WHAT IF Check report

This file was created 2011-12-18 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 pdb1zr4.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 124191.773
Volume of the Unit Cell V= 2129762.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.287
Vm by authors and this calculated Vm agree reasonably well
Matthews coefficient read from REMARK 280 Vm= 3.930

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

  20 DADE  (  20-)  Z  -   P    150 SER   (  10-)  A  -   OG
  55 DADE  (  20-)  I  -   P    332 SER   (  10-)  B  -   OG
  90 DADE  (  20-)  W  -   P    515 SER   (  10-)  E  -   OG
 125 DADE  (  20-)  O  -   P    697 SER   (  10-)  D  -   OG

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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.

 753 LEU   (  66-)  D  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: D

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'.

 753 LEU   (  66-)  D      O

Warning: B-factors outside the range 0.0 - 100.0

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

   1 DTHY  (   1-)  X    High
   2 DCYT  (   2-)  X    High
   3 DADE  (   3-)  X    High
   4 DGUA  (   4-)  X    High
   5 DTHY  (   5-)  X    High
   6 DGUA  (   6-)  X    High
   7 DTHY  (   7-)  X    High
   8 DCYT  (   8-)  X    High
   9 DCYT  (   9-)  X    High
  10 DGUA  (  10-)  X    High
  11 DADE  (  11-)  X    High
  12 DTHY  (  12-)  X    High
  13 DADE  (  13-)  X    High
  14 DADE  (  14-)  X    High
  15 DTHY  (  15-)  X    High
  16 DTHY  (  16-)  X    High
  17 DTHY  (  17-)  X    High
  18 DADE  (  18-)  X    High
  19 DTHY  (  19-)  X    High
  21 DADE  (  21-)  Z    High
  22 DADE  (  22-)  Z    High
  23 DTHY  (  23-)  Y    High
  24 DTHY  (  24-)  Y    High
  25 DADE  (  25-)  Y    High
  26 DTHY  (  26-)  Y    High
And so on for a total of 588 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 12

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: E

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Tyrosine convention problem

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

 146 TYR   (   6-)  A
 242 TYR   ( 102-)  A
 316 TYR   ( 176-)  A
 328 TYR   (   6-)  B
 424 TYR   ( 102-)  B
 498 TYR   ( 176-)  B
 511 TYR   (   6-)  E
 607 TYR   ( 102-)  E
 681 TYR   ( 176-)  E
 693 TYR   (   6-)  D
 789 TYR   ( 102-)  D
 863 TYR   ( 176-)  D

Warning: Phenylalanine convention problem

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

 144 PHE   (   4-)  A
 223 PHE   (  83-)  A
 232 PHE   (  92-)  A
 280 PHE   ( 140-)  A
 326 PHE   (   4-)  B
 405 PHE   (  83-)  B
 462 PHE   ( 140-)  B
 509 PHE   (   4-)  E
 588 PHE   (  83-)  E
 645 PHE   ( 140-)  E
 691 PHE   (   4-)  D
 770 PHE   (  83-)  D
 779 PHE   (  92-)  D
 827 PHE   ( 140-)  D

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.

 165 ASP   (  25-)  A
 212 ASP   (  72-)  A
 347 ASP   (  25-)  B
 394 ASP   (  72-)  B
 397 ASP   (  75-)  B
 422 ASP   ( 100-)  B
 530 ASP   (  25-)  E
 605 ASP   ( 100-)  E
 712 ASP   (  25-)  D
 762 ASP   (  75-)  D
 787 ASP   ( 100-)  D

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 440 GLU   ( 118-)  B
 503 GLU   ( 181-)  B
 637 GLU   ( 132-)  E
 686 GLU   ( 181-)  E
 805 GLU   ( 118-)  D
 868 GLU   ( 181-)  D

Geometric checks

Warning: Unusual bond lengths

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

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

   2 DCYT  (   2-)  X      C1'  N1    1.54    6.2
  19 DTHY  (  19-)  X      C1'  N1    1.54    4.6
  71 DTHY  (   1-)  U      C1'  N1    1.54    4.7
  78 DCYT  (   8-)  U      C1'  N1    1.52    4.2
  79 DCYT  (   9-)  U      C1'  N1    1.53    5.0
  97 DCYT  (  27-)  V      C1'  N1    1.52    4.2
 103 DCYT  (  33-)  V      C1'  N1    1.53    5.1
 106 DTHY  (   1-)  M      C1'  N1    1.55    5.8
 108 DADE  (   3-)  M      C3'  O3'   1.49    4.5
 114 DCYT  (   9-)  M      O5'  C5'   1.37   -4.1
 116 DADE  (  11-)  M      O5'  C5'   1.37   -4.2
 133 DGUA  (  28-)  N      O5'  C5'   1.37   -4.7
 134 DGUA  (  29-)  N      O5'  C5'   1.37   -4.3
 136 DCYT  (  31-)  N      C1'  N1    1.53    4.8
 139 DTHY  (  34-)  N      C1'  N1    1.57    6.6

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

 |  0.999147 -0.000064  0.000388|
 | -0.000064  0.997985  0.000041|
 |  0.000388  0.000041  0.997878|
Proposed new scale matrix

 |  0.008399  0.000000 -0.000003|
 |  0.000000  0.007872  0.000000|
 | -0.000003  0.000000  0.007137|
With corresponding cell

    A    = 119.060  B   = 127.035  C    = 140.112
    Alpha=  90.002  Beta=  89.955  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 119.158  B   = 127.290  C    = 140.419
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 327.543
(Under-)estimated Z-score: 13.338

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.

   1 DTHY  (   1-)  X      C3'  C2'  C1'  92.38   -7.4
   1 DTHY  (   1-)  X      C4'  O4'  C1' 101.09   -6.1
   1 DTHY  (   1-)  X      O4'  C1'  N1  116.56   10.9
   1 DTHY  (   1-)  X      C2'  C1'  N1  122.59    5.2
   1 DTHY  (   1-)  X      C5   C4   O4  121.12   -5.4
   1 DTHY  (   1-)  X      O4   C4   N3  122.42    4.2
   2 DCYT  (   2-)  X      P   -C3* -O3* 129.36    8.1
   2 DCYT  (   2-)  X      P    O5'  C5' 127.43    4.1
   2 DCYT  (   2-)  X      C5'  C4'  O4' 118.03    5.4
   2 DCYT  (   2-)  X      C4'  O4'  C1' 102.16   -5.4
   2 DCYT  (   2-)  X      O4'  C1'  N1  118.95   13.9
   2 DCYT  (   2-)  X      C6   N1   C2  118.55   -4.4
   3 DADE  (   3-)  X      C3'  C4'  C5' 121.55    4.6
   3 DADE  (   3-)  X      O5'  C5'  C4' 118.92    6.2
   4 DGUA  (   4-)  X      P   -C3* -O3* 125.39    4.7
   4 DGUA  (   4-)  X      N9   C8   N7  114.05    5.9
   5 DTHY  (   5-)  X      C6   C5   C7  120.41   -4.1
   5 DTHY  (   5-)  X      C5   C4   O4  121.90   -4.3
   6 DGUA  (   6-)  X      N9   C8   N7  113.68    5.2
   7 DTHY  (   7-)  X      P   -C3* -O3* 126.24    5.4
   7 DTHY  (   7-)  X      C6   C5   C7  120.33   -4.3
   9 DCYT  (   9-)  X      O5*  P   -O3*  95.40   -4.5
   9 DCYT  (   9-)  X      P   -C3* -O3* 124.56    4.0
   9 DCYT  (   9-)  X      C3'  C4'  C5' 106.68   -5.3
   9 DCYT  (   9-)  X      O4'  C1'  N1  112.15    5.4
And so on for a total of 162 lines.

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.

 165 ASP   (  25-)  A
 212 ASP   (  72-)  A
 347 ASP   (  25-)  B
 394 ASP   (  72-)  B
 397 ASP   (  75-)  B
 422 ASP   ( 100-)  B
 440 GLU   ( 118-)  B
 503 GLU   ( 181-)  B
 530 ASP   (  25-)  E
 605 ASP   ( 100-)  E
 637 GLU   ( 132-)  E
 686 GLU   ( 181-)  E
 712 ASP   (  25-)  D
 762 ASP   (  75-)  D
 787 ASP   ( 100-)  D
 805 GLU   ( 118-)  D
 868 GLU   ( 181-)  D

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.

 825 VAL   ( 138-)  D    5.40
 848 ALA   ( 161-)  D    4.64
 824 GLY   ( 137-)  D    4.62

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

 131 DTHY  (  26-)  N    0.15
 112 DTHY  (   7-)  M    0.14
 104 DTHY  (  34-)  V    0.13
  85 DTHY  (  15-)  U    0.12
  24 DTHY  (  24-)  Y    0.11
 120 DTHY  (  15-)  M    0.11
  23 DTHY  (  23-)  Y    0.11
  15 DTHY  (  15-)  X    0.10
  12 DTHY  (  12-)  X    0.10
 Ramachandran Z-score : -3.884

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.884

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.

 419 ILE   (  97-)  B    -2.6
 602 ILE   (  97-)  E    -2.4
 364 SER   (  42-)  B    -2.4
 237 ILE   (  97-)  A    -2.3
 730 SER   (  43-)  D    -2.2
 172 ARG   (  32-)  A    -2.2
 608 ILE   ( 103-)  E    -2.1
 148 ARG   (   8-)  A    -2.1
 338 LEU   (  16-)  B    -2.1
 330 ARG   (   8-)  B    -2.1
 729 SER   (  42-)  D    -2.1
 750 VAL   (  63-)  D    -2.1
 205 LYS   (  65-)  A    -2.1
 513 ARG   (   8-)  E    -2.1
 331 VAL   (   9-)  B    -2.1
 514 VAL   (   9-)  E    -2.1
 613 VAL   ( 108-)  E    -2.1
 695 ARG   (   8-)  D    -2.1
 568 VAL   (  63-)  E    -2.1
 696 VAL   (   9-)  D    -2.1
 823 LYS   ( 136-)  D    -2.0
 187 GLY   (  47-)  A    -2.0
 149 VAL   (   9-)  A    -2.0
 185 ARG   (  45-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

 153 GLN   (  13-)  A  Poor phi/psi
 154 GLN   (  14-)  A  Poor phi/psi
 155 SER   (  15-)  A  Poor phi/psi
 170 ALA   (  30-)  A  omega poor
 179 SER   (  39-)  A  Poor phi/psi
 182 SER   (  42-)  A  Poor phi/psi
 285 LYS   ( 145-)  A  omega poor
 307 THR   ( 167-)  A  omega poor
 335 GLN   (  13-)  B  Poor phi/psi
 336 GLN   (  14-)  B  Poor phi/psi
 353 ASN   (  31-)  B  Poor phi/psi
 364 SER   (  42-)  B  Poor phi/psi
 366 ASP   (  44-)  B  Poor phi/psi
 390 ARG   (  68-)  B  Poor phi/psi
 467 LYS   ( 145-)  B  Poor phi/psi
 472 ALA   ( 150-)  B  Poor phi/psi
 490 MET   ( 168-)  B  Poor phi/psi
 518 GLN   (  13-)  E  Poor phi/psi
 519 GLN   (  14-)  E  Poor phi/psi
 539 PHE   (  34-)  E  omega poor
 547 SER   (  42-)  E  Poor phi/psi
 548 SER   (  43-)  E  Poor phi/psi
 638 ALA   ( 133-)  E  Poor phi/psi
 655 ALA   ( 150-)  E  Poor phi/psi
 674 ASN   ( 169-)  E  Poor phi/psi
 700 GLN   (  13-)  D  Poor phi/psi
 701 GLN   (  14-)  D  Poor phi/psi
 702 SER   (  15-)  D  Poor phi/psi
 718 ASN   (  31-)  D  omega poor
 750 VAL   (  63-)  D  omega poor
 754 ASP   (  67-)  D  Poor phi/psi
 780 ILE   (  93-)  D  Poor phi/psi
 791 GLY   ( 104-)  D  Poor phi/psi
 823 LYS   ( 136-)  D  Poor phi/psi, omega poor
 824 GLY   ( 137-)  D  omega poor
 856 ASN   ( 169-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.263

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 : -5.263

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!

   3 DADE  (   3-)  X      0
   4 DGUA  (   4-)  X      0
   5 DTHY  (   5-)  X      0
   6 DGUA  (   6-)  X      0
   7 DTHY  (   7-)  X      0
   8 DCYT  (   8-)  X      0
   9 DCYT  (   9-)  X      0
  10 DGUA  (  10-)  X      0
  11 DADE  (  11-)  X      0
  12 DTHY  (  12-)  X      0
  13 DADE  (  13-)  X      0
  14 DADE  (  14-)  X      0
  15 DTHY  (  15-)  X      0
  16 DTHY  (  16-)  X      0
  17 DTHY  (  17-)  X      0
  18 DADE  (  18-)  X      0
  19 DTHY  (  19-)  X      0
  20 DADE  (  20-)  Z      0
  21 DADE  (  21-)  Z      0
  22 DADE  (  22-)  Z      0
  23 DTHY  (  23-)  Y      0
  24 DTHY  (  24-)  Y      0
  25 DADE  (  25-)  Y      0
  26 DTHY  (  26-)  Y      0
  27 DCYT  (  27-)  Y      0
And so on for a total of 367 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 663 GLY   ( 158-)  E   1.59   80

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 238 SER   (  98-)  A   2.22

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.

 119 DADE  (  14-)  M      N1   <->   128 DTHY  (  23-)  N      N3   0.45    2.55  INTRA BF
 557 ARG   (  52-)  E      NH1  <->   587 GLU   (  82-)  E      OE1  0.41    2.29  INTRA BL
 104 DTHY  (  34-)  V      C2'  <->   105 DGUA  (  35-)  V      C8   0.40    2.80  INTRA BF
   6 DGUA  (   6-)  X      N7   <->   312 ARG   ( 172-)  A      NH2  0.39    2.61  INTRA BF
 121 DTHY  (  16-)  M      N3   <->   126 DADE  (  21-)  O      N1   0.37    2.63  INTRA BF
  76 DGUA  (   6-)  U      N7   <->   677 ARG   ( 172-)  E      NH2  0.36    2.64  INTRA BF
 109 DGUA  (   4-)  M      N1   <->   138 DCYT  (  33-)  N      N3   0.35    2.65  INTRA BF
   2 DCYT  (   2-)  X      C2'  <->     3 DADE  (   3-)  X      OP2  0.31    2.39  INTRA BF
 213 THR   (  73-)  A      N    <->   256 GLN   ( 116-)  A      OE1  0.28    2.42  INTRA BL
  77 DTHY  (   7-)  U      N3   <->   100 DADE  (  30-)  V      N1   0.26    2.74  INTRA BF
 109 DGUA  (   4-)  M      C2   <->   139 DTHY  (  34-)  N      O2   0.26    2.54  INTRA BF
 513 ARG   (   8-)  E      O    <->   524 GLN   (  19-)  E      NE2  0.25    2.45  INTRA BF
 337 SER   (  15-)  B      C    <->   339 ASP   (  17-)  B      N    0.24    2.66  INTRA BF
 122 DTHY  (  17-)  M      N3   <->   125 DADE  (  20-)  O      N1   0.23    2.77  INTRA BL
 111 DGUA  (   6-)  M      N7   <->   859 ARG   ( 172-)  D      NH2  0.22    2.78  INTRA BF
 367 ARG   (  45-)  B      NH2  <->   397 ASP   (  75-)  B      OD1  0.21    2.49  INTRA BF
  51 DTHY  (  16-)  J      N3   <->    56 DADE  (  21-)  I      N1   0.21    2.79  INTRA BF
  34 DTHY  (  34-)  Y      C2'  <->    35 DGUA  (  35-)  Y      C8   0.20    3.00  INTRA BL
 326 PHE   (   4-)  B      O    <->   384 LEU   (  62-)  B      N    0.19    2.51  INTRA BL
 691 PHE   (   4-)  D      O    <->   749 LEU   (  62-)  D      N    0.19    2.51  INTRA BL
 148 ARG   (   8-)  A      O    <->   159 GLN   (  19-)  A      NE2  0.19    2.51  INTRA BF
  81 DADE  (  11-)  U      N1   <->    96 DTHY  (  26-)  V      N3   0.19    2.81  INTRA BF
 695 ARG   (   8-)  D      O    <->   706 GLN   (  19-)  D      NE2  0.18    2.52  INTRA BF
  30 DADE  (  30-)  Y      C2'  <->    31 DCYT  (  31-)  Y      C5'  0.18    3.02  INTRA BF
 112 DTHY  (   7-)  M      N3   <->   135 DADE  (  30-)  N      N1   0.18    2.82  INTRA BF
And so on for a total of 153 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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 831 ARG   ( 144-)  D      -7.48
 758 ARG   (  71-)  D      -7.40
 211 ARG   (  71-)  A      -7.35
 280 PHE   ( 140-)  A      -7.22
 466 ARG   ( 144-)  B      -7.18
 393 ARG   (  71-)  B      -7.16
 462 PHE   ( 140-)  B      -7.08
 649 ARG   ( 144-)  E      -6.94
 576 ARG   (  71-)  E      -6.82
 645 PHE   ( 140-)  E      -6.70
 827 PHE   ( 140-)  D      -6.63
 755 ARG   (  68-)  D      -6.28
 284 ARG   ( 144-)  A      -6.16
 464 ARG   ( 142-)  B      -6.01
 829 ARG   ( 142-)  D      -6.01
 647 ARG   ( 142-)  E      -5.95
 661 GLN   ( 156-)  E      -5.57
 208 ARG   (  68-)  A      -5.57
 282 ARG   ( 142-)  A      -5.53
 390 ARG   (  68-)  B      -5.42
 573 ARG   (  68-)  E      -5.37
 491 ASN   ( 169-)  B      -5.37
 226 GLN   (  86-)  A      -5.30
 408 GLN   (  86-)  B      -5.24
 644 VAL   ( 139-)  E      -5.16
 296 GLN   ( 156-)  A      -5.08
 353 ASN   (  31-)  B      -5.07
 536 ASN   (  31-)  E      -5.06
 826 VAL   ( 139-)  D      -5.06
 695 ARG   (   8-)  D      -5.04
 279 VAL   ( 139-)  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.

 464 ARG   ( 142-)  B       466 - ARG    144- ( B)         -5.74
 647 ARG   ( 142-)  E       649 - ARG    144- ( E)         -5.78
 829 ARG   ( 142-)  D       832 - LYS    145- ( D)         -5.64

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: 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: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 281 GLY   ( 141-)  A   -2.96
 463 GLY   ( 141-)  B   -2.96
 646 GLY   ( 141-)  E   -2.96
 828 GLY   ( 141-)  D   -2.96
 462 PHE   ( 140-)  B   -2.81
 827 PHE   ( 140-)  D   -2.69
 280 PHE   ( 140-)  A   -2.66
 330 ARG   (   8-)  B   -2.57

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.

 279 VAL   ( 139-)  A     -  283 LYS   ( 143-)  A        -2.10
 461 VAL   ( 139-)  B     -  465 LYS   ( 143-)  B        -2.13
 644 VAL   ( 139-)  E     -  647 ARG   ( 142-)  E        -2.12
 826 VAL   ( 139-)  D     -  830 LYS   ( 143-)  D        -2.12

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: E

Note: Second generation quality Z-score plot

Chain identifier: D

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.

 293 ASN   ( 153-)  A
 297 GLN   ( 157-)  A
 625 GLN   ( 120-)  E
 662 GLN   ( 157-)  E

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.

   1 DTHY  (   1-)  X      N3
  35 DGUA  (  35-)  Y      N1
 139 DTHY  (  34-)  N      N3
 148 ARG   (   8-)  A      NE
 157 ASP   (  17-)  A      N
 193 MET   (  53-)  A      N
 204 LYS   (  64-)  A      N
 205 LYS   (  65-)  A      N
 210 GLY   (  70-)  A      N
 211 ARG   (  71-)  A      N
 230 ILE   (  90-)  A      N
 235 ASP   (  95-)  A      N
 239 THR   (  99-)  A      OG1
 243 ILE   ( 103-)  A      N
 282 ARG   ( 142-)  A      NE
 297 GLN   ( 157-)  A      N
 299 LEU   ( 159-)  A      N
 325 LEU   (   3-)  B      N
 330 ARG   (   8-)  B      N
 368 LYS   (  46-)  B      N
 377 VAL   (  55-)  B      N
 386 LYS   (  64-)  B      N
 387 LYS   (  65-)  B      N
 391 LEU   (  69-)  B      N
 393 ARG   (  71-)  B      N
And so on for a total of 78 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.

 341 GLN   (  19-)  B      OE1
 524 GLN   (  19-)  E      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.

 165 ASP   (  25-)  A   H-bonding suggests Asn; but Alt-Rotamer
 199 ASP   (  59-)  A   H-bonding suggests Asn; but Alt-Rotamer
 347 ASP   (  25-)  B   H-bonding suggests Asn
 371 ASP   (  49-)  B   H-bonding suggests Asn
 530 ASP   (  25-)  E   H-bonding suggests Asn; but Alt-Rotamer
 549 ASP   (  44-)  E   H-bonding suggests Asn; but Alt-Rotamer
 564 ASP   (  59-)  E   H-bonding suggests Asn; but Alt-Rotamer
 712 ASP   (  25-)  D   H-bonding suggests Asn
 736 ASP   (  49-)  D   H-bonding suggests Asn
 746 ASP   (  59-)  D   H-bonding suggests Asn
 805 GLU   ( 118-)  D   H-bonding suggests Gln
 815 GLU   ( 128-)  D   H-bonding suggests Gln

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 :  -1.445
  2nd generation packing quality :  -1.893
  Ramachandran plot appearance   :  -3.884 (poor)
  chi-1/chi-2 rotamer normality  :  -5.263 (bad)
  Backbone conformation          :   0.654

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.690
  Bond angles                    :   1.123
  Omega angle restraints         :   0.909
  Side chain planarity           :   0.327 (tight)
  Improper dihedral distribution :   0.628
  B-factor distribution          :   0.367
  Inside/Outside distribution    :   0.975

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.690
  Bond angles                    :   1.123
  Omega angle restraints         :   0.909
  Side chain planarity           :   0.327 (tight)
  Improper dihedral distribution :   0.628
  B-factor distribution          :   0.367
  Inside/Outside distribution    :   0.975
==============

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.