WHAT IF Check report

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

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

Verification log for pdb3v4z.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 583 PGE   ( 501-)  A  -
 584 PEG   ( 502-)  A  -

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

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

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.

  31 GLU   (  32-)  A    High
  48 GLN   (  49-)  A    High
  51 GLU   (  52-)  A    High
  64 ARG   (  65-)  A    High
 119 GLN   ( 120-)  A    High
 147 GLU   ( 148-)  A    High
 148 GLY   ( 149-)  A    High
 149 SER   ( 150-)  A    High
 150 SER   ( 151-)  A    High
 168 GLU   ( 169-)  A    High
 171 GLN   ( 172-)  A    High
 172 HIS   ( 173-)  A    High
 194 ASP   ( 195-)  A    High
 207 LYS   ( 220-)  A    High
 219 GLU   ( 232-)  A    High
 222 GLN   ( 235-)  A    High
 267 HIS   ( 280-)  A    High
 290 MET   ( 303-)  A    High
 325 GLU   (  32-)  B    High
 345 GLU   (  52-)  B    High
 358 ARG   (  65-)  B    High
 413 GLN   ( 120-)  B    High
 420 PRO   ( 127-)  B    High
 421 GLU   ( 128-)  B    High
 422 GLU   ( 129-)  B    High
 440 HIS   ( 147-)  B    High
 447 HIS   ( 159-)  B    High
 470 TRP   ( 182-)  B    High
 472 SER   ( 184-)  B    High
 483 ASP   ( 195-)  B    High
 484 GLU   ( 196-)  B    High
 492 GLN   ( 204-)  B    High
 493 PRO   ( 205-)  B    High
 494 PRO   ( 206-)  B    High
 495 THR   ( 221-)  B    High
 498 PHE   ( 224-)  B    High
 509 GLN   ( 235-)  B    High
 536 ARG   ( 262-)  B    High
 537 ASP   ( 263-)  B    High
 554 HIS   ( 280-)  B    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: 2

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

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.

 412 ARG   ( 119-)  B

Warning: Tyrosine convention problem

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

 113 TYR   ( 114-)  A
 232 TYR   ( 245-)  A
 254 TYR   ( 267-)  A
 376 TYR   (  83-)  B
 519 TYR   ( 245-)  B
 541 TYR   ( 267-)  B

Warning: Phenylalanine convention problem

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

 211 PHE   ( 224-)  A
 338 PHE   (  45-)  B
 371 PHE   (  78-)  B
 476 PHE   ( 188-)  B
 498 PHE   ( 224-)  B
 568 PHE   ( 294-)  B

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.

 173 ASP   ( 174-)  A
 194 ASP   ( 195-)  A
 248 ASP   ( 261-)  A
 250 ASP   ( 263-)  A
 293 ASP   ( 306-)  A
 462 ASP   ( 174-)  B
 483 ASP   ( 195-)  B
 535 ASP   ( 261-)  B
 537 ASP   ( 263-)  B
 580 ASP   ( 306-)  B

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.

  14 GLU   (  15-)  A
  31 GLU   (  32-)  A
  67 GLU   (  68-)  A
 147 GLU   ( 148-)  A
 179 GLU   ( 180-)  A
 195 GLU   ( 196-)  A
 219 GLU   ( 232-)  A
 308 GLU   (  15-)  B
 361 GLU   (  68-)  B
 416 GLU   ( 123-)  B
 421 GLU   ( 128-)  B
 450 GLU   ( 162-)  B
 457 GLU   ( 169-)  B
 468 GLU   ( 180-)  B
 475 GLU   ( 187-)  B
 484 GLU   ( 196-)  B

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.

 252 HIS   ( 265-)  A      CG   CD2   1.40    4.0
 267 HIS   ( 280-)  A      CG   CD2   1.40    4.3
 356 HIS   (  63-)  B      CG   CD2   1.41    4.6
 554 HIS   ( 280-)  B      CG   CD2   1.40    4.4

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

 |  0.999032  0.000134  0.000105|
 |  0.000134  0.999458 -0.000756|
 |  0.000105 -0.000756  0.997761|
Proposed new scale matrix

 |  0.009946  0.005739  0.000003|
 | -0.000002  0.011480  0.000009|
 |  0.000000  0.000007  0.009086|
With corresponding cell

    A    = 100.537  B   = 100.559  C    = 110.055
    Alpha=  90.078  Beta=  89.995  Gamma= 119.977

The CRYST1 cell dimensions

    A    = 100.637  B   = 100.637  C    = 110.304
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 35.876
(Under-)estimated Z-score: 4.414

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.

  62 HIS   (  63-)  A      CG   ND1  CE1 109.62    4.0
 146 HIS   ( 147-)  A      CG   ND1  CE1 109.74    4.1
 158 HIS   ( 159-)  A      CG   ND1  CE1 109.61    4.0
 232 TYR   ( 245-)  A      CA   CB   CG  121.91    4.4
 249 ARG   ( 262-)  A      CB   CG   CD  103.60   -5.2
 285 VAL   ( 298-)  A      C    CA   CB  120.40    5.4
 392 ARG   (  99-)  B      CA   CB   CG  105.61   -4.2
 408 VAL   ( 115-)  B      N    CA   C    98.38   -4.6
 418 LEU   ( 125-)  B      CA   CB   CG  130.49    4.1
 461 HIS   ( 173-)  B      CG   ND1  CE1 109.97    4.4

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.

  14 GLU   (  15-)  A
  31 GLU   (  32-)  A
  67 GLU   (  68-)  A
 147 GLU   ( 148-)  A
 173 ASP   ( 174-)  A
 179 GLU   ( 180-)  A
 194 ASP   ( 195-)  A
 195 GLU   ( 196-)  A
 219 GLU   ( 232-)  A
 248 ASP   ( 261-)  A
 250 ASP   ( 263-)  A
 293 ASP   ( 306-)  A
 308 GLU   (  15-)  B
 361 GLU   (  68-)  B
 412 ARG   ( 119-)  B
 416 GLU   ( 123-)  B
 421 GLU   ( 128-)  B
 450 GLU   ( 162-)  B
 457 GLU   ( 169-)  B
 462 ASP   ( 174-)  B
 468 GLU   ( 180-)  B
 475 GLU   ( 187-)  B
 483 ASP   ( 195-)  B
 484 GLU   ( 196-)  B
 535 ASP   ( 261-)  B
 537 ASP   ( 263-)  B
 580 ASP   ( 306-)  B

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.

 131 ALA   ( 132-)  A    5.71
 560 ALA   ( 286-)  B    5.15
 408 VAL   ( 115-)  B    4.51
 563 GLN   ( 289-)  B    4.07
 138 LEU   ( 139-)  A    4.05

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 126 PRO   ( 127-)  A    -2.9
  47 THR   (  48-)  A    -2.7
 121 PHE   ( 122-)  A    -2.6
 110 ILE   ( 111-)  A    -2.4
 240 TRP   ( 253-)  A    -2.4
   8 LEU   (   9-)  A    -2.2
  79 GLN   (  80-)  A    -2.2
 475 GLU   ( 187-)  B    -2.2
 407 TYR   ( 114-)  B    -2.2
 527 TRP   ( 253-)  B    -2.2
 492 GLN   ( 204-)  B    -2.2
 302 LEU   (   9-)  B    -2.2
 138 LEU   ( 139-)  A    -2.1
  56 LYS   (  57-)  A    -2.1
 176 VAL   ( 177-)  A    -2.1
 147 GLU   ( 148-)  A    -2.1
 340 VAL   (  47-)  B    -2.1
  21 SER   (  22-)  A    -2.1
 433 PRO   ( 140-)  B    -2.1
 408 VAL   ( 115-)  B    -2.1
 257 GLU   ( 270-)  A    -2.0
 566 LEU   ( 292-)  B    -2.0
  67 GLU   (  68-)  A    -2.0
 523 ASP   ( 249-)  B    -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.

  28 GLY   (  29-)  A  Poor phi/psi
  35 ASP   (  36-)  A  omega poor
  46 VAL   (  47-)  A  omega poor
  66 GLY   (  67-)  A  Poor phi/psi
 120 GLN   ( 121-)  A  omega poor
 138 LEU   ( 139-)  A  PRO omega poor
 147 GLU   ( 148-)  A  Poor phi/psi
 148 GLY   ( 149-)  A  Poor phi/psi, omega poor
 154 SER   ( 155-)  A  omega poor
 172 HIS   ( 173-)  A  Poor phi/psi
 179 GLU   ( 180-)  A  omega poor
 183 SER   ( 184-)  A  omega poor
 184 GLY   ( 185-)  A  PRO omega poor
 192 LEU   ( 193-)  A  omega poor
 211 PHE   ( 224-)  A  omega poor
 212 CYS   ( 225-)  A  PRO omega poor
 236 ASP   ( 249-)  A  Poor phi/psi
 238 SER   ( 251-)  A  Poor phi/psi
 240 TRP   ( 253-)  A  Poor phi/psi
 256 LEU   ( 269-)  A  omega poor
 257 GLU   ( 270-)  A  Poor phi/psi
 260 THR   ( 273-)  A  omega poor
 263 GLY   ( 276-)  A  Poor phi/psi
 265 THR   ( 278-)  A  Poor phi/psi
 266 SER   ( 279-)  A  omega poor
 267 HIS   ( 280-)  A  omega poor
 346 GLN   (  53-)  B  omega poor
 360 GLY   (  67-)  B  Poor phi/psi
 373 GLN   (  80-)  B  omega poor
 427 VAL   ( 134-)  B  Poor phi/psi
 432 LEU   ( 139-)  B  PRO omega poor
 473 GLY   ( 185-)  B  PRO omega poor
 481 LEU   ( 193-)  B  omega poor
 491 ILE   ( 203-)  B  omega poor
 499 CYS   ( 225-)  B  PRO omega poor
 523 ASP   ( 249-)  B  Poor phi/psi
 565 GLY   ( 291-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.146

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

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

chi-1/chi-2 correlation Z-score : -4.146

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.

 282 SER   ( 295-)  A    0.35
  21 SER   (  22-)  A    0.37
  90 SER   (  91-)  A    0.38

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!

   8 LEU   (   9-)  A      0
  11 THR   (  12-)  A      0
  14 GLU   (  15-)  A      0
  35 ASP   (  36-)  A      0
  52 GLN   (  53-)  A      0
  54 PHE   (  55-)  A      0
  60 ALA   (  61-)  A      0
  62 HIS   (  63-)  A      0
  64 ARG   (  65-)  A      0
  67 GLU   (  68-)  A      0
  68 ASP   (  69-)  A      0
  70 THR   (  71-)  A      0
  83 THR   (  84-)  A      0
  94 MET   (  95-)  A      0
 106 LEU   ( 107-)  A      0
 108 LEU   ( 109-)  A      0
 112 PRO   ( 113-)  A      0
 136 LEU   ( 137-)  A      0
 138 LEU   ( 139-)  A      0
 145 SER   ( 146-)  A      0
 147 GLU   ( 148-)  A      0
 151 VAL   ( 152-)  A      0
 170 PHE   ( 171-)  A      0
 172 HIS   ( 173-)  A      0
 175 ASP   ( 176-)  A      0
And so on for a total of 170 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!

   9 GLY   (  10-)  A   3.05   14
 482 GLY   ( 194-)  B   2.53   16

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].

  45 PRO   (  46-)  A    -3.0 envelop N (0 degrees)
  81 PRO   (  82-)  A  -114.7 envelop C-gamma (-108 degrees)
 112 PRO   ( 113-)  A  -160.1 half-chair N/C-delta (-162 degrees)
 126 PRO   ( 127-)  A   144.5 envelop C-alpha (144 degrees)
 204 PRO   ( 205-)  A  -128.1 half-chair C-delta/C-gamma (-126 degrees)
 271 PRO   ( 284-)  A   100.3 envelop C-beta (108 degrees)
 339 PRO   (  46-)  B  -115.3 envelop C-gamma (-108 degrees)
 375 PRO   (  82-)  B  -115.0 envelop C-gamma (-108 degrees)
 433 PRO   ( 140-)  B   -60.4 half-chair C-beta/C-alpha (-54 degrees)
 438 PRO   ( 145-)  B  -115.1 envelop C-gamma (-108 degrees)
 487 PRO   ( 199-)  B   100.2 envelop C-beta (108 degrees)
 493 PRO   ( 205-)  B   -20.2 half-chair C-alpha/N (-18 degrees)
 494 PRO   ( 206-)  B    52.8 half-chair C-delta/C-gamma (54 degrees)
 500 PRO   ( 226-)  B  -123.1 half-chair C-delta/C-gamma (-126 degrees)
 549 PRO   ( 275-)  B    47.7 half-chair C-delta/C-gamma (54 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.

 195 GLU   ( 196-)  A      OE2 <->  287 ARG   ( 300-)  A      NH1    0.44    2.26  INTRA BF
  63 GLY   (  64-)  A      N   <->   67 GLU   (  68-)  A      OE2    0.36    2.34  INTRA BF
 146 HIS   ( 147-)  A      ND1 <->  173 ASP   ( 174-)  A      OD2    0.28    2.42  INTRA BF
 357 GLY   (  64-)  B      N   <->  361 GLU   (  68-)  B      OE2    0.22    2.48  INTRA BF
 157 ASP   ( 158-)  A      N   <->  161 GLU   ( 162-)  A      OE1    0.19    2.51  INTRA BF
 557 VAL   ( 283-)  B      N   <->  586 HOH   ( 310 )  B      O      0.18    2.52  INTRA BL
 491 ILE   ( 203-)  B      CG2 <->  492 GLN   ( 204-)  B      N      0.17    2.83  INTRA BF
 146 HIS   ( 147-)  A      ND1 <->  173 ASP   ( 174-)  A      CG     0.16    2.94  INTRA BF
 318 ALA   (  25-)  B      CB  <->  568 PHE   ( 294-)  B      CZ     0.16    3.04  INTRA BL
 118 ARG   ( 119-)  A      N   <->  174 SER   ( 175-)  A      O      0.16    2.54  INTRA BF
 510 GLN   ( 236-)  B      O   <->  514 LEU   ( 240-)  B      N      0.14    2.56  INTRA BL
 173 ASP   ( 174-)  A      OD1 <->  174 SER   ( 175-)  A      N      0.13    2.47  INTRA BF
 476 PHE   ( 188-)  B      N   <->  532 VAL   ( 258-)  B      O      0.13    2.57  INTRA BF
 394 LYS   ( 101-)  B      NZ  <->  405 SER   ( 112-)  B      OG     0.12    2.58  INTRA BF
 230 GLN   ( 243-)  A      O   <->  234 ALA   ( 247-)  A      N      0.11    2.59  INTRA BL
  50 LYS   (  51-)  A      O   <->   52 GLN   (  53-)  A      N      0.10    2.60  INTRA BF
  10 GLY   (  11-)  A      O   <->   15 ARG   (  16-)  A      NH1    0.10    2.60  INTRA BF
 412 ARG   ( 119-)  B      NH2 <->  459 PHE   ( 171-)  B      O      0.10    2.60  INTRA BF
 560 ALA   ( 286-)  B      N   <->  561 ALA   ( 287-)  B      N      0.10    2.50  INTRA BL
 499 CYS   ( 225-)  B      CA  <->  500 PRO   ( 226-)  B      C      0.09    2.91  INTRA BF
 275 ARG   ( 288-)  A      C   <->  277 TYR   ( 290-)  A      N      0.09    2.81  INTRA BF
 398 GLN   ( 105-)  B      NE2 <->  407 TYR   ( 114-)  B      OH     0.09    2.61  INTRA BL
 246 MET   ( 259-)  A      O   <->  254 TYR   ( 267-)  A      N      0.09    2.61  INTRA BL
 507 SER   ( 233-)  B      O   <->  511 LEU   ( 237-)  B      N      0.08    2.62  INTRA BL
 133 VAL   ( 134-)  A      O   <->  136 LEU   ( 137-)  A      N      0.08    2.62  INTRA BL
And so on for a total of 76 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

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.

  64 ARG   (  65-)  A      -7.67
 358 ARG   (  65-)  B      -7.36
 536 ARG   ( 262-)  B      -7.32
 249 ARG   ( 262-)  A      -7.26
 276 GLN   ( 289-)  A      -5.48
 563 GLN   ( 289-)  B      -5.43
 554 HIS   ( 280-)  B      -5.14

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

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.

 215 GLY   ( 228-)  A   -2.52

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

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 585 HOH   ( 311 )  A      O
 585 HOH   ( 314 )  A      O
 585 HOH   ( 316 )  A      O

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.

  23 GLN   (  24-)  A
 252 HIS   ( 265-)  A

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.

  12 SER   (  13-)  A      N
  16 GLU   (  17-)  A      N
  46 VAL   (  47-)  A      N
  47 THR   (  48-)  A      N
  47 THR   (  48-)  A      OG1
  50 LYS   (  51-)  A      N
  51 GLU   (  52-)  A      N
  61 LEU   (  62-)  A      N
  98 ARG   (  99-)  A      NH1
 148 GLY   ( 149-)  A      N
 158 HIS   ( 159-)  A      N
 163 GLN   ( 164-)  A      N
 214 SER   ( 227-)  A      N
 219 GLU   ( 232-)  A      N
 232 TYR   ( 245-)  A      OH
 249 ARG   ( 262-)  A      N
 258 VAL   ( 271-)  A      N
 268 SER   ( 281-)  A      N
 310 GLU   (  17-)  B      N
 344 LYS   (  51-)  B      N
 345 GLU   (  52-)  B      N
 355 LEU   (  62-)  B      N
 362 ASP   (  69-)  B      N
 377 THR   (  84-)  B      OG1
 429 LYS   ( 136-)  B      N
 447 HIS   ( 159-)  B      N
 488 SER   ( 200-)  B      OG
 502 GLY   ( 228-)  B      N

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.

 223 GLN   ( 236-)  A      OE1
 461 HIS   ( 173-)  B      ND1
 580 ASP   ( 306-)  B      OD1

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.

 175 ASP   ( 176-)  A   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 :   0.385
  2nd generation packing quality :  -0.811
  Ramachandran plot appearance   :  -2.393
  chi-1/chi-2 rotamer normality  :  -4.146 (bad)
  Backbone conformation          :   1.240

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.749
  Bond angles                    :   0.895
  Omega angle restraints         :   1.172
  Side chain planarity           :   0.571 (tight)
  Improper dihedral distribution :   0.966
  B-factor distribution          :   0.773
  Inside/Outside distribution    :   0.990

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 : 2.69


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.7
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :   1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.749
  Bond angles                    :   0.895
  Omega angle restraints         :   1.172
  Side chain planarity           :   0.571 (tight)
  Improper dihedral distribution :   0.966
  B-factor distribution          :   0.773
  Inside/Outside distribution    :   0.990
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
    G.Vriend and C.Sander,
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      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,
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      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.