WHAT IF Check report

This file was created 2012-01-05 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1pa3.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.920
CA-only RMS fit for the two chains : 0.483

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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: 0

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

   4 TYR   (   8-)  A
   5 TYR   (   9-)  A
  74 TYR   (  78-)  A
  79 TYR   (  83-)  A
 150 TYR   ( 160-)  A
 159 TYR   ( 169-)  A
 166 TYR   ( 176-)  A
 192 TYR   ( 202-)  A
 201 TYR   (   9-)  B
 270 TYR   (  78-)  B
 275 TYR   (  83-)  B
 346 TYR   ( 160-)  B
 362 TYR   ( 176-)  B
 388 TYR   ( 202-)  B

Warning: Phenylalanine convention problem

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

  31 PHE   (  35-)  A
  41 PHE   (  45-)  A
  44 PHE   (  48-)  A
  52 PHE   (  56-)  A
 106 PHE   ( 110-)  A
 131 PHE   ( 135-)  A
 143 PHE   ( 153-)  A
 156 PHE   ( 166-)  A
 227 PHE   (  35-)  B
 234 PHE   (  42-)  B
 237 PHE   (  45-)  B
 240 PHE   (  48-)  B
 248 PHE   (  56-)  B
 302 PHE   ( 110-)  B
 308 PHE   ( 116-)  B
 315 PHE   ( 123-)  B
 327 PHE   ( 135-)  B
 339 PHE   ( 153-)  B
 369 PHE   ( 183-)  B

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.

   7 ASP   (  11-)  A
  28 ASP   (  32-)  A
  49 ASP   (  53-)  A
  93 ASP   (  97-)  A
 123 ASP   ( 127-)  A
 224 ASP   (  32-)  B

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.

  53 GLU   (  57-)  A
 318 GLU   ( 126-)  B

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.

 262 ALA   (  70-)  B      N    CA   C   126.07    5.3
 363 PRO   ( 177-)  B      N    CA   C   121.81    4.0

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.

   7 ASP   (  11-)  A
  28 ASP   (  32-)  A
  49 ASP   (  53-)  A
  53 GLU   (  57-)  A
  93 ASP   (  97-)  A
 123 ASP   ( 127-)  A
 224 ASP   (  32-)  B
 318 GLU   ( 126-)  B

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.

 363 PRO   ( 177-)  B      N      7.0    20.60    -2.48
The average deviation= 0.793

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.

 312 GLU   ( 120-)  B    7.06
 262 ALA   (  70-)  B    6.09
 319 ASP   ( 127-)  B    5.21
  89 GLU   (  93-)  A    5.16
 116 GLU   ( 120-)  A    4.92
 197 ILE   (   5-)  B    4.11

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 : 1.628

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.

 363 PRO   ( 177-)  B    -3.1
 383 PRO   ( 197-)  B    -3.0
   5 TYR   (   9-)  A    -2.8
 201 TYR   (   9-)  B    -2.8
 364 SER   ( 178-)  B    -2.7
 379 ILE   ( 193-)  B    -2.5
 111 LEU   ( 115-)  A    -2.5
  81 ILE   (  85-)  A    -2.4
 298 ILE   ( 106-)  B    -2.4
  26 TYR   (  30-)  A    -2.3
  24 ILE   (  28-)  A    -2.2
 187 PRO   ( 197-)  A    -2.1
 219 GLY   (  27-)  B    -2.1
  68 SER   (  72-)  A    -2.0
 183 ILE   ( 193-)  A    -2.0
 189 ILE   ( 199-)  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.

   7 ASP   (  11-)  A  Poor phi/psi
   9 ARG   (  13-)  A  Poor phi/psi
  55 VAL   (  59-)  A  PRO omega poor
  67 GLN   (  71-)  A  Poor phi/psi
 141 TYR   ( 151-)  A  Poor phi/psi
 201 TYR   (   9-)  B  Poor phi/psi
 230 ASN   (  38-)  B  Poor phi/psi
 249 GLU   (  57-)  B  Poor phi/psi
 251 VAL   (  59-)  B  PRO omega poor
 337 TYR   ( 151-)  B  Poor phi/psi
 363 PRO   ( 177-)  B  Poor phi/psi
 364 SER   ( 178-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.080

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.080

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 272 SER   (  80-)  B    0.37

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!

   4 TYR   (   8-)  A      0
   5 TYR   (   9-)  A      0
   6 PHE   (  10-)  A      0
   7 ASP   (  11-)  A      0
   9 ARG   (  13-)  A      0
  10 GLY   (  14-)  A      0
  11 LYS   (  15-)  A      0
  25 GLU   (  29-)  A      0
  31 PHE   (  35-)  A      0
  33 VAL   (  37-)  A      0
  34 ASN   (  38-)  A      0
  47 GLU   (  51-)  A      0
  51 PRO   (  55-)  A      0
  54 GLN   (  58-)  A      0
  55 VAL   (  59-)  A      0
  60 ILE   (  64-)  A      0
  62 ASP   (  66-)  A      0
  66 ALA   (  70-)  A      0
  67 GLN   (  71-)  A      0
  79 TYR   (  83-)  A      0
  81 ILE   (  85-)  A      0
  82 CYS   (  86-)  A      0
  84 GLU   (  88-)  A      0
 109 THR   ( 113-)  A      0
 114 GLN   ( 118-)  A      0
And so on for a total of 117 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 : 1.339

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]

 363 PRO   ( 177-)  B    0.48 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 383 PRO   ( 197-)  B    99.5 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 193 ILE   ( 203-)  A      CD1 <->  196 ARG   ( 206-)  A      NH1    0.28    2.82  INTRA BF
  39 VAL   (  43-)  A      O   <->   43 ASN   (  47-)  A      ND2    0.21    2.49  INTRA BF
 304 ASN   ( 112-)  B      O   <->  311 ASN   ( 119-)  B      ND2    0.18    2.52  INTRA
 139 HIS   ( 143-)  A      NE2 <->  393 HOH   ( 217 )  A      O      0.15    2.55  INTRA BF
 353 ASN   ( 167-)  B      ND2 <->  394 HOH   ( 224 )  B      O      0.14    2.56  INTRA BL
 180 ASN   ( 190-)  A      CB  <->  393 HOH   ( 215 )  A      O      0.13    2.67  INTRA BL
 107 ASN   ( 111-)  A      O   <->  306 ASN   ( 114-)  B      ND2    0.13    2.57  INTRA BL
  19 PHE   (  23-)  A      CD1 <->   24 ILE   (  28-)  A      CD1    0.11    3.09  INTRA
 328 GLU   ( 136-)  B      OE2 <->  372 LEU   ( 186-)  B      N      0.11    2.59  INTRA
 306 ASN   ( 114-)  B      OD1 <->  309 LYS   ( 117-)  B      N      0.11    2.59  INTRA BL
 244 LYS   (  52-)  B      NZ  <->  255 GLN   (  63-)  B      OE1    0.10    2.60  INTRA BF
  13 GLU   (  17-)  A      OE2 <->  192 TYR   ( 202-)  A      OH     0.10    2.30  INTRA
 268 VAL   (  76-)  B      CG2 <->  269 ARG   (  77-)  B      N      0.09    2.91  INTRA BL
 263 GLN   (  71-)  B      O   <->  266 ALA   (  74-)  B      N      0.09    2.61  INTRA BL
 328 GLU   ( 136-)  B      OE2 <->  371 LEU   ( 185-)  B      N      0.08    2.62  INTRA
 236 GLU   (  44-)  B      O   <->  240 PHE   (  48-)  B      N      0.07    2.63  INTRA BF
   9 ARG   (  13-)  A      CZ  <->  196 ARG   ( 206-)  A      NH2    0.07    3.03  INTRA BF
 138 ASN   ( 142-)  A      ND2 <->  142 TYR   ( 152-)  A      O      0.07    2.63  INTRA BF
 342 ASN   ( 156-)  B      N   <->  343 ASN   ( 157-)  B      N      0.06    2.54  INTRA BF
   6 PHE   (  10-)  A      O   <->    8 ALA   (  12-)  A      N      0.06    2.64  INTRA BL
 132 GLU   ( 136-)  A      OE2 <->  176 LEU   ( 186-)  A      N      0.06    2.64  INTRA BL
 132 GLU   ( 136-)  A      O   <->  136 LYS   ( 140-)  A      N      0.05    2.65  INTRA BL
 160 ASP   ( 170-)  A      OD2 <->  196 ARG   ( 206-)  A      NH2    0.05    2.65  INTRA BF
  62 ASP   (  66-)  A      N   <->   63 LEU   (  67-)  A      N      0.05    2.55  INTRA BF
 277 ILE   (  85-)  B      N   <->  278 CYS   (  86-)  B      N      0.05    2.55  INTRA BL
 356 ASP   ( 170-)  B      OD2 <->  392 ARG   ( 206-)  B      NH2    0.05    2.65  INTRA BF
 360 THR   ( 174-)  B      N   <->  361 LYS   ( 175-)  B      N      0.05    2.55  INTRA BF
 110 ASN   ( 114-)  A      ND2 <->  113 LYS   ( 117-)  A      N      0.04    2.81  INTRA
 362 TYR   ( 176-)  B      CB  <->  363 PRO   ( 177-)  B      CD     0.04    3.06  INTRA BF
  69 GLN   (  73-)  A      OE1 <->  100 GLN   ( 104-)  A      NE2    0.04    2.66  INTRA BF
 157 ASN   ( 167-)  A      ND2 <->  393 HOH   ( 213 )  A      O      0.04    2.66  INTRA BL
 323 TRP   ( 131-)  B      C   <->  325 GLY   ( 133-)  B      N      0.04    2.86  INTRA BL
 291 ILE   (  99-)  B      CD1 <->  330 LEU   ( 138-)  B      CD1    0.04    3.16  INTRA BL
  39 VAL   (  43-)  A      CG1 <->   43 ASN   (  47-)  A      ND2    0.03    3.07  INTRA BF
 363 PRO   ( 177-)  B      CB  <->  364 SER   ( 178-)  B      N      0.03    2.67  INTRA BF
 143 PHE   ( 153-)  A      N   <->  152 ASP   ( 162-)  A      OD1    0.03    2.67  INTRA BL
 202 PHE   (  10-)  B      O   <->  204 ALA   (  12-)  B      N      0.03    2.67  INTRA BL
 189 ILE   ( 199-)  A      CG1 <->  190 LYS   ( 200-)  A      N      0.03    2.97  INTRA
 138 ASN   ( 142-)  A      O   <->  139 HIS   ( 143-)  A      C      0.02    2.58  INTRA BF
 381 ASN   ( 195-)  B      C   <->  382 LEU   ( 196-)  B      C      0.02    2.78  INTRA BF
 152 ASP   ( 162-)  A      OD1 <->  179 HIS   ( 189-)  A      NE2    0.02    2.68  INTRA BL
 324 SER   ( 132-)  B      N   <->  325 GLY   ( 133-)  B      N      0.02    2.58  INTRA BL
 334 ASN   ( 142-)  B      N   <->  335 HIS   ( 143-)  B      N      0.02    2.58  INTRA BF
 124 LEU   ( 128-)  A      N   <->  125 PRO   ( 129-)  A      CD     0.02    2.98  INTRA BL
   5 TYR   (   9-)  A      CG  <->    6 PHE   (  10-)  A      N      0.02    2.98  INTRA BL
 135 LEU   ( 139-)  A      O   <->  139 HIS   ( 143-)  A      N      0.01    2.69  INTRA BF
 156 PHE   ( 166-)  A      CD2 <->  157 ASN   ( 167-)  A      N      0.01    2.99  INTRA BL
 180 ASN   ( 190-)  A      CA  <->  393 HOH   ( 215 )  A      O      0.01    2.79  INTRA BL

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

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.

 337 TYR   ( 151-)  B      -6.23
  84 GLU   (  88-)  A      -6.09
 280 GLU   (  88-)  B      -5.98
  52 PHE   (  56-)  A      -5.66
 248 PHE   (  56-)  B      -5.47
 172 ASN   ( 182-)  A      -5.46
 221 GLU   (  29-)  B      -5.36
 368 ASN   ( 182-)  B      -5.35
 391 ASN   ( 205-)  B      -5.34
 138 ASN   ( 142-)  A      -5.28
  25 GLU   (  29-)  A      -5.24
 230 ASN   (  38-)  B      -5.22
 141 TYR   ( 151-)  A      -5.15
 317 ASN   ( 125-)  B      -5.15
 250 GLN   (  58-)  B      -5.14
  34 ASN   (  38-)  A      -5.08
 342 ASN   ( 156-)  B      -5.01

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

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.

 229 VAL   (  37-)  B   -2.75

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.

 110 ASN   ( 114-)  A     -  113 LYS   ( 117-)  A        -1.78

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

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

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

 393 HOH   ( 214 )  A      O
 393 HOH   ( 228 )  A      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.

  59 GLN   (  63-)  A
 107 ASN   ( 111-)  A
 110 ASN   ( 114-)  A
 147 ASN   ( 157-)  A
 188 ASN   ( 198-)  A
 195 ASN   ( 205-)  A
 265 GLN   (  73-)  B
 303 ASN   ( 111-)  B
 343 ASN   ( 157-)  B
 376 ASN   ( 190-)  B
 384 ASN   ( 198-)  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.

   6 PHE   (  10-)  A      N
  32 GLY   (  36-)  A      N
  38 PHE   (  42-)  A      N
  46 LYS   (  50-)  A      N
  54 GLN   (  58-)  A      N
  66 ALA   (  70-)  A      N
  73 ARG   (  77-)  A      NH1
  73 ARG   (  77-)  A      NH2
 110 ASN   ( 114-)  A      N
 116 GLU   ( 120-)  A      N
 170 LEU   ( 180-)  A      N
 202 PHE   (  10-)  B      N
 234 PHE   (  42-)  B      N
 262 ALA   (  70-)  B      N
 263 GLN   (  71-)  B      N
 269 ARG   (  77-)  B      NH1
 296 GLN   ( 104-)  B      NE2
 303 ASN   ( 111-)  B      ND2
 306 ASN   ( 114-)  B      N
 312 GLU   ( 120-)  B      N
 376 ASN   ( 190-)  B      ND2

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.

  47 GLU   (  51-)  A   H-bonding suggests Gln
 132 GLU   ( 136-)  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:

  1st generation packing quality :  -0.086
  2nd generation packing quality :  -1.068
  Ramachandran plot appearance   :  -2.339
  chi-1/chi-2 rotamer normality  :  -3.080 (poor)
  Backbone conformation          :  -0.050

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.353 (tight)
  Bond angles                    :   0.673
  Omega angle restraints         :   0.243 (tight)
  Side chain planarity           :   0.269 (tight)
  Improper dihedral distribution :   0.701
  B-factor distribution          :   0.470
  Inside/Outside distribution    :   1.035

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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.1
  2nd generation packing quality :   0.5
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.353 (tight)
  Bond angles                    :   0.673
  Omega angle restraints         :   0.243 (tight)
  Side chain planarity           :   0.269 (tight)
  Improper dihedral distribution :   0.701
  B-factor distribution          :   0.470
  Inside/Outside distribution    :   1.035
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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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,
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    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,
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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.