WHAT IF Check report

This file was created 2013-12-10 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 pdb4fbu.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  52.774  B   = 181.458  C    =  52.744
    Alpha=  90.000  Beta= 109.490  Gamma=  90.000

Dimensions of a reduced cell

    A    =  52.744  B   =  52.774  C    = 181.458
    Alpha=  90.000  Beta=  90.000  Gamma= 109.490

Dimensions of the conventional cell

    A    =  60.907  B   =  86.165  C    = 181.458
    Alpha=  90.000  Beta=  90.000  Gamma=  89.965

Transformation to conventional cell

 |  1.000000  0.000000  1.000000|
 |  1.000000  0.000000 -1.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: 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 B

All-atom RMS fit for the two chains : 1.117
CA-only RMS fit for the two chains : 0.683

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

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

 736 DG8   (   3-)  T  -
 741 DG8   (   3-)  C  -

Administrative problems that can generate validation failures

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

 697 DCYT  (   6-)  T  -              696 DGUA  (   4-)  T  -           3.2

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'.

 332 ARG   ( 332-)  A      CG
 332 ARG   ( 332-)  A      CD
 332 ARG   ( 332-)  A      NE
 332 ARG   ( 332-)  A      CZ
 332 ARG   ( 332-)  A      NH1
 332 ARG   ( 332-)  A      NH2
 377 ARG   (  36-)  B      CG
 377 ARG   (  36-)  B      CD
 377 ARG   (  36-)  B      NE
 377 ARG   (  36-)  B      CZ
 377 ARG   (  36-)  B      NH1
 377 ARG   (  36-)  B      NH2
 521 ILE   ( 180-)  B      CG1
 521 ILE   ( 180-)  B      CG2
 521 ILE   ( 180-)  B      CD1
 673 ARG   ( 332-)  B      CG
 673 ARG   ( 332-)  B      CD
 673 ARG   ( 332-)  B      NE
 673 ARG   ( 332-)  B      CZ
 673 ARG   ( 332-)  B      NH1
 673 ARG   ( 332-)  B      NH2
 683 DCYT  (   2-)  P      O5'
 708 DCYT  (   2-)  D      O5'

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.

  35 GLY   (  35-)  A    High
  36 ARG   (  36-)  A    High
  38 GLU   (  38-)  A    High
 116 ARG   ( 116-)  A    High
 169 GLU   ( 169-)  A    High
 172 LYS   ( 172-)  A    High
 176 ARG   ( 176-)  A    High
 177 GLU   ( 177-)  A    High
 179 ASP   ( 179-)  A    High
 192 GLU   ( 192-)  A    High
 193 LYS   ( 193-)  A    High
 194 LEU   ( 194-)  A    High
 195 LYS   ( 195-)  A    High
 196 LYS   ( 196-)  A    High
 197 LEU   ( 197-)  A    High
 198 GLY   ( 198-)  A    High
 199 ILE   ( 199-)  A    High
 200 ASN   ( 200-)  A    High
 201 LYS   ( 201-)  A    High
 204 ASP   ( 204-)  A    High
 205 THR   ( 205-)  A    High
 207 SER   ( 207-)  A    High
 208 ILE   ( 208-)  A    High
 209 GLU   ( 209-)  A    High
 210 PHE   ( 210-)  A    High
And so on for a total of 134 lines.

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 12

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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.

 579 ARG   ( 238-)  B

Warning: Tyrosine convention problem

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

  10 TYR   (  10-)  A
  73 TYR   (  73-)  A
  95 TYR   (  95-)  A
 108 TYR   ( 108-)  A
 122 TYR   ( 122-)  A
 264 TYR   ( 264-)  A
 312 TYR   ( 312-)  A
 351 TYR   (  10-)  B
 449 TYR   ( 108-)  B
 463 TYR   ( 122-)  B
 614 TYR   ( 273-)  B
 653 TYR   ( 312-)  B

Warning: Phenylalanine convention problem

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

  37 PHE   (  37-)  A
 374 PHE   (  33-)  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.

 292 ASP   ( 292-)  A
 326 ASP   ( 326-)  A
 509 ASP   ( 168-)  B
 667 ASP   ( 326-)  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.

  49 GLU   (  49-)  A
 177 GLU   ( 177-)  A
 260 GLU   ( 260-)  A
 291 GLU   ( 291-)  A
 314 GLU   ( 314-)  A
 324 GLU   ( 324-)  A
 379 GLU   (  38-)  B
 390 GLU   (  49-)  B
 447 GLU   ( 106-)  B
 533 GLU   ( 192-)  B
 550 GLU   ( 209-)  B
 576 GLU   ( 235-)  B
 632 GLU   ( 291-)  B
 655 GLU   ( 314-)  B
 665 GLU   ( 324-)  B
 666 GLU   ( 325-)  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.

 723 DCYT  (   6-)  C      C3'  O3'   1.38   -4.3

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.

  36 ARG   (  36-)  A      C    CA   CB  101.01   -4.8
  37 PHE   (  37-)  A      N    CA   C    95.17   -5.7
 265 LEU   ( 265-)  A     -C    N    CA  131.19    5.3
 265 LEU   ( 265-)  A      N    CA   C   129.62    6.6
 265 LEU   ( 265-)  A      C    CA   CB  102.26   -4.1
 684 DCYT  (   3-)  P      O5'  C5'  C4' 116.90    4.8
 688 DTHY  (   7-)  P      O4   C4   N3  122.82    4.9
 690 DCYT  (   9-)  P      O4'  C1'  N1  113.40    7.0
 693 DGUA  (  12-)  P      N9   C8   N7  113.61    5.0
 694 DTHY  (  13-)  P      C5   C4   O4  121.78   -4.5
 694 DTHY  (  13-)  P      O4   C4   N3  122.69    4.7
 695 DCYT  (  14-)  P      O5'  C5'  C4' 116.25    4.3
 696 DGUA  (   4-)  T      C3'  C4'  C5' 106.52   -5.5
 696 DGUA  (   4-)  T      N9   C8   N7  113.86    5.5
 697 DCYT  (   6-)  T      O4'  C1'  N1  112.25    5.6
 699 DGUA  (   8-)  T      N9   C8   N7  114.06    5.9
 700 DGUA  (   9-)  T      N9   C8   N7  113.21    4.2
 703 DTHY  (  12-)  T      O4   C4   N3  122.77    4.8
 704 DTHY  (  13-)  T      O4'  C1'  N1  111.10    4.1
 705 DGUA  (  14-)  T      N9   C8   N7  113.99    5.8
 706 DGUA  (  15-)  T      N9   C8   N7  113.93    5.7
 707 DGUA  (  16-)  T      P   -C3* -O3* 109.55   -8.5
 707 DGUA  (  16-)  T      C3'  C4'  O4' 101.03   -4.6
 707 DGUA  (  16-)  T      C3'  C2'  C1'  93.95   -6.3
 707 DGUA  (  16-)  T      C4'  C3'  C2'  96.94   -6.3
And so on for a total of 52 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  49 GLU   (  49-)  A
 177 GLU   ( 177-)  A
 260 GLU   ( 260-)  A
 291 GLU   ( 291-)  A
 292 ASP   ( 292-)  A
 314 GLU   ( 314-)  A
 324 GLU   ( 324-)  A
 326 ASP   ( 326-)  A
 379 GLU   (  38-)  B
 390 GLU   (  49-)  B
 447 GLU   ( 106-)  B
 509 ASP   ( 168-)  B
 533 GLU   ( 192-)  B
 550 GLU   ( 209-)  B
 576 GLU   ( 235-)  B
 579 ARG   ( 238-)  B
 632 GLU   ( 291-)  B
 655 GLU   ( 314-)  B
 665 GLU   ( 324-)  B
 666 GLU   ( 325-)  B
 667 ASP   ( 326-)  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.

 265 LEU   ( 265-)  A    7.44
  37 PHE   (  37-)  A    6.19

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.

 501 PRO   ( 160-)  B    -2.8
 160 PRO   ( 160-)  A    -2.7
 386 THR   (  45-)  B    -2.7
 409 LEU   (  68-)  B    -2.6
 677 ARG   ( 336-)  B    -2.5
 352 PHE   (  11-)  B    -2.5
 525 PRO   ( 184-)  B    -2.5
 248 ILE   ( 248-)  A    -2.5
  10 TYR   (  10-)  A    -2.4
 575 ASN   ( 234-)  B    -2.3
 336 ARG   ( 336-)  A    -2.3
 486 SER   ( 145-)  B    -2.3
 478 LYS   ( 137-)  B    -2.3
  45 THR   (  45-)  A    -2.3
 264 TYR   ( 264-)  A    -2.3
 335 VAL   ( 335-)  A    -2.3
 676 VAL   ( 335-)  B    -2.2
 351 TYR   (  10-)  B    -2.2
 574 TYR   ( 233-)  B    -2.2
 324 GLU   ( 324-)  A    -2.1
 145 SER   ( 145-)  A    -2.0
 333 ILE   ( 333-)  A    -2.0
 178 LEU   ( 178-)  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.

  10 TYR   (  10-)  A  Poor phi/psi
  39 ASP   (  39-)  A  Poor phi/psi
  70 ASN   (  70-)  A  omega poor
 137 LYS   ( 137-)  A  Poor phi/psi
 159 LYS   ( 159-)  A  PRO omega poor
 200 ASN   ( 200-)  A  Poor phi/psi
 231 ASP   ( 231-)  A  Poor phi/psi
 255 SER   ( 255-)  A  Poor phi/psi
 262 LYS   ( 262-)  A  PRO omega poor
 264 TYR   ( 264-)  A  omega poor
 277 ASP   ( 277-)  A  Poor phi/psi
 278 LYS   ( 278-)  A  Poor phi/psi, omega poor
 293 LEU   ( 293-)  A  Poor phi/psi
 325 GLU   ( 325-)  A  Poor phi/psi
 351 TYR   (  10-)  B  Poor phi/psi, omega poor
 377 ARG   (  36-)  B  Poor phi/psi
 378 PHE   (  37-)  B  Poor phi/psi
 380 ASP   (  39-)  B  Poor phi/psi
 444 SER   ( 103-)  B  Poor phi/psi
 478 LYS   ( 137-)  B  Poor phi/psi
 500 LYS   ( 159-)  B  PRO omega poor
 517 ARG   ( 176-)  B  Poor phi/psi
 521 ILE   ( 180-)  B  Poor phi/psi
 522 ALA   ( 181-)  B  Poor phi/psi
 526 GLY   ( 185-)  B  omega poor
 532 ALA   ( 191-)  B  Poor phi/psi
 552 ASP   ( 211-)  B  Poor phi/psi
 572 ASP   ( 231-)  B  Poor phi/psi
 596 SER   ( 255-)  B  omega poor
 618 ASP   ( 277-)  B  Poor phi/psi
 634 LEU   ( 293-)  B  Poor phi/psi
 680 LYS   ( 339-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.976

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.

 481 VAL   ( 140-)  B    0.36

Warning: Unusual backbone conformations

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

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

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

   9 ASP   (   9-)  A      0
  10 TYR   (  10-)  A      0
  22 SER   (  22-)  A      0
  24 LYS   (  24-)  A      0
  36 ARG   (  36-)  A      0
  37 PHE   (  37-)  A      0
  38 GLU   (  38-)  A      0
  40 SER   (  40-)  A      0
  44 ALA   (  44-)  A      0
  45 THR   (  45-)  A      0
  53 PHE   (  53-)  A      0
  56 LYS   (  56-)  A      0
  57 ALA   (  57-)  A      0
  68 LEU   (  68-)  A      0
  76 MET   (  76-)  A      0
  77 ARG   (  77-)  A      0
  95 TYR   (  95-)  A      0
  97 GLU   (  97-)  A      0
  98 LYS   (  98-)  A      0
 102 ALA   ( 102-)  A      0
 105 ASP   ( 105-)  A      0
 106 GLU   ( 106-)  A      0
 111 ILE   ( 111-)  A      0
 136 GLU   ( 136-)  A      0
 146 LYS   ( 146-)  A      0
And so on for a total of 285 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]

 368 PRO   (  27-)  B    0.18 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].

  27 PRO   (  27-)  A    51.9 half-chair C-delta/C-gamma (54 degrees)
 184 PRO   ( 184-)  A   102.6 envelop C-beta (108 degrees)
 281 PRO   ( 281-)  A   -27.0 half-chair C-alpha/N (-18 degrees)
 303 PRO   ( 303-)  A    50.7 half-chair C-delta/C-gamma (54 degrees)
 501 PRO   ( 160-)  B   -20.3 half-chair C-alpha/N (-18 degrees)
 525 PRO   ( 184-)  B   120.1 half-chair C-beta/C-alpha (126 degrees)
 577 PRO   ( 236-)  B    38.9 envelop C-delta (36 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.

 697 DCYT  (   6-)  T      N4  <->  736 DG8   (   3-)  T      C5'    0.81    2.29  INTRA BF
 634 LEU   ( 293-)  B      CD1 <->  741 DG8   (   3-)  C      N3     0.57    2.53  INTRA BF
 711 DADE  (   5-)  D      N1  <->  730 DTHY  (  13-)  C      N3     0.43    2.57  INTRA BF
 716 DCYT  (  10-)  D      N3  <->  725 DGUA  (   8-)  C      N1     0.41    2.59  INTRA BL
 634 LEU   ( 293-)  B      CD1 <->  741 DG8   (   3-)  C      O1P    0.39    2.41  INTRA BF
 710 DCYT  (   4-)  D      C2' <->  711 DADE  (   5-)  D      C8     0.39    2.81  INTRA BF
 173 ARG   ( 173-)  A      NH1 <->  177 GLU   ( 177-)  A      OE2    0.38    2.32  INTRA BF
 704 DTHY  (  13-)  T      C2' <->  705 DGUA  (  14-)  T      C8     0.36    2.84  INTRA BF
  14 GLN   (  14-)  A      NE2 <->  139 THR   ( 139-)  A      N      0.35    2.50  INTRA BL
 708 DCYT  (   2-)  D      N4  <->  733 DGUA  (  16-)  C      O6     0.35    2.35  INTRA BF
 355 GLN   (  14-)  B      NE2 <->  480 THR   ( 139-)  B      N      0.33    2.52  INTRA BL
 689 DADE  (   8-)  P      N1  <->  701 DTHY  (  10-)  T      N3     0.31    2.69  INTRA BF
  36 ARG   (  36-)  A      NH1 <->  331 ARG   ( 331-)  A      NH1    0.31    2.54  INTRA BF
 686 DADE  (   5-)  P      N1  <->  704 DTHY  (  13-)  T      N3     0.30    2.70  INTRA BF
 336 ARG   ( 336-)  A      NH2 <->  698 DTHY  (   7-)  T      C6     0.28    2.82  INTRA BF
 597 ARG   ( 256-)  B      NH1 <->  669 ARG   ( 328-)  B      O      0.28    2.42  INTRA BF
 719 DTHY  (  13-)  D      N3  <->  722 DADE  (   5-)  C      N1     0.27    2.73  INTRA BL
 706 DGUA  (  15-)  T      C2' <->  707 DGUA  (  16-)  T      C8     0.27    2.93  INTRA BF
 696 DGUA  (   4-)  T      C5' <->  736 DG8   (   3-)  T      C31    0.25    2.95  INTRA BF
 255 SER   ( 255-)  A      O   <->  330 ILE   ( 330-)  A      N      0.25    2.45  INTRA BF
 730 DTHY  (  13-)  C      C2' <->  731 DGUA  (  14-)  C      C8     0.25    2.95  INTRA BF
 264 TYR   ( 264-)  A      N   <->  267 ARG   ( 267-)  A      N      0.25    2.60  INTRA BF
 457 ARG   ( 116-)  B      NH2 <->  743 HOH   ( 557 )  B      O      0.25    2.45  INTRA BF
 683 DCYT  (   2-)  P      C2' <->  684 DCYT  (   3-)  P      O4'    0.25    2.55  INTRA BF
 434 ARG   (  93-)  B      NH2 <->  743 HOH   ( 587 )  B      O      0.24    2.46  INTRA BL
And so on for a total of 183 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.

 574 TYR   ( 233-)  B      -8.46
 116 ARG   ( 116-)  A      -7.21
 457 ARG   ( 116-)  B      -7.13
 253 ARG   ( 253-)  A      -6.30
 242 ARG   ( 242-)  A      -5.99
 594 ARG   ( 253-)  B      -5.90
 230 ARG   ( 230-)  A      -5.51
 583 ARG   ( 242-)  B      -5.41
 593 LYS   ( 252-)  B      -5.35
 581 ARG   ( 240-)  B      -5.28
 252 LYS   ( 252-)  A      -5.10

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.

  36 ARG   (  36-)  A        38 - GLU     38- ( A)         -4.34
 240 ARG   ( 240-)  A       243 - LYS    243- ( A)         -4.74
 573 GLU   ( 232-)  B       576 - GLU    235- ( B)         -5.20

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.

 377 ARG   (  36-)  B   -3.48
 206 LEU   ( 206-)  A   -2.85
 547 LEU   ( 206-)  B   -2.60
 521 ILE   ( 180-)  B   -2.56

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 742 HOH   ( 569 )  A      O     11.82  -33.71  -25.49
 742 HOH   ( 607 )  A      O    -11.66  -86.62   46.03
 743 HOH   ( 513 )  B      O      7.66  -56.41   13.55
 743 HOH   ( 523 )  B      O      3.96  -47.88  -19.18
 743 HOH   ( 569 )  B      O    -31.44  -54.39   43.08

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.

 742 HOH   ( 507 )  A      O
 742 HOH   ( 508 )  A      O
 742 HOH   ( 543 )  A      O
 742 HOH   ( 579 )  A      O
 742 HOH   ( 598 )  A      O
 743 HOH   ( 513 )  B      O
 743 HOH   ( 518 )  B      O
 743 HOH   ( 536 )  B      O
 743 HOH   ( 540 )  B      O
 743 HOH   ( 549 )  B      O
 743 HOH   ( 554 )  B      O
 743 HOH   ( 556 )  B      O
 743 HOH   ( 565 )  B      O
 743 HOH   ( 596 )  B      O
 745 HOH   ( 104 )  T      O
 747 HOH   ( 102 )  C      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.

  14 GLN   (  14-)  A
 234 ASN   ( 234-)  A
 304 HIS   ( 304-)  A
 355 GLN   (  14-)  B
 464 ASN   ( 123-)  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.

  11 PHE   (  11-)  A      N
  34 SER   (  34-)  A      OG
  47 ASN   (  47-)  A      ND2
  98 LYS   (  98-)  A      N
 103 SER   ( 103-)  A      OG
 113 ASP   ( 113-)  A      N
 117 ASP   ( 117-)  A      N
 140 VAL   ( 140-)  A      N
 147 ASN   ( 147-)  A      N
 148 LYS   ( 148-)  A      N
 149 VAL   ( 149-)  A      N
 167 ASP   ( 167-)  A      N
 196 LYS   ( 196-)  A      N
 198 GLY   ( 198-)  A      N
 200 ASN   ( 200-)  A      N
 201 LYS   ( 201-)  A      N
 202 LEU   ( 202-)  A      N
 203 VAL   ( 203-)  A      N
 221 LYS   ( 221-)  A      N
 235 GLU   ( 235-)  A      N
 244 SER   ( 244-)  A      N
 247 ARG   ( 247-)  A      NE
 262 LYS   ( 262-)  A      N
 264 TYR   ( 264-)  A      N
 266 PHE   ( 266-)  A      N
And so on for a total of 69 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

   7 ASP   (   7-)  A      OD1
  17 GLU   (  17-)  A      OE2
 446 ASP   ( 105-)  B      OD1
 572 ASP   ( 231-)  B      OD1
 575 ASN   ( 234-)  B      OD1
 611 GLU   ( 270-)  B      OE1
 655 GLU   ( 314-)  B      OE2

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+.

 737  CA   ( 401-)  A   -.-  -.-  Part of ionic cluster
 737  CA   ( 401-)  A     0.57   0.74 Scores about as good as NA
 738  CA   ( 402-)  A   -.-  -.-  Part of ionic cluster
 738  CA   ( 402-)  A     0.35   1.06 Is perhaps  K
 739  CA   ( 401-)  B   -.-  -.-  Part of ionic cluster
 739  CA   ( 401-)  B     0.51   0.70 Scores about as good as NA
 740  CA   ( 402-)  B   -.-  -.-  Part of ionic cluster
 740  CA   ( 402-)  B     0.59   0.79 Scores about as good as NA

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.

  17 GLU   (  17-)  A   H-bonding suggests Gln; but Alt-Rotamer
 179 ASP   ( 179-)  A   H-bonding suggests Asn
 232 GLU   ( 232-)  A   H-bonding suggests Gln; but Alt-Rotamer
 350 ASP   (   9-)  B   H-bonding suggests Asn
 520 ASP   ( 179-)  B   H-bonding suggests Asn
 523 ASP   ( 182-)  B   H-bonding suggests Asn; but Alt-Rotamer
 552 ASP   ( 211-)  B   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 :  -0.098
  2nd generation packing quality :  -1.143
  Ramachandran plot appearance   :  -2.408
  chi-1/chi-2 rotamer normality  :  -2.976
  Backbone conformation          :   0.212

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.491 (tight)
  Bond angles                    :   0.806
  Omega angle restraints         :   0.874
  Side chain planarity           :   0.270 (tight)
  Improper dihedral distribution :   0.576
  B-factor distribution          :   0.791
  Inside/Outside distribution    :   0.988

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.1
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.491 (tight)
  Bond angles                    :   0.806
  Omega angle restraints         :   0.874
  Side chain planarity           :   0.270 (tight)
  Improper dihedral distribution :   0.576
  B-factor distribution          :   0.791
  Inside/Outside distribution    :   0.988
==============

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.