WHAT IF Check report

This file was created 2011-12-21 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 pdb1bxc.ent

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

Note: Ramachandran plot

Chain identifier: D

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'.

  65 GLN   (  65-)  A      CG
  65 GLN   (  65-)  A      CD
  65 GLN   (  65-)  A      OE1
  65 GLN   (  65-)  A      NE2
 452 GLN   (  65-)  B      CG
 452 GLN   (  65-)  B      CD
 452 GLN   (  65-)  B      OE1
 452 GLN   (  65-)  B      NE2
 839 GLN   (  65-)  C      CG
 839 GLN   (  65-)  C      CD
 839 GLN   (  65-)  C      OE1
 839 GLN   (  65-)  C      NE2
1226 GLN   (  65-)  D      CG
1226 GLN   (  65-)  D      CD
1226 GLN   (  65-)  D      OE1
1226 GLN   (  65-)  D      NE2

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) :287.000

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 : 14.24

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

Note: B-factor plot

Chain identifier: D

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

 |  1.000654 -0.000233  0.000007|
 | -0.000233  0.998953  0.000084|
 |  0.000007  0.000084  0.998307|
Proposed new scale matrix

 |  0.011847  0.000003  0.000000|
 |  0.000002  0.008099  0.000000|
 |  0.000000  0.000000  0.007143|
With corresponding cell

    A    =  84.408  B   = 123.465  C    = 139.995
    Alpha=  90.002  Beta=  90.001  Gamma=  90.027

The CRYST1 cell dimensions

    A    =  84.350  B   = 123.600  C    = 140.240
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 46.008
(Under-)estimated Z-score: 4.999

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.

 822 HIS   (  48-)  C      CG   ND1  CE1 109.65    4.0

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.

 132 ILE   ( 132-)  A      C     -6.4    -8.35     0.03
 502 PHE   ( 115-)  B      C     -6.2    -9.84     0.23
 906 ILE   ( 132-)  C      C     -6.2    -8.07     0.03
1276 PHE   ( 115-)  D      C     -6.3   -10.10     0.23
1293 ILE   ( 132-)  D      C     -6.2    -8.07     0.03
The average deviation= 1.503

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.

 340 LEU   ( 340-)  A    4.08

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 889 PHE   ( 115-)  C      CB   6.28
 502 PHE   ( 115-)  B      CB   6.03
1276 PHE   ( 115-)  D      CB   5.68
 115 PHE   ( 115-)  A      CB   5.65
 578 TYR   ( 191-)  B      OH   5.39
 242 HIS   ( 242-)  A      CB   5.11
1016 HIS   ( 242-)  C      CB   4.83
 629 HIS   ( 242-)  B      CB   4.61
1403 HIS   ( 242-)  D      CB   4.41
 966 PHE   ( 192-)  C      CB   4.05
 672 PHE   ( 285-)  B      CB   4.05
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.197

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.

 252 ARG   ( 252-)  A    -2.8
1026 ARG   ( 252-)  C    -2.8
 639 ARG   ( 252-)  B    -2.8
1413 ARG   ( 252-)  D    -2.8
 137 PRO   ( 137-)  A    -2.8
 728 PRO   ( 341-)  B    -2.7
 341 PRO   ( 341-)  A    -2.7
1115 PRO   ( 341-)  C    -2.7
1502 PRO   ( 341-)  D    -2.6
1298 PRO   ( 137-)  D    -2.6
 524 PRO   ( 137-)  B    -2.6
 633 ASN   ( 246-)  B    -2.6
1213 LEU   (  52-)  D    -2.6
 826 LEU   (  52-)  C    -2.5
1407 ASN   ( 246-)  D    -2.5
 439 LEU   (  52-)  B    -2.5
  52 LEU   (  52-)  A    -2.5
1020 ASN   ( 246-)  C    -2.5
 246 ASN   ( 246-)  A    -2.5
  89 THR   (  89-)  A    -2.4
 911 PRO   ( 137-)  C    -2.4
1276 PHE   ( 115-)  D    -2.4
1521 PRO   ( 360-)  D    -2.4
 139 ARG   ( 139-)  A    -2.4
 913 ARG   ( 139-)  C    -2.4
And so on for a total of 53 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.

   9 ARG   (   9-)  A  Poor phi/psi
  52 LEU   (  52-)  A  omega poor
  93 PHE   (  93-)  A  Poor phi/psi
 142 ALA   ( 142-)  A  omega poor
 152 LYS   ( 152-)  A  omega poor
 175 TYR   ( 175-)  A  omega poor
 185 GLU   ( 185-)  A  Poor phi/psi, PRO omega poor
 192 PHE   ( 192-)  A  omega poor
 213 LEU   ( 213-)  A  omega poor
 246 ASN   ( 246-)  A  Poor phi/psi
 251 ASN   ( 251-)  A  Poor phi/psi
 332 TYR   ( 332-)  A  omega poor
 341 PRO   ( 341-)  A  omega poor
 344 ASP   ( 344-)  A  Poor phi/psi, PRO omega poor
 346 TYR   ( 346-)  A  omega poor
 360 PRO   ( 360-)  A  omega poor
 370 ALA   ( 370-)  A  Poor phi/psi
 386 ARG   ( 386-)  A  Poor phi/psi
 396 ARG   (   9-)  B  Poor phi/psi
 439 LEU   (  52-)  B  omega poor
 480 PHE   (  93-)  B  Poor phi/psi
 529 ALA   ( 142-)  B  omega poor
 539 LYS   ( 152-)  B  omega poor
 562 TYR   ( 175-)  B  omega poor
 572 GLU   ( 185-)  B  Poor phi/psi, PRO omega poor
And so on for a total of 66 lines.

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!

   8 HIS   (   8-)  A      0
   9 ARG   (   9-)  A      0
  10 PHE   (  10-)  A      0
  22 ARG   (  22-)  A      0
  23 ASP   (  23-)  A      0
  25 PHE   (  25-)  A      0
  45 LEU   (  45-)  A      0
  48 HIS   (  48-)  A      0
  60 ARG   (  60-)  A      0
  86 PRO   (  86-)  A      0
  92 LEU   (  92-)  A      0
  93 PHE   (  93-)  A      0
  94 SER   (  94-)  A      0
  98 PHE   (  98-)  A      0
 100 ASP   ( 100-)  A      0
 103 PHE   ( 103-)  A      0
 105 SER   ( 105-)  A      0
 106 ARG   ( 106-)  A      0
 128 LEU   ( 128-)  A      0
 130 ALA   ( 130-)  A      0
 131 GLU   ( 131-)  A      0
 137 PRO   ( 137-)  A      0
 140 GLU   ( 140-)  A      0
 145 GLU   ( 145-)  A      0
 147 THR   ( 147-)  A      0
And so on for a total of 511 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!

 174 GLY   ( 174-)  A   2.23   10
 561 GLY   ( 174-)  B   2.21   10

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].

 181 PRO   ( 181-)  A     9.9 half-chair N/C-delta (18 degrees)
 215 PRO   ( 215-)  A    36.4 envelop C-delta (36 degrees)
 341 PRO   ( 341-)  A   -62.2 half-chair C-beta/C-alpha (-54 degrees)
 345 PRO   ( 345-)  A    50.0 half-chair C-delta/C-gamma (54 degrees)
 568 PRO   ( 181-)  B     7.4 envelop N (0 degrees)
 602 PRO   ( 215-)  B    39.3 envelop C-delta (36 degrees)
 728 PRO   ( 341-)  B   -60.7 half-chair C-beta/C-alpha (-54 degrees)
 732 PRO   ( 345-)  B    49.1 half-chair C-delta/C-gamma (54 degrees)
 955 PRO   ( 181-)  C     9.7 half-chair N/C-delta (18 degrees)
 989 PRO   ( 215-)  C    43.8 envelop C-delta (36 degrees)
1115 PRO   ( 341-)  C   -62.8 half-chair C-beta/C-alpha (-54 degrees)
1119 PRO   ( 345-)  C    51.1 half-chair C-delta/C-gamma (54 degrees)
1342 PRO   ( 181-)  D    20.3 half-chair N/C-delta (18 degrees)
1376 PRO   ( 215-)  D    39.5 envelop C-delta (36 degrees)
1502 PRO   ( 341-)  D   -60.0 half-chair C-beta/C-alpha (-54 degrees)
1506 PRO   ( 345-)  D    48.2 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 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.

 493 ARG   ( 106-)  B      NE  <-> 1493 TYR   ( 332-)  D      CD1    0.40    2.70  INTRA BF
 106 ARG   ( 106-)  A      NE  <-> 1106 TYR   ( 332-)  C      CD1    0.39    2.71  INTRA
 719 TYR   ( 332-)  B      CD1 <-> 1267 ARG   ( 106-)  D      NE     0.37    2.73  INTRA
 493 ARG   ( 106-)  B      NE  <-> 1493 TYR   ( 332-)  D      CE1    0.37    2.73  INTRA
 332 TYR   ( 332-)  A      CD1 <->  880 ARG   ( 106-)  C      NE     0.37    2.73  INTRA BF
 719 TYR   ( 332-)  B      CE1 <-> 1267 ARG   ( 106-)  D      NE     0.36    2.74  INTRA
1166 LYS   (   5-)  D      N   <-> 1169 HIS   (   8-)  D      ND1    0.35    2.65  INTRA
 392 LYS   (   5-)  B      N   <->  395 HIS   (   8-)  B      ND1    0.35    2.65  INTRA BL
 106 ARG   ( 106-)  A      NE  <-> 1106 TYR   ( 332-)  C      CE1    0.35    2.75  INTRA
   5 LYS   (   5-)  A      N   <->    8 HIS   (   8-)  A      ND1    0.33    2.67  INTRA
 332 TYR   ( 332-)  A      CE1 <->  880 ARG   ( 106-)  C      NE     0.32    2.78  INTRA
 779 LYS   (   5-)  C      N   <->  782 HIS   (   8-)  C      ND1    0.32    2.68  INTRA
 502 PHE   ( 115-)  B      CZ  <->  550 PHE   ( 163-)  B      CB     0.31    2.89  INTRA BF
 493 ARG   ( 106-)  B      NH2 <-> 1493 TYR   ( 332-)  D      CE1    0.31    2.79  INTRA
 889 PHE   ( 115-)  C      CZ  <->  937 PHE   ( 163-)  C      CB     0.31    2.89  INTRA BF
 115 PHE   ( 115-)  A      CZ  <->  163 PHE   ( 163-)  A      CB     0.30    2.90  INTRA BF
 719 TYR   ( 332-)  B      CE1 <-> 1267 ARG   ( 106-)  D      NH2    0.30    2.80  INTRA
 106 ARG   ( 106-)  A      NH2 <-> 1106 TYR   ( 332-)  C      CE1    0.30    2.80  INTRA
1276 PHE   ( 115-)  D      CZ  <-> 1324 PHE   ( 163-)  D      CB     0.29    2.91  INTRA BF
 493 ARG   ( 106-)  B      CZ  <-> 1493 TYR   ( 332-)  D      CE1    0.29    2.91  INTRA BL
 880 ARG   ( 106-)  C      NH2 <->  921 THR   ( 147-)  C      CG2    0.29    2.81  INTRA
 332 TYR   ( 332-)  A      CE1 <->  880 ARG   ( 106-)  C      NH2    0.28    2.82  INTRA
 106 ARG   ( 106-)  A      CZ  <-> 1106 TYR   ( 332-)  C      CE1    0.28    2.92  INTRA BL
 493 ARG   ( 106-)  B      NH2 <->  534 THR   ( 147-)  B      CG2    0.28    2.82  INTRA
 590 HIS   ( 203-)  B      ND1 <-> 1364 HIS   ( 203-)  D      ND1    0.28    2.72  INTRA BF
And so on for a total of 308 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

  60 ARG   (  60-)  A      -6.80
1441 GLN   ( 280-)  D      -6.77
 834 ARG   (  60-)  C      -6.76
 280 GLN   ( 280-)  A      -6.75
 667 GLN   ( 280-)  B      -6.74
1221 ARG   (  60-)  D      -6.72
 447 ARG   (  60-)  B      -6.72
1054 GLN   ( 280-)  C      -6.68
1160 ARG   ( 386-)  C      -6.41
1547 ARG   ( 386-)  D      -6.39
 773 ARG   ( 386-)  B      -6.38
 796 ARG   (  22-)  C      -6.38
 386 ARG   ( 386-)  A      -6.31
1183 ARG   (  22-)  D      -6.31
  22 ARG   (  22-)  A      -6.31
 409 ARG   (  22-)  B      -6.25
   8 HIS   (   8-)  A      -5.87
 782 HIS   (   8-)  C      -5.86
1169 HIS   (   8-)  D      -5.83
 395 HIS   (   8-)  B      -5.80
 743 ARG   ( 356-)  B      -5.67
 356 ARG   ( 356-)  A      -5.67
1130 ARG   ( 356-)  C      -5.67
1517 ARG   ( 356-)  D      -5.66
 526 ARG   ( 139-)  B      -5.61
 139 ARG   ( 139-)  A      -5.59
 913 ARG   ( 139-)  C      -5.53
1300 ARG   ( 139-)  D      -5.51
 358 GLU   ( 358-)  A      -5.38
 745 GLU   ( 358-)  B      -5.38
 171 GLN   ( 171-)  A      -5.38
 806 ARG   (  32-)  C      -5.37
 945 GLN   ( 171-)  C      -5.37
 558 GLN   ( 171-)  B      -5.36
1332 GLN   ( 171-)  D      -5.35
1519 GLU   ( 358-)  D      -5.35
1132 GLU   ( 358-)  C      -5.35
  32 ARG   (  32-)  A      -5.30
 419 ARG   (  32-)  B      -5.24
1193 ARG   (  32-)  D      -5.21

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

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: D

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.

 610 ALA   ( 223-)  B   -2.84
 997 ALA   ( 223-)  C   -2.82
1384 ALA   ( 223-)  D   -2.80
 359 LEU   ( 359-)  A   -2.59
1133 LEU   ( 359-)  C   -2.57
 746 LEU   ( 359-)  B   -2.54
1520 LEU   ( 359-)  D   -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

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

1552 HOH   ( 689 )  D      O

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.

1549 HOH   ( 526 )  A      O    -20.15 -128.62  174.98
1549 HOH   ( 533 )  A      O    -20.55 -120.55  180.03
1549 HOH   ( 535 )  A      O     -7.40 -134.28  188.06
1549 HOH   ( 544 )  A      O    -27.97 -124.50  175.95
1549 HOH   ( 548 )  A      O     -2.68 -142.42  181.46
1549 HOH   ( 550 )  A      O    -22.47 -104.56  176.84
1549 HOH   ( 552 )  A      O    -29.15 -121.85  185.84
1549 HOH   ( 558 )  A      O     38.69 -112.13  225.69
1549 HOH   ( 560 )  A      O    -21.46 -128.57  155.62
1549 HOH   ( 561 )  A      O      8.93 -131.59  182.72
1549 HOH   ( 568 )  A      O    -25.68 -137.25  189.94
1549 HOH   ( 575 )  A      O    -30.89 -127.51  186.46
1549 HOH   ( 577 )  A      O    -19.30 -102.14  204.86
1549 HOH   ( 643 )  A      O     12.74  -97.21  201.74
1549 HOH   ( 646 )  A      O     16.43 -146.62  155.23
1549 HOH   ( 652 )  A      O     24.02 -107.61  201.21
1549 HOH   ( 662 )  A      O     18.52 -144.36  154.80
1549 HOH   ( 675 )  A      O     40.39 -169.60  189.69
1549 HOH   ( 695 )  A      O     52.72  -98.12  200.67
1550 HOH   ( 546 )  B      O     37.49 -126.59  216.54
1550 HOH   ( 553 )  B      O    -27.04 -152.40  195.33
1550 HOH   ( 555 )  B      O     29.54 -137.06  202.58
1550 HOH   ( 564 )  B      O    -31.81 -145.73  199.92
1550 HOH   ( 568 )  B      O     28.21 -146.44  208.96
1550 HOH   ( 570 )  B      O      6.92 -142.89  221.73
And so on for a total of 72 lines.

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.

1549 HOH   ( 550 )  A      O
1549 HOH   ( 552 )  A      O
1549 HOH   ( 572 )  A      O
1549 HOH   ( 575 )  A      O
1549 HOH   ( 641 )  A      O
1549 HOH   ( 644 )  A      O
1549 HOH   ( 675 )  A      O
1549 HOH   ( 695 )  A      O
1550 HOH   ( 546 )  B      O
1550 HOH   ( 553 )  B      O
1550 HOH   ( 564 )  B      O
1550 HOH   ( 572 )  B      O
1550 HOH   ( 579 )  B      O
1550 HOH   ( 581 )  B      O
1550 HOH   ( 585 )  B      O
1550 HOH   ( 591 )  B      O
1550 HOH   ( 594 )  B      O
1550 HOH   ( 630 )  B      O
1550 HOH   ( 680 )  B      O
1550 HOH   ( 683 )  B      O
1550 HOH   ( 691 )  B      O
1551 HOH   ( 536 )  C      O
1551 HOH   ( 567 )  C      O
1551 HOH   ( 587 )  C      O
1551 HOH   ( 645 )  C      O
1551 HOH   ( 656 )  C      O
1551 HOH   ( 666 )  C      O
1552 HOH   ( 536 )  D      O
1552 HOH   ( 581 )  D      O
1552 HOH   ( 588 )  D      O
1552 HOH   ( 655 )  D      O
1552 HOH   ( 662 )  D      O
1552 HOH   ( 677 )  D      O
1552 HOH   ( 681 )  D      O
1552 HOH   ( 689 )  D      O
1552 HOH   ( 694 )  D      O

Error: HIS, ASN, GLN side chain flips

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

  40 HIS   (  40-)  A
  48 HIS   (  48-)  A
  51 ASN   (  51-)  A
  69 GLN   (  69-)  A
 203 HIS   ( 203-)  A
 219 HIS   ( 219-)  A
 229 HIS   ( 229-)  A
 233 GLN   ( 233-)  A
 246 ASN   ( 246-)  A
 248 GLN   ( 248-)  A
 376 GLN   ( 376-)  A
 427 HIS   (  40-)  B
 435 HIS   (  48-)  B
 456 GLN   (  69-)  B
 571 ASN   ( 184-)  B
 590 HIS   ( 203-)  B
 606 HIS   ( 219-)  B
 616 HIS   ( 229-)  B
 620 GLN   ( 233-)  B
 633 ASN   ( 246-)  B
 635 GLN   ( 248-)  B
 638 ASN   ( 251-)  B
 763 GLN   ( 376-)  B
 814 HIS   (  40-)  C
 822 HIS   (  48-)  C
 977 HIS   ( 203-)  C
 993 HIS   ( 219-)  C
1003 HIS   ( 229-)  C
1020 ASN   ( 246-)  C
1022 GLN   ( 248-)  C
1150 GLN   ( 376-)  C
1209 HIS   (  48-)  D
1345 ASN   ( 184-)  D
1364 HIS   ( 203-)  D
1380 HIS   ( 219-)  D
1390 HIS   ( 229-)  D
1394 GLN   ( 233-)  D
1407 ASN   ( 246-)  D
1409 GLN   ( 248-)  D
1537 GLN   ( 376-)  D

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.

  15 TRP   (  15-)  A      N
  28 ALA   (  28-)  A      N
  36 VAL   (  36-)  A      N
 106 ARG   ( 106-)  A      NE
 106 ARG   ( 106-)  A      NH2
 136 TRP   ( 136-)  A      NE1
 139 ARG   ( 139-)  A      NE
 151 ARG   ( 151-)  A      NE
 151 ARG   ( 151-)  A      NH2
 154 TRP   ( 154-)  A      N
 175 TYR   ( 175-)  A      N
 184 ASN   ( 184-)  A      N
 184 ASN   ( 184-)  A      ND2
 187 ARG   ( 187-)  A      N
 187 ARG   ( 187-)  A      NH1
 192 PHE   ( 192-)  A      N
 194 THR   ( 194-)  A      N
 210 ARG   ( 210-)  A      NE
 210 ARG   ( 210-)  A      NH2
 214 ASN   ( 214-)  A      ND2
 243 ILE   ( 243-)  A      N
 246 ASN   ( 246-)  A      N
 249 ARG   ( 249-)  A      NH1
 251 ASN   ( 251-)  A      ND2
 252 ARG   ( 252-)  A      N
And so on for a total of 135 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.

 216 GLU   ( 216-)  A      OE1
 380 GLU   ( 380-)  A      OE1
 487 ASP   ( 100-)  B      OD2
 567 GLU   ( 180-)  B      OE2
 603 GLU   ( 216-)  B      OE1
 638 ASN   ( 251-)  B      OD1
 767 GLU   ( 380-)  B      OE1
 874 ASP   ( 100-)  C      OD2
 954 GLU   ( 180-)  C      OE2
 990 GLU   ( 216-)  C      OE1
1154 GLU   ( 380-)  C      OE1
1261 ASP   ( 100-)  D      OD2
1341 GLU   ( 180-)  D      OE2
1377 GLU   ( 216-)  D      OE1
1541 GLU   ( 380-)  D      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.

1550 HOH   ( 532 )  B      O  0.96  K  4
1550 HOH   ( 668 )  B      O  0.93  K  4
1551 HOH   ( 607 )  C      O  0.96  K  4
1552 HOH   ( 641 )  D      O  1.05  K  4

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.

  68 ASP   (  68-)  A   H-bonding suggests Asn
  79 ASP   (  79-)  A   H-bonding suggests Asn
 123 ASP   ( 123-)  A   H-bonding suggests Asn
 327 GLU   ( 327-)  A   H-bonding suggests Gln
 344 ASP   ( 344-)  A   H-bonding suggests Asn
 455 ASP   (  68-)  B   H-bonding suggests Asn
 466 ASP   (  79-)  B   H-bonding suggests Asn
 510 ASP   ( 123-)  B   H-bonding suggests Asn; but Alt-Rotamer
 714 GLU   ( 327-)  B   H-bonding suggests Gln
 731 ASP   ( 344-)  B   H-bonding suggests Asn
 842 ASP   (  68-)  C   H-bonding suggests Asn
 897 ASP   ( 123-)  C   H-bonding suggests Asn; but Alt-Rotamer
1101 GLU   ( 327-)  C   H-bonding suggests Gln
1118 ASP   ( 344-)  C   H-bonding suggests Asn
1229 ASP   (  68-)  D   H-bonding suggests Asn
1284 ASP   ( 123-)  D   H-bonding suggests Asn; but Alt-Rotamer
1488 GLU   ( 327-)  D   H-bonding suggests Gln
1505 ASP   ( 344-)  D   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 :  -0.717
  2nd generation packing quality :  -0.927
  Ramachandran plot appearance   :  -1.197
  chi-1/chi-2 rotamer normality  :  -2.763
  Backbone conformation          :   0.092

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.383 (tight)
  Bond angles                    :   0.564 (tight)
  Omega angle restraints         :   1.147
  Side chain planarity           :   0.978
  Improper dihedral distribution :   1.373
  Inside/Outside distribution    :   1.013

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.383 (tight)
  Bond angles                    :   0.564 (tight)
  Omega angle restraints         :   1.147
  Side chain planarity           :   0.978
  Improper dihedral distribution :   1.373
  Inside/Outside distribution    :   1.013
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      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,
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    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.