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 pdb3ir7.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some 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 two or less which PRODRUG also cannot cope with), 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.

1977 MD1   (1247-)  A  -         OK
1978 SF4   (1248-)  A  -         Atom types
1980 SF4   ( 802-)  B  -         Atom types
1981 SF4   ( 803-)  B  -         Atom types
1982 SF4   ( 804-)  B  -         Atom types
1983 F3S   ( 805-)  B  -         Atom types
1986 AGA   (1249-)  C  -         OK
1987 MD1   (1251-)  A  -         OK
1988 FME   (   1-)  C  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1752 GLN   (   2-)  C  -   N   bound to 1988 FME   (   1-)  C  -   C

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

   7 PHE   (   7-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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'.

   7 PHE   (   7-)  A      O
   8 PHE   (  10-)  A      CG
   8 PHE   (  10-)  A      CD1
   8 PHE   (  10-)  A      CD2
   8 PHE   (  10-)  A      CE1
   8 PHE   (  10-)  A      CE2
   8 PHE   (  10-)  A      CZ
 360 ASP   ( 362-)  A      CG
 360 ASP   ( 362-)  A      OD1
 360 ASP   ( 362-)  A      OD2
1827 TYR   (  77-)  C      CG
1827 TYR   (  77-)  C      CD1
1827 TYR   (  77-)  C      CD2
1827 TYR   (  77-)  C      CE1
1827 TYR   (  77-)  C      CE2
1827 TYR   (  77-)  C      CZ
1827 TYR   (  77-)  C      OH
1828 GLU   (  78-)  C      CG
1828 GLU   (  78-)  C      CD
1828 GLU   (  78-)  C      OE1
1828 GLU   (  78-)  C      OE2

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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.

   6 ARG   (   6-)  A
  27 ARG   (  29-)  A
  34 ARG   (  36-)  A
  36 ARG   (  38-)  A
  44 ARG   (  46-)  A
  77 ARG   (  79-)  A
 152 ARG   ( 154-)  A
 157 ARG   ( 159-)  A
 202 ARG   ( 204-)  A
 258 ARG   ( 260-)  A
 313 ARG   ( 315-)  A
 351 ARG   ( 353-)  A
 354 ARG   ( 356-)  A
 513 ARG   ( 515-)  A
 518 ARG   ( 520-)  A
 521 ARG   ( 523-)  A
 533 ARG   ( 535-)  A
 601 ARG   ( 603-)  A
 635 ARG   ( 637-)  A
 646 ARG   ( 648-)  A
 691 ARG   ( 693-)  A
 772 ARG   ( 774-)  A
 888 ARG   ( 890-)  A
 896 ARG   ( 898-)  A
 926 ARG   ( 928-)  A
And so on for a total of 56 lines.

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   (  35-)  A
  60 TYR   (  62-)  A
  75 TYR   (  77-)  A
  99 TYR   ( 101-)  A
 101 TYR   ( 103-)  A
 203 TYR   ( 205-)  A
 242 TYR   ( 244-)  A
 246 TYR   ( 248-)  A
 282 TYR   ( 284-)  A
 331 TYR   ( 333-)  A
 347 TYR   ( 349-)  A
 494 TYR   ( 496-)  A
 500 TYR   ( 502-)  A
 546 TYR   ( 548-)  A
 610 TYR   ( 612-)  A
 728 TYR   ( 730-)  A
 790 TYR   ( 792-)  A
1020 TYR   (1022-)  A
1024 TYR   (1026-)  A
1099 TYR   (1101-)  A
1204 TYR   (1206-)  A
1208 TYR   (1210-)  A
1280 TYR   (  38-)  B
1304 TYR   (  62-)  B
1343 TYR   ( 101-)  B
1411 TYR   ( 169-)  B
1421 TYR   ( 179-)  B
1444 TYR   ( 202-)  B
1511 TYR   ( 269-)  B
1517 TYR   ( 275-)  B
1631 TYR   ( 389-)  B
1657 TYR   ( 415-)  B
1686 TYR   ( 444-)  B
1688 TYR   ( 446-)  B
1783 TYR   (  33-)  C
1963 TYR   ( 213-)  C
1968 TYR   ( 218-)  C

Warning: Phenylalanine convention problem

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

 146 PHE   ( 148-)  A
 264 PHE   ( 266-)  A
 315 PHE   ( 317-)  A
 324 PHE   ( 326-)  A
 375 PHE   ( 377-)  A
 523 PHE   ( 525-)  A
 561 PHE   ( 563-)  A
 592 PHE   ( 594-)  A
 609 PHE   ( 611-)  A
 771 PHE   ( 773-)  A
 803 PHE   ( 805-)  A
 897 PHE   ( 899-)  A
 975 PHE   ( 977-)  A
1206 PHE   (1208-)  A
1219 PHE   (1221-)  A
1283 PHE   (  41-)  B
1542 PHE   ( 300-)  B
1720 PHE   ( 478-)  B
1736 PHE   ( 494-)  B
1753 PHE   (   3-)  C
1758 PHE   (   8-)  C
1805 PHE   (  55-)  C
1817 PHE   (  67-)  C
1896 PHE   ( 146-)  C
1948 PHE   ( 198-)  C
1950 PHE   ( 200-)  C

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.

   5 ASP   (   5-)  A
  40 ASP   (  42-)  A
 128 ASP   ( 130-)  A
 216 ASP   ( 218-)  A
 220 ASP   ( 222-)  A
 234 ASP   ( 236-)  A
 281 ASP   ( 283-)  A
 318 ASP   ( 320-)  A
 344 ASP   ( 346-)  A
 404 ASP   ( 406-)  A
 422 ASP   ( 424-)  A
 462 ASP   ( 464-)  A
 487 ASP   ( 489-)  A
 525 ASP   ( 527-)  A
 595 ASP   ( 597-)  A
 632 ASP   ( 634-)  A
 642 ASP   ( 644-)  A
 753 ASP   ( 755-)  A
 756 ASP   ( 758-)  A
 764 ASP   ( 766-)  A
 770 ASP   ( 772-)  A
 794 ASP   ( 796-)  A
 873 ASP   ( 875-)  A
 989 ASP   ( 991-)  A
1121 ASP   (1123-)  A
1124 ASP   (1126-)  A
1131 ASP   (1133-)  A
1237 ASP   (1239-)  A
1297 ASP   (  55-)  B
1340 ASP   (  98-)  B
1341 ASP   (  99-)  B
1349 ASP   ( 107-)  B
1389 ASP   ( 147-)  B
1455 ASP   ( 213-)  B
1457 ASP   ( 215-)  B
1518 ASP   ( 276-)  B
1520 ASP   ( 278-)  B
1533 ASP   ( 291-)  B
1540 ASP   ( 298-)  B
1547 ASP   ( 305-)  B
1621 ASP   ( 379-)  B
1668 ASP   ( 426-)  B
1724 ASP   ( 482-)  B
1730 ASP   ( 488-)  B
1760 ASP   (  10-)  C
1779 ASP   (  29-)  C

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.

  30 GLU   (  32-)  A
  86 GLU   (  88-)  A
 138 GLU   ( 140-)  A
 162 GLU   ( 164-)  A
 165 GLU   ( 167-)  A
 237 GLU   ( 239-)  A
 267 GLU   ( 269-)  A
 284 GLU   ( 286-)  A
 341 GLU   ( 343-)  A
 365 GLU   ( 367-)  A
 380 GLU   ( 382-)  A
 409 GLU   ( 411-)  A
 412 GLU   ( 414-)  A
 426 GLU   ( 428-)  A
 438 GLU   ( 440-)  A
 444 GLU   ( 446-)  A
 446 GLU   ( 448-)  A
 522 GLU   ( 524-)  A
 619 GLU   ( 621-)  A
 624 GLU   ( 626-)  A
 625 GLU   ( 627-)  A
 669 GLU   ( 671-)  A
 687 GLU   ( 689-)  A
 695 GLU   ( 697-)  A
 751 GLU   ( 753-)  A
And so on for a total of 51 lines.

Geometric checks

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

 |  0.998963  0.000000 -0.000050|
 |  0.000000  0.998748 -0.000142|
 | -0.000050 -0.000142  0.998957|
Proposed new scale matrix

 |  0.006507  0.000000  0.000000|
 |  0.000000  0.004152  0.000000|
 |  0.000000  0.000001  0.007152|
With corresponding cell

    A    = 153.687  B   = 240.836  C    = 139.812
    Alpha=  90.010  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 153.851  B   = 241.147  C    = 139.966
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 83.177
(Under-)estimated Z-score: 6.722

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.

 581 LEU   ( 583-)  A      N    CA   C    99.80   -4.1
 605 SER   ( 607-)  A      N    CA   C   123.34    4.3
 806 PRO   ( 808-)  A      N    CA   C   121.87    4.0
 807 LEU   ( 809-)  A      N    CA   C    96.52   -5.2
1014 GLU   (1016-)  A      N    CA   C    98.42   -4.6
1147 VAL   (1149-)  A      N    CA   C    99.93   -4.0
1272 TRP   (  30-)  B      N    CA   C   123.51    4.4
1649 LYS   ( 407-)  B      C    CA   CB  121.53    6.0

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.

   5 ASP   (   5-)  A
   6 ARG   (   6-)  A
  27 ARG   (  29-)  A
  30 GLU   (  32-)  A
  34 ARG   (  36-)  A
  36 ARG   (  38-)  A
  40 ASP   (  42-)  A
  44 ARG   (  46-)  A
  77 ARG   (  79-)  A
  86 GLU   (  88-)  A
 128 ASP   ( 130-)  A
 138 GLU   ( 140-)  A
 152 ARG   ( 154-)  A
 157 ARG   ( 159-)  A
 162 GLU   ( 164-)  A
 165 GLU   ( 167-)  A
 202 ARG   ( 204-)  A
 216 ASP   ( 218-)  A
 220 ASP   ( 222-)  A
 234 ASP   ( 236-)  A
 237 GLU   ( 239-)  A
 258 ARG   ( 260-)  A
 267 GLU   ( 269-)  A
 281 ASP   ( 283-)  A
 284 GLU   ( 286-)  A
And so on for a total of 153 lines.

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.

 605 SER   ( 607-)  A    7.33
1272 TRP   (  30-)  B    6.43
 100 LEU   ( 102-)  A    6.04
 314 GLU   ( 316-)  A    5.67
 807 LEU   ( 809-)  A    5.59
1717 GLY   ( 475-)  B    5.25
 584 GLN   ( 586-)  A    5.06
 331 TYR   ( 333-)  A    5.01
 254 VAL   ( 256-)  A    4.99
1958 SER   ( 208-)  C    4.82
1636 LEU   ( 394-)  B    4.80
1522 ILE   ( 280-)  B    4.80
 581 LEU   ( 583-)  A    4.65
 806 PRO   ( 808-)  A    4.57
1014 GLU   (1016-)  A    4.44
1833 ILE   (  83-)  C    4.39
 194 MET   ( 196-)  A    4.18
1601 LEU   ( 359-)  B    4.16
1342 TYR   ( 100-)  B    4.09
1662 THR   ( 420-)  B    4.04
 330 ARG   ( 332-)  A    4.02
1147 VAL   (1149-)  A    4.01

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.

 500 TYR   ( 502-)  A    -3.1
 188 PRO   ( 190-)  A    -3.1
 222 PRO   ( 224-)  A    -3.0
 599 PRO   ( 601-)  A    -3.0
1866 PRO   ( 116-)  C    -2.8
 806 PRO   ( 808-)  A    -2.8
  87 PRO   (  89-)  A    -2.7
1488 PHE   ( 246-)  B    -2.7
  52 THR   (  54-)  A    -2.7
1030 LEU   (1032-)  A    -2.7
 802 PRO   ( 804-)  A    -2.6
1365 ILE   ( 123-)  B    -2.6
1425 LEU   ( 183-)  B    -2.6
 531 HIS   ( 533-)  A    -2.6
1403 PHE   ( 161-)  B    -2.6
 219 CYS   ( 221-)  A    -2.5
1142 LEU   (1144-)  A    -2.5
  46 THR   (  48-)  A    -2.4
1933 ILE   ( 183-)  C    -2.4
 388 ILE   ( 390-)  A    -2.4
 233 THR   ( 235-)  A    -2.3
 598 ARG   ( 600-)  A    -2.3
1170 PRO   (1172-)  A    -2.3
 934 GLU   ( 936-)  A    -2.3
1339 ILE   (  97-)  B    -2.3
 918 THR   ( 920-)  A    -2.3
 765 LEU   ( 767-)  A    -2.2
1206 PHE   (1208-)  A    -2.2
 761 GLY   ( 763-)  A    -2.2
1809 ILE   (  59-)  C    -2.2
 258 ARG   ( 260-)  A    -2.2
 811 VAL   ( 813-)  A    -2.2
 423 GLU   ( 425-)  A    -2.2
 400 LEU   ( 402-)  A    -2.2
 382 VAL   ( 384-)  A    -2.2
1541 VAL   ( 299-)  B    -2.2
 469 THR   ( 471-)  A    -2.1
1463 ARG   ( 221-)  B    -2.1
1831 LEU   (  81-)  C    -2.1
1209 TYR   (1211-)  A    -2.1
1954 ILE   ( 204-)  C    -2.1
 285 ILE   ( 287-)  A    -2.1
 614 SER   ( 616-)  A    -2.1
1113 PRO   (1115-)  A    -2.1
1231 LEU   (1233-)  A    -2.0
  69 GLU   (  71-)  A    -2.0
1600 PRO   ( 358-)  B    -2.0
  90 CYS   (  92-)  A    -2.0
1833 ILE   (  83-)  C    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

  41 LYS   (  43-)  A  Poor phi/psi
  46 THR   (  48-)  A  Poor phi/psi
  51 CYS   (  53-)  A  Poor phi/psi
  52 THR   (  54-)  A  Poor phi/psi
  54 SER   (  56-)  A  Poor phi/psi
  63 ASN   (  65-)  A  Poor phi/psi
  86 GLU   (  88-)  A  PRO omega poor
  88 ARG   (  90-)  A  Poor phi/psi
 158 SER   ( 160-)  A  Poor phi/psi
 189 ILE   ( 191-)  A  Poor phi/psi
 219 CYS   ( 221-)  A  Poor phi/psi
 233 THR   ( 235-)  A  Poor phi/psi
 343 ARG   ( 345-)  A  Poor phi/psi
 361 ALA   ( 363-)  A  Poor phi/psi
 393 GLY   ( 395-)  A  Poor phi/psi
 423 GLU   ( 425-)  A  Poor phi/psi
 445 LEU   ( 447-)  A  Poor phi/psi
 499 ALA   ( 501-)  A  Poor phi/psi
 500 TYR   ( 502-)  A  Poor phi/psi
 531 HIS   ( 533-)  A  Poor phi/psi
 576 VAL   ( 578-)  A  Poor phi/psi
 583 PRO   ( 585-)  A  Poor phi/psi
 598 ARG   ( 600-)  A  PRO omega poor
 656 ALA   ( 658-)  A  PRO omega poor
 711 ARG   ( 713-)  A  Poor phi/psi
And so on for a total of 67 lines.

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.

 832 SER   ( 834-)  A    0.35
 170 SER   ( 172-)  A    0.35
 135 SER   ( 137-)  A    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 ARG   (   6-)  A      0
   7 PHE   (   7-)  A      0
   8 PHE   (  10-)  A      0
   9 LYS   (  11-)  A      0
  13 GLU   (  15-)  A      0
  15 PHE   (  17-)  A      0
  16 ALA   (  18-)  A      0
  17 ASP   (  19-)  A      0
  19 HIS   (  21-)  A      0
  25 THR   (  27-)  A      0
  26 ASN   (  28-)  A      0
  27 ARG   (  29-)  A      0
  40 ASP   (  42-)  A      0
  44 ARG   (  46-)  A      0
  50 ASN   (  52-)  A      0
  51 CYS   (  53-)  A      0
  52 THR   (  54-)  A      0
  63 ASN   (  65-)  A      0
  67 THR   (  69-)  A      0
  68 TRP   (  70-)  A      0
  73 THR   (  75-)  A      0
  74 ASP   (  76-)  A      0
  75 TYR   (  77-)  A      0
  77 ARG   (  79-)  A      0
  85 HIS   (  87-)  A      0
And so on for a total of 775 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 : 1.301

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 419 GLY   ( 421-)  A   1.77   58

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

1161 HIS   (1163-)  A   2.41

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]

 697 PRO   ( 699-)  A    0.45 HIGH
 806 PRO   ( 808-)  A    0.47 HIGH

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].

 188 PRO   ( 190-)  A   -65.7 envelop C-beta (-72 degrees)
1866 PRO   ( 116-)  C  -117.1 half-chair C-delta/C-gamma (-126 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.

1752 GLN   (   2-)  C      N   <-> 1988 FME   (   1-)  C      C      1.35    1.35  INTRA B3
1977 MD1   (1247-)  A      S12 <-> 1987 MD1   (1251-)  A      S13    0.91    2.69  INTRA BF
1752 GLN   (   2-)  C      CA  <-> 1988 FME   (   1-)  C      C      0.76    2.44  INTRA
1977 MD1   (1247-)  A      S13 <-> 1987 MD1   (1251-)  A      S12    0.66    2.94  INTRA BF
1096 HIS   (1098-)  A      CE1 <-> 1987 MD1   (1251-)  A      S13    0.52    2.88  INTRA
1096 HIS   (1098-)  A      CE1 <-> 1977 MD1   (1247-)  A      S12    0.44    2.96  INTRA BF
1536 GLN   ( 294-)  B      N   <-> 1989 HOH   ( 554 )  B      O      0.41    2.29  INTRA BL
 860 GLN   ( 862-)  A      NE2 <-> 1990 HOH   (1260 )  A      O      0.41    2.29  INTRA BF
 789 TRP   ( 791-)  A      NE1 <-> 1977 MD1   (1247-)  A      N7     0.37    2.63  INTRA
1711 ALA   ( 469-)  B      N   <-> 1989 HOH   ( 526 )  B      O      0.34    2.36  INTRA BL
1501 CYS   ( 259-)  B      SG  <-> 1510 ARG   ( 268-)  B      NH1    0.31    2.99  INTRA BL
1096 HIS   (1098-)  A      C   <-> 1162 ALA   (1164-)  A      CB     0.29    2.91  INTRA
1274 SER   (  32-)  B      N   <-> 1989 HOH   ( 556 )  B      O      0.28    2.42  INTRA BL
 722 HIS   ( 724-)  A      NE2 <-> 1165 ARG   (1167-)  A      NH1    0.26    2.74  INTRA BL
  49 VAL   (  51-)  A      C   <->  192 MET   ( 194-)  A      SD     0.26    3.14  INTRA
1204 TYR   (1206-)  A      CG  <-> 1205 GLY   (1207-)  A      N      0.26    2.74  INTRA BL
1232 ASP   (1234-)  A      OD2 <-> 1367 ARG   ( 125-)  B      NH1    0.23    2.47  INTRA BL
1004 ILE   (1006-)  A      CD1 <-> 1990 HOH   (1323 )  A      O      0.23    2.57  INTRA
1216 ARG   (1218-)  A      CD  <-> 1990 HOH   (1319 )  A      O      0.23    2.57  INTRA
1088 THR   (1090-)  A      OG1 <-> 1977 MD1   (1247-)  A      N17    0.22    2.48  INTRA BF
1816 HIS   (  66-)  C      NE2 <-> 1985 HEM   ( 807-)  C      ND     0.22    2.78  INTRA BF
 580 LYS   ( 582-)  A      NZ  <->  582 ARG   ( 584-)  A      NH1    0.22    2.63  INTRA BF
1816 HIS   (  66-)  C      CD2 <-> 1985 HEM   ( 807-)  C      NB     0.21    2.89  INTRA BF
 218 TYR   ( 220-)  A      CE1 <->  718 SER   ( 720-)  A      CB     0.21    2.99  INTRA BF
1800 LEU   (  50-)  C      CD1 <-> 1804 LEU   (  54-)  C      CD1    0.20    3.00  INTRA
And so on for a total of 303 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: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

   6 ARG   (   6-)  A      -7.00
1974 ARG   ( 224-)  C      -6.71
 598 ARG   ( 600-)  A      -6.56
 157 ARG   ( 159-)  A      -6.34
1319 ARG   (  77-)  B      -6.25
1826 MET   (  76-)  C      -6.19
1361 LYS   ( 119-)  B      -6.15
 862 LEU   ( 864-)  A      -6.05
1241 GLU   (1243-)  A      -5.96
1722 PHE   ( 480-)  B      -5.94
1612 GLU   ( 370-)  B      -5.92
1312 ILE   (  70-)  B      -5.80
 744 GLN   ( 746-)  A      -5.74
1795 ARG   (  45-)  C      -5.72
 711 ARG   ( 713-)  A      -5.69
 444 GLU   ( 446-)  A      -5.67
1110 ARG   (1112-)  A      -5.61
1320 MET   (  78-)  B      -5.59
 743 GLN   ( 745-)  A      -5.52
1613 LEU   ( 371-)  B      -5.51
1825 TRP   (  75-)  C      -5.49
 483 ARG   ( 485-)  A      -5.48
 733 GLU   ( 735-)  A      -5.44
  37 TRP   (  39-)  A      -5.42
  77 ARG   (  79-)  A      -5.38
1901 MET   ( 151-)  C      -5.38
 406 LYS   ( 408-)  A      -5.37
1060 ARG   (1062-)  A      -5.33
1830 TRP   (  80-)  C      -5.30
 930 TYR   ( 932-)  A      -5.23
 177 ASN   ( 179-)  A      -5.23
 747 VAL   ( 749-)  A      -5.16
1416 ASN   ( 174-)  B      -5.10
 343 ARG   ( 345-)  A      -5.09
 687 GLU   ( 689-)  A      -5.06
1178 ARG   (1180-)  A      -5.06
 152 ARG   ( 154-)  A      -5.06
1716 ASN   ( 474-)  B      -5.03

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.

1074 GLN   (1076-)  A      1076 - SER   1078- ( A)         -4.39
1176 GLN   (1178-)  A      1178 - ARG   1180- ( A)         -4.82
1824 HIS   (  74-)  C      1826 - MET     76- ( C)         -5.44
1899 GLN   ( 149-)  C      1901 - MET    151- ( C)         -4.90

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

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.

 937 ALA   ( 939-)  A   -2.98
1091 GLN   (1093-)  A   -2.63
 417 LEU   ( 419-)  A   -2.58

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  84 ASN   (  86-)  A
 126 HIS   ( 128-)  A
 177 ASN   ( 179-)  A
 243 ASN   ( 245-)  A
 402 GLN   ( 404-)  A
1402 ASN   ( 160-)  B
1536 GLN   ( 294-)  B
1803 ASN   (  53-)  C

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.

  27 ARG   (  29-)  A      N
  48 GLY   (  50-)  A      N
  49 VAL   (  51-)  A      N
  50 ASN   (  52-)  A      ND2
  54 SER   (  56-)  A      N
  55 CYS   (  57-)  A      N
  57 TRP   (  59-)  A      NE1
  68 TRP   (  70-)  A      NE1
  75 TYR   (  77-)  A      OH
  86 GLU   (  88-)  A      N
  88 ARG   (  90-)  A      NH1
  90 CYS   (  92-)  A      N
  96 TYR   (  98-)  A      OH
 101 TYR   ( 103-)  A      N
 108 TYR   ( 110-)  A      N
 112 ARG   ( 114-)  A      NH1
 153 GLY   ( 155-)  A      N
 181 ASP   ( 183-)  A      N
 189 ILE   ( 191-)  A      N
 191 ALA   ( 193-)  A      N
 193 SER   ( 195-)  A      OG
 210 THR   ( 212-)  A      OG1
 218 TYR   ( 220-)  A      OH
 232 GLN   ( 234-)  A      N
 252 SER   ( 254-)  A      N
And so on for a total of 217 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.

  85 HIS   (  87-)  A      NE2
 164 ASN   ( 166-)  A      OD1
 227 GLN   ( 229-)  A      OE1
 263 HIS   ( 265-)  A      NE2
 300 ASP   ( 302-)  A      OD2
 364 GLN   ( 366-)  A      OE1
 385 ASN   ( 387-)  A      OD1
 611 ASN   ( 613-)  A      OD1
 612 HIS   ( 614-)  A      ND1
1021 ASN   (1023-)  A      OD1
1054 GLU   (1056-)  A      OE1
1090 HIS   (1092-)  A      ND1
1194 HIS   (1196-)  A      ND1
1456 GLN   ( 214-)  B      OE1
1656 HIS   ( 414-)  B      ND1
1834 GLU   (  84-)  C      OE2
1837 GLN   (  87-)  C      OE1
1886 GLN   ( 136-)  C      OE1

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.

   5 ASP   (   5-)  A   H-bonding suggests Asn; but Alt-Rotamer
  69 GLU   (  71-)  A   H-bonding suggests Gln
 267 GLU   ( 269-)  A   H-bonding suggests Gln
 300 ASP   ( 302-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 333 ASP   ( 335-)  A   H-bonding suggests Asn
 446 GLU   ( 448-)  A   H-bonding suggests Gln
 794 ASP   ( 796-)  A   H-bonding suggests Asn
 887 GLU   ( 889-)  A   H-bonding suggests Gln
 959 GLU   ( 961-)  A   H-bonding suggests Gln
1218 GLU   (1220-)  A   H-bonding suggests Gln
1427 GLU   ( 185-)  B   H-bonding suggests Gln
1706 GLU   ( 464-)  B   H-bonding suggests Gln
1760 ASP   (  10-)  C   H-bonding suggests Asn
1928 ASP   ( 178-)  C   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.305
  2nd generation packing quality :  -1.975
  Ramachandran plot appearance   :  -2.268
  chi-1/chi-2 rotamer normality  :  -1.765
  Backbone conformation          :  -0.888

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.297 (tight)
  Bond angles                    :   0.637 (tight)
  Omega angle restraints         :   0.237 (tight)
  Side chain planarity           :   0.244 (tight)
  Improper dihedral distribution :   0.595
  B-factor distribution          :   0.442
  Inside/Outside distribution    :   1.103

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.297 (tight)
  Bond angles                    :   0.637 (tight)
  Omega angle restraints         :   0.237 (tight)
  Side chain planarity           :   0.244 (tight)
  Improper dihedral distribution :   0.595
  B-factor distribution          :   0.442
  Inside/Outside distribution    :   1.103
==============

WHAT IF
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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
    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.