WHAT IF Check report

This file was created 2012-01-30 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 pdb3e42.ent

Checks that need to be done early-on in validation

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

 520  CA   (  15-)  B  E

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: 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'.

   4 LYS   (   5-)  A      CE
   4 LYS   (   5-)  A      NZ
   8 GLN   (   9-)  A      CG
   8 GLN   (   9-)  A      CD
   8 GLN   (   9-)  A      OE1
   8 GLN   (   9-)  A      NE2
  18 LYS   (  19-)  A      CG
  18 LYS   (  19-)  A      CD
  18 LYS   (  19-)  A      CE
  18 LYS   (  19-)  A      NZ
  19 VAL   (  20-)  A      CG1
  19 VAL   (  20-)  A      CG2
  20 LYS   (  21-)  A      CG
  20 LYS   (  21-)  A      CD
  20 LYS   (  21-)  A      CE
  20 LYS   (  21-)  A      NZ
  21 ARG   (  22-)  A      CG
  21 ARG   (  22-)  A      CD
  21 ARG   (  22-)  A      NE
  21 ARG   (  22-)  A      CZ
  21 ARG   (  22-)  A      NH1
  21 ARG   (  22-)  A      NH2
  26 GLU   (  35-)  A      CG
  26 GLU   (  35-)  A      CD
  26 GLU   (  35-)  A      OE1
And so on for a total of 187 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.

  22 PRO   (  23-)  A    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: 0

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.

  82 ARG   (  91-)  A
 322 ARG   (  91-)  B

Warning: Tyrosine convention problem

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

  33 TYR   (  42-)  A
 274 TYR   (  42-)  B
 399 TYR   ( 168-)  B
 487 TYR   ( 256-)  B

Warning: Phenylalanine convention problem

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

  28 PHE   (  37-)  A
  35 PHE   (  44-)  A
  45 PHE   (  54-)  A
  55 PHE   (  64-)  A
  96 PHE   ( 105-)  A
 129 PHE   ( 138-)  A
 178 PHE   ( 187-)  A
 182 PHE   ( 191-)  A
 225 PHE   ( 234-)  A
 336 PHE   ( 105-)  B
 369 PHE   ( 138-)  B
 392 PHE   ( 161-)  B
 395 PHE   ( 164-)  B
 418 PHE   ( 187-)  B
 422 PHE   ( 191-)  B
 465 PHE   ( 234-)  B
 484 PHE   ( 253-)  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.

 102 ASP   ( 111-)  A
 105 ASP   ( 114-)  A
 111 ASP   ( 120-)  A
 148 ASP   ( 157-)  A
 283 ASP   (  51-)  B
 294 ASP   (  62-)  B
 342 ASP   ( 111-)  B
 388 ASP   ( 157-)  B
 478 ASP   ( 247-)  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.

  88 GLU   (  97-)  A
  98 GLU   ( 107-)  A
 115 GLU   ( 124-)  A
 180 GLU   ( 189-)  A
 290 GLU   (  58-)  B
 355 GLU   ( 124-)  B
 391 GLU   ( 160-)  B
 405 GLU   ( 174-)  B
 420 GLU   ( 189-)  B
 428 GLU   ( 197-)  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.

 506 DGUA  (   4-)  F      C2   N3    1.36    4.1
 513 DCYT  (  11-)  F      C1'  N1    1.53    5.2

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.

 268 PRO   (  36-)  B      N    CA   CB  110.09    6.4
 489 DGUA  (   1-)  E      N9   C8   N7  113.63    5.1
 492 DGUA  (   4-)  E      N9   C8   N7  113.60    5.0
 493 DGUA  (   5-)  E      O4'  C1'  N9  111.79    5.0
 493 DGUA  (   5-)  E      N9   C8   N7  113.20    4.2
 494 DTHY  (   6-)  E      C6   C5   C7  125.73    4.7
 494 DTHY  (   6-)  E      C5   C4   O4  119.32   -8.0
 494 DTHY  (   6-)  E      C4   C5   C7  116.14   -4.8
 494 DTHY  (   6-)  E      O4   C4   N3  124.21    7.2
 496 DGUA  (   8-)  E      O4'  C1'  N9  111.94    5.2
 496 DGUA  (   8-)  E      N9   C8   N7  114.27    6.3
 497 DADE  (   9-)  E      O4'  C1'  C2'  99.99   -5.6
 497 DADE  (   9-)  E      O4'  C1'  N9  112.42    5.8
 498 DCYT  (  10-)  E      P   -C3* -O3* 125.26    4.6
 499 DCYT  (  11-)  E      N4   C4   N3  115.03   -4.2
 499 DCYT  (  11-)  E      N3   C2   O2  118.23   -5.2
 500 DGUA  (  12-)  E      O4'  C1'  N9  111.10    4.1
 501 DGUA  (  13-)  E      O4'  C1'  N9  111.69    4.9
 502 DCYT  (  14-)  E      P   -C3* -O3* 113.21   -5.4
 503 DGUA  (   1-)  F      C3'  C4'  O4' 101.49   -4.1
 503 DGUA  (   1-)  F      N9   C8   N7  113.42    4.6
 504 DCYT  (   2-)  F      O4'  C1'  N1  104.21   -4.5
 505 DCYT  (   3-)  F      P    O5'  C5' 113.34   -4.7
 506 DGUA  (   4-)  F      P   -C3* -O3* 114.38   -4.4
 506 DGUA  (   4-)  F      C5   C6   O6  125.88   -4.5
 508 DTHY  (   6-)  F      O4'  C1'  N1  111.20    4.2
 509 DCYT  (   7-)  F      C3'  C4'  O4'  99.41   -6.2
 510 DGUA  (   8-)  F      O4'  C1'  N9  114.32    8.2
 510 DGUA  (   8-)  F      N9   C8   N7  113.26    4.3
 512 DCYT  (  10-)  F      O4'  C1'  N1  111.54    4.7
 512 DCYT  (  10-)  F      C6   N1   C2  122.17    4.7
 513 DCYT  (  11-)  F      N3   C2   O2  118.33   -5.1
 514 DGUA  (  12-)  F      O4'  C1'  N9  112.67    6.1
 514 DGUA  (  12-)  F      N9   C8   N7  113.11    4.0
 514 DGUA  (  12-)  F      C5   C6   O6  126.17   -4.0
 516 DCYT  (  14-)  F      C4'  C3'  C2'  98.66   -4.5
 516 DCYT  (  14-)  F      O4'  C1'  N1  112.49    5.9

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.

  82 ARG   (  91-)  A
  88 GLU   (  97-)  A
  98 GLU   ( 107-)  A
 102 ASP   ( 111-)  A
 105 ASP   ( 114-)  A
 111 ASP   ( 120-)  A
 115 GLU   ( 124-)  A
 148 ASP   ( 157-)  A
 180 GLU   ( 189-)  A
 283 ASP   (  51-)  B
 290 GLU   (  58-)  B
 294 ASP   (  62-)  B
 322 ARG   (  91-)  B
 342 ASP   ( 111-)  B
 355 GLU   ( 124-)  B
 388 ASP   ( 157-)  B
 391 GLU   ( 160-)  B
 405 GLU   ( 174-)  B
 420 GLU   ( 189-)  B
 428 GLU   ( 197-)  B
 478 ASP   ( 247-)  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.

 313 SER   (  82-)  B    4.27

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 : -3.131

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.

 382 THR   ( 151-)  B    -2.7
 369 PHE   ( 138-)  B    -2.5
 303 ILE   (  71-)  B    -2.5
 371 PRO   ( 140-)  B    -2.4
 129 PHE   ( 138-)  A    -2.4
  73 SER   (  82-)  A    -2.3
 364 ILE   ( 133-)  B    -2.2
  36 LEU   (  45-)  A    -2.2
 365 SER   ( 134-)  B    -2.1
 441 PHE   ( 210-)  B    -2.1
 250 PHE   (   3-)  B    -2.1
 224 HIS   ( 233-)  A    -2.1
  58 ASN   (  67-)  A    -2.1
  11 ASN   (  12-)  A    -2.1
 188 GLU   ( 197-)  A    -2.0
  92 ILE   ( 101-)  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.

  41 SER   (  50-)  A  Poor phi/psi
  45 PHE   (  54-)  A  omega poor
  73 SER   (  82-)  A  Poor phi/psi
 127 SER   ( 136-)  A  Poor phi/psi
 154 LEU   ( 163-)  A  omega poor
 175 SER   ( 184-)  A  Poor phi/psi
 197 MET   ( 206-)  A  Poor phi/psi
 198 GLN   ( 207-)  A  omega poor
 212 GLY   ( 221-)  A  Poor phi/psi
 282 SER   (  50-)  B  Poor phi/psi
 284 LEU   (  52-)  B  Poor phi/psi
 286 PHE   (  54-)  B  omega poor
 323 GLY   (  92-)  B  omega poor
 351 ASP   ( 120-)  B  Poor phi/psi
 352 GLN   ( 121-)  B  Poor phi/psi
 394 LEU   ( 163-)  B  Poor phi/psi
 435 ALA   ( 204-)  B  Poor phi/psi
 436 ALA   ( 205-)  B  Poor phi/psi
 437 MET   ( 206-)  B  Poor phi/psi
 441 PHE   ( 210-)  B  omega poor
 450 PHE   ( 219-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.772

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.

 260 SER   (  13-)  B    0.36
 460 SER   ( 229-)  B    0.37

Warning: Unusual backbone conformations

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

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

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

   6 ILE   (   7-)  A      0
  15 ILE   (  16-)  A      0
  21 ARG   (  22-)  A      0
  22 PRO   (  23-)  A      0
  23 ALA   (  32-)  A      0
  24 ALA   (  33-)  A      0
  39 ASN   (  48-)  A      0
  40 LEU   (  49-)  A      0
  41 SER   (  50-)  A      0
  44 THR   (  53-)  A      0
  61 ILE   (  70-)  A      0
  62 ILE   (  71-)  A      0
  64 HIS   (  73-)  A      0
  71 PHE   (  80-)  A      0
  72 ASN   (  81-)  A      0
  73 SER   (  82-)  A      0
  90 TRP   (  99-)  A      0
  94 ASN   ( 103-)  A      0
 103 THR   ( 112-)  A      0
 104 ALA   ( 113-)  A      0
 122 ARG   ( 131-)  A      0
 126 LYS   ( 135-)  A      0
 128 ALA   ( 137-)  A      0
 130 ALA   ( 139-)  A      0
 132 ASN   ( 141-)  A      0
And so on for a total of 204 lines.

Warning: Unusual PRO puckering amplitudes

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

 268 PRO   (  36-)  B    0.00 LOW

Warning: Unusual PRO puckering phases

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

 131 PRO   ( 140-)  A   -56.9 half-chair C-beta/C-alpha (-54 degrees)
 186 PRO   ( 195-)  A    99.5 envelop C-beta (108 degrees)
 253 PRO   (   6-)  B   101.3 envelop C-beta (108 degrees)
 371 PRO   ( 140-)  B   -59.1 half-chair C-beta/C-alpha (-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.

 499 DCYT  (  11-)  E      N3  <->  506 DGUA  (   4-)  F      N2     0.69    2.31  INTRA BL
 492 DGUA  (   4-)  E      N2  <->  513 DCYT  (  11-)  F      N3     0.66    2.34  INTRA BL
 499 DCYT  (  11-)  E      C2  <->  506 DGUA  (   4-)  F      N2     0.40    2.70  INTRA BL
 499 DCYT  (  11-)  E      O2  <->  506 DGUA  (   4-)  F      N2     0.38    2.32  INTRA BL
 495 DCYT  (   7-)  E      N3  <->  510 DGUA  (   8-)  F      N1     0.38    2.62  INTRA BL
 499 DCYT  (  11-)  E      N3  <->  506 DGUA  (   4-)  F      N1     0.36    2.64  INTRA BL
 322 ARG   (  91-)  B      NH2 <->  337 GLU   ( 106-)  B      O      0.33    2.37  INTRA BF
 492 DGUA  (   4-)  E      N1  <->  513 DCYT  (  11-)  F      N4     0.33    2.52  INTRA BL
 492 DGUA  (   4-)  E      N2  <->  513 DCYT  (  11-)  F      C2     0.32    2.78  INTRA BL
 499 DCYT  (  11-)  E      N4  <->  506 DGUA  (   4-)  F      N1     0.32    2.53  INTRA BL
 132 ASN   ( 141-)  A      ND2 <->  510 DGUA  (   8-)  F      N7     0.31    2.69  INTRA BL
 492 DGUA  (   4-)  E      N1  <->  513 DCYT  (  11-)  F      N3     0.31    2.69  INTRA BL
 277 LEU   (  45-)  B      O   <->  281 LEU   (  49-)  B      N      0.28    2.42  INTRA BF
 492 DGUA  (   4-)  E      N2  <->  513 DCYT  (  11-)  F      O2     0.26    2.44  INTRA BL
 192 ASN   ( 201-)  A      ND2 <->  493 DGUA  (   5-)  E      N7     0.25    2.75  INTRA BL
 101 ASN   ( 110-)  A      CG  <->  521 HOH   ( 271 )  A      O      0.25    2.55  INTRA BL
 503 DGUA  (   1-)  F      N7  <->  524 HOH   (  31 )  F      O      0.23    2.47  INTRA BL
 426 PRO   ( 195-)  B      O   <->  428 GLU   ( 197-)  B      N      0.23    2.47  INTRA BF
  84 LYS   (  93-)  A      NZ  <->  521 HOH   ( 266 )  A      O      0.22    2.48  INTRA BL
 500 DGUA  (  12-)  E      N1  <->  505 DCYT  (   3-)  F      N3     0.22    2.78  INTRA BL
 396 ASP   ( 165-)  B      OD1 <->  454 ARG   ( 223-)  B      NH2    0.21    2.49  INTRA BF
 499 DCYT  (  11-)  E      N3  <->  506 DGUA  (   4-)  F      C2     0.21    2.89  INTRA BL
 305 HIS   (  73-)  B      N   <->  328 GLU   (  97-)  B      OE1    0.20    2.50  INTRA BF
 373 ILE   ( 142-)  B      N   <->  439 ILE   ( 208-)  B      O      0.20    2.50  INTRA BL
 453 THR   ( 222-)  B      O   <->  456 GLU   ( 225-)  B      N      0.20    2.50  INTRA BF
And so on for a total of 114 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: 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.

  21 ARG   (  22-)  A   -3.61
 126 LYS   ( 135-)  A   -3.37
 350 LYS   ( 119-)  B   -3.10
 183 LYS   ( 192-)  A   -3.01
 340 GLN   ( 109-)  B   -2.99
 101 ASN   ( 110-)  A   -2.97
 369 PHE   ( 138-)  B   -2.95
 129 PHE   ( 138-)  A   -2.93
  26 GLU   (  35-)  A   -2.70
 110 LYS   ( 119-)  A   -2.66
 100 GLN   ( 109-)  A   -2.51
 352 GLN   ( 121-)  B   -2.50
 112 GLN   ( 121-)  A   -2.50

Warning: Abnormal packing Z-score for sequential residues

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

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

 338 GLU   ( 107-)  B     -  341 ASN   ( 110-)  B        -1.78

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.

 521 HOH   ( 270 )  A      O
 521 HOH   ( 324 )  A      O
 521 HOH   ( 325 )  A      O
 521 HOH   ( 327 )  A      O
 521 HOH   ( 329 )  A      O
 521 HOH   ( 335 )  A      O
 522 HOH   ( 266 )  B      O
 522 HOH   ( 268 )  B      O
 522 HOH   ( 270 )  B      O
 522 HOH   ( 272 )  B      O
 522 HOH   ( 278 )  B      O
 522 HOH   ( 286 )  B      O
 523 HOH   (  20 )  E      O
 524 HOH   ( 123 )  F      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.

  39 ASN   (  48-)  A
 101 ASN   ( 110-)  A
 228 GLN   ( 237-)  A
 280 ASN   (  48-)  B
 305 HIS   (  73-)  B
 341 ASN   ( 110-)  B

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.

  30 LYS   (  39-)  A      N
  48 TYR   (  57-)  A      N
  49 GLU   (  58-)  A      N
  99 LYS   ( 108-)  A      N
 101 ASN   ( 110-)  A      N
 134 ILE   ( 143-)  A      N
 155 PHE   ( 164-)  A      N
 158 ASN   ( 167-)  A      ND2
 164 TRP   ( 173-)  A      NE1
 177 SER   ( 186-)  A      OG
 201 PHE   ( 210-)  A      N
 204 ARG   ( 213-)  A      NE
 215 GLU   ( 224-)  A      N
 249 SER   (   2-)  B      OG
 250 PHE   (   3-)  B      N
 289 TYR   (  57-)  B      N
 304 GLY   (  72-)  B      N
 341 ASN   ( 110-)  B      ND2
 395 PHE   ( 164-)  B      N
 397 ILE   ( 166-)  B      N
 398 ASN   ( 167-)  B      ND2
 404 TRP   ( 173-)  B      NE1
 422 PHE   ( 191-)  B      N
 427 SER   ( 196-)  B      N
 434 ALA   ( 203-)  B      N
 442 HIS   ( 211-)  B      NE2
 444 ARG   ( 213-)  B      NE

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.

 163 ASP   ( 172-)  A      OD1
 355 GLU   ( 124-)  B      OE1
 358 ASP   ( 127-)  B      OD1
 398 ASN   ( 167-)  B      OD1
 403 ASP   ( 172-)  B      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 517  NA   ( 259-)  A    0.45  -.-   Poor packing (Few ligands (4) )
 518  CA   ( 260-)  A     0.49   0.70 Is perhaps NA *1 and *2
 519  NA   ( 259-)  B    0.35  -.-   Poor packing (Few ligands (4) )
 520  CA   (  15-)  B     0.34   0.83 Is perhaps  K

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.

 148 ASP   ( 157-)  A   H-bonding suggests Asn; but Alt-Rotamer
 478 ASP   ( 247-)  B   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:

  2nd generation packing quality :  -2.626
  Ramachandran plot appearance   :  -3.131 (poor)
  chi-1/chi-2 rotamer normality  :  -2.772
  Backbone conformation          :  -0.840

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.492 (tight)
  Bond angles                    :   0.842
  Omega angle restraints         :   0.960
  Side chain planarity           :   0.270 (tight)
  Improper dihedral distribution :   0.547
  B-factor distribution          :   0.867
  Inside/Outside distribution    :   1.009

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 : 2.68


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.492 (tight)
  Bond angles                    :   0.842
  Omega angle restraints         :   0.960
  Side chain planarity           :   0.270 (tight)
  Improper dihedral distribution :   0.547
  B-factor distribution          :   0.867
  Inside/Outside distribution    :   1.009
==============

WHAT IF
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    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
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      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
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      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.