WHAT IF Check report

This file was created 2011-12-13 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 pdb1dhk.ent

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.

 693 NAG   ( 511-)  B  -   O4  bound to  692 NAG   ( 510-)  B  -   C1
 695 NAG   ( 509-)  B  -   O4  bound to  694 NAG   ( 508-)  B  -   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: A

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'.

 570 ARG   (  74-)  B      CG
 570 ARG   (  74-)  B      CD
 570 ARG   (  74-)  B      NE
 570 ARG   (  74-)  B      CZ
 570 ARG   (  74-)  B      NH1
 570 ARG   (  74-)  B      NH2

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) :293.000

Note: B-factor plot

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

Chain identifier: A

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.

 424 ARG   ( 424-)  A

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.

   8 SER   (   8-)  A      CA   C     1.38   -7.1
 216 ASN   ( 216-)  A      CA   CB    1.34   -9.3
 424 ARG   ( 424-)  A      CD   NE    1.32   -7.6
 583 ASP   (  96-)  B      CA   C     1.64    5.4
 583 ASP   (  96-)  B      CA   CB    1.26  -13.5
 595 ARG   ( 108-)  B      CD   NE    1.31   -8.5

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: 0.412
RMS-deviation in bond distances: 0.009

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 PCA   (   1-)  A      N    CD   OE  147.10    4.6
   8 SER   (   8-)  A      N    CA   C   123.61    4.4
   8 SER   (   8-)  A      CA   C    O   106.88   -8.2
   9 GLY   (   9-)  A     -CA  -C    N   129.67    6.7
   9 GLY   (   9-)  A      CA   C    O   107.55   -6.3
  10 ARG   (  10-)  A     -O   -C    N   131.94    5.6
  20 ARG   (  20-)  A      CG   CD   NE  122.44    7.0
 110 GLY   ( 110-)  A     -C    N    CA  112.91   -4.5
 111 THR   ( 111-)  A      N    CA   CB  101.86   -5.1
 111 THR   ( 111-)  A      C    CA   CB  118.97    4.7
 157 VAL   ( 157-)  A      CA   CB   CG2 117.90    4.4
 162 LEU   ( 162-)  A      CB   CG   CD1  91.72   -6.3
 162 LEU   ( 162-)  A      CB   CG   CD2 132.08    7.1
 165 LEU   ( 165-)  A      CB   CG   CD2 138.29    9.2
 176 ARG   ( 176-)  A      CA   CB   CG  123.23    4.6
 176 ARG   ( 176-)  A      NE   CZ   NH1 110.94   -4.8
 176 ARG   ( 176-)  A      NE   CZ   NH2 129.66    5.1
 195 ARG   ( 195-)  A      N    CA   C    99.48   -4.2
 216 ASN   ( 216-)  A      CA   CB   CG  119.87    7.3
 244 SER   ( 244-)  A      CA   CB   OG   98.47   -6.3
 267 ARG   ( 267-)  A      CG   CD   NE  123.42    7.6
 293 LEU   ( 293-)  A      N    CA   C    99.14   -4.3
 424 ARG   ( 424-)  A      CG   CD   NE  122.03    6.8
 424 ARG   ( 424-)  A      CD   NE   CZ  137.92    9.0
 469 VAL   ( 469-)  A      CA   CB   CG1 130.51   11.8
 500 THR   (   4-)  B     -C    N    CA  113.76   -4.4
 555 VAL   (  59-)  B      CA   CB   CG2 120.09    5.6
 563 THR   (  67-)  B      CA   CB   CG2 133.76   13.7
 563 THR   (  67-)  B      CA   CB   OG1 117.21    5.1
 567 ARG   (  71-)  B      CG   CD   NE   92.43  -10.6
 583 ASP   (  96-)  B      CA   C    O   131.45    6.3
 583 ASP   (  96-)  B      N    CA   CB  101.98   -5.0
 583 ASP   (  96-)  B      C    CA   CB  136.18   13.7
 583 ASP   (  96-)  B      CA   CB   CG  157.10   44.5
 584 THR   (  97-)  B     -CA  -C    N   105.61   -5.3
 585 VAL   (  98-)  B      CA   CB   CG1 122.32    7.0
 595 ARG   ( 108-)  B      CG   CD   NE  100.35   -6.0
 595 ARG   ( 108-)  B      CD   NE   CZ  133.50    6.6
 595 ARG   ( 108-)  B      NE   CZ   NH1 131.37    6.0
 595 ARG   ( 108-)  B      NE   CZ   NH2 111.06   -4.7
 598 ILE   ( 111-)  B      N    CA   C    98.27   -4.6
 619 ASN   ( 132-)  B      CA   CB   CG  119.50    6.9
 677 TYR   ( 190-)  B      N    CA   C   124.48    4.7

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.

 424 ARG   ( 424-)  A

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.

   8 SER   (   8-)  A      CA    -7.2    20.96    34.32
 165 LEU   ( 165-)  A      CG    11.6   -12.63   -33.01
 469 VAL   ( 469-)  A      CB     9.9   -19.98   -32.96
 563 THR   (  67-)  B      CB   -14.0     2.73    34.09
 583 ASP   (  96-)  B      CA   -10.2    13.50    33.73
The average deviation= 1.087

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.

 677 TYR   ( 190-)  B    5.05
 318 ALA   ( 318-)  A    5.03
 292 ALA   ( 292-)  A    4.72
 598 ILE   ( 111-)  B    4.62
 195 ARG   ( 195-)  A    4.60
   8 SER   (   8-)  A    4.58
 293 LEU   ( 293-)  A    4.44
 510 THR   (  14-)  B    4.34
 579 LEU   (  86-)  B    4.20
 336 THR   ( 336-)  A    4.15

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.

 674 GLN   ( 187-)  B    6.44
 424 ARG   ( 424-)  A    5.53
 595 ARG   ( 108-)  B    4.44

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.

 650 THR   ( 163-)  B    -2.9
   8 SER   (   8-)  A    -2.6
 595 ARG   ( 108-)  B    -2.6
 673 TYR   ( 186-)  B    -2.4
 529 SER   (  33-)  B    -2.4
 111 THR   ( 111-)  A    -2.3
 512 LEU   (  16-)  B    -2.3
 653 GLU   ( 166-)  B    -2.2
 163 VAL   ( 163-)  A    -2.2
 240 GLU   ( 240-)  A    -2.1
 560 THR   (  64-)  B    -2.1
  56 ARG   (  56-)  A    -2.1
 270 SER   ( 270-)  A    -2.1
 401 VAL   ( 401-)  A    -2.1
 637 LEU   ( 150-)  B    -2.1
  66 SER   (  66-)  A    -2.1
  45 PRO   (  45-)  A    -2.0
 341 SER   ( 341-)  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.

   5 GLN   (   5-)  A  Poor phi/psi
   7 GLN   (   7-)  A  omega poor
   8 SER   (   8-)  A  Poor phi/psi
  18 GLU   (  18-)  A  Poor phi/psi
  53 ASN   (  53-)  A  PRO omega poor
  65 VAL   (  65-)  A  Poor phi/psi
 102 MET   ( 102-)  A  Poor phi/psi
 129 VAL   ( 129-)  A  PRO omega poor
 221 TRP   ( 221-)  A  Poor phi/psi
 268 LYS   ( 268-)  A  Poor phi/psi
 350 ASN   ( 350-)  A  Poor phi/psi
 376 THR   ( 376-)  A  Poor phi/psi
 380 ASN   ( 380-)  A  Poor phi/psi
 381 ASP   ( 381-)  A  Poor phi/psi
 414 SER   ( 414-)  A  Poor phi/psi
 486 PRO   ( 486-)  A  Poor phi/psi
 529 SER   (  33-)  B  Poor phi/psi
 569 HIS   (  73-)  B  Poor phi/psi
 594 SER   ( 107-)  B  Poor phi/psi
 601 ASN   ( 114-)  B  Poor phi/psi
 602 ASN   ( 115-)  B  Poor phi/psi
 631 LYS   ( 144-)  B  Poor phi/psi
 655 GLU   ( 168-)  B  Poor phi/psi
 673 TYR   ( 186-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.807

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!

   5 GLN   (   5-)  A      0
   7 GLN   (   7-)  A      0
   8 SER   (   8-)  A      0
  12 SER   (  12-)  A      0
  17 PHE   (  17-)  A      0
  18 GLU   (  18-)  A      0
  19 TRP   (  19-)  A      0
  30 ARG   (  30-)  A      0
  31 TYR   (  31-)  A      0
  32 LEU   (  32-)  A      0
  45 PRO   (  45-)  A      0
  48 ASN   (  48-)  A      0
  52 THR   (  52-)  A      0
  53 ASN   (  53-)  A      0
  54 PRO   (  54-)  A      0
  55 SER   (  55-)  A      0
  56 ARG   (  56-)  A      0
  57 PRO   (  57-)  A      0
  58 TRP   (  58-)  A      0
  59 TRP   (  59-)  A      0
  62 TYR   (  62-)  A      0
  63 GLN   (  63-)  A      0
  64 PRO   (  64-)  A      0
  67 TYR   (  67-)  A      0
  69 LEU   (  69-)  A      0
And so on for a total of 307 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 : 1.915

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]

 121 PRO   ( 121-)  A    0.45 HIGH

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.

 577 PHE   (  84-)  B      CD1 <->  703 HOH   ( 513 )  B      O      1.67    1.13  INTRA BL
 577 PHE   (  84-)  B      CE1 <->  703 HOH   ( 513 )  B      O      0.96    1.84  INTRA BL
 125 GLU   ( 125-)  A      CB  <->  702 HOH   ( 741 )  A      O      0.65    2.15  INTRA
 577 PHE   (  84-)  B      CG  <->  703 HOH   ( 513 )  B      O      0.62    2.18  INTRA BL
 132 SER   ( 132-)  A      OG  <->  134 TRP   ( 134-)  A      CE2    0.55    2.25  INTRA BF
 337 ARG   ( 337-)  A      NH2 <->  699  CL   ( 498-)  A     CL      0.36    2.74  INTRA BL
 125 GLU   ( 125-)  A      CA  <->  702 HOH   ( 741 )  A      O      0.31    2.49  INTRA BL
 125 GLU   ( 125-)  A      C   <->  702 HOH   ( 741 )  A      O      0.28    2.52  INTRA BL
 317 ASP   ( 317-)  A      OD2 <->  702 HOH   ( 750 )  A      O      0.27    2.13  INTRA
 392 ARG   ( 392-)  A      NH2 <->  702 HOH   ( 599 )  A      O      0.27    2.43  INTRA
 132 SER   ( 132-)  A      OG  <->  134 TRP   ( 134-)  A      NE1    0.21    2.49  INTRA BF
 301 ASN   ( 301-)  A      O   <->  305 HIS   ( 305-)  A      NE2    0.17    2.53  INTRA BL
 127 PRO   ( 127-)  A      CD  <->  702 HOH   ( 741 )  A      O      0.16    2.64  INTRA BL
 140 LYS   ( 140-)  A      CE  <->  702 HOH   ( 654 )  A      O      0.15    2.65  INTRA
 642 THR   ( 155-)  B      CG2 <->  644 LYS   ( 157-)  B      CG     0.15    3.05  INTRA BF
 561 ASN   (  65-)  B      ND2 <->  695 NAG   ( 509-)  B      C7     0.14    2.96  INTRA
 699  CL   ( 498-)  A     CL   <->  702 HOH   ( 523 )  A      O      0.13    2.67  INTRA BL
 500 THR   (   4-)  B      CG2 <->  545 ILE   (  49-)  B      CD1    0.13    3.07  INTRA
 132 SER   ( 132-)  A      OG  <->  134 TRP   ( 134-)  A      CD2    0.13    2.67  INTRA BF
 627 ASN   ( 140-)  B      ND2 <->  696 NAG   ( 512-)  B      C7     0.13    2.97  INTRA BF
  11 THR   (  11-)  A      OG1 <->  399 ASN   ( 399-)  A      ND2    0.13    2.57  INTRA BL
  20 ARG   (  20-)  A      NH2 <->  369 GLU   ( 369-)  A      CB     0.13    2.97  INTRA
 521 SER   (  25-)  B      OG  <->  523 ASN   (  27-)  B      ND2    0.10    2.60  INTRA
 140 LYS   ( 140-)  A      NZ  <->  171 GLU   ( 171-)  A      CD     0.09    3.01  INTRA
   7 GLN   (   7-)  A      N   <->  702 HOH   ( 539 )  A      O      0.09    2.61  INTRA
And so on for a total of 56 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

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.

  72 ARG   (  72-)  A      -7.24
 118 TYR   ( 118-)  A      -6.82
   7 GLN   (   7-)  A      -5.89
 284 TRP   ( 284-)  A      -5.47
   2 TYR   (   2-)  A      -5.34
 279 ASN   ( 279-)  A      -5.32
  30 ARG   (  30-)  A      -5.30
 343 ARG   ( 343-)  A      -5.28
  88 ASN   (  88-)  A      -5.28
 267 ARG   ( 267-)  A      -5.18
  53 ASN   (  53-)  A      -5.18

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

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.

 570 ARG   (  74-)  B   -2.85

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

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.

 702 HOH   ( 751 )  A      O    116.36   59.62   -8.17
 702 HOH   ( 757 )  A      O    105.97   25.02   -0.23

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.

   5 GLN   (   5-)  A
  41 GLN   (  41-)  A
 201 HIS   ( 201-)  A
 279 ASN   ( 279-)  A
 302 GLN   ( 302-)  A
 399 ASN   ( 399-)  A
 408 ASN   ( 408-)  A
 527 GLN   (  31-)  B

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.

  12 SER   (  12-)  A      N
  59 TRP   (  59-)  A      N
  87 ASN   (  87-)  A      ND2
 101 HIS   ( 101-)  A      N
 175 VAL   ( 175-)  A      N
 182 TYR   ( 182-)  A      OH
 193 GLY   ( 193-)  A      N
 241 ALA   ( 241-)  A      N
 273 LYS   ( 273-)  A      N
 281 GLY   ( 281-)  A      N
 295 PHE   ( 295-)  A      N
 316 TRP   ( 316-)  A      NE1
 337 ARG   ( 337-)  A      NH2
 344 TRP   ( 344-)  A      N
 346 ARG   ( 346-)  A      N
 370 VAL   ( 370-)  A      N
 424 ARG   ( 424-)  A      NE
 434 TRP   ( 434-)  A      N
 495 LYS   ( 495-)  A      N
 506 ALA   (  10-)  B      N
 520 VAL   (  24-)  B      N
 525 ASN   (  29-)  B      N
 543 ALA   (  47-)  B      N
 548 ARG   (  52-)  B      NE
 597 SER   ( 110-)  B      OG
 644 LYS   ( 157-)  B      N
 654 LEU   ( 167-)  B      N
 670 SER   ( 183-)  B      OG
 672 ALA   ( 185-)  B      N
 684 SER   ( 197-)  B      N
Only metal coordination for  100 ASN  ( 100-) A      OD1
Only metal coordination for  599 ASP  ( 112-) B      OD2
Only metal coordination for  604 ASP  ( 117-) B      OD1

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.

  15 HIS   (  15-)  A      NE2
 201 HIS   ( 201-)  A      ND1
 565 ASN   (  69-)  B      OD1
 588 GLU   ( 101-)  B      OE1

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+.

 698  CA   ( 500-)  A     1.48   0.78 Scores about as good as MG
 701  CA   ( 499-)  B     1.51   0.86 Scores about as good as MG

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.

 702 HOH   ( 527 )  A      O  0.87  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.

 181 ASP   ( 181-)  A   H-bonding suggests Asn
 353 ASP   ( 353-)  A   H-bonding suggests Asn; but Alt-Rotamer
 576 ASP   (  83-)  B   H-bonding suggests Asn; but Alt-Rotamer
 590 ASP   ( 103-)  B   H-bonding suggests Asn
 616 ASP   ( 129-)  B   H-bonding suggests Asn
 660 ASP   ( 173-)  B   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 :  -0.125
  2nd generation packing quality :  -1.267
  Ramachandran plot appearance   :  -1.010
  chi-1/chi-2 rotamer normality  :  -1.807
  Backbone conformation          :  -0.663

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.412 (tight)
  Bond angles                    :   0.791
  Omega angle restraints         :   0.348 (tight)
  Side chain planarity           :   0.701
  Improper dihedral distribution :   1.098
  B-factor distribution          :   0.667
  Inside/Outside distribution    :   0.997

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 : 1.85


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -1.1
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.412 (tight)
  Bond angles                    :   0.791
  Omega angle restraints         :   0.348 (tight)
  Side chain planarity           :   0.701
  Improper dihedral distribution :   1.098
  B-factor distribution          :   0.667
  Inside/Outside distribution    :   0.997
==============

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.