WHAT IF Check report

This file was created 2011-12-17 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 pdb1ncd.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 91692.602
Volume of the Unit Cell V= 3458056.3
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.714
Vm by authors and this calculated Vm agree remarkably well
Matthews coefficient read from REMARK 280 Vm= 4.740

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 833 MAN   ( 472-)  N  -
 834 MAN   ( 473-)  N  -
 836 MAN   ( 474-)  N  -
 837 BMA   ( 471-)  N  -

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.

 825 NAG   ( 469A)  N  -   O4  bound to  826 NAG   ( 470B)  N  -   C1
 826 NAG   ( 470B)  N  -   O4  bound to  837 BMA   ( 471-)  N  -   C1
 828 NAG   ( 476A)  N  -   O4  bound to  829 NAG   ( 477B)  N  -   C1

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: N

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: H

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:

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.

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 21.83

Note: B-factor plot

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

Chain identifier: N

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: H

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

   1 ILE   (  81-)  N      CA   CB    1.62    4.7
   3 GLU   (  83-)  N      CA   CB    1.44   -4.3
  77 ASP   ( 157-)  N      CB   CG    1.64    4.8
 125 VAL   ( 204-)  N      CA   CB    1.63    5.0
 208 VAL   ( 287-)  N      CA   CB    1.63    5.2
 232 THR   ( 311-)  N      CA   CB    1.45   -4.1
 318 LEU   ( 399-)  N      CB   CG    1.45   -4.2
 359 TRP   ( 438-)  N      CD1  NE1   1.28   -4.4
 378 ASN   ( 457-)  N      CG   ND2   1.21   -5.5
 379 TRP   ( 458-)  N      NE1  CE2   1.32   -4.3
 424 TRP   (  35-)  L      NE1  CE2   1.32   -4.4
 445 ILE   (  56-)  L      CA   CB    1.63    5.2
 447 VAL   (  58-)  L      CA   CB    1.61    4.1
 480 HIS   (  91-)  L      CD2  NE2   1.29   -4.2
 486 THR   (  97-)  L      CA   CB    1.63    4.9
 591 THR   ( 202-)  L      CA   CB    1.63    5.1
 653 TRP   (  50-)  H      CG   CD2   1.36   -4.2
 764 TRP   ( 157-)  H      CG   CD2   1.36   -4.2

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.002863 -0.000091  0.000295|
 | -0.000091  1.002660 -0.000628|
 |  0.000295 -0.000628  1.003170|
Proposed new scale matrix

 |  0.005971  0.000000 -0.000002|
 |  0.000000  0.005972  0.000004|
 | -0.000002  0.000005  0.008040|
With corresponding cell

    A    = 167.479  B   = 167.445  C    = 124.386
    Alpha=  90.072  Beta=  89.966  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 167.000  B   = 167.000  C    = 124.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 233.260
(Under-)estimated Z-score: 11.256

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.

   1 ILE   (  81-)  N      N    CA   C    99.44   -4.2
   1 ILE   (  81-)  N      CB   CG1  CD1 124.07    4.9
   3 GLU   (  83-)  N      N    CA   CB  101.68   -5.2
   5 ASN   (  85-)  N      ND2  CG   OD1 118.26   -4.3
  14 ILE   (  94-)  N      CA   CB   CG2 101.94   -5.0
  14 ILE   (  94-)  N      CA   CB   CG1 118.44    4.7
  17 TRP   (  97-)  N      CB   CG   CD1 118.96   -5.3
  17 TRP   (  97-)  N      CE3  CD2  CG  140.61    6.7
  17 TRP   (  97-)  N      CG   CD2  CE2 100.96   -5.2
  19 ILE   (  99-)  N     -CA  -C    N   124.87    4.3
  19 ILE   (  99-)  N      N    CA   CB  121.18    6.3
  19 ILE   (  99-)  N      C    CA   CB   99.54   -5.6
  20 TYR   ( 100-)  N     -CA  -C    N   106.24   -5.0
  21 GLY   ( 101-)  N     -CA  -C    N   124.34    4.1
  23 ASP   ( 103-)  N      CA   CB   CG  118.70    6.1
  26 VAL   ( 106-)  N      CG1  CB   CG2 101.38   -4.3
  29 GLY   ( 109-)  N     -C    N    CA  128.36    4.6
  31 ASP   ( 111-)  N      CA   CB   CG  116.87    4.3
  38 ARG   ( 118-)  N      CA   CB   CG  123.77    4.8
  41 TYR   ( 121-)  N      CA   CB   CG  122.24    4.5
  45 ASP   ( 125-)  N      CA   CB   CG  119.31    6.7
  47 ASP   ( 127-)  N      N    CA   CB  100.69   -5.8
  47 ASP   ( 127-)  N      CA   CB   CG  117.62    5.0
  48 GLU   ( 128-)  N      CA   CB   CG  122.87    4.4
  49 CYS   ( 129-)  N     -CA  -C    N   126.14    5.0
And so on for a total of 342 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.

  26 VAL   ( 106-)  N      CB    -6.4   -41.34   -32.96
 125 VAL   ( 204-)  N      C     -6.8    -9.16     0.15
 143 ILE   ( 222-)  N      CB     6.4    40.68    32.31
 175 ILE   ( 254-)  N      CB     6.2    40.37    32.31
 445 ILE   (  56-)  L      C     -7.4    -9.72     0.03
 640 VAL   (  37-)  H      CB    -7.7   -43.04   -32.96
The average deviation= 1.607

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.

 147 GLN   ( 226-)  N    6.84
 558 LYS   ( 169-)  L    6.15
 642 GLN   (  39-)  H    5.35
 785 TYR   ( 185-)  H    5.25
 769 LEU   ( 166-)  H    5.19
 823 ARG   ( 226-)  H    4.92
  25 ALA   ( 105-)  N    4.74
 583 CYS   ( 194-)  L    4.70
 198 GLU   ( 277-)  N    4.69
  95 GLU   ( 174-)  N    4.68
 214 ASP   ( 293-)  N    4.63
 820 ILE   ( 223-)  H    4.58
 715 GLN   ( 105-)  H    4.57
 188 PRO   ( 267-)  N    4.45
 274 TYR   ( 354-)  N    4.29
 144 LEU   ( 223-)  N    4.22
 434 LYS   (  45-)  L    4.15
 699 CYS   (  92-)  H    4.03
 527 ASN   ( 138-)  L    4.02

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.875

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 378 ASN   ( 457-)  N   11.03
 142 ASN   ( 221-)  N    4.96

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.

 742 THR   ( 134-)  H    -3.5
 757 PRO   ( 149-)  H    -3.0
 759 PRO   ( 151-)  H    -2.9
 712 TYR   ( 102-)  H    -2.9
  40 PRO   ( 120-)  N    -2.9
 466 SER   (  77-)  L    -2.6
 307 ARG   ( 387-)  N    -2.6
  38 ARG   ( 118-)  N    -2.6
 784 LEU   ( 184-)  H    -2.6
 766 SER   ( 163-)  H    -2.6
 680 SER   (  76-)  H    -2.6
 419 SER   (  30-)  L    -2.6
 741 THR   ( 133-)  H    -2.5
 591 THR   ( 202-)  L    -2.5
 284 ARG   ( 364-)  N    -2.5
 143 ILE   ( 222-)  N    -2.4
 677 THR   (  73-)  H    -2.4
 497 ARG   ( 108-)  L    -2.4
 174 ARG   ( 253-)  N    -2.4
 172 GLU   ( 251-)  N    -2.4
 391 ILE   (   2-)  L    -2.4
 439 TRP   (  50-)  L    -2.4
  68 THR   ( 148-)  N    -2.4
 145 ARG   ( 224-)  N    -2.4
 765 ASN   ( 162-)  H    -2.3
And so on for a total of 77 lines.

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.

  38 ARG   ( 118-)  N  Poor phi/psi
  39 GLU   ( 119-)  N  Poor phi/psi
  41 TYR   ( 121-)  N  Poor phi/psi
  67 GLY   ( 147-)  N  Poor phi/psi
  84 SER   ( 164-)  N  Poor phi/psi
  91 ASN   ( 170-)  N  Poor phi/psi
  96 CYS   ( 175-)  N  Poor phi/psi
 117 GLY   ( 196-)  N  PRO omega poor
 129 ASN   ( 208-)  N  Poor phi/psi
 148 GLU   ( 227-)  N  Poor phi/psi
 155 ASN   ( 234-)  N  Poor phi/psi
 169 GLY   ( 248-)  N  PRO omega poor
 178 PHE   ( 257-)  N  omega poor
 181 GLY   ( 260-)  N  Poor phi/psi
 198 GLU   ( 277-)  N  Poor phi/psi
 212 CYS   ( 291-)  N  Poor phi/psi
 216 TRP   ( 295-)  N  Poor phi/psi
 246 ASN   ( 325-)  N  PRO omega poor
 248 ARG   ( 327-)  N  PRO omega poor
 266 ASN   ( 346-)  N  Poor phi/psi
 323 SER   ( 404-)  N  Poor phi/psi
 351 ARG   ( 430-)  N  PRO omega poor
 378 ASN   ( 457-)  N  omega poor
 396 SER   (   7-)  L  PRO omega poor
 420 THR   (  31-)  L  Poor phi/psi
And so on for a total of 53 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -5.048

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 LYS   (  89-)  N      0
  15 ASN   (  95-)  N      0
  16 SER   (  96-)  N      0
  31 ASP   ( 111-)  N      0
  32 SER   ( 112-)  N      0
  33 ASP   ( 113-)  N      0
  38 ARG   ( 118-)  N      0
  39 GLU   ( 119-)  N      0
  40 PRO   ( 120-)  N      0
  41 TYR   ( 121-)  N      0
  47 ASP   ( 127-)  N      0
  48 GLU   ( 128-)  N      0
  56 GLN   ( 136-)  N      0
  64 HIS   ( 144-)  N      0
  66 ASN   ( 146-)  N      0
  68 THR   ( 148-)  N      0
  69 ILE   ( 149-)  N      0
  70 HIS   ( 150-)  N      0
  72 ARG   ( 152-)  N      0
  76 ARG   ( 156-)  N      0
  81 TRP   ( 161-)  N      0
  83 LEU   ( 163-)  N      0
  84 SER   ( 164-)  N      0
  88 THR   ( 168-)  N      0
  90 TYR   ( 169-)  N      0
And so on for a total of 413 lines.

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!

 430 GLY   (  41-)  L   1.53   11

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...

 632 PHE   (  29-)  H   1.89

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]

 188 PRO   ( 267-)  N    0.49 HIGH
 300 PRO   ( 380-)  N    0.46 HIGH
 310 PRO   ( 390-)  N    0.49 HIGH
 380 PRO   ( 459-)  N    0.02 LOW
 397 PRO   (   8-)  L    0.47 HIGH
 483 PRO   (  94-)  L    0.48 HIGH
 508 PRO   ( 119-)  L    0.51 HIGH
 530 PRO   ( 141-)  L    0.46 HIGH
 593 PRO   ( 204-)  L    0.46 HIGH
 644 PRO   (  41-)  H    0.47 HIGH
 759 PRO   ( 151-)  H    0.46 HIGH
 822 PRO   ( 225-)  H    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].

  40 PRO   ( 120-)  N   -58.1 half-chair C-beta/C-alpha (-54 degrees)
  46 PRO   ( 126-)  N  -113.8 envelop C-gamma (-108 degrees)
  82 PRO   ( 162-)  N  -122.7 half-chair C-delta/C-gamma (-126 degrees)
 247 PRO   ( 326-)  N    43.3 envelop C-delta (36 degrees)
 260 PRO   ( 340-)  N  -125.1 half-chair C-delta/C-gamma (-126 degrees)
 484 PRO   (  95-)  L   -43.8 envelop C-alpha (-36 degrees)
 661 PRO   (  57-)  H   -11.4 half-chair C-alpha/N (-18 degrees)
 729 PRO   ( 119-)  H   -54.0 half-chair C-beta/C-alpha (-54 degrees)
 757 PRO   ( 149-)  H   -50.1 half-chair C-beta/C-alpha (-54 degrees)
 759 PRO   ( 151-)  H   -62.8 half-chair C-beta/C-alpha (-54 degrees)
 799 PRO   ( 200-)  H    51.4 half-chair C-delta/C-gamma (54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

 834 MAN   ( 473-)  N      O2   <->   836 MAN   ( 474-)  N      C1   0.99    1.41  INTRA B3
 826 NAG   ( 470-)  N      O4   <->   837 BMA   ( 471-)  N      C1   0.97    1.43  INTRA B3
 826 NAG   ( 470-)  N      C4   <->   837 BMA   ( 471-)  N      C1   0.73    2.47  INTRA
 834 MAN   ( 473-)  N      C2   <->   836 MAN   ( 474-)  N      C1   0.71    2.49  INTRA
 312 GLN   ( 392-)  N      NE2  <->   373 PHE   ( 452-)  N      CE2  0.27    2.83  INTRA BL
 349 ARG   ( 428-)  N      NH1  <->   381 ASP   ( 460-)  N      OD2  0.23    2.47  INTRA BL
 384 LYS   ( 463-)  N      C    <->   386 GLU   ( 465-)  N      N    0.18    2.72  INTRA
 609 GLN   (   6-)  H      NE2  <->   699 CYS   (  92-)  H      SG   0.17    3.13  INTRA
 448 PRO   (  59-)  L      O    <->   450 ARG   (  61-)  L      N    0.16    2.54  INTRA
 379 TRP   ( 458-)  N      CA   <->   380 PRO   ( 459-)  N      CD   0.15    2.65  INTRA BL
 384 LYS   ( 463-)  N      O    <->   386 GLU   ( 465-)  N      N    0.14    2.56  INTRA
  17 TRP   (  97-)  N      N    <->   314 GLN   ( 395-)  N      NE2  0.12    2.73  INTRA BL
  88 THR   ( 168-)  N      CB   <->    91 ASN   ( 170-)  N      ND2  0.12    2.98  INTRA
 177 TYR   ( 256-)  N      O    <->   184 LEU   ( 263-)  N      N    0.11    2.59  INTRA BL
 349 ARG   ( 428-)  N      O    <->   361 SER   ( 440-)  N      N    0.11    2.59  INTRA BL
 379 TRP   ( 458-)  N      NE1  <->   838 HOH   ( 537 )  N      O    0.10    2.60  INTRA
 391 ILE   (   2-)  L      CD1  <->   479 GLN   (  90-)  L      NE2  0.10    3.00  INTRA
 427 GLN   (  38-)  L      OE1  <->   642 GLN   (  39-)  H      NE2  0.10    2.60  INTRA
 526 ASN   ( 137-)  L      ND2  <->   774 HIS   ( 172-)  H      CD2  0.10    3.00  INTRA
 733 PRO   ( 123-)  H      CD   <->   818 LYS   ( 221-)  H      NZ   0.10    3.00  INTRA
  66 ASN   ( 146-)  N      ND2  <->   828 NAG   ( 476-)  N      C7   0.09    3.01  INTRA BF
 220 ASN   ( 299-)  N      OD1  <->   261 TYR   ( 341-)  N      N    0.09    2.61  INTRA
 394 THR   (   5-)  L      N    <->   413 LYS   (  24-)  L      O    0.09    2.61  INTRA
 765 ASN   ( 162-)  H      OD1  <->   804 THR   ( 206-)  H      N    0.08    2.62  INTRA
 337 GLU   ( 416-)  N      N    <->   338 CYS   ( 417-)  N      N    0.08    2.52  INTRA BL
And so on for a total of 67 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: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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   ( 211-)  L      -7.96
 823 ARG   ( 226-)  H      -7.41
   2 ARG   (  82-)  N      -7.41
 545 GLN   ( 156-)  L      -6.58
 431 GLN   (  42-)  L      -6.43
  72 ARG   ( 152-)  N      -6.26
 577 ARG   ( 188-)  L      -6.22
 602 GLU   ( 213-)  L      -6.15
 335 GLU   ( 414-)  N      -6.15
 646 LYS   (  43-)  H      -6.06
  90 TYR   ( 169-)  N      -5.85
  74 GLN   ( 154-)  N      -5.80
 261 TYR   ( 341-)  N      -5.59
 376 GLN   ( 455-)  N      -5.58
 445 ILE   (  56-)  L      -5.48
 205 GLN   ( 284-)  N      -5.42
 337 GLU   ( 416-)  N      -5.38
 758 GLU   ( 150-)  H      -5.27
 108 ARG   ( 187-)  N      -5.24
 130 ARG   ( 209-)  N      -5.24
 481 TYR   (  92-)  L      -5.21
  61 ARG   ( 141-)  N      -5.15
 765 ASN   ( 162-)  H      -5.07

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.

 666 GLU   (  62-)  H       668 - LYS     64- ( H)         -4.51

Note: Quality value plot

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

Chain identifier: N

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: L

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: H

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.

 314 GLN   ( 395-)  N   -2.51

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: N

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: H

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 838 HOH   ( 491 )  N      O
Bound group on Asn; dont flip    6 ASN  (  86-) N
Bound to:  827 NAG  ( 475-) N
Bound group on Asn; dont flip   66 ASN  ( 146-) N
Bound to:  828 NAG  ( 476-) N
Bound group on Asn; dont flip  121 ASN  ( 200-) N
Bound to:  825 NAG  ( 469-) N

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.

  64 HIS   ( 144-)  N
 137 ASN   ( 216-)  N
 147 GLN   ( 226-)  N
 205 GLN   ( 284-)  N
 236 GLN   ( 315-)  N
 312 GLN   ( 392-)  N
 376 GLN   ( 455-)  N
 527 ASN   ( 138-)  L
 609 GLN   (   6-)  H

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.

   3 GLU   (  83-)  N      N
  17 TRP   (  97-)  N      N
  17 TRP   (  97-)  N      NE1
  22 LYS   ( 102-)  N      NZ
  32 SER   ( 112-)  N      OG
  34 VAL   ( 114-)  N      N
  38 ARG   ( 118-)  N      NH1
  41 TYR   ( 121-)  N      OH
  44 CYS   ( 124-)  N      N
  47 ASP   ( 127-)  N      N
  58 THR   ( 138-)  N      N
  69 ILE   ( 149-)  N      N
  73 SER   ( 153-)  N      N
  84 SER   ( 164-)  N      N
  88 THR   ( 168-)  N      OG1
  90 TYR   ( 169-)  N      N
 103 SER   ( 182-)  N      N
 144 LEU   ( 223-)  N      N
 145 ARG   ( 224-)  N      NH1
 147 GLN   ( 226-)  N      NE2
 149 SER   ( 228-)  N      N
 156 GLY   ( 235-)  N      N
 195 HIS   ( 274-)  N      N
 201 CYS   ( 280-)  N      N
 211 THR   ( 290-)  N      OG1
And so on for a total of 81 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.

 197 GLU   ( 276-)  N      OE2
 264 ASN   ( 344-)  N      OD1
 584 GLU   ( 195-)  L      OE1
 638 ASN   (  35-)  H      OD1
 683 ASN   (  79-)  H      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Unusual ion packing

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

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

 835  CA   (   0-)  N     1.66   0.80 Scores about as good as MG

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.

  77 ASP   ( 157-)  N   H-bonding suggests Asn
 106 ASP   ( 185-)  N   H-bonding suggests Asn; but Alt-Rotamer
 148 GLU   ( 227-)  N   H-bonding suggests Gln
 164 ASP   ( 243-)  N   H-bonding suggests Asn; but Alt-Rotamer
 187 GLU   ( 266-)  N   H-bonding suggests Gln
 494 GLU   ( 105-)  L   H-bonding suggests Gln
 556 ASP   ( 167-)  L   H-bonding suggests Asn; but Alt-Rotamer
 619 GLU   (  16-)  H   H-bonding suggests Gln
 704 ASP   (  97-)  H   H-bonding suggests Asn
 740 ASP   ( 130-)  H   H-bonding suggests Asn
 817 ASP   ( 220-)  H   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.801
  2nd generation packing quality :  -1.500
  Ramachandran plot appearance   :  -2.888
  chi-1/chi-2 rotamer normality  :  -5.048 (bad)
  Backbone conformation          :  -0.973

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.888
  Bond angles                    :   1.807
  Omega angle restraints         :   1.052
  Side chain planarity           :   1.081
  Improper dihedral distribution :   1.366
  Inside/Outside distribution    :   1.001

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.888
  Bond angles                    :   1.807
  Omega angle restraints         :   1.052
  Side chain planarity           :   1.081
  Improper dihedral distribution :   1.366
  Inside/Outside distribution    :   1.001
==============

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.