WHAT IF Check report

This file was created 2012-04-04 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 pdb3o5k.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 B

All-atom RMS fit for the two chains : 0.912
CA-only RMS fit for the two chains : 0.669

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.828
CA-only RMS fit for the two chains : 0.648

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.946
CA-only RMS fit for the two chains : 0.807

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.743
CA-only RMS fit for the two chains : 0.605

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.880
CA-only RMS fit for the two chains : 0.705

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and D

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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'.

   8 GLU   (  20-)  A      CG
   8 GLU   (  20-)  A      CD
   8 GLU   (  20-)  A      OE1
   8 GLU   (  20-)  A      OE2
  11 GLU   (  23-)  A      CG
  11 GLU   (  23-)  A      CD
  11 GLU   (  23-)  A      OE1
  11 GLU   (  23-)  A      OE2
  32 GLU   (  44-)  A      CG
  32 GLU   (  44-)  A      CD
  32 GLU   (  44-)  A      OE1
  32 GLU   (  44-)  A      OE2
  63 GLU   (  75-)  A      CG
  63 GLU   (  75-)  A      CD
  63 GLU   (  75-)  A      OE1
  63 GLU   (  75-)  A      OE2
 159 GLU   (  44-)  B      CG
 159 GLU   (  44-)  B      CD
 159 GLU   (  44-)  B      OE1
 159 GLU   (  44-)  B      OE2
 188 ARG   (  73-)  B      CG
 188 ARG   (  73-)  B      CD
 188 ARG   (  73-)  B      NE
 188 ARG   (  73-)  B      CZ
 188 ARG   (  73-)  B      NH1
And so on for a total of 122 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.

 357 SER   ( 115-)  C    High
 358 ALA   ( 116-)  C    High
 361 LEU   ( 119-)  C    High
 362 PRO   ( 120-)  C    High
 363 LYS   ( 121-)  C    High
 366 SER   ( 124-)  C    High
 424 TYR   (  54-)  D    High
 426 HIS   (  56-)  D    High
 433 ASN   (  63-)  D    High
 435 LYS   (  65-)  D    High
 436 LYS   (  66-)  D    High
 437 PHE   (  67-)  D    High
 438 ASP   (  68-)  D    High
 439 SER   (  69-)  D    High
 440 SER   (  70-)  D    High
 441 HIS   (  71-)  D    High
 442 ASP   (  72-)  D    High
 443 ARG   (  73-)  D    High
 444 ASN   (  74-)  D    High
 445 GLU   (  75-)  D    High
 446 PRO   (  76-)  D    High
 447 PHE   (  77-)  D    High
 448 VAL   (  78-)  D    High
 450 SER   (  80-)  D    High
 453 LYS   (  83-)  D    High
 454 GLY   (  84-)  D    High
 455 GLN   (  85-)  D    High
 483 TYR   ( 113-)  D    High
 484 GLY   ( 114-)  D    High
 485 SER   ( 115-)  D    High
 486 ALA   ( 116-)  D    High
 487 GLY   ( 117-)  D    High
 488 SER   ( 118-)  D    High
 489 LEU   ( 119-)  D    High
 490 PRO   ( 120-)  D    High
 491 LYS   ( 121-)  D    High
 492 ILE   ( 122-)  D    High
 493 PRO   ( 123-)  D    High
 494 SER   ( 124-)  D    High
 495 ASN   ( 125-)  D    High
 508 LYS   ( 138-)  D    High
 509 GLY   ( 139-)  D    High
 510 GLU   ( 140-)  D    High

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 4

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

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

  42 TYR   (  54-)  A
  45 TYR   (  57-)  A
  99 TYR   ( 111-)  A
 101 TYR   ( 113-)  A
 169 TYR   (  54-)  B
 172 TYR   (  57-)  B
 226 TYR   ( 111-)  B
 296 TYR   (  54-)  C
 299 TYR   (  57-)  C
 353 TYR   ( 111-)  C
 355 TYR   ( 113-)  C
 424 TYR   (  54-)  D
 427 TYR   (  57-)  D
 483 TYR   ( 113-)  D

Warning: Phenylalanine convention problem

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

  67 PHE   (  79-)  A
 192 PHE   (  77-)  B
 194 PHE   (  79-)  B
 321 PHE   (  79-)  C
 371 PHE   ( 129-)  C
 449 PHE   (  79-)  D
 507 PHE   ( 137-)  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.

  18 ASP   (  30-)  A
 145 ASP   (  30-)  B
 272 ASP   (  30-)  C
 400 ASP   (  30-)  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.

  33 GLU   (  45-)  A
 119 GLU   ( 131-)  A
 135 GLU   (  20-)  B
 510 GLU   ( 140-)  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.

 255 GLY   (  13-)  C      N    CA    1.66   13.3
 445 GLU   (  75-)  D      CD   OE1   1.36    5.8
 445 GLU   (  75-)  D      CD   OE2   1.37    6.2

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

 |  0.996701 -0.000053  0.000245|
 | -0.000053  0.996885 -0.000079|
 |  0.000245 -0.000079  0.997747|
Proposed new scale matrix

 |  0.014372  0.000001  0.006538|
 |  0.000001  0.020713  0.000002|
 | -0.000004  0.000001  0.014432|
With corresponding cell

    A    =  69.573  B   =  48.280  C    =  76.118
    Alpha=  90.006  Beta= 114.448  Gamma=  90.006

The CRYST1 cell dimensions

    A    =  69.802  B   =  48.430  C    =  76.317
    Alpha=  90.000  Beta= 114.500  Gamma=  90.000

Variance: 134.390
(Under-)estimated Z-score: 8.544

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 ASP   (  30-)  A
  33 GLU   (  45-)  A
 119 GLU   ( 131-)  A
 135 GLU   (  20-)  B
 145 ASP   (  30-)  B
 272 ASP   (  30-)  C
 400 ASP   (  30-)  D
 510 GLU   ( 140-)  D

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.

 490 PRO   ( 120-)  D    -2.7
 360 SER   ( 118-)  C    -2.5
 362 PRO   ( 120-)  C    -2.4
  33 GLU   (  45-)  A    -2.3
 488 SER   ( 118-)  D    -2.3
 108 PRO   ( 120-)  A    -2.3
  36 MET   (  48-)  A    -2.2
 106 SER   ( 118-)  A    -2.1
 493 PRO   ( 123-)  D    -2.1
 476 LEU   ( 106-)  D    -2.1
 233 SER   ( 118-)  B    -2.0
 361 LEU   ( 119-)  C    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   2 ALA   (  14-)  A  Poor phi/psi
  17 LYS   (  29-)  A  Poor phi/psi
  19 ARG   (  31-)  A  Poor phi/psi
  30 ASN   (  42-)  A  omega poor
  31 GLY   (  43-)  A  Poor phi/psi, omega poor
  32 GLU   (  44-)  A  omega poor
  43 VAL   (  55-)  A  omega poor
  52 GLY   (  64-)  A  Poor phi/psi
  62 ASN   (  74-)  A  Poor phi/psi
  89 GLU   ( 101-)  A  omega poor
  93 LEU   ( 105-)  A  omega poor
 100 ALA   ( 112-)  A  Poor phi/psi
 107 LEU   ( 119-)  A  PRO omega poor
 123 LEU   ( 135-)  A  omega poor
 144 LYS   (  29-)  B  Poor phi/psi
 146 ARG   (  31-)  B  Poor phi/psi
 150 LYS   (  35-)  B  omega poor
 175 LYS   (  60-)  B  omega poor
 183 ASP   (  68-)  B  Poor phi/psi
 227 ALA   ( 112-)  B  Poor phi/psi
 234 LEU   ( 119-)  B  PRO omega poor
 236 LYS   ( 121-)  B  omega poor
 240 ASN   ( 125-)  B  Poor phi/psi
 241 ALA   ( 126-)  B  omega poor
 245 PHE   ( 130-)  B  omega poor
 271 LYS   (  29-)  C  Poor phi/psi
 273 ARG   (  31-)  C  Poor phi/psi
 297 VAL   (  55-)  C  omega poor
 316 ASN   (  74-)  C  Poor phi/psi
 354 ALA   ( 112-)  C  Poor phi/psi
 361 LEU   ( 119-)  C  PRO omega poor
 367 ASN   ( 125-)  C  Poor phi/psi
 372 PHE   ( 130-)  C  omega poor
 399 LYS   (  29-)  D  Poor phi/psi
 401 ARG   (  31-)  D  Poor phi/psi
 425 VAL   (  55-)  D  omega poor
 482 ALA   ( 112-)  D  Poor phi/psi
 488 SER   ( 118-)  D  Poor phi/psi
 489 LEU   ( 119-)  D  PRO omega poor
 493 PRO   ( 123-)  D  Poor phi/psi
 495 ASN   ( 125-)  D  Poor phi/psi
 500 PHE   ( 130-)  D  omega poor
 506 ASP   ( 136-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.635

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!

  13 ILE   (  25-)  A      0
  19 ARG   (  31-)  A      0
  23 LYS   (  35-)  A      0
  26 LYS   (  38-)  A      0
  27 ARG   (  39-)  A      0
  30 ASN   (  42-)  A      0
  31 GLY   (  43-)  A      0
  32 GLU   (  44-)  A      0
  33 GLU   (  45-)  A      0
  36 MET   (  48-)  A      0
  37 ILE   (  49-)  A      0
  54 LYS   (  66-)  A      0
  56 ASP   (  68-)  A      0
  57 SER   (  69-)  A      0
  61 ARG   (  73-)  A      0
  62 ASN   (  74-)  A      0
  69 LEU   (  81-)  A      0
  73 GLN   (  85-)  A      0
  74 VAL   (  86-)  A      0
  87 LYS   (  99-)  A      0
  99 TYR   ( 111-)  A      0
 100 ALA   ( 112-)  A      0
 101 TYR   ( 113-)  A      0
 103 SER   ( 115-)  A      0
 104 ALA   ( 116-)  A      0
And so on for a total of 215 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!

 179 GLY   (  64-)  B   1.50   80

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].

  97 PRO   ( 109-)  A  -125.6 half-chair C-delta/C-gamma (-126 degrees)
 108 PRO   ( 120-)  A     1.2 envelop N (0 degrees)
 235 PRO   ( 120-)  B   -29.8 envelop C-alpha (-36 degrees)
 351 PRO   ( 109-)  C  -126.4 half-chair C-delta/C-gamma (-126 degrees)
 362 PRO   ( 120-)  C    -9.4 half-chair C-alpha/N (-18 degrees)
 479 PRO   ( 109-)  D  -134.7 half-chair C-delta/C-gamma (-126 degrees)
 490 PRO   ( 120-)  D    11.9 half-chair N/C-delta (18 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

  30 ASN   (  42-)  A      C   <->   31 GLY   (  43-)  A      O      0.21    2.39  INTRA BL
 260 VAL   (  18-)  C      O   <->  264 GLY   (  22-)  C      N      0.19    2.51  INTRA BF
  44 HIS   (  56-)  A      ND1 <->   58 SER   (  70-)  A      OG     0.18    2.52  INTRA BL
  45 TYR   (  57-)  A      OH  <->   56 ASP   (  68-)  A      OD2    0.18    2.22  INTRA BL
 408 LYS   (  38-)  D      N   <->  472 ILE   ( 102-)  D      O      0.17    2.53  INTRA BF
 384 ALA   (  14-)  D      N   <->  385 PRO   (  15-)  D      CD     0.17    2.83  INTRA BF
  30 ASN   (  42-)  A      N   <->   87 LYS   (  99-)  A      O      0.16    2.54  INTRA BL
   2 ALA   (  14-)  A      CB  <->    5 THR   (  17-)  A      OG1    0.15    2.65  INTRA BL
  34 THR   (  46-)  A      CG2 <->   85 MET   (  97-)  A      O      0.13    2.67  INTRA BL
 298 HIS   (  56-)  C      ND1 <->  312 SER   (  70-)  C      OG     0.13    2.57  INTRA BF
 265 GLU   (  23-)  C      N   <->  277 LYS   (  35-)  C      O      0.12    2.58  INTRA BL
 360 SER   ( 118-)  C      O   <->  364 ILE   ( 122-)  C      N      0.12    2.58  INTRA BF
 452 GLY   (  82-)  D      N   <->  461 ASP   (  91-)  D      OD1    0.10    2.60  INTRA BF
  38 GLY   (  50-)  A      N   <->   69 LEU   (  81-)  A      O      0.10    2.60  INTRA BL
 475 LEU   ( 105-)  D      N   <->  500 PHE   ( 130-)  D      O      0.08    2.62  INTRA BF
 301 GLY   (  59-)  C      N   <->  310 ASP   (  68-)  C      O      0.08    2.62  INTRA BF
 383 GLY   (  13-)  D      C   <->  385 PRO   (  15-)  D      CD     0.07    3.13  INTRA BF
  30 ASN   (  42-)  A      C   <->   31 GLY   (  43-)  A      C      0.07    2.73  INTRA BL
 174 GLY   (  59-)  B      N   <->  183 ASP   (  68-)  B      O      0.07    2.63  INTRA BL
  77 ALA   (  89-)  A      O   <->   81 GLY   (  93-)  A      N      0.07    2.63  INTRA BL
 426 HIS   (  56-)  D      O   <->  503 GLU   ( 133-)  D      N      0.07    2.63  INTRA BF
  48 LYS   (  60-)  A      N   <->  117 PHE   ( 129-)  A      O      0.06    2.64  INTRA BL
  20 GLY   (  32-)  A      O   <->   96 LYS   ( 108-)  A      N      0.06    2.64  INTRA BL
 176 LEU   (  61-)  B      N   <->  180 LYS   (  65-)  B      O      0.05    2.65  INTRA BL
  44 HIS   (  56-)  A      O   <->  121 GLU   ( 133-)  A      N      0.05    2.65  INTRA BL
 388 VAL   (  18-)  D      CG1 <->  476 LEU   ( 106-)  D      CB     0.05    3.15  INTRA BF
 459 ALA   (  89-)  D      CB  <->  477 CYS   ( 107-)  D      SG     0.05    3.35  INTRA BF
 488 SER   ( 118-)  D      N   <->  492 ILE   ( 122-)  D      O      0.05    2.65  INTRA BF
 459 ALA   (  89-)  D      O   <->  463 GLY   (  93-)  D      N      0.04    2.66  INTRA BF
 296 TYR   (  54-)  C      N   <->  378 ASP   ( 136-)  C      O      0.03    2.67  INTRA BL
   7 ALA   (  19-)  A      O   <->   19 ARG   (  31-)  A      NH2    0.03    2.67  INTRA BL
 349 CYS   ( 107-)  C      N   <->  370 LEU   ( 128-)  C      O      0.03    2.67  INTRA BL
 150 LYS   (  35-)  B      NZ  <->  216 GLU   ( 101-)  B      OE2    0.03    2.67  INTRA BL
  97 PRO   ( 109-)  A      O   <->  102 GLY   ( 114-)  A      N      0.03    2.67  INTRA BL
 431 LEU   (  61-)  D      N   <->  435 LYS   (  65-)  D      O      0.03    2.67  INTRA BF
 477 CYS   ( 107-)  D      N   <->  498 LEU   ( 128-)  D      O      0.02    2.68  INTRA BF
  31 GLY   (  43-)  A      C   <->   33 GLU   (  45-)  A      N      0.02    2.88  INTRA BL
   5 THR   (  17-)  A      O   <->    9 GLN   (  21-)  A      N      0.02    2.68  INTRA BL
 443 ARG   (  73-)  D      N   <->  444 ASN   (  74-)  D      N      0.02    2.58  INTRA BF
 387 THR   (  17-)  D      O   <->  391 GLN   (  21-)  D      N      0.01    2.69  INTRA BF
 221 LEU   ( 106-)  B      CD1 <->  242 THR   ( 127-)  B      CG2    0.01    3.19  INTRA BL
 355 TYR   ( 113-)  C      O   <->  359 GLY   ( 117-)  C      N      0.01    2.69  INTRA BF
  36 MET   (  48-)  A      N   <->   39 ASP   (  51-)  A      OD2    0.01    2.69  INTRA BL
 424 TYR   (  54-)  D      N   <->  506 ASP   ( 136-)  D      O      0.01    2.69  INTRA BF
  30 ASN   (  42-)  A      O   <->   31 GLY   (  43-)  A      C      0.01    2.59  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

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

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

 489 LEU   ( 119-)  D      -6.53
 455 GLN   (  85-)  D      -6.23
 433 ASN   (  63-)  D      -6.03
 107 LEU   ( 119-)  A      -5.98
  61 ARG   (  73-)  A      -5.85
 483 TYR   ( 113-)  D      -5.84
   9 GLN   (  21-)  A      -5.79
 236 LYS   ( 121-)  B      -5.75
  36 MET   (  48-)  A      -5.60
 136 GLN   (  21-)  B      -5.58
 290 MET   (  48-)  C      -5.52
 410 VAL   (  40-)  D      -5.38
 282 VAL   (  40-)  C      -5.27
 200 GLN   (  85-)  B      -5.26
 163 MET   (  48-)  B      -5.25
 228 TYR   ( 113-)  B      -5.23
 327 GLN   (  85-)  C      -5.22
 157 ASN   (  42-)  B      -5.12
 101 TYR   ( 113-)  A      -5.07
 437 PHE   (  67-)  D      -5.02
  73 GLN   (  85-)  A      -5.01

Warning: Abnormal packing environment for sequential residues

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

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

 432 SER   (  62-)  D       434 - GLY     64- ( D)         -4.82

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Warning: Low packing Z-score for some residues

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

 469 LYS   (  99-)  D   -3.17
 363 LYS   ( 121-)  C   -3.11
  63 GLU   (  75-)  A   -2.83
 188 ARG   (  73-)  B   -2.63
 412 ASN   (  42-)  D   -2.58
 453 LYS   (  83-)  D   -2.57

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

 444 ASN   (  74-)  D
 495 ASN   ( 125-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  21 VAL   (  33-)  A      N
  34 THR   (  46-)  A      OG1
  61 ARG   (  73-)  A      N
  73 GLN   (  85-)  A      N
  74 VAL   (  86-)  A      N
  78 TRP   (  90-)  A      NE1
  98 GLU   ( 110-)  A      N
 109 LYS   ( 121-)  A      N
 148 VAL   (  33-)  B      N
 160 GLU   (  45-)  B      N
 161 THR   (  46-)  B      N
 200 GLN   (  85-)  B      N
 201 VAL   (  86-)  B      N
 205 TRP   (  90-)  B      NE1
 210 ALA   (  95-)  B      N
 225 GLU   ( 110-)  B      N
 260 VAL   (  18-)  C      N
 275 VAL   (  33-)  C      N
 283 GLY   (  41-)  C      N
 287 GLU   (  45-)  C      N
 288 THR   (  46-)  C      N
 305 ASN   (  63-)  C      N
 316 ASN   (  74-)  C      N
 327 GLN   (  85-)  C      N
 328 VAL   (  86-)  C      N
 332 TRP   (  90-)  C      NE1
 337 ALA   (  95-)  C      N
 379 PHE   ( 137-)  C      N
 403 VAL   (  33-)  D      N
 418 MET   (  48-)  D      N
 443 ARG   (  73-)  D      N
 444 ASN   (  74-)  D      N
 456 VAL   (  86-)  D      N
 460 TRP   (  90-)  D      NE1
 469 LYS   (  99-)  D      N
 480 GLU   ( 110-)  D      N

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.

 135 GLU   (  20-)  B   H-bonding suggests Gln
 138 GLU   (  23-)  B   H-bonding suggests Gln
 266 ASP   (  24-)  C   H-bonding suggests Asn; but Alt-Rotamer
 314 ASP   (  72-)  C   H-bonding suggests Asn; but Alt-Rotamer
 394 ASP   (  24-)  D   H-bonding suggests Asn
 442 ASP   (  72-)  D   H-bonding suggests Asn

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 :  -1.012
  2nd generation packing quality :  -1.767
  Ramachandran plot appearance   :  -1.868
  chi-1/chi-2 rotamer normality  :  -2.635
  Backbone conformation          :  -0.199

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.474 (tight)
  Bond angles                    :   0.627 (tight)
  Omega angle restraints         :   1.170
  Side chain planarity           :   0.295 (tight)
  Improper dihedral distribution :   0.603
  B-factor distribution          :   0.671
  Inside/Outside distribution    :   0.982

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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.474 (tight)
  Bond angles                    :   0.627 (tight)
  Omega angle restraints         :   1.170
  Side chain planarity           :   0.295 (tight)
  Improper dihedral distribution :   0.603
  B-factor distribution          :   0.671
  Inside/Outside distribution    :   0.982
==============

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.