WHAT IF Check report

This file was created 2012-01-05 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 pdb1q16.ent

Checks that need to be done early-on in validation

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected.

1991 HOH   (1448 )  A      O       3

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.

1978 MD1   (1300-)  A  -         OK
1980 SF4   (1401-)  A  -         Atom types
1981 SF4   (1402-)  B  -         Atom types
1982 SF4   (1403-)  B  -         Atom types
1983 SF4   (1404-)  B  -         Atom types
1984 F3S   (1405-)  B  -         Atom types
1987 3PH   (1310-)  C  -         OK
1988 AGA   (1309-)  C  -         OK
1989 MD1   (1301-)  A  -         OK
1990 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.

1754 GLN   (   2-)  C  -   N   bound to 1990 FME   (   1-)  C  -   C

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: 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: 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
   8 ARG   (   8-)  A
  29 ARG   (  29-)  A
  36 ARG   (  36-)  A
  38 ARG   (  38-)  A
  46 ARG   (  46-)  A
  79 ARG   (  79-)  A
 154 ARG   ( 154-)  A
 159 ARG   ( 159-)  A
 204 ARG   ( 204-)  A
 260 ARG   ( 260-)  A
 315 ARG   ( 315-)  A
 353 ARG   ( 353-)  A
 356 ARG   ( 356-)  A
 515 ARG   ( 515-)  A
 520 ARG   ( 520-)  A
 523 ARG   ( 523-)  A
 535 ARG   ( 535-)  A
 603 ARG   ( 603-)  A
 637 ARG   ( 637-)  A
 648 ARG   ( 648-)  A
 693 ARG   ( 693-)  A
 774 ARG   ( 774-)  A
 890 ARG   ( 890-)  A
 898 ARG   ( 898-)  A
And so on for a total of 57 lines.

Warning: Tyrosine convention problem

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

  35 TYR   (  35-)  A
  62 TYR   (  62-)  A
  77 TYR   (  77-)  A
 101 TYR   ( 101-)  A
 103 TYR   ( 103-)  A
 205 TYR   ( 205-)  A
 244 TYR   ( 244-)  A
 248 TYR   ( 248-)  A
 284 TYR   ( 284-)  A
 333 TYR   ( 333-)  A
 496 TYR   ( 496-)  A
 502 TYR   ( 502-)  A
 548 TYR   ( 548-)  A
 612 TYR   ( 612-)  A
 730 TYR   ( 730-)  A
 792 TYR   ( 792-)  A
1022 TYR   (1022-)  A
1026 TYR   (1026-)  A
1101 TYR   (1101-)  A
1206 TYR   (1206-)  A
1210 TYR   (1210-)  A
1282 TYR   (  38-)  B
1306 TYR   (  62-)  B
1345 TYR   ( 101-)  B
1413 TYR   ( 169-)  B
1423 TYR   ( 179-)  B
1446 TYR   ( 202-)  B
1513 TYR   ( 269-)  B
1575 TYR   ( 331-)  B
1659 TYR   ( 415-)  B
1688 TYR   ( 444-)  B
1690 TYR   ( 446-)  B
1780 TYR   (  28-)  C
1785 TYR   (  33-)  C
1964 TYR   ( 213-)  C
1969 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.

  10 PHE   (  10-)  A
  17 PHE   (  17-)  A
 148 PHE   ( 148-)  A
 266 PHE   ( 266-)  A
 317 PHE   ( 317-)  A
 326 PHE   ( 326-)  A
 377 PHE   ( 377-)  A
 434 PHE   ( 434-)  A
 525 PHE   ( 525-)  A
 563 PHE   ( 563-)  A
 594 PHE   ( 594-)  A
 611 PHE   ( 611-)  A
 773 PHE   ( 773-)  A
 805 PHE   ( 805-)  A
 899 PHE   ( 899-)  A
 977 PHE   ( 977-)  A
1138 PHE   (1138-)  A
1208 PHE   (1208-)  A
1221 PHE   (1221-)  A
1285 PHE   (  41-)  B
1348 PHE   ( 104-)  B
1350 PHE   ( 106-)  B
1544 PHE   ( 300-)  B
1722 PHE   ( 478-)  B
1738 PHE   ( 494-)  B
1760 PHE   (   8-)  C
1807 PHE   (  55-)  C
1815 PHE   (  63-)  C
1949 PHE   ( 198-)  C
1951 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
  42 ASP   (  42-)  A
 130 ASP   ( 130-)  A
 218 ASP   ( 218-)  A
 222 ASP   ( 222-)  A
 236 ASP   ( 236-)  A
 283 ASP   ( 283-)  A
 320 ASP   ( 320-)  A
 346 ASP   ( 346-)  A
 362 ASP   ( 362-)  A
 406 ASP   ( 406-)  A
 424 ASP   ( 424-)  A
 464 ASP   ( 464-)  A
 489 ASP   ( 489-)  A
 527 ASP   ( 527-)  A
 597 ASP   ( 597-)  A
 634 ASP   ( 634-)  A
 644 ASP   ( 644-)  A
 755 ASP   ( 755-)  A
 758 ASP   ( 758-)  A
 766 ASP   ( 766-)  A
 772 ASP   ( 772-)  A
 796 ASP   ( 796-)  A
 875 ASP   ( 875-)  A
1123 ASP   (1123-)  A
1126 ASP   (1126-)  A
1133 ASP   (1133-)  A
1239 ASP   (1239-)  A
1299 ASP   (  55-)  B
1342 ASP   (  98-)  B
1343 ASP   (  99-)  B
1351 ASP   ( 107-)  B
1391 ASP   ( 147-)  B
1457 ASP   ( 213-)  B
1459 ASP   ( 215-)  B
1520 ASP   ( 276-)  B
1522 ASP   ( 278-)  B
1535 ASP   ( 291-)  B
1542 ASP   ( 298-)  B
1549 ASP   ( 305-)  B
1623 ASP   ( 379-)  B
1670 ASP   ( 426-)  B
1726 ASP   ( 482-)  B
1732 ASP   ( 488-)  B
1762 ASP   (  10-)  C
1781 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.

  32 GLU   (  32-)  A
  88 GLU   (  88-)  A
 140 GLU   ( 140-)  A
 164 GLU   ( 164-)  A
 167 GLU   ( 167-)  A
 239 GLU   ( 239-)  A
 269 GLU   ( 269-)  A
 286 GLU   ( 286-)  A
 343 GLU   ( 343-)  A
 367 GLU   ( 367-)  A
 382 GLU   ( 382-)  A
 411 GLU   ( 411-)  A
 414 GLU   ( 414-)  A
 428 GLU   ( 428-)  A
 440 GLU   ( 440-)  A
 446 GLU   ( 446-)  A
 448 GLU   ( 448-)  A
 524 GLU   ( 524-)  A
 621 GLU   ( 621-)  A
 626 GLU   ( 626-)  A
 627 GLU   ( 627-)  A
 671 GLU   ( 671-)  A
 673 GLU   ( 673-)  A
 689 GLU   ( 689-)  A
 697 GLU   ( 697-)  A
And so on for a total of 51 lines.

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.259
RMS-deviation in bond distances: 0.006

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

 |  0.998780  0.000092 -0.000262|
 |  0.000092  0.998555 -0.000026|
 | -0.000262 -0.000026  0.998942|
Proposed new scale matrix

 |  0.006494  0.000000  0.000002|
 |  0.000000  0.004149  0.000000|
 |  0.000002  0.000000  0.007177|
With corresponding cell

    A    = 153.990  B   = 241.022  C    = 139.342
    Alpha=  90.002  Beta=  90.030  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 154.175  B   = 241.376  C    = 139.494
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 105.265
(Under-)estimated Z-score: 7.562

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.

  10 PHE   (  10-)  A      C    CA   CB  121.04    5.8
 362 ASP   ( 362-)  A      C    CA   CB  121.01    5.7
 501 ALA   ( 501-)  A      CA   C    O   110.71   -5.9
 501 ALA   ( 501-)  A      N    CA   CB  119.01    5.7
 502 TYR   ( 502-)  A     -CA  -C    N   124.32    4.1
 502 TYR   ( 502-)  A     -C    N    CA  146.96   14.0
 502 TYR   ( 502-)  A      N    CA   C   122.47    4.0
 502 TYR   ( 502-)  A      C    CA   CB  119.58    5.0
 502 TYR   ( 502-)  A      CA   CB   CG  127.49    7.3
 502 TYR   ( 502-)  A      CB   CG   CD1 127.11    4.2
 502 TYR   ( 502-)  A      CB   CG   CD2 114.49   -4.2
 583 LEU   ( 583-)  A      N    CA   C    99.52   -4.2
 808 PRO   ( 808-)  A      N    CA   C   123.59    4.7
 809 LEU   ( 809-)  A      N    CA   C    96.02   -5.4
 863 PRO   ( 863-)  A      N    CA   C   121.95    4.1
1016 GLU   (1016-)  A      N    CA   C    99.40   -4.2
1035 TRP   (1035-)  A      N    CA   C    99.46   -4.2
1097 ILE   (1097-)  A      N    CA   C    98.20   -4.6
1149 VAL   (1149-)  A      N    CA   C    98.94   -4.4
1164 ALA   (1164-)  A     -O   -C    N   109.13   -8.7
1164 ALA   (1164-)  A     -C    N    CA  155.04   18.5
1164 ALA   (1164-)  A      N    CA   CB  117.49    4.7
1274 TRP   (  30-)  B      N    CA   C   123.56    4.4
1623 ASP   ( 379-)  B      N    CA   C    99.56   -4.2

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.632
RMS-deviation in bond angles: 1.386

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
   8 ARG   (   8-)  A
  29 ARG   (  29-)  A
  32 GLU   (  32-)  A
  36 ARG   (  36-)  A
  38 ARG   (  38-)  A
  42 ASP   (  42-)  A
  46 ARG   (  46-)  A
  79 ARG   (  79-)  A
  88 GLU   (  88-)  A
 130 ASP   ( 130-)  A
 140 GLU   ( 140-)  A
 154 ARG   ( 154-)  A
 159 ARG   ( 159-)  A
 164 GLU   ( 164-)  A
 167 GLU   ( 167-)  A
 204 ARG   ( 204-)  A
 218 ASP   ( 218-)  A
 222 ASP   ( 222-)  A
 236 ASP   ( 236-)  A
 239 GLU   ( 239-)  A
 260 ARG   ( 260-)  A
 269 GLU   ( 269-)  A
 283 ASP   ( 283-)  A
And so on for a total of 154 lines.

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.

 501 ALA   ( 501-)  A      CA    -9.5    22.08    34.09
 501 ALA   ( 501-)  A      C     -9.1   -13.81     0.08
 502 TYR   ( 502-)  A      CA   -13.8    12.16    34.03
1164 ALA   (1164-)  A      CA    -8.5    23.28    34.09
The average deviation= 0.701

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.

1274 TRP   (  30-)  B    6.45
 607 SER   ( 607-)  A    5.97
 809 LEU   ( 809-)  A    5.81
1638 LEU   ( 394-)  B    5.50
 808 PRO   ( 808-)  A    5.34
 256 VAL   ( 256-)  A    5.05
1344 TYR   ( 100-)  B    4.86
 583 LEU   ( 583-)  A    4.76
1959 SER   ( 208-)  C    4.68
1357 THR   ( 113-)  B    4.64
 586 GLN   ( 586-)  A    4.58
 316 GLU   ( 316-)  A    4.54
1035 TRP   (1035-)  A    4.53
1149 VAL   (1149-)  A    4.46
1603 LEU   ( 359-)  B    4.42
 333 TYR   ( 333-)  A    4.41
 101 TYR   ( 101-)  A    4.38
1865 PHE   ( 114-)  C    4.37
1719 GLY   ( 475-)  B    4.34
 502 TYR   ( 502-)  A    4.29
 261 THR   ( 261-)  A    4.22
1016 GLU   (1016-)  A    4.11
1664 THR   ( 420-)  B    4.09
1097 ILE   (1097-)  A    4.07
 730 TYR   ( 730-)  A    4.02
  74 GLN   (  74-)  A    4.02
 196 MET   ( 196-)  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.

   9 TYR   (   9-)  A    -3.6
 190 PRO   ( 190-)  A    -3.1
 224 PRO   ( 224-)  A    -3.0
 804 PRO   ( 804-)  A    -2.9
  48 THR   (  48-)  A    -2.8
 601 PRO   ( 601-)  A    -2.7
 533 HIS   ( 533-)  A    -2.7
1367 ILE   ( 123-)  B    -2.6
1006 ILE   (1006-)  A    -2.6
1490 PHE   ( 246-)  B    -2.6
1405 PHE   ( 161-)  B    -2.6
 808 PRO   ( 808-)  A    -2.6
 390 ILE   ( 390-)  A    -2.5
1032 LEU   (1032-)  A    -2.5
  89 PRO   (  89-)  A    -2.5
1867 PRO   ( 116-)  C    -2.5
 221 CYS   ( 221-)  A    -2.4
 936 GLU   ( 936-)  A    -2.4
1144 LEU   (1144-)  A    -2.4
 767 LEU   ( 767-)  A    -2.3
1427 LEU   ( 183-)  B    -2.3
 235 THR   ( 235-)  A    -2.3
 322 PRO   ( 322-)  A    -2.3
1172 PRO   (1172-)  A    -2.3
 195 SER   ( 195-)  A    -2.2
 920 THR   ( 920-)  A    -2.2
  54 THR   (  54-)  A    -2.2
 402 LEU   ( 402-)  A    -2.2
 578 VAL   ( 578-)  A    -2.2
 260 ARG   ( 260-)  A    -2.2
 348 TYR   ( 348-)  A    -2.2
 319 LEU   ( 319-)  A    -2.1
 384 VAL   ( 384-)  A    -2.1
 461 GLN   ( 461-)  A    -2.1
1703 PRO   ( 459-)  B    -2.1
 502 TYR   ( 502-)  A    -2.1
1955 ILE   ( 204-)  C    -2.1
1341 ILE   (  97-)  B    -2.1
1211 TYR   (1211-)  A    -2.1
 287 ILE   ( 287-)  A    -2.0
1465 ARG   ( 221-)  B    -2.0
  56 SER   (  56-)  A    -2.0
1110 LEU   (1110-)  A    -2.0
1571 GLN   ( 327-)  B    -2.0
  71 GLU   (  71-)  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.

  43 LYS   (  43-)  A  Poor phi/psi
  54 THR   (  54-)  A  Poor phi/psi
  65 ASN   (  65-)  A  Poor phi/psi
  88 GLU   (  88-)  A  PRO omega poor
  90 ARG   (  90-)  A  Poor phi/psi
 160 SER   ( 160-)  A  Poor phi/psi
 191 ILE   ( 191-)  A  Poor phi/psi
 221 CYS   ( 221-)  A  Poor phi/psi
 235 THR   ( 235-)  A  Poor phi/psi
 361 VAL   ( 361-)  A  Poor phi/psi
 364 LEU   ( 364-)  A  Poor phi/psi
 422 SER   ( 422-)  A  Poor phi/psi
 447 LEU   ( 447-)  A  Poor phi/psi
 488 ASN   ( 488-)  A  Poor phi/psi
 501 ALA   ( 501-)  A  omega poor
 533 HIS   ( 533-)  A  Poor phi/psi
 578 VAL   ( 578-)  A  Poor phi/psi
 585 PRO   ( 585-)  A  Poor phi/psi
 600 ARG   ( 600-)  A  PRO omega poor
 658 ALA   ( 658-)  A  PRO omega poor
 713 ARG   ( 713-)  A  Poor phi/psi
 718 GLY   ( 718-)  A  Poor phi/psi
 719 SER   ( 719-)  A  Poor phi/psi
 817 TRP   ( 817-)  A  Poor phi/psi
 855 ASP   ( 855-)  A  Poor phi/psi
And so on for a total of 57 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.

 834 SER   ( 834-)  A    0.35
 137 SER   ( 137-)  A    0.38

Warning: Unusual backbone conformations

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

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

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

   9 TYR   (   9-)  A      0
  15 GLU   (  15-)  A      0
  17 PHE   (  17-)  A      0
  18 ALA   (  18-)  A      0
  19 ASP   (  19-)  A      0
  21 HIS   (  21-)  A      0
  28 ASN   (  28-)  A      0
  29 ARG   (  29-)  A      0
  42 ASP   (  42-)  A      0
  46 ARG   (  46-)  A      0
  52 ASN   (  52-)  A      0
  53 CYS   (  53-)  A      0
  54 THR   (  54-)  A      0
  69 THR   (  69-)  A      0
  70 TRP   (  70-)  A      0
  75 THR   (  75-)  A      0
  76 ASP   (  76-)  A      0
  77 TYR   (  77-)  A      0
  79 ARG   (  79-)  A      0
  87 HIS   (  87-)  A      0
  88 GLU   (  88-)  A      0
  89 PRO   (  89-)  A      0
  90 ARG   (  90-)  A      0
 102 LEU   ( 102-)  A      0
 103 TYR   ( 103-)  A      0
And so on for a total of 790 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 : 1.405

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].

  85 PRO   (  85-)  A  -113.4 envelop C-gamma (-108 degrees)
 190 PRO   ( 190-)  A   -63.3 envelop C-beta (-72 degrees)
 808 PRO   ( 808-)  A   -62.8 half-chair C-beta/C-alpha (-54 degrees)
1867 PRO   ( 116-)  C  -115.0 envelop C-gamma (-108 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.

1754 GLN   (   2-)  C      N   <-> 1990 FME   (   1-)  C      C      1.36    1.34  INTRA B3
1978 MD1   (1300-)  A      S12 <-> 1989 MD1   (1301-)  A      S13    0.93    2.67  INTRA
1754 GLN   (   2-)  C      CA  <-> 1990 FME   (   1-)  C      C      0.76    2.44  INTRA
1978 MD1   (1300-)  A      S13 <-> 1989 MD1   (1301-)  A      S12    0.57    3.03  INTRA
1098 HIS   (1098-)  A      CE1 <-> 1989 MD1   (1301-)  A      S13    0.52    2.88  INTRA
1098 HIS   (1098-)  A      CE1 <-> 1978 MD1   (1300-)  A      S12    0.51    2.89  INTRA
1082 GLN   (1082-)  A      NE2 <-> 1991 HOH   (1629 )  A      O      0.36    2.34  INTRA
 619 ARG   ( 619-)  A      NH1 <-> 1991 HOH   (1939 )  A      O      0.31    2.39  INTRA
 791 TRP   ( 791-)  A      NE1 <-> 1978 MD1   (1300-)  A      N7     0.31    2.69  INTRA BL
  52 ASN   (  52-)  A      ND2 <-> 1978 MD1   (1300-)  A      S12    0.30    3.00  INTRA
 586 GLN   ( 586-)  A      NE2 <->  590 GLN   ( 590-)  A      CG     0.24    2.86  INTRA
 641 HIS   ( 641-)  A      ND1 <->  642 LEU   ( 642-)  A      N      0.23    2.67  INTRA
1818 HIS   (  66-)  C      CD2 <-> 1986 HEM   ( 807-)  C      NB     0.22    2.88  INTRA
1428 CYS   ( 184-)  B      SG  <-> 1487 LYS   ( 243-)  B      NZ     0.22    3.08  INTRA BL
 378 ASN   ( 378-)  A      ND2 <->  382 GLU   ( 382-)  A      CB     0.21    2.89  INTRA BF
1818 HIS   (  66-)  C      NE2 <-> 1986 HEM   ( 807-)  C      ND     0.21    2.79  INTRA
 641 HIS   ( 641-)  A      ND1 <->  643 ILE   ( 643-)  A      N      0.20    2.80  INTRA
1808 HIS   (  56-)  C      NE2 <-> 1985 HEM   ( 806-)  C      NA     0.20    2.80  INTRA BL
 366 GLN   ( 366-)  A      CG  <->  373 LYS   ( 373-)  A      NZ     0.18    2.92  INTRA
1006 ILE   (1006-)  A      CD1 <-> 1016 GLU   (1016-)  A      CD     0.18    3.02  INTRA
 190 PRO   ( 190-)  A      O   <->  713 ARG   ( 713-)  A      NH1    0.18    2.52  INTRA
1818 HIS   (  66-)  C      NE2 <-> 1986 HEM   ( 807-)  C      NA     0.18    2.82  INTRA
1956 HIS   ( 205-)  C      NE2 <-> 1985 HEM   ( 806-)  C      ND     0.17    2.83  INTRA BL
1381 LYS   ( 137-)  B      NZ  <-> 1992 HOH   (1491 )  B      O      0.17    2.53  INTRA BL
 498 ASP   ( 498-)  A      OD2 <->  500 LYS   ( 500-)  A      NZ     0.17    2.53  INTRA
And so on for a total of 251 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.

 600 ARG   ( 600-)  A      -6.99
1975 ARG   ( 224-)  C      -6.68
1321 ARG   (  77-)  B      -6.40
 864 LEU   ( 864-)  A      -6.14
1243 GLU   (1243-)  A      -6.04
 159 ARG   ( 159-)  A      -6.03
1614 GLU   ( 370-)  B      -5.95
1363 LYS   ( 119-)  B      -5.93
1314 ILE   (  70-)  B      -5.81
1724 PHE   ( 480-)  B      -5.77
1797 ARG   (  45-)  C      -5.77
 713 ARG   ( 713-)  A      -5.68
1322 MET   (  78-)  B      -5.65
 446 GLU   ( 446-)  A      -5.64
1112 ARG   (1112-)  A      -5.63
1062 ARG   (1062-)  A      -5.45
  39 TRP   (  39-)  A      -5.43
1615 LEU   ( 371-)  B      -5.34
 932 TYR   ( 932-)  A      -5.32
1019 HIS   (1019-)  A      -5.24
 735 GLU   ( 735-)  A      -5.23
 179 ASN   ( 179-)  A      -5.23
 408 LYS   ( 408-)  A      -5.22
  79 ARG   (  79-)  A      -5.22
 485 ARG   ( 485-)  A      -5.20
  12 GLN   (  12-)  A      -5.19
 749 VAL   ( 749-)  A      -5.18
 931 ASN   ( 931-)  A      -5.17
1902 MET   ( 151-)  C      -5.14
1827 TRP   (  75-)  C      -5.14
 569 GLN   ( 569-)  A      -5.09
1418 ASN   ( 174-)  B      -5.06
 689 GLU   ( 689-)  A      -5.06
1718 ASN   ( 474-)  B      -5.04
1274 TRP   (  30-)  B      -5.03
 936 GLU   ( 936-)  A      -5.01
1900 GLN   ( 149-)  C      -5.01

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.

1076 GLN   (1076-)  A      1078 - SER   1078- ( A)         -4.30
1178 GLN   (1178-)  A      1180 - ARG   1180- ( A)         -4.75
1900 GLN   ( 149-)  C      1902 - MET    151- ( C)         -4.91

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.

 102 LEU   ( 102-)  A   -2.75
 419 LEU   ( 419-)  A   -2.65
1183 ILE   (1183-)  A   -2.62
1081 ASN   (1081-)  A   -2.57
1093 GLN   (1093-)  A   -2.55
1955 ILE   ( 204-)  C   -2.53

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

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.

1991 HOH   (1732 )  A      O   -164.52  -67.98  -18.21
1991 HOH   (1951 )  A      O   -180.33  -46.62   -5.41
1991 HOH   (1968 )  A      O   -182.93  -45.33   -5.41
1992 HOH   (1425 )  B      O   -134.48  -32.89  -22.87
1992 HOH   (1780 )  B      O   -121.57  -37.98  -27.91

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.

1991 HOH   (2038 )  A      O
1991 HOH   (2059 )  A      O
1991 HOH   (2100 )  A      O
1992 HOH   (1753 )  B      O
1993 HOH   ( 871 )  C      O
Metal-coordinating Histidine residue  49 fixed to   1
Metal-coordinating Histidine residue1808 fixed to   1
Metal-coordinating Histidine residue1956 fixed to   1
Metal-coordinating Histidine residue1818 fixed to   1
Metal-coordinating Histidine residue1938 fixed to   1

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.

  74 GLN   (  74-)  A
  86 ASN   (  86-)  A
 179 ASN   ( 179-)  A
 245 ASN   ( 245-)  A
 369 ASN   ( 369-)  A
 404 GLN   ( 404-)  A
 559 ASN   ( 559-)  A
 704 ASN   ( 704-)  A
 919 ASN   ( 919-)  A
 942 GLN   ( 942-)  A
1076 GLN   (1076-)  A
1404 ASN   ( 160-)  B
1415 GLN   ( 171-)  B
1538 GLN   ( 294-)  B
1695 ASN   ( 451-)  B
1805 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.

  50 GLY   (  50-)  A      N
  52 ASN   (  52-)  A      ND2
  57 CYS   (  57-)  A      N
  59 TRP   (  59-)  A      NE1
  70 TRP   (  70-)  A      NE1
  77 TYR   (  77-)  A      N
  92 CYS   (  92-)  A      N
  98 TYR   (  98-)  A      OH
 191 ILE   ( 191-)  A      N
 212 THR   ( 212-)  A      OG1
 254 SER   ( 254-)  A      N
 255 ASN   ( 255-)  A      N
 256 VAL   ( 256-)  A      N
 259 THR   ( 259-)  A      OG1
 260 ARG   ( 260-)  A      NH2
 271 ARG   ( 271-)  A      N
 300 GLY   ( 300-)  A      N
 302 ASP   ( 302-)  A      N
 394 TRP   ( 394-)  A      N
 399 LYS   ( 399-)  A      N
 448 GLU   ( 448-)  A      N
 502 TYR   ( 502-)  A      N
 536 SER   ( 536-)  A      N
 542 ALA   ( 542-)  A      N
 567 VAL   ( 567-)  A      N
And so on for a total of 121 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.

 366 GLN   ( 366-)  A      OE1
 604 HIS   ( 604-)  A      ND1
1023 ASN   (1023-)  A      OD1
1092 HIS   (1092-)  A      ND1
1098 HIS   (1098-)  A      ND1
1163 HIS   (1163-)  A      NE2
1887 GLN   ( 136-)  C      OE1

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.

1991 HOH   (1462 )  A      O  0.84  K  5 *2
1991 HOH   (1481 )  A      O  1.10  K  4 *2
1991 HOH   (1512 )  A      O  0.83  K  5 *2
1991 HOH   (1534 )  A      O  0.99  K  4 *2
1991 HOH   (1654 )  A      O  1.03  K  4 *2
1991 HOH   (1693 )  A      O  0.95  K  4 *2
1991 HOH   (1732 )  A      O  0.97  K  4 *2 Ion-B
1991 HOH   (1850 )  A      O  1.15  K  4 *2 Ion-B
1991 HOH   (1867 )  A      O  0.94  K  4 *2 Ion-B H2O-B
1991 HOH   (1868 )  A      O  0.83  K  4 *2 Ion-B
1992 HOH   (1425 )  B      O  1.16  K  4 *2
1992 HOH   (1442 )  B      O  1.10  K  4 *2
1992 HOH   (1522 )  B      O  1.06  K  4 *2
1992 HOH   (1540 )  B      O  1.08  K  4 *2
1992 HOH   (1549 )  B      O  1.15  K  4 *2
1992 HOH   (1558 )  B      O  1.03  K  4 *2
1992 HOH   (1652 )  B      O  1.00  K  4 *2 Ion-B
1992 HOH   (1714 )  B      O  0.87  K  4 *2 ION-B
1992 HOH   (1795 )  B      O  0.78  K  4 *2 ION-B H2O-B

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
  71 GLU   (  71-)  A   H-bonding suggests Gln
 233 GLU   ( 233-)  A   H-bonding suggests Gln
 269 GLU   ( 269-)  A   H-bonding suggests Gln; but Alt-Rotamer
 302 ASP   ( 302-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 335 ASP   ( 335-)  A   H-bonding suggests Asn
 448 GLU   ( 448-)  A   H-bonding suggests Gln
 925 ASP   ( 925-)  A   H-bonding suggests Asn
 961 GLU   ( 961-)  A   H-bonding suggests Gln
1220 GLU   (1220-)  A   H-bonding suggests Gln
1406 ASP   ( 162-)  B   H-bonding suggests Asn; but Alt-Rotamer
1429 GLU   ( 185-)  B   H-bonding suggests Gln
1542 ASP   ( 298-)  B   H-bonding suggests Asn
1762 ASP   (  10-)  C   H-bonding suggests Asn
1929 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 :  -1.050
  2nd generation packing quality :  -1.928
  Ramachandran plot appearance   :  -1.187
  chi-1/chi-2 rotamer normality  :  -0.801
  Backbone conformation          :  -0.898

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.259 (tight)
  Bond angles                    :   0.632 (tight)
  Omega angle restraints         :   0.255 (tight)
  Side chain planarity           :   0.247 (tight)
  Improper dihedral distribution :   0.653
  B-factor distribution          :   0.681
  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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.259 (tight)
  Bond angles                    :   0.632 (tight)
  Omega angle restraints         :   0.255 (tight)
  Side chain planarity           :   0.247 (tight)
  Improper dihedral distribution :   0.653
  B-factor distribution          :   0.681
  Inside/Outside distribution    :   1.103
==============

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.