WHAT IF Check report

This file was created 2015-07-02 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 pdb4m75.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: F and M

All-atom RMS fit for the two chains : 0.852
CA-only RMS fit for the two chains : 0.423

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: F and M

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

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'.

  90 ASP   ( 121-)  A      CG
  90 ASP   ( 121-)  A      OD1
  90 ASP   ( 121-)  A      OD2
  93 LEU   ( 124-)  A      CG
  93 LEU   ( 124-)  A      CD1
  93 LEU   ( 124-)  A      CD2
 119 HIS   ( 152-)  A      CG
 119 HIS   ( 152-)  A      ND1
 119 HIS   ( 152-)  A      CD2
 119 HIS   ( 152-)  A      CE1
 119 HIS   ( 152-)  A      NE2
 120 LYS   ( 153-)  A      CG
 120 LYS   ( 153-)  A      CD
 120 LYS   ( 153-)  A      CE
 120 LYS   ( 153-)  A      NZ
 126 ARG   ( 159-)  A      CG
 126 ARG   ( 159-)  A      CD
 126 ARG   ( 159-)  A      NE
 126 ARG   ( 159-)  A      CZ
 126 ARG   ( 159-)  A      NH1
 126 ARG   ( 159-)  A      NH2
 178 LYS   (  39-)  B      CD
 178 LYS   (  39-)  B      CE
 178 LYS   (  39-)  B      NZ
 278 SER   (  57-)  C      OG
And so on for a total of 267 lines.

Warning: B-factors outside the range 0.0 - 100.0

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

  59 GLU   (  90-)  A    High
  60 GLU   (  91-)  A    High
  61 ASN   (  92-)  A    High
  62 LYS   (  93-)  A    High
  85 ASP   ( 116-)  A    High
  86 ILE   ( 117-)  A    High
  87 ASP   ( 118-)  A    High
  90 ASP   ( 121-)  A    High
  91 GLN   ( 122-)  A    High
  92 PRO   ( 123-)  A    High
  95 GLU   ( 128-)  A    High
 101 GLU   ( 134-)  A    High
 108 LYS   ( 141-)  A    High
 109 ASN   ( 142-)  A    High
 110 ASP   ( 143-)  A    High
 111 GLU   ( 144-)  A    High
 113 ARG   ( 146-)  A    High
 115 LYS   ( 148-)  A    High
 118 THR   ( 151-)  A    High
 119 HIS   ( 152-)  A    High
 122 LYS   ( 155-)  A    High
 123 LYS   ( 156-)  A    High
 124 MSE   ( 157-)  A    High
 125 ALA   ( 158-)  A    High
 126 ARG   ( 159-)  A    High
And so on for a total of 251 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.

  32 MSE   (  63-)  A    0.38
  72 MSE   ( 103-)  A    0.66
  80 MSE   ( 111-)  A    0.65
  94 MSE   ( 127-)  A    0.69
 124 MSE   ( 157-)  A    0.76
 138 MSE   ( 171-)  A    0.43
 140 MSE   (   1-)  B    0.43
 215 MSE   (  76-)  B    0.93
 230 MSE   (  91-)  B    0.59
 286 MSE   (  65-)  C    0.87
 332 MSE   (  45-)  D    0.55
 428 MSE   (  65-)  E    0.86
 434 MSE   (  71-)  E    0.78
 474 MSE   (  43-)  F    0.70
 490 MSE   (  59-)  F    0.82
 501 MSE   (  70-)  F    0.35
 544 MSE   (  15-)  G    0.68
 565 MSE   (  36-)  G    0.60
 630 MSE   (  63-)  H    0.44
 670 MSE   ( 103-)  H    0.64
 678 MSE   ( 111-)  H    0.70
 694 MSE   ( 127-)  H    0.85
 724 MSE   ( 157-)  H    0.65
 738 MSE   ( 171-)  H    0.45
 739 MSE   (   1-)  I    0.47
 812 MSE   (  76-)  I    0.88
 885 MSE   (  65-)  J    0.72
 935 MSE   (  45-)  K    0.63
 965 MSE   (  79-)  K    0.76
1025 MSE   (  65-)  L    0.77
1031 MSE   (  71-)  L    0.73
1060 MSE   (  43-)  M    0.69
1076 MSE   (  59-)  M    0.67
1087 MSE   (  70-)  M    0.83
1116 MSE   (   1-)  N    0.74
1130 MSE   (  15-)  N    0.89
1151 MSE   (  36-)  N    0.68

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: 14

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: 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

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.

  28 ARG   (  59-)  A
 197 ARG   (  58-)  B
 585 ARG   (  72-)  G
 626 ARG   (  59-)  H
 696 ARG   ( 129-)  H
 799 ARG   (  63-)  I
 843 ARG   (  21-)  J
 846 ARG   (  24-)  J
1169 ARG   (  72-)  N

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.

  76 GLU   ( 107-)  A
  83 GLU   ( 114-)  A
  89 GLU   ( 120-)  A
  95 GLU   ( 128-)  A
 111 GLU   ( 144-)  A
 116 GLU   ( 149-)  A
 117 GLU   ( 150-)  A
 153 GLU   (  14-)  B
 157 GLU   (  18-)  B
 187 GLU   (  48-)  B
 273 GLU   (  46-)  C
 341 GLU   (  54-)  D
 370 GLU   (  83-)  D
 396 GLU   (  29-)  E
 417 GLU   (  50-)  E
 547 GLU   (  18-)  G
 581 GLU   (  68-)  G
 651 GLU   (  84-)  H
 663 GLU   (  96-)  H
 664 GLU   (  97-)  H
 681 GLU   ( 114-)  H
 756 GLU   (  18-)  I
 762 GLU   (  24-)  I
 868 GLU   (  46-)  J
 929 GLU   (  39-)  K
 944 GLU   (  54-)  K
 994 GLU   (  29-)  L
 996 GLU   (  31-)  L
1015 GLU   (  50-)  L
1022 GLU   (  62-)  L
1133 GLU   (  18-)  N

Geometric checks

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

 |  1.004975  0.000303 -0.000064|
 |  0.000303  1.004803 -0.000034|
 | -0.000064 -0.000034  1.005139|
Proposed new scale matrix

 |  0.014923  0.007373  0.006760|
 | -0.000005  0.016366  0.003812|
 |  0.000000  0.000000  0.010947|
With corresponding cell

    A    =  67.002  B   =  68.146  C    =  98.747
    Alpha=  93.142  Beta= 108.219  Gamma= 116.277

The CRYST1 cell dimensions

    A    =  66.672  B   =  67.835  C    =  98.235
    Alpha=  93.140  Beta= 108.210  Gamma= 116.300

Variance: 932.701
(Under-)estimated Z-score: 22.508

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.

  59 GLU   (  90-)  A     -C    N    CA  114.31   -4.1
 454 PRO   (  22-)  F      N    CA   CB  110.64    6.9
 678 MSE   ( 111-)  H      N    CA   CB  101.40   -5.4
1031 MSE   (  71-)  L      N    CA   CB  103.11   -4.3

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.

  28 ARG   (  59-)  A
  76 GLU   ( 107-)  A
  83 GLU   ( 114-)  A
  89 GLU   ( 120-)  A
  95 GLU   ( 128-)  A
 111 GLU   ( 144-)  A
 116 GLU   ( 149-)  A
 117 GLU   ( 150-)  A
 153 GLU   (  14-)  B
 157 GLU   (  18-)  B
 187 GLU   (  48-)  B
 197 ARG   (  58-)  B
 273 GLU   (  46-)  C
 341 GLU   (  54-)  D
 370 GLU   (  83-)  D
 396 GLU   (  29-)  E
 417 GLU   (  50-)  E
 547 GLU   (  18-)  G
 581 GLU   (  68-)  G
 585 ARG   (  72-)  G
 626 ARG   (  59-)  H
 651 GLU   (  84-)  H
 663 GLU   (  96-)  H
 664 GLU   (  97-)  H
 681 GLU   ( 114-)  H
 696 ARG   ( 129-)  H
 756 GLU   (  18-)  I
 762 GLU   (  24-)  I
 799 ARG   (  63-)  I
 843 ARG   (  21-)  J
 846 ARG   (  24-)  J
 868 GLU   (  46-)  J
 929 GLU   (  39-)  K
 944 GLU   (  54-)  K
 994 GLU   (  29-)  L
 996 GLU   (  31-)  L
1015 GLU   (  50-)  L
1022 GLU   (  62-)  L
1133 GLU   (  18-)  N
1169 ARG   (  72-)  N

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.

 191 PRO   (  52-)  B      N     -6.1   -22.33    -2.48
 690 PRO   ( 123-)  H      N     -6.2   -22.80    -2.48
1043 PRO   (  83-)  L      N     -8.5   -30.34    -2.48
The average deviation= 0.915

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.

 613 ILE   (  46-)  H    4.67
  75 GLY   ( 106-)  A    4.58
 673 GLY   ( 106-)  H    4.56
 234 LEU   (   7-)  C    4.36
1185 LYS   (  88-)  N    4.28
 963 GLN   (  77-)  K    4.17
 459 LEU   (  28-)  F    4.16

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.

 349 LYS   (  62-)  D    -2.9
1101 ILE   (  98-)  M    -2.7
 731 TYR   ( 164-)  H    -2.7
 515 ILE   (  98-)  F    -2.6
 859 SER   (  37-)  J    -2.6
 529 SER   (   0-)  G    -2.6
  38 ARG   (  69-)  A    -2.6
 931 ILE   (  41-)  K    -2.6
 211 LEU   (  72-)  B    -2.6
 252 THR   (  25-)  C    -2.6
 619 ARG   (  52-)  H    -2.6
 813 VAL   (  77-)  I    -2.6
 590 LYS   (  77-)  G    -2.6
 567 LEU   (  38-)  G    -2.5
 504 ARG   (  87-)  F    -2.5
  57 PHE   (  88-)  A    -2.5
 993 ARG   (  28-)  L    -2.5
 895 LEU   (  75-)  J    -2.5
 154 VAL   (  15-)  B    -2.5
 679 LEU   ( 112-)  H    -2.5
 808 LEU   (  72-)  I    -2.4
 492 LEU   (  61-)  F    -2.4
 264 SER   (  37-)  C    -2.4
 629 ARG   (  62-)  H    -2.4
1078 LEU   (  61-)  M    -2.4
And so on for a total of 117 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.

  20 ASP   (  51-)  A  Poor phi/psi
  50 ASP   (  81-)  A  Poor phi/psi
  61 ASN   (  92-)  A  Poor phi/psi
  74 ARG   ( 105-)  A  omega poor
 128 GLY   ( 161-)  A  Poor phi/psi
 151 ASP   (  12-)  B  Poor phi/psi
 160 ASN   (  21-)  B  omega poor
 161 ASP   (  22-)  B  Poor phi/psi
 175 LEU   (  36-)  B  Poor phi/psi, omega poor
 198 ASN   (  59-)  B  omega poor
 208 TYR   (  69-)  B  omega poor
 240 ASP   (  13-)  C  Poor phi/psi
 249 GLY   (  22-)  C  Poor phi/psi
 250 ALA   (  23-)  C  Poor phi/psi
 260 PHE   (  33-)  C  omega poor
 264 SER   (  37-)  C  Poor phi/psi
 270 ASP   (  43-)  C  Poor phi/psi
 291 GLY   (  70-)  C  Poor phi/psi
 298 SER   (  77-)  C  Poor phi/psi
 324 ARG   (  37-)  D  omega poor
 338 SER   (  51-)  D  Poor phi/psi
 344 GLU   (  57-)  D  Poor phi/psi
 349 LYS   (  62-)  D  Poor phi/psi
 362 GLY   (  75-)  D  Poor phi/psi
 384 ASN   (  17-)  E  Poor phi/psi
And so on for a total of 59 lines.

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

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

chi-1/chi-2 correlation Z-score : -6.120

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.

 886 VAL   (  66-)  J    0.36

Warning: Unusual backbone conformations

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

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

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

   6 GLN   (  37-)  A      0
   7 TYR   (  38-)  A      0
   9 PHE   (  40-)  A      0
  19 VAL   (  50-)  A      0
  32 MSE   (  63-)  A      0
  34 PHE   (  65-)  A      0
  39 THR   (  70-)  A      0
  45 ASN   (  76-)  A      0
  49 GLN   (  80-)  A      0
  51 CYS   (  82-)  A      0
  57 PHE   (  88-)  A      0
  58 SER   (  89-)  A      0
  60 GLU   (  91-)  A      0
  62 LYS   (  93-)  A      0
  68 ARG   (  99-)  A      0
  70 ILE   ( 101-)  A      0
  72 MSE   ( 103-)  A      0
  80 MSE   ( 111-)  A      0
  88 LYS   ( 119-)  A      0
  89 GLU   ( 120-)  A      0
  92 PRO   ( 123-)  A      0
  93 LEU   ( 124-)  A      0
  94 MSE   ( 127-)  A      0
  95 GLU   ( 128-)  A      0
 124 MSE   ( 157-)  A      0
And so on for a total of 539 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 454 PRO   (  22-)  F    0.00 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].

1043 PRO   (  83-)  L   118.8 half-chair C-beta/C-alpha (126 degrees)
1118 PRO   (   3-)  N   110.9 envelop C-beta (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.

1130 MSE   (  15-)  N      CE   <->  1176 ILE   (  79-)  N      CG2  1.08    2.12  INTRA BL
 977 ILE   (  12-)  L      CG2  <->  1002 PHE   (  37-)  L      CE2  1.01    2.19  INTRA BF
 994 GLU   (  29-)  L      CD   <->  1018 ILE   (  53-)  L      CD1  1.01    2.19  INTRA BL
 124 MSE   ( 157-)  A      CE   <->   131 TYR   ( 164-)  A      CD2  0.99    2.21  INTRA BF
 461 LEU   (  30-)  F      CB   <->   486 TYR   (  55-)  F      CE2  0.97    2.23  INTRA BF
 490 MSE   (  59-)  F      CE   <->   516 LEU   (  99-)  F      CD2  0.97    2.23  INTRA BF
 230 MSE   (  91-)  B      CE   <->   260 PHE   (  33-)  C      CE2  0.97    2.23  INTRA BF
 494 LEU   (  63-)  F      CD1  <->   511 ILE   (  94-)  F      CD1  0.87    2.33  INTRA BL
 303 LEU   (  16-)  D      CA   <->   306 ILE   (  19-)  D      CG2  0.86    2.34  INTRA BF
 524 LEU   (  -5-)  G      CD2  <->   530 MSE   (   1-)  G      CB   0.86    2.34  INTRA BF
   4 LEU   (  35-)  A      CD1  <->  1151 MSE   (  36-)  N      CE   0.86    2.34  INTRA BL
 943 THR   (  53-)  K      CG2  <->   952 LYS   (  66-)  K      CB   0.85    2.35  INTRA BF
 848 LEU   (  26-)  J      CD2  <->   888 ILE   (  68-)  J      CD1  0.83    2.37  INTRA BF
 312 ASN   (  25-)  D      OD1  <->   371 GLN   (  84-)  D      NE2  0.78    1.92  INTRA BF
 819 GLN   (  83-)  I      NE2  <->   853 GLN   (  31-)  J      OE1  0.77    1.93  INTRA BF
 269 SER   (  42-)  C      CB   <->   286 MSE   (  65-)  C      CE   0.76    2.44  INTRA BF
1065 VAL   (  48-)  M      CG2  <->  1084 VAL   (  67-)  M      O    0.75    2.05  INTRA BF
 848 LEU   (  26-)  J      CD1  <->   863 LEU   (  41-)  J      CD1  0.75    2.45  INTRA BF
 530 MSE   (   1-)  G      CE   <->   602 VAL   (  89-)  G      CG1  0.74    2.46  INTRA BF
 524 LEU   (  -5-)  G      CD2  <->   530 MSE   (   1-)  G      CG   0.72    2.48  INTRA BF
 303 LEU   (  16-)  D      C    <->   306 ILE   (  19-)  D      CG2  0.72    2.48  INTRA BF
 945 HIS   (  55-)  K      NE2  <->   950 LEU   (  64-)  K      CB   0.72    2.38  INTRA BF
  84 VAL   ( 115-)  A      CG1  <->    85 ASP   ( 116-)  A      N    0.72    2.28  INTRA BF
 994 GLU   (  29-)  L      OE2  <->  1018 ILE   (  53-)  L      CD1  0.70    2.10  INTRA BL
   7 TYR   (  38-)  A      C    <->  1117 LEU   (   2-)  N      CD1  0.70    2.50  INTRA BL
And so on for a total of 690 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

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.

  91 GLN   ( 122-)  A      -7.70
 787 TYR   (  51-)  I      -7.45
 488 GLN   (  57-)  F      -7.44
1074 GLN   (  57-)  M      -7.36
 486 TYR   (  55-)  F      -7.02
 719 HIS   ( 152-)  H      -6.53
 946 TYR   (  56-)  K      -6.50
  43 TYR   (  74-)  A      -6.49
 733 PHE   ( 166-)  H      -6.38
  96 ARG   ( 129-)  A      -6.30
 248 ARG   (  21-)  C      -6.16
 331 PHE   (  44-)  D      -5.98
 934 PHE   (  44-)  K      -5.89
 837 ARG   (  15-)  J      -5.84
 526 PHE   (  -3-)  G      -5.82
 843 ARG   (  21-)  J      -5.73
 505 LYS   (  88-)  F      -5.71
 696 ARG   ( 129-)  H      -5.66
1188 GLN   (  91-)  N      -5.61
 709 ASN   ( 142-)  H      -5.61
 283 ARG   (  62-)  C      -5.57
 823 ARG   (  87-)  I      -5.55
  56 TYR   (  87-)  A      -5.53
 343 TYR   (  56-)  D      -5.53
 153 GLU   (  14-)  B      -5.50
 963 GLN   (  77-)  K      -5.49
 227 ARG   (  88-)  B      -5.47
 626 ARG   (  59-)  H      -5.43
 690 PRO   ( 123-)  H      -5.41
 371 GLN   (  84-)  D      -5.36
 169 GLN   (  30-)  B      -5.26
 734 HIS   ( 167-)  H      -5.23
 229 VAL   (  90-)  B      -5.22
 543 GLN   (  14-)  G      -5.20
 872 GLN   (  50-)  J      -5.19
 689 GLN   ( 122-)  H      -5.12
1028 HIS   (  68-)  L      -5.09
 563 ASN   (  34-)  G      -5.09
1112 PHE   (  -3-)  N      -5.06
 133 PHE   ( 166-)  A      -5.02

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.

 227 ARG   (  88-)  B       229 - VAL     90- ( B)         -5.00

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

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.

1051 LYS   (  34-)  M   -3.85
 126 ARG   ( 159-)  A   -2.92
 515 ILE   (  98-)  F   -2.85
 449 LYS   (  17-)  F   -2.81
 423 ARG   (  60-)  E   -2.80
1101 ILE   (  98-)  M   -2.76
  93 LEU   ( 124-)  A   -2.75
 502 SER   (  71-)  F   -2.74
 461 LEU   (  30-)  F   -2.72
 691 LEU   ( 124-)  H   -2.58
 451 PHE   (  19-)  F   -2.57
 612 ALA   (  45-)  H   -2.51
 576 SER   (  47-)  G   -2.50

Warning: Abnormal packing Z-score for sequential residues

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

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

 210 TYR   (  71-)  B     -  213 LYS   (  74-)  B        -1.40
 447 GLY   (  84-)  E     -  452 GLU   (  20-)  F        -1.83
 949 LEU   (  63-)  K     -  952 LYS   (  66-)  K        -2.11

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

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.

 127 HIS   ( 160-)  A
 160 ASN   (  21-)  B
 212 ASN   (  73-)  B
 265 ASN   (  38-)  C
 364 GLN   (  77-)  D
 409 ASN   (  42-)  E
 595 GLN   (  82-)  G
 727 HIS   ( 160-)  H
 833 ASN   (  11-)  J
 858 HIS   (  36-)  J
 945 HIS   (  55-)  K
 983 GLN   (  18-)  L
 992 ASN   (  27-)  L
1149 ASN   (  34-)  N
1189 GLN   (  92-)  N

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.

   2 LEU   (  33-)  A      N
   5 ASP   (  36-)  A      N
   7 TYR   (  38-)  A      N
  17 SER   (  48-)  A      N
  39 THR   (  70-)  A      N
  55 ILE   (  86-)  A      N
  59 GLU   (  90-)  A      N
  74 ARG   ( 105-)  A      NE
  85 ASP   ( 116-)  A      N
  87 ASP   ( 118-)  A      N
  89 GLU   ( 120-)  A      N
  90 ASP   ( 121-)  A      N
  91 GLN   ( 122-)  A      N
 113 ARG   ( 146-)  A      N
 123 LYS   ( 156-)  A      N
 126 ARG   ( 159-)  A      N
 130 VAL   ( 163-)  A      N
 135 LYS   ( 168-)  A      N
 137 ASP   ( 170-)  A      N
 141 LEU   (   2-)  B      N
 142 PHE   (   3-)  B      N
 143 PHE   (   4-)  B      N
 152 GLN   (  13-)  B      N
 160 ASN   (  21-)  B      N
 162 ILE   (  23-)  B      N
And so on for a total of 133 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.

 157 GLU   (  18-)  B      OE1
 192 HIS   (  53-)  B      ND1
 198 ASN   (  59-)  B      OD1
 258 GLN   (  31-)  C      OE1
 312 ASN   (  25-)  D      OD1
 499 GLU   (  68-)  F      OE1
 499 GLU   (  68-)  F      OE2
 932 ASP   (  42-)  K      OD2
1128 GLN   (  13-)  N      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.

   5 ASP   (  36-)  A   H-bonding suggests Asn; but Alt-Rotamer
  87 ASP   ( 118-)  A   H-bonding suggests Asn; but Alt-Rotamer
 161 ASP   (  22-)  B   H-bonding suggests Asn
 357 ASP   (  70-)  D   H-bonding suggests Asn; but Alt-Rotamer
 405 ASP   (  38-)  E   H-bonding suggests Asn; but Alt-Rotamer
 487 ASP   (  56-)  F   H-bonding suggests Asn; but Alt-Rotamer
 562 ASP   (  33-)  G   H-bonding suggests Asn; but Alt-Rotamer
 683 ASP   ( 116-)  H   H-bonding suggests Asn; but Alt-Rotamer
 687 GLU   ( 120-)  H   H-bonding suggests Gln
 771 ASP   (  33-)  I   H-bonding suggests Asn; but Alt-Rotamer
 779 ASP   (  41-)  I   H-bonding suggests Asn; but Alt-Rotamer
 856 ASP   (  34-)  J   H-bonding suggests Asn; but Alt-Rotamer
 908 ASP   (  18-)  K   H-bonding suggests Asn; but Alt-Rotamer
 956 ASP   (  70-)  K   H-bonding suggests Asn
1052 ASP   (  35-)  M   H-bonding suggests Asn
1073 ASP   (  56-)  M   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 :  -0.717
  2nd generation packing quality :  -1.654
  Ramachandran plot appearance   :  -2.166
  chi-1/chi-2 rotamer normality  :  -6.120 (bad)
  Backbone conformation          :  -0.431

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.533 (tight)
  Bond angles                    :   0.627 (tight)
  Omega angle restraints         :   1.018
  Side chain planarity           :   0.243 (tight)
  Improper dihedral distribution :   0.851
  B-factor distribution          :   0.507
  Inside/Outside distribution    :   1.040

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 : 2.95


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -3.5 (poor)
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.533 (tight)
  Bond angles                    :   0.627 (tight)
  Omega angle restraints         :   1.018
  Side chain planarity           :   0.243 (tight)
  Improper dihedral distribution :   0.851
  B-factor distribution          :   0.507
  Inside/Outside distribution    :   1.040
==============

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.