WHAT IF Check report

This file was created 2011-12-18 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb1xsl.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

1395 CAC   ( 950-)  D  -         Atom types

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: E

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: M

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'.

 380 LYS   ( 544-)  A      CG
 380 LYS   ( 544-)  A      CD
 380 LYS   ( 544-)  A      CE
 380 LYS   ( 544-)  A      NZ
 381 VAL   ( 545-)  A      CG1
 381 VAL   ( 545-)  A      CG2
 415 LEU   ( 254-)  E      CG
 415 LEU   ( 254-)  E      CD1
 415 LEU   ( 254-)  E      CD2
 426 LYS   ( 265-)  E      CG
 426 LYS   ( 265-)  E      CD
 426 LYS   ( 265-)  E      CE
 426 LYS   ( 265-)  E      NZ
 472 GLU   ( 311-)  E      CG
 472 GLU   ( 311-)  E      CD
 472 GLU   ( 311-)  E      OE1
 472 GLU   ( 311-)  E      OE2
 484 ARG   ( 323-)  E      CG
 484 ARG   ( 323-)  E      CD
 484 ARG   ( 323-)  E      NE
 484 ARG   ( 323-)  E      CZ
 484 ARG   ( 323-)  E      NH1
 484 ARG   ( 323-)  E      NH2
 491 GLU   ( 330-)  E      CG
 491 GLU   ( 330-)  E      CD
And so on for a total of 94 lines.

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

1199 GLU   ( 385-)  M    0.50

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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

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: E

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: M

Nomenclature related problems

Warning: Tyrosine convention problem

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

 132 TYR   ( 296-)  A
 403 TYR   ( 567-)  A
 541 TYR   ( 380-)  E
 579 TYR   ( 418-)  E
 728 TYR   ( 567-)  E
 840 TYR   ( 353-)  I
1054 TYR   ( 567-)  I
1110 TYR   ( 296-)  M
1381 TYR   ( 567-)  M

Warning: Phenylalanine convention problem

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

 125 PHE   ( 289-)  A
 174 PHE   ( 338-)  A
 193 PHE   ( 357-)  A
 242 PHE   ( 406-)  A
 342 PHE   ( 506-)  A
 348 PHE   ( 512-)  A
 396 PHE   ( 560-)  A
 450 PHE   ( 289-)  E
 499 PHE   ( 338-)  E
 518 PHE   ( 357-)  E
 567 PHE   ( 406-)  E
 667 PHE   ( 506-)  E
 673 PHE   ( 512-)  E
 721 PHE   ( 560-)  E
 776 PHE   ( 289-)  I
 825 PHE   ( 338-)  I
 844 PHE   ( 357-)  I
 993 PHE   ( 506-)  I
 999 PHE   ( 512-)  I
1103 PHE   ( 289-)  M
1152 PHE   ( 338-)  M
1171 PHE   ( 357-)  M
1220 PHE   ( 406-)  M
1320 PHE   ( 506-)  M
1326 PHE   ( 512-)  M

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.

 198 ASP   ( 362-)  A
 326 ASP   ( 490-)  A
 410 ASP   ( 574-)  A
 523 ASP   ( 362-)  E
 590 ASP   ( 429-)  E
 651 ASP   ( 490-)  E
 735 ASP   ( 574-)  E
 849 ASP   ( 362-)  I
 977 ASP   ( 490-)  I
1061 ASP   ( 574-)  I
1176 ASP   ( 362-)  M
1241 ASP   ( 427-)  M
1273 ASP   ( 459-)  M
1304 ASP   ( 490-)  M
1388 ASP   ( 574-)  M

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.

  94 GLU   ( 258-)  A
 172 GLU   ( 336-)  A
 197 GLU   ( 361-)  A
 290 GLU   ( 454-)  A
 301 GLU   ( 465-)  A
 302 GLU   ( 466-)  A
 392 GLU   ( 556-)  A
 405 GLU   ( 569-)  A
 419 GLU   ( 258-)  E
 479 GLU   ( 318-)  E
 497 GLU   ( 336-)  E
 546 GLU   ( 385-)  E
 627 GLU   ( 466-)  E
 717 GLU   ( 556-)  E
 730 GLU   ( 569-)  E
 823 GLU   ( 336-)  I
 941 GLU   ( 454-)  I
1043 GLU   ( 556-)  I
1056 GLU   ( 569-)  I
1072 GLU   ( 258-)  M
1150 GLU   ( 336-)  M
1279 GLU   ( 465-)  M
1370 GLU   ( 556-)  M
1383 GLU   ( 569-)  M

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.

 275 SER   ( 439-)  A      N   -C     1.24   -4.7
1053 PRO   ( 566-)  I      N   -C     1.49    8.2

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999415  0.000095 -0.000052|
 |  0.000095  0.999304  0.000134|
 | -0.000052  0.000134  0.999337|
Proposed new scale matrix

 |  0.005225  0.000000  0.000000|
 |  0.000000  0.010127 -0.000001|
 |  0.000000 -0.000001  0.009574|
With corresponding cell

    A    = 191.385  B   =  98.745  C    = 104.446
    Alpha=  89.985  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 191.504  B   =  98.812  C    = 104.519
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 36.606
(Under-)estimated Z-score: 4.459

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.

   3 DGUA  (   3-)  B      N9   C8   N7  113.17    4.1
   8 DGUA  (   8-)  B      N9   C8   N7  113.22    4.2
  14 DGUA  (   3-)  C      N9   C8   N7  113.15    4.1
  21 DGUA  (   4-)  D      N9   C8   N7  113.12    4.0
  23 DGUA  (   2-)  F      N9   C8   N7  113.10    4.0
  27 DGUA  (   6-)  F      N9   C8   N7  113.11    4.0
  33 DGUA  (   1-)  G      N9   C8   N7  113.16    4.1
  35 DGUA  (   3-)  G      N9   C8   N7  113.19    4.2
  39 DGUA  (   1-)  H      OP1  P    OP2 112.94   -4.4
  50 DGUA  (   8-)  J      N9   C8   N7  113.25    4.3
  54 DGUA  (   1-)  K      N9   C8   N7  113.20    4.2
  56 DGUA  (   3-)  K      N9   C8   N7  113.22    4.2
  60 DGUA  (   1-)  L      OP1  P    OP2 113.29   -4.2
  63 DGUA  (   4-)  L      N9   C8   N7  113.11    4.0
  69 DGUA  (   6-)  N      N9   C8   N7  113.13    4.1
  71 DGUA  (   8-)  N      N9   C8   N7  113.15    4.1
  77 DGUA  (   3-)  O      N9   C8   N7  113.20    4.2
  81 DGUA  (   1-)  P      C2'  C1'  N9  107.80   -4.0
 275 SER   ( 439-)  A     -O   -C    N   115.39   -4.8
 275 SER   ( 439-)  A     -CA  -C    N   124.59    4.2
 368 LEU   ( 532-)  A      N    CA   C    99.36   -4.2
1053 PRO   ( 566-)  I     -CA  -C    N   107.09   -6.5

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.

  94 GLU   ( 258-)  A
 172 GLU   ( 336-)  A
 197 GLU   ( 361-)  A
 198 ASP   ( 362-)  A
 290 GLU   ( 454-)  A
 301 GLU   ( 465-)  A
 302 GLU   ( 466-)  A
 326 ASP   ( 490-)  A
 392 GLU   ( 556-)  A
 405 GLU   ( 569-)  A
 410 ASP   ( 574-)  A
 419 GLU   ( 258-)  E
 479 GLU   ( 318-)  E
 497 GLU   ( 336-)  E
 523 ASP   ( 362-)  E
 546 GLU   ( 385-)  E
 590 ASP   ( 429-)  E
 627 GLU   ( 466-)  E
 651 ASP   ( 490-)  E
 717 GLU   ( 556-)  E
 730 GLU   ( 569-)  E
 735 ASP   ( 574-)  E
 823 GLU   ( 336-)  I
 849 ASP   ( 362-)  I
 941 GLU   ( 454-)  I
 977 ASP   ( 490-)  I
1043 GLU   ( 556-)  I
1056 GLU   ( 569-)  I
1061 ASP   ( 574-)  I
1072 GLU   ( 258-)  M
1150 GLU   ( 336-)  M
1176 ASP   ( 362-)  M
1241 ASP   ( 427-)  M
1273 ASP   ( 459-)  M
1279 GLU   ( 465-)  M
1304 ASP   ( 490-)  M
1370 GLU   ( 556-)  M
1383 GLU   ( 569-)  M
1388 ASP   ( 574-)  M

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

1051 GLY   ( 564-)  I      C     -6.8    -8.94     0.06
1052 LEU   ( 565-)  I      C     13.0    20.81     0.20
The average deviation= 0.648

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.

1179 SER   ( 365-)  M    4.80
 479 GLU   ( 318-)  E    4.55
 201 SER   ( 365-)  A    4.35
 521 LEU   ( 360-)  E    4.35
 368 LEU   ( 532-)  A    4.34
 853 GLN   ( 366-)  I    4.25
1200 ARG   ( 386-)  M    4.17
 434 LYS   ( 273-)  E    4.13

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.

 269 THR   ( 433-)  A    -2.9
1247 THR   ( 433-)  M    -2.9
 594 THR   ( 433-)  E    -2.7
 920 THR   ( 433-)  I    -2.6
 731 PRO   ( 570-)  E    -2.3
 127 LYS   ( 291-)  A    -2.3
 452 LYS   ( 291-)  E    -2.2
 382 GLY   ( 546-)  A    -2.1
 801 ILE   ( 314-)  I    -2.1
 908 GLY   ( 421-)  I    -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.

 127 LYS   ( 291-)  A  Poor phi/psi
 194 ARG   ( 358-)  A  Poor phi/psi
 251 CYS   ( 415-)  A  Poor phi/psi
 274 ARG   ( 438-)  A  Poor phi/psi
 344 GLY   ( 508-)  A  omega poor
 482 HIS   ( 321-)  E  Poor phi/psi
 576 CYS   ( 415-)  E  Poor phi/psi
 599 ARG   ( 438-)  E  Poor phi/psi
 669 GLY   ( 508-)  E  omega poor
 692 ALA   ( 531-)  E  Poor phi/psi
 700 ASN   ( 539-)  E  Poor phi/psi
 759 ASP   ( 272-)  I  Poor phi/psi
 806 SER   ( 319-)  I  Poor phi/psi
 807 GLY   ( 320-)  I  Poor phi/psi
 845 ARG   ( 358-)  I  Poor phi/psi
 853 GLN   ( 366-)  I  Poor phi/psi
 902 CYS   ( 415-)  I  Poor phi/psi
 995 GLY   ( 508-)  I  omega poor
1018 ALA   ( 531-)  I  Poor phi/psi
1051 GLY   ( 564-)  I  omega poor
1180 GLN   ( 366-)  M  Poor phi/psi
1229 CYS   ( 415-)  M  Poor phi/psi
1252 ARG   ( 438-)  M  Poor phi/psi
1322 GLY   ( 508-)  M  omega poor
1345 ALA   ( 531-)  M  Poor phi/psi
1353 ASN   ( 539-)  M  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.763

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.

 286 SER   ( 450-)  A    0.36
1329 SER   ( 515-)  M    0.36
1259 SER   ( 445-)  M    0.36
 868 SER   ( 381-)  I    0.38
 542 SER   ( 381-)  E    0.39
 937 SER   ( 450-)  I    0.39

Warning: Unusual backbone conformations

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

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

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

   3 DGUA  (   3-)  B      0
   4 DCYT  (   4-)  B      0
   5 DADE  (   5-)  B      0
   6 DGUA  (   6-)  B      0
   7 DCYT  (   7-)  B      0
   8 DGUA  (   8-)  B      0
   9 DCYT  (   9-)  B      0
  10 DADE  (  10-)  B      0
  11 DCYT  (  11-)  B      0
  12 DGUA  (   1-)  C      0
  13 DTHY  (   2-)  C      0
  14 DGUA  (   3-)  C      0
  15 DCYT  (   4-)  C      0
  16 DGUA  (   5-)  C      0
  17 DCYT  (   6-)  C      0
  18 DGUA  (   1-)  D      0
  19 DCYT  (   2-)  D      0
  20 DCYT  (   3-)  D      0
  21 DGUA  (   4-)  D      0
  22 DCYT  (   1-)  F      0
  23 DGUA  (   2-)  F      0
  24 DGUA  (   3-)  F      0
  25 DCYT  (   4-)  F      0
  26 DADE  (   5-)  F      0
  27 DGUA  (   6-)  F      0
And so on for a total of 468 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.323

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

1325 HIS   ( 511-)  M      ND1  <->  1328 ARG   ( 514-)  M      NH2  0.47    2.53  INTRA BL
 998 HIS   ( 511-)  I      ND1  <->  1001 ARG   ( 514-)  I      NH2  0.45    2.55  INTRA BF
 794 LYS   ( 307-)  I      NZ   <->  1418 HOH   (1033 )  I      O    0.38    2.32  INTRA BF
 404 ARG   ( 568-)  A      NH2  <->  1390 TRP   ( 575-)  A      O''  0.29    2.41  INTRA BL
  32 DCYT  (  11-)  F      N3   <->    33 DGUA  (   1-)  G      N1   0.27    2.73  INTRA BF
  31 DADE  (  10-)  F      C2'  <->    32 DCYT  (  11-)  F      C5'  0.25    2.95  INTRA BF
  64 DCYT  (   1-)  N      N3   <->    84 DGUA  (   4-)  P      N1   0.25    2.75  INTRA BL
1333 LEU   ( 519-)  M      CD2  <->  1379 LEU   ( 565-)  M      CD1  0.25    2.95  INTRA BL
   1 DCYT  (   1-)  B      N3   <->    21 DGUA  (   4-)  D      N1   0.24    2.76  INTRA BL
 258 LYS   ( 422-)  A      NZ   <->   410 ASP   ( 574-)  A      OD2  0.24    2.46  INTRA BF
 433 ASP   ( 272-)  E      OD2  <->   436 ARG   ( 275-)  E      NH1  0.23    2.47  INTRA BF
1250 ASP   ( 436-)  M      OD1  <->  1252 ARG   ( 438-)  M      N    0.21    2.49  INTRA BL
1201 MET   ( 387-)  M      CE   <->  1206 ALA   ( 392-)  M      N    0.21    2.89  INTRA BL
 909 LYS   ( 422-)  I      NZ   <->  1061 ASP   ( 574-)  I      OD2  0.21    2.49  INTRA BF
 700 ASN   ( 539-)  E      ND2  <->   704 CYS   ( 543-)  E      CB   0.20    2.90  INTRA BF
  53 DCYT  (  11-)  J      N3   <->    54 DGUA  (   1-)  K      N1   0.20    2.80  INTRA BF
  37 DGUA  (   5-)  G      N7   <->  1408 HOH   ( 651 )  G      O    0.20    2.50  INTRA BF
 101 LYS   ( 265-)  A      NZ   <->   172 GLU   ( 336-)  A      CD   0.20    2.90  INTRA BF
 662 CYS   ( 501-)  E      SG   <->   692 ALA   ( 531-)  E      CA   0.19    3.21  INTRA BL
  43 DCYT  (   1-)  J      N3   <->    63 DGUA  (   4-)  L      N1   0.18    2.82  INTRA BF
1356 GLY   ( 542-)  M      C    <->  1357 CYS   ( 543-)  M      SG   0.18    3.12  INTRA BF
   2 DGUA  (   2-)  B      N1   <->    20 DCYT  (   3-)  D      N3   0.18    2.82  INTRA BL
 988 CYS   ( 501-)  I      SG   <->  1018 ALA   ( 531-)  I      CA   0.17    3.23  INTRA
1281 ASN   ( 467-)  M      OD1  <->  1344 HIS   ( 530-)  M      NE2  0.17    2.53  INTRA BL
 375 ASN   ( 539-)  A      O    <->   378 GLY   ( 542-)  A      N    0.16    2.54  INTRA BF
And so on for a total of 216 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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

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.

 873 ARG   ( 386-)  I      -6.56
 222 ARG   ( 386-)  A      -6.30
1200 ARG   ( 386-)  M      -6.18
 413 HIS   ( 252-)  E      -6.15
 699 ARG   ( 538-)  E      -6.15
 814 HIS   ( 327-)  I      -6.07
 126 HIS   ( 290-)  A      -6.02
 547 ARG   ( 386-)  E      -5.87
 451 HIS   ( 290-)  E      -5.74
1104 HIS   ( 290-)  M      -5.64
1025 ARG   ( 538-)  I      -5.60
 289 GLN   ( 453-)  A      -5.59
 928 ARG   ( 441-)  I      -5.58
 940 GLN   ( 453-)  I      -5.58
 841 GLN   ( 354-)  I      -5.58
 374 ARG   ( 538-)  A      -5.56
 515 GLN   ( 354-)  E      -5.56
1352 ARG   ( 538-)  M      -5.55
1168 GLN   ( 354-)  M      -5.55
1267 GLN   ( 453-)  M      -5.55
 777 HIS   ( 290-)  I      -5.55
 190 GLN   ( 354-)  A      -5.54
 602 ARG   ( 441-)  E      -5.51
1028 HIS   ( 541-)  I      -5.51
 971 ARG   ( 484-)  I      -5.50
 853 GLN   ( 366-)  I      -5.49
 527 GLN   ( 366-)  E      -5.47
1180 GLN   ( 366-)  M      -5.43
 202 GLN   ( 366-)  A      -5.39
 255 ARG   ( 419-)  A      -5.33
 580 ARG   ( 419-)  E      -5.32
 906 ARG   ( 419-)  I      -5.30
 277 ARG   ( 441-)  A      -5.26
1233 ARG   ( 419-)  M      -5.25
 314 ARG   ( 478-)  A      -5.24
1292 ARG   ( 478-)  M      -5.23
 645 ARG   ( 484-)  E      -5.17
1172 ARG   ( 358-)  M      -5.17
1055 ARG   ( 568-)  I      -5.12
1024 VAL   ( 537-)  I      -5.11
1255 ARG   ( 441-)  M      -5.07
1382 ARG   ( 568-)  M      -5.04

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.

 200 ARG   ( 364-)  A       202 - GLN    366- ( A)         -4.74
 525 ARG   ( 364-)  E       527 - GLN    366- ( E)         -4.85
 639 ARG   ( 478-)  E       641 - PRO    480- ( E)         -4.52
 851 ARG   ( 364-)  I       853 - GLN    366- ( I)         -4.75
 965 ARG   ( 478-)  I       967 - PRO    480- ( I)         -4.44
1178 ARG   ( 364-)  M      1180 - GLN    366- ( M)         -4.56
1292 ARG   ( 478-)  M      1294 - PRO    480- ( M)         -4.51

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: E

Note: Quality value plot

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

Chain identifier: I

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: M

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.

 127 LYS   ( 291-)  A   -2.59
 808 HIS   ( 321-)  I   -2.57

Warning: Abnormal packing Z-score for sequential residues

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

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

1279 GLU   ( 465-)  M     - 1282 GLY   ( 468-)  M        -1.52

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: E

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: M

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.

1410 HOH   ( 896 )  J      O     24.32   66.63   75.12
1417 HOH   (1032 )  E      O     23.28   81.68   69.87
1417 HOH   (1039 )  E      O     20.59   80.78   68.95
1419 HOH   (1074 )  M      O     55.07   30.25   39.59

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.

 300 GLN   ( 464-)  A
 628 ASN   ( 467-)  E
 631 GLN   ( 470-)  E
 739 HIS   ( 252-)  I
 954 ASN   ( 467-)  I
1066 HIS   ( 252-)  M
1069 HIS   ( 255-)  M
1278 GLN   ( 464-)  M

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.

  92 ILE   ( 256-)  A      N
 111 ARG   ( 275-)  A      NE
 127 LYS   ( 291-)  A      N
 226 GLU   ( 390-)  A      N
 365 GLU   ( 529-)  A      N
 374 ARG   ( 538-)  A      NE
 404 ARG   ( 568-)  A      N
 452 LYS   ( 291-)  E      N
 456 SER   ( 295-)  E      N
 533 GLN   ( 372-)  E      N
 547 ARG   ( 386-)  E      N
 588 ASP   ( 427-)  E      N
 602 ARG   ( 441-)  E      NE
 607 ARG   ( 446-)  E      N
 645 ARG   ( 484-)  E      N
 647 HIS   ( 486-)  E      N
 678 ARG   ( 517-)  E      NH1
 729 ARG   ( 568-)  E      N
 739 HIS   ( 252-)  I      N
 778 LYS   ( 291-)  I      N
 782 SER   ( 295-)  I      N
 933 ARG   ( 446-)  I      NE
 942 GLY   ( 455-)  I      N
 951 GLN   ( 464-)  I      N
 974 ARG   ( 487-)  I      NH1
1028 HIS   ( 541-)  I      N
1030 CYS   ( 543-)  I      N
1055 ARG   ( 568-)  I      N
1073 LYS   ( 259-)  M      N
1089 ARG   ( 275-)  M      NE
1105 LYS   ( 291-)  M      N
1109 SER   ( 295-)  M      N
1382 ARG   ( 568-)  M      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.

 590 ASP   ( 429-)  E      OD1
 627 GLU   ( 466-)  E      OE1
 883 GLU   ( 396-)  I      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+.

1397  MG   ( 993-)  H   -.-  -.-  Low probability ion. B= 85.8
1399  NA   ( 966-)  N     1.58   1.37 Scores about as good as CA (Few ligands (4) )
1401  NA   ( 962-)  E     0.66   1.25 Scores about as good as  K

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and 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 nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple 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 method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1416 HOH   ( 970 )  A      O  0.95  K  4 NCS 1/1

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.

  97 GLU   ( 261-)  A   H-bonding suggests Gln; but Alt-Rotamer
 295 ASP   ( 459-)  A   H-bonding suggests Asn
 620 ASP   ( 459-)  E   H-bonding suggests Asn; but Alt-Rotamer
 936 ASP   ( 449-)  I   H-bonding suggests Asn
 946 ASP   ( 459-)  I   H-bonding suggests Asn
 947 ASP   ( 460-)  I   H-bonding suggests Asn; but Alt-Rotamer
1263 ASP   ( 449-)  M   H-bonding suggests Asn; but Alt-Rotamer
1273 ASP   ( 459-)  M   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.199
  2nd generation packing quality :  -0.830
  Ramachandran plot appearance   :  -0.752
  chi-1/chi-2 rotamer normality  :  -0.763
  Backbone conformation          :   0.696

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.341 (tight)
  Bond angles                    :   0.637 (tight)
  Omega angle restraints         :   0.241 (tight)
  Side chain planarity           :   0.230 (tight)
  Improper dihedral distribution :   0.592
  B-factor distribution          :   0.456
  Inside/Outside distribution    :   0.962

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.341 (tight)
  Bond angles                    :   0.637 (tight)
  Omega angle restraints         :   0.241 (tight)
  Side chain planarity           :   0.230 (tight)
  Improper dihedral distribution :   0.592
  B-factor distribution          :   0.456
  Inside/Outside distribution    :   0.962
==============

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.