (  16-)  K      N     -6.3   -23.29    -2.48
1735 PRO   ( 114-)  K      N      7.5    22.19    -2.48
2349 PRO   ( 148-)  O      N      9.0    27.07    -2.48
2455 PRO   (  16-)  P      N      7.4    21.93    -2.48
2553 PRO   ( 114-)  P      N      7.0    20.45    -2.48
The average deviation= 0.954

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.

1887 GLU   (  87-)  L    5.09
1105 PRO   ( 124-)  G    4.84
1924 PRO   ( 124-)  L    4.59
 293 PRO   ( 124-)  B    4.55
1053 LYS   (  65-)  G    4.29
1223 ASN   (  37-)  I    4.25
2742 PRO   ( 124-)  Q    4.25
1966 ARG   ( 166-)  L    4.13
 467 ALA   (  93-)  D    4.13
 405 LEU   (  31-)  D    4.09
1188 GLN   (   2-)  I    4.08
1233 TYR   (  47-)  I    4.08
 421 TYR   (  47-)  D    4.05

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.

2830 PRO   (   7-)  S    -3.1
2012 PRO   (   7-)  N    -3.1
 381 PRO   (   7-)  D    -3.1
 578 PRO   (   8-)  E    -3.1
2209 PRO   (   8-)  O    -3.0
1908 PRO   ( 108-)  L    -3.0
3027 PRO   (   8-)  T    -3.0
2726 PRO   ( 108-)  Q    -3.0
1924 PRO   ( 124-)  L    -3.0
2240 PRO   (  39-)  O    -3.0
 111 PRO   ( 114-)  A    -2.9
1105 PRO   ( 124-)  G    -2.9
1457 PHE   (  74-)  J    -2.9
1735 PRO   ( 114-)  K    -2.9
2553 PRO   ( 114-)  P    -2.9
  93 PRO   (  96-)  A    -2.9
 293 PRO   ( 124-)  B    -2.9
1444 PRO   (  61-)  J    -2.8
1234 ILE   (  48-)  I    -2.8
2455 PRO   (  16-)  P    -2.8
 922 PRO   ( 114-)  F    -2.8
 422 ILE   (  48-)  D    -2.8
3093 PHE   (  74-)  T    -2.7
2566 PRO   ( 127-)  P    -2.7
 439 THR   (  65-)  D    -2.7
And so on for a total of 176 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.

   5 ILE   (   8-)  A  omega poor
   9 PHE   (  12-)  A  omega poor
  11 LEU   (  14-)  A  omega poor
  15 GLN   (  18-)  A  Poor phi/psi, omega poor
  24 ASP   (  27-)  A  Poor phi/psi
  52 GLU   (  55-)  A  omega poor
  76 TYR   (  79-)  A  Poor phi/psi
  84 PRO   (  87-)  A  omega poor
  97 ARG   ( 100-)  A  Poor phi/psi
 106 ILE   ( 109-)  A  omega poor
 108 LYS   ( 111-)  A  Poor phi/psi
 110 THR   ( 113-)  A  PRO omega poor
 111 PRO   ( 114-)  A  Poor phi/psi
 112 PRO   ( 115-)  A  Poor phi/psi
 121 ASN   ( 124-)  A  Poor phi/psi
 140 HIS   ( 143-)  A  Poor phi/psi
 144 LYS   ( 147-)  A  Poor phi/psi
 155 GLU   ( 158-)  A  omega poor
 159 ASP   ( 162-)  A  omega poor
 166 GLY   ( 169-)  A  Poor phi/psi
 173 LYS   ( 176-)  A  omega poor
 195 ASN   (  19-)  B  Poor phi/psi
 210 GLN   (  34-)  B  Poor phi/psi
 213 SER   (  37-)  B  Poor phi/psi
 226 VAL   (  50-)  B  omega poor
And so on for a total of 243 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.101

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.

2486 GLU   (  47-)  P    0.36
 504 VAL   ( 130-)  D    0.38
 702 SER   ( 132-)  E    0.38
2515 ARG   (  76-)  P    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!

   7 ALA   (  10-)  A      0
   8 GLU   (  11-)  A      0
  12 ASN   (  15-)  A      0
  15 GLN   (  18-)  A      0
  16 SER   (  19-)  A      0
  23 PHE   (  26-)  A      0
  29 PHE   (  32-)  A      0
  41 ARG   (  44-)  A      0
  48 PHE   (  51-)  A      0
  53 ALA   (  56-)  A      0
  76 TYR   (  79-)  A      0
  93 PRO   (  96-)  A      0
  96 LEU   (  99-)  A      0
  97 ARG   ( 100-)  A      0
 100 ASN   ( 103-)  A      0
 107 ASP   ( 110-)  A      0
 108 LYS   ( 111-)  A      0
 110 THR   ( 113-)  A      0
 111 PRO   ( 114-)  A      0
 112 PRO   ( 115-)  A      0
 113 VAL   ( 116-)  A      0
 120 ARG   ( 123-)  A      0
 121 ASN   ( 124-)  A      0
 127 THR   ( 130-)  A      0
 129 VAL   ( 132-)  A      0
And so on for a total of 1403 lines.

Warning: Omega angle restraints not strong enough

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

Standard deviation of omega values : 8.936

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!

 294 GLY   ( 125-)  B   2.20   64
1106 GLY   ( 125-)  G   2.11   46
 337 GLY   ( 168-)  B   1.87   80
1149 GLY   ( 168-)  G   1.81   80
2743 GLY   ( 125-)  Q   1.80   31
2097 GLY   (  92-)  N   1.77   18
2915 GLY   (  92-)  S   1.75   11
1434 GLY   (  51-)  J   1.56   11

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]

 696 PRO   ( 126-)  E    0.18 LOW
 824 PRO   (  16-)  F    0.47 HIGH
1085 PRO   (  97-)  G    0.09 LOW
2349 PRO   ( 148-)  O    0.46 HIGH
2872 PRO   (  49-)  S    0.18 LOW

Warning: Unusual PRO puckering phases

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

  13 PRO   (  16-)  A   -41.5 envelop C-alpha (-36 degrees)
  84 PRO   (  87-)  A   -58.4 half-chair C-beta/C-alpha (-54 degrees)
  93 PRO   (  96-)  A  -154.9 half-chair N/C-delta (-162 degrees)
  99 PRO   ( 102-)  A   101.5 envelop C-beta (108 degrees)
 111 PRO   ( 114-)  A   172.7 envelop N (180 degrees)
 149 PRO   ( 152-)  A    50.5 half-chair C-delta/C-gamma (54 degrees)
 170 PRO   ( 173-)  A  -117.1 half-chair C-delta/C-gamma (-126 degrees)
 293 PRO   ( 124-)  B    43.3 envelop C-delta (36 degrees)
 352 PRO   ( 183-)  B    18.4 half-chair N/C-delta (18 degrees)
 381 PRO   (   7-)  D  -168.2 half-chair N/C-delta (-162 degrees)
 382 PRO   (   8-)  D   110.2 envelop C-beta (108 degrees)
 571 PRO   ( 197-)  D    47.6 half-chair C-delta/C-gamma (54 degrees)
 578 PRO   (   8-)  E   171.6 envelop N (180 degrees)
 609 PRO   (  39-)  E  -119.8 half-chair C-delta/C-gamma (-126 degrees)
 718 PRO   ( 148-)  E   171.6 envelop N (180 degrees)
 770 PRO   ( 200-)  E    42.9 envelop C-delta (36 degrees)
 824 PRO   (  16-)  F   152.4 envelop C-alpha (144 degrees)
 894 PRO   (  86-)  F    49.2 half-chair C-delta/C-gamma (54 degrees)
 904 PRO   (  96-)  F  -116.6 envelop C-gamma (-108 degrees)
 910 PRO   ( 102-)  F   103.5 envelop C-beta (108 degrees)
 922 PRO   ( 114-)  F   173.1 envelop N (180 degrees)
 981 PRO   ( 173-)  F  -114.8 envelop C-gamma (-108 degrees)
1105 PRO   ( 124-)  G    37.4 envelop C-delta (36 degrees)
1164 PRO   ( 183-)  G  -140.4 envelop C-delta (-144 degrees)
1184 PRO   (  35-)  H  -112.1 envelop C-gamma (-108 degrees)
And so on for a total of 70 lines.

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.

2742 PRO   ( 124-)  Q      CD   <->  2795 HIS   ( 177-)  Q      NE2  0.65    2.45  INTRA BL
2036 LEU   (  31-)  N      CD2  <->  2074 SER   (  69-)  N      CB   0.65    2.55  INTRA BL
2664 GLU   (  46-)  Q      OE2  <->  2666 ARG   (  48-)  Q      NH1  0.59    2.11  INTRA BL
1034 GLU   (  46-)  G      OE2  <->  1036 ARG   (  48-)  G      NH2  0.52    2.18  INTRA BL
 375 ILE   (   1-)  D      N    <->   401 SER   (  27-)  D      CB   0.51    2.59  INTRA
 881 MET   (  73-)  F      SD   <->  1041 LEU   (  53-)  G      CD2  0.45    2.95  INTRA BL
 165 TRP   ( 168-)  A      NE1  <->   179 THR   (   3-)  B      CG2  0.45    2.65  INTRA BL
 811 GLU   (   3-)  F      OE2  <->  1004 HIS   (  16-)  G      ND1  0.44    2.26  INTRA
 664 THR   (  94-)  E      CG2  <->   669 GLY   (  99-)  E      CA   0.42    2.78  INTRA BL
 377 VAL   (   3-)  D      CG1  <->   460 CYS   (  86-)  D      SG   0.42    2.98  INTRA BL
 717 PHE   ( 147-)  E      CD2  <->   718 PRO   ( 148-)  E      CD   0.39    2.81  INTRA BL
1887 GLU   (  87-)  L      CG   <->  1892 GLN   (  92-)  L      NE2  0.39    2.71  INTRA BL
1212 ASP   (  26-)  I      OD1  <->  1253 ARG   (  67-)  I      NH1  0.38    2.32  INTRA
1846 GLU   (  46-)  L      OE2  <->  1848 ARG   (  48-)  L      NH1  0.38    2.32  INTRA BL
3224 ARG   ( 205-)  T      NH1  <->  3226 GLN   ( 207-)  T      OE1  0.38    2.32  INTRA BL
2580 GLU   ( 141-)  P      OE2  <->  2647 ARG   (  29-)  Q      NH2  0.37    2.33  INTRA BL
2992 SER   ( 169-)  S      OG   <->  3208 ARG   ( 189-)  T      CD   0.36    2.44  INTRA BL
 953 PHE   ( 145-)  F      CZ   <->   998 GLN   (  10-)  G      NE2  0.36    2.74  INTRA BL
1530 PHE   ( 147-)  J      CD2  <->  1531 PRO   ( 148-)  J      CD   0.36    2.84  INTRA BL
1804 ARG   (   4-)  L      O    <->  1806 ARG   (   6-)  L      NH1  0.35    2.35  INTRA BL
 144 LYS   ( 147-)  A      NZ   <->   146 HIS   ( 149-)  A      CE1  0.34    2.76  INTRA
2348 PHE   ( 147-)  O      CD2  <->  2349 PRO   ( 148-)  O      CD   0.33    2.87  INTRA BL
 757 SER   ( 187-)  E      OG   <->   759 ARG   ( 189-)  E      NH2  0.33    2.37  INTRA
1037 ALA   (  49-)  G      O    <->  2166 ARG   ( 161-)  N      NH1  0.33    2.37  INTRA
 266 THR   (  90-)  B      OG1  <->   267 VAL   (  91-)  B      N    0.33    2.27  INTRA BL
And so on for a total of 514 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: 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: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

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: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

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.

2622 ARG   (   4-)  Q      -7.72
1804 ARG   (   4-)  L      -7.47
 180 ARG   (   4-)  B      -7.37
 992 ARG   (   4-)  G      -7.35
2116 GLN   ( 111-)  N      -6.42
 485 GLN   ( 111-)  D      -6.41
2934 GLN   ( 111-)  S      -6.39
1297 GLN   ( 111-)  I      -6.30
2105 GLN   ( 100-)  N      -6.16
 358 ARG   ( 189-)  B      -6.14
1721 ARG   ( 100-)  K      -6.10
2439 ARG   ( 238-)  O      -6.09
2757 LYS   ( 139-)  Q      -6.00
2334 HIS   ( 133-)  O      -5.94
3060 MET   (  41-)  T      -5.91
2242 MET   (  41-)  O      -5.85
 177 PHE   ( 180-)  A      -5.84
1286 GLN   ( 100-)  I      -5.75
  15 GLN   (  18-)  A      -5.73
1894 ARG   (  94-)  L      -5.72
1310 LYS   ( 124-)  I      -5.67
1424 MET   (  41-)  J      -5.66
1361 ASN   ( 175-)  I      -5.66
1170 ARG   ( 189-)  G      -5.64
 703 HIS   ( 133-)  E      -5.59
And so on for a total of 67 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

 990 ASP   (   2-)  G       992 - ARG      4- ( G)         -5.30
2727 LEU   ( 109-)  Q      2729 - HIS    111- ( Q)         -4.46
3257 ARG   ( 238-)  T      3259 - ASP    240- ( T)         -4.46

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

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: 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: L

Note: Quality value plot

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

Chain identifier: 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: N

Note: Quality value plot

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

Chain identifier: 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: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

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.

2349 PRO   ( 148-)  O   -2.95
 824 PRO   (  16-)  F   -2.91
1604 GLN   ( 221-)  J   -2.85
1610 VAL   ( 227-)  J   -2.79
 797 VAL   ( 227-)  E   -2.64
3246 VAL   ( 227-)  T   -2.63
3007 ALA   ( 184-)  S   -2.60
2887 ALA   (  64-)  S   -2.60
2879 GLY   (  56-)  S   -2.58
2189 ALA   ( 184-)  N   -2.57
1370 ALA   ( 184-)  I   -2.54
2061 GLY   (  56-)  N   -2.52
2428 VAL   ( 227-)  O   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

2210 LYS   (   9-)  O     - 2213 ILE   (  12-)  O        -1.53

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: 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: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

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: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  12 ASN   (  15-)  A
 146 HIS   ( 149-)  A
 186 GLN   (  10-)  B
 209 ASN   (  33-)  B
 319 ASN   ( 150-)  B
 325 GLN   ( 156-)  B
 367 ASN   (  30-)  C
 379 GLN   (   5-)  D
 409 HIS   (  35-)  D
 451 GLN   (  77-)  D
 542 ASN   ( 168-)  D
 560 ASN   ( 186-)  D
 561 ASN   ( 187-)  D
 576 GLN   (   6-)  E
 666 HIS   (  96-)  E
 779 GLN   ( 209-)  E
 957 HIS   ( 149-)  F
 998 GLN   (  10-)  G
1021 ASN   (  33-)  G
1131 ASN   ( 150-)  G
1179 ASN   (  30-)  H
1191 GLN   (   5-)  I
1221 HIS   (  35-)  I
1263 GLN   (  77-)  I
1325 GLN   ( 139-)  I
And so on for a total of 60 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.

  16 SER   (  19-)  A      N
  29 PHE   (  32-)  A      N
  42 LEU   (  45-)  A      N
  52 GLU   (  55-)  A      N
 110 THR   ( 113-)  A      OG1
 118 TRP   ( 121-)  A      NE1
 137 ARG   ( 140-)  A      NE
 169 GLU   ( 172-)  A      N
 183 PHE   (   7-)  B      N
 185 TRP   (   9-)  B      NE1
 186 GLN   (  10-)  B      NE2
 210 GLN   (  34-)  B      N
 213 SER   (  37-)  B      OG
 222 GLU   (  46-)  B      N
 251 VAL   (  75-)  B      N
 253 THR   (  77-)  B      OG1
 282 ASN   ( 113-)  B      N
 283 LEU   ( 114-)  B      N
 327 LEU   ( 158-)  B      N
 365 THR   (  28-)  C      N
 365 THR   (  28-)  C      OG1
 368 ALA   (  31-)  C      N
 379 GLN   (   5-)  D      NE2
 399 SER   (  25-)  D      OG
 405 LEU   (  31-)  D      N
And so on for a total of 260 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.

   8 GLU   (  11-)  A      OE1
  63 ASP   (  66-)  A      OD1
  63 ASP   (  66-)  A      OD2
 397 ASN   (  23-)  D      OD1
 542 ASN   ( 168-)  D      OD1
 681 GLU   ( 111-)  E      OE1
 819 GLU   (  11-)  F      OE1
 874 ASP   (  66-)  F      OD2
1004 HIS   (  16-)  G      ND1
1045 ASP   (  57-)  G      OD2
1191 GLN   (   5-)  I      OE1
1354 ASN   ( 168-)  I      OD1
1623 ASP   ( 240-)  J      OD1
1632 GLU   (  11-)  K      OE1
1646 ASP   (  25-)  K      OD2
1687 ASP   (  66-)  K      OD2
1770 HIS   ( 149-)  K      ND1
2286 GLN   (  85-)  O      OE1
2442 GLU   (   3-)  P      OE2
2450 GLU   (  11-)  P      OE1
2457 GLN   (  18-)  P      OE1
2496 GLN   (  57-)  P      OE1
2505 ASP   (  66-)  P      OD2
2582 HIS   ( 143-)  P      ND1
2588 HIS   ( 149-)  P      ND1
2598 ASP   ( 159-)  P      OD2
2628 GLN   (  10-)  Q      OE1
2792 GLN   ( 174-)  Q      OE1
2794 GLU   ( 176-)  Q      OE1
3149 GLU   ( 130-)  T      OE1

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.

  18 GLU   (  21-)  A   H-bonding suggests Gln
  24 ASP   (  27-)  A   H-bonding suggests Asn; but Alt-Rotamer
 496 ASP   ( 122-)  D   H-bonding suggests Asn; but Alt-Rotamer
 501 ASP   ( 127-)  D   H-bonding suggests Asn
 690 GLU   ( 120-)  E   H-bonding suggests Gln
 829 GLU   (  21-)  F   H-bonding suggests Gln
 874 ASP   (  66-)  F   H-bonding suggests Asn
1308 ASP   ( 122-)  I   H-bonding suggests Asn; but Alt-Rotamer
1340 ASP   ( 154-)  I   H-bonding suggests Asn
1503 GLU   ( 120-)  J   H-bonding suggests Gln
1642 GLU   (  21-)  K   H-bonding suggests Gln
1687 ASP   (  66-)  K   H-bonding suggests Asn
1783 ASP   ( 162-)  K   H-bonding suggests Asn; but Alt-Rotamer
2127 ASP   ( 122-)  N   H-bonding suggests Asn
2132 ASP   ( 127-)  N   H-bonding suggests Asn; but Alt-Rotamer
2198 ASP   ( 193-)  N   H-bonding suggests Asn
2227 ASP   (  26-)  O   H-bonding suggests Asn
2257 ASP   (  56-)  O   H-bonding suggests Asn; but Alt-Rotamer
2418 ASP   ( 217-)  O   H-bonding suggests Asn
2460 GLU   (  21-)  P   H-bonding suggests Gln
2505 ASP   (  66-)  P   H-bonding suggests Asn
2620 ASP   ( 181-)  P   H-bonding suggests Asn
2653 GLU   (  35-)  Q   H-bonding suggests Gln
2945 ASP   ( 122-)  S   H-bonding suggests Asn
2950 ASP   ( 127-)  S   H-bonding suggests Asn; but Alt-Rotamer
3016 ASP   ( 193-)  S   H-bonding suggests Asn
3045 ASP   (  26-)  T   H-bonding suggests Asn
3075 ASP   (  56-)  T   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 :  -0.197
  2nd generation packing quality :  -1.355
  Ramachandran plot appearance   :  -1.558
  chi-1/chi-2 rotamer normality  :  -4.101 (bad)
  Backbone conformation          :  -0.289

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.565 (tight)
  Bond angles                    :   0.749
  Omega angle restraints         :   1.625 (loose)
  Side chain planarity           :   0.473 (tight)
  Improper dihedral distribution :   0.829
  B-factor distribution          :   0.482
  Inside/Outside distribution    :   1.038

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.1
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.565 (tight)
  Bond angles                    :   0.749
  Omega angle restraints         :   1.625 (loose)
  Side chain planarity           :   0.473 (tight)
  Improper dihedral distribution :   0.829
  B-factor distribution          :   0.482
  Inside/Outside distribution    :   1.038
==============

WHAT IF
    G.Vriend,
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    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.