WHAT IF Check report

This file was created 2013-12-09 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 pdb3vnn.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

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'.

   6 LYS   ( 273-)  A      CG
   6 LYS   ( 273-)  A      CD
   6 LYS   ( 273-)  A      CE
   6 LYS   ( 273-)  A      NZ
  16 LYS   ( 283-)  A      CG
  16 LYS   ( 283-)  A      CD
  16 LYS   ( 283-)  A      CE
  16 LYS   ( 283-)  A      NZ
  17 ASP   ( 284-)  A      CG
  17 ASP   ( 284-)  A      OD1
  17 ASP   ( 284-)  A      OD2
  22 LYS   ( 289-)  A      CG
  22 LYS   ( 289-)  A      CD
  22 LYS   ( 289-)  A      CE
  22 LYS   ( 289-)  A      NZ
  38 SER   ( 305-)  A      OG
  46 ILE   ( 315-)  A      CG1
  46 ILE   ( 315-)  A      CG2
  46 ILE   ( 315-)  A      CD1
  51 LYS   ( 320-)  A      CG
  51 LYS   ( 320-)  A      CD
  51 LYS   ( 320-)  A      CE
  51 LYS   ( 320-)  A      NZ
  74 MET   ( 343-)  A      CG
  74 MET   ( 343-)  A      SD
And so on for a total of 69 lines.

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 PHE   ( 268-)  A    High
   2 TYR   ( 269-)  A    High
   3 ILE   ( 270-)  A    High
   4 GLU   ( 271-)  A    High
   6 LYS   ( 273-)  A    High
   8 ASP   ( 275-)  A    High
   9 GLY   ( 276-)  A    High
  10 GLU   ( 277-)  A    High
  11 ARG   ( 278-)  A    High
  12 MET   ( 279-)  A    High
  13 GLN   ( 280-)  A    High
  14 MET   ( 281-)  A    High
  15 HIS   ( 282-)  A    High
  16 LYS   ( 283-)  A    High
  17 ASP   ( 284-)  A    High
  18 GLY   ( 285-)  A    High
  19 ASP   ( 286-)  A    High
  20 VAL   ( 287-)  A    High
  21 TYR   ( 288-)  A    High
  22 LYS   ( 289-)  A    High
  23 TYR   ( 290-)  A    High
  24 PHE   ( 291-)  A    High
  25 SER   ( 292-)  A    High
  26 ARG   ( 293-)  A    High
  27 ASN   ( 294-)  A    High
And so on for a total of 116 lines.

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 1

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.674 over 188 bonds
Average difference in B over a bond : 7.56
RMS difference in B over a bond : 9.48

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.

 117 ARG   ( 399-)  A

Warning: Tyrosine convention problem

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

   2 TYR   ( 269-)  A
  21 TYR   ( 288-)  A
  31 TYR   ( 298-)  A
  66 TYR   ( 335-)  A
 104 TYR   ( 386-)  A

Warning: Phenylalanine convention problem

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

 111 PHE   ( 393-)  A

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  77 ASP   ( 359-)  A

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  41 GLU   ( 308-)  A
 119 GLU   ( 401-)  A

Geometric checks

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.

  21 TYR   ( 288-)  A      CA   CB   CG  122.77    4.8
  22 LYS   ( 289-)  A     -C    N    CA  129.76    4.5
  29 TYR   ( 296-)  A      N    CA   C    99.98   -4.0
  47 HIS   ( 316-)  A      CG   ND1  CE1 109.67    4.1
  49 ALA   ( 318-)  A      N    CA   C    99.96   -4.0
  72 THR   ( 341-)  A      C    CA   CB  101.33   -4.6
  89 MET   ( 371-)  A      CB   CG   SD  124.78    4.0
 111 PHE   ( 393-)  A      N    CA   C   127.92    6.0

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  41 GLU   ( 308-)  A
  77 ASP   ( 359-)  A
 117 ARG   ( 399-)  A
 119 GLU   ( 401-)  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.

 111 PHE   ( 393-)  A      CA    -8.9    19.78    33.98
The average deviation= 1.210

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.

 111 PHE   ( 393-)  A    6.43
 110 ILE   ( 392-)  A    5.41
  49 ALA   ( 318-)  A    4.75
  29 TYR   ( 296-)  A    4.28

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 : 1.702

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.817

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.

  43 THR   ( 312-)  A    -3.1
  18 GLY   ( 285-)  A    -2.4
  47 HIS   ( 316-)  A    -2.3
  91 ASN   ( 373-)  A    -2.3
 121 VAL   ( 403-)  A    -2.2
  90 VAL   ( 372-)  A    -2.1
 118 ILE   ( 400-)  A    -2.1
  71 GLN   ( 340-)  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.

  17 ASP   ( 284-)  A  omega poor
  18 GLY   ( 285-)  A  Poor phi/psi
  19 ASP   ( 286-)  A  Poor phi/psi
  27 ASN   ( 294-)  A  omega poor
  29 TYR   ( 296-)  A  Poor phi/psi
  35 PHE   ( 302-)  A  omega poor
  43 THR   ( 312-)  A  PRO omega poor
  44 PRO   ( 313-)  A  omega poor
  48 ASN   ( 317-)  A  omega poor
  51 LYS   ( 320-)  A  omega poor
  52 ALA   ( 321-)  A  Poor phi/psi
  71 GLN   ( 340-)  A  Poor phi/psi
  78 LEU   ( 360-)  A  Poor phi/psi
  83 CYS   ( 365-)  A  omega poor
  92 ASN   ( 374-)  A  Poor phi/psi, omega poor
 110 ILE   ( 392-)  A  omega poor
 111 PHE   ( 393-)  A  omega poor
 112 THR   ( 394-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -6.507

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 : -6.507

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 ASP   ( 275-)  A      0
  11 ARG   ( 278-)  A      0
  16 LYS   ( 283-)  A      0
  17 ASP   ( 284-)  A      0
  19 ASP   ( 286-)  A      0
  31 TYR   ( 298-)  A      0
  35 PHE   ( 302-)  A      0
  37 ALA   ( 304-)  A      0
  40 THR   ( 307-)  A      0
  41 GLU   ( 308-)  A      0
  42 LEU   ( 311-)  A      0
  43 THR   ( 312-)  A      0
  44 PRO   ( 313-)  A      0
  48 ASN   ( 317-)  A      0
  49 ALA   ( 318-)  A      0
  50 PHE   ( 319-)  A      0
  52 ALA   ( 321-)  A      0
  54 ILE   ( 323-)  A      0
  60 ASP   ( 329-)  A      0
  70 THR   ( 339-)  A      0
  71 GLN   ( 340-)  A      0
  74 MET   ( 343-)  A      0
  75 GLN   ( 344-)  A      0
  76 LYS   ( 345-)  A      0
  77 ASP   ( 359-)  A      0
And so on for a total of 61 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 9.446

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!

  18 GLY   ( 285-)  A   3.55   10
  28 GLY   ( 295-)  A   2.94   36

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].

  39 PRO   ( 306-)  A  -122.8 half-chair C-delta/C-gamma (-126 degrees)
  44 PRO   ( 313-)  A  -126.1 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

  87 VAL   ( 369-)  A      CG1 <->  107 LEU   ( 389-)  A      CD1    1.65    1.55  INTRA BF
   7 LEU   ( 274-)  A      CD2 <->   75 GLN   ( 344-)  A      NE2    0.89    2.21  INTRA BF
  98 GLU   ( 380-)  A      O   <->  103 ARG   ( 385-)  A      NH1    0.61    2.09  INTRA BF
  53 ASP   ( 322-)  A      O   <->   91 ASN   ( 373-)  A      ND2    0.52    2.18  INTRA BF
  35 PHE   ( 302-)  A      O   <->   42 LEU   ( 311-)  A      N      0.39    2.31  INTRA BF
  56 ILE   ( 325-)  A      O   <->   91 ASN   ( 373-)  A      N      0.39    2.31  INTRA BF
  67 ASN   ( 336-)  A      O   <->   71 GLN   ( 340-)  A      N      0.33    2.37  INTRA BF
 110 ILE   ( 392-)  A      CG2 <->  111 PHE   ( 393-)  A      CD1    0.33    2.87  INTRA BF
  66 TYR   ( 335-)  A      CE1 <->  116 GLY   ( 398-)  A      O      0.29    2.51  INTRA BF
  13 GLN   ( 280-)  A      OE1 <->   15 HIS   ( 282-)  A      NE2    0.28    2.42  INTRA BF
  75 GLN   ( 344-)  A      O   <->   76 LYS   ( 345-)  A      C      0.25    2.35  INTRA BF
  55 GLN   ( 324-)  A      N   <->   91 ASN   ( 373-)  A      OD1    0.25    2.45  INTRA BF
  86 ASP   ( 368-)  A      OD1 <->   87 VAL   ( 369-)  A      N      0.20    2.40  INTRA BL
   8 ASP   ( 275-)  A      N   <->   75 GLN   ( 344-)  A      OE1    0.20    2.50  INTRA BF
  87 VAL   ( 369-)  A      CB  <->  107 LEU   ( 389-)  A      CD1    0.19    3.01  INTRA BF
  87 VAL   ( 369-)  A      CG1 <->  107 LEU   ( 389-)  A      CG     0.18    3.02  INTRA BL
  96 GLY   ( 378-)  A      N   <->   97 HIS   ( 379-)  A      N      0.16    2.44  INTRA BF
  58 ILE   ( 327-)  A      N   <->   89 MET   ( 371-)  A      O      0.15    2.55  INTRA BF
  52 ALA   ( 321-)  A      CB  <->   53 ASP   ( 322-)  A      N      0.12    2.58  INTRA BF
  29 TYR   ( 296-)  A      CD1 <->   30 ASN   ( 297-)  A      N      0.12    2.88  INTRA BF
  64 MET   ( 333-)  A      O   <->   81 CYS   ( 363-)  A      N      0.11    2.59  INTRA BF
  64 MET   ( 333-)  A      N   <->   81 CYS   ( 363-)  A      O      0.09    2.61  INTRA BL
  66 TYR   ( 335-)  A      CE1 <->  116 GLY   ( 398-)  A      CA     0.09    3.11  INTRA BF
  66 TYR   ( 335-)  A      CE1 <->  116 GLY   ( 398-)  A      C      0.09    3.11  INTRA BF
  67 ASN   ( 336-)  A      N   <->   72 THR   ( 341-)  A      O      0.08    2.62  INTRA BF
 106 ILE   ( 388-)  A      O   <->  109 SER   ( 391-)  A      N      0.07    2.63  INTRA BF
  75 GLN   ( 344-)  A      C   <->   76 LYS   ( 345-)  A      C      0.07    2.73  INTRA BF
  70 THR   ( 339-)  A      O   <->   72 THR   ( 341-)  A      N      0.07    2.63  INTRA BF
 100 LEU   ( 382-)  A      C   <->  101 ARG   ( 383-)  A      C      0.06    2.74  INTRA BF
  12 MET   ( 279-)  A      SD  <->   24 PHE   ( 291-)  A      C      0.05    3.35  INTRA BL
  86 ASP   ( 368-)  A      C   <->   87 VAL   ( 369-)  A      CG1    0.05    3.05  INTRA BL
  66 TYR   ( 335-)  A      CZ  <->  116 GLY   ( 398-)  A      CA     0.05    3.15  INTRA BF
  23 TYR   ( 290-)  A      CD1 <->   35 PHE   ( 302-)  A      CD2    0.04    3.16  INTRA BF
 115 PRO   ( 397-)  A      CA  <->  119 GLU   ( 401-)  A      OE2    0.04    2.76  INTRA BF
  81 CYS   ( 363-)  A      SG  <->  118 ILE   ( 400-)  A      N      0.04    3.26  INTRA BF
  16 LYS   ( 283-)  A      CB  <->   57 CYS   ( 326-)  A      SG     0.04    3.36  INTRA BF
  14 MET   ( 281-)  A      CE  <->   57 CYS   ( 326-)  A      SG     0.03    3.37  INTRA BF
  13 GLN   ( 280-)  A      N   <->   24 PHE   ( 291-)  A      O      0.03    2.67  INTRA BL
 114 ILE   ( 396-)  A      C   <->  115 PRO   ( 397-)  A      CA     0.02    2.28  INTRA BL
  66 TYR   ( 335-)  A      CD1 <->  116 GLY   ( 398-)  A      O      0.02    2.78  INTRA BF
  45 PHE   ( 314-)  A      C   <->   47 HIS   ( 316-)  A      N      0.01    2.89  INTRA BF
  70 THR   ( 339-)  A      C   <->   72 THR   ( 341-)  A      N      0.01    2.89  INTRA BF
  90 VAL   ( 372-)  A      O   <->   93 LYS   ( 375-)  A      N      0.01    2.69  INTRA BF

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: 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.

  95 LEU   ( 377-)  A   -2.93
  74 MET   ( 343-)  A   -2.74
  51 LYS   ( 320-)  A   -2.59

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

  92 ASN   ( 374-)  A     -   95 LEU   ( 377-)  A        -2.13

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.

 125 HOH   ( 501 )  A      O     -0.32    6.14   81.47

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.

  69 ASN   ( 338-)  A

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.

  25 SER   ( 292-)  A      OG
  36 GLY   ( 303-)  A      N
  38 SER   ( 305-)  A      N
  45 PHE   ( 314-)  A      N
  89 MET   ( 371-)  A      N
  92 ASN   ( 374-)  A      N
  97 HIS   ( 379-)  A      N
  98 GLU   ( 380-)  A      N
 111 PHE   ( 393-)  A      N
 117 ARG   ( 399-)  A      NE

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.

  30 ASN   ( 297-)  A      OD1

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.

   8 ASP   ( 275-)  A   H-bonding suggests Asn; but Alt-Rotamer
  19 ASP   ( 286-)  A   H-bonding suggests Asn
  41 GLU   ( 308-)  A   H-bonding suggests Gln

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:

  2nd generation packing quality :  -3.937 (poor)
  Ramachandran plot appearance   :  -3.817 (poor)
  chi-1/chi-2 rotamer normality  :  -6.507 (bad)
  Backbone conformation          :  -1.093

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.643 (tight)
  Bond angles                    :   0.931
  Omega angle restraints         :   1.717 (loose)
  Side chain planarity           :   0.550 (tight)
  Improper dihedral distribution :   1.087
  B-factor distribution          :   1.674 (loose)
  Inside/Outside distribution    :   1.101

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:

  2nd generation packing quality :  -1.9
  Ramachandran plot appearance   :  -1.3
  chi-1/chi-2 rotamer normality  :  -3.9 (poor)
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.643 (tight)
  Bond angles                    :   0.931
  Omega angle restraints         :   1.717 (loose)
  Side chain planarity           :   0.550 (tight)
  Improper dihedral distribution :   1.087
  B-factor distribution          :   1.674 (loose)
  Inside/Outside distribution    :   1.101
==============

WHAT IF
    G.Vriend,
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WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
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    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.