WHAT IF Check report

This file was created 2011-12-17 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb3prb.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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'.

 223 LYS   ( 223-)  A      CG
 223 LYS   ( 223-)  A      CD
 223 LYS   ( 223-)  A      CE
 223 LYS   ( 223-)  A      NZ
 446 LYS   ( 223-)  B      CG
 446 LYS   ( 223-)  B      CD
 446 LYS   ( 223-)  B      CE
 446 LYS   ( 223-)  B      NZ
 447 LYS   ( 224-)  B      CG
 447 LYS   ( 224-)  B      CD
 447 LYS   ( 224-)  B      CE
 447 LYS   ( 224-)  B      NZ

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

Crystal temperature (K) :100.000

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

  15 TYR   (  15-)  A
 238 TYR   (  15-)  B
 258 TYR   (  35-)  B
 364 TYR   ( 141-)  B

Warning: Phenylalanine convention problem

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

  47 PHE   (  47-)  A
  80 PHE   (  80-)  A
 189 PHE   ( 189-)  A
 244 PHE   (  21-)  B
 270 PHE   (  47-)  B
 303 PHE   (  80-)  B
 353 PHE   ( 130-)  B
 439 PHE   ( 216-)  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.

  17 ASP   (  17-)  A
  22 ASP   (  22-)  A
  65 ASP   (  65-)  A
  84 ASP   (  84-)  A
 151 ASP   ( 151-)  A
 240 ASP   (  17-)  B
 281 ASP   (  58-)  B
 373 ASP   ( 150-)  B
 433 ASP   ( 210-)  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.

  59 GLU   (  59-)  A
  63 GLU   (  63-)  A
  68 GLU   (  68-)  A
 147 GLU   ( 147-)  A
 158 GLU   ( 158-)  A
 212 GLU   ( 212-)  A
 221 GLU   ( 221-)  A
 249 GLU   (  26-)  B
 250 GLU   (  27-)  B
 255 GLU   (  32-)  B
 286 GLU   (  63-)  B
 291 GLU   (  68-)  B
 294 GLU   (  71-)  B
 370 GLU   ( 147-)  B
 426 GLU   ( 203-)  B
 441 GLU   ( 218-)  B

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.997402  0.001122 -0.000633|
 |  0.001122  0.995548  0.000158|
 | -0.000633  0.000158  0.996223|
Proposed new scale matrix

 |  0.018055 -0.000020  0.000011|
 | -0.000017  0.015407 -0.000002|
 |  0.000004 -0.000001  0.006755|
With corresponding cell

    A    =  55.387  B   =  64.907  C    = 148.049
    Alpha=  89.982  Beta=  90.073  Gamma=  89.871

The CRYST1 cell dimensions

    A    =  55.532  B   =  65.199  C    = 148.616
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 193.209
(Under-)estimated Z-score: 10.244

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.

 142 ARG   ( 142-)  A      CG   CD   NE  117.71    4.2

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.

  17 ASP   (  17-)  A
  22 ASP   (  22-)  A
  59 GLU   (  59-)  A
  63 GLU   (  63-)  A
  65 ASP   (  65-)  A
  68 GLU   (  68-)  A
  84 ASP   (  84-)  A
 147 GLU   ( 147-)  A
 151 ASP   ( 151-)  A
 158 GLU   ( 158-)  A
 212 GLU   ( 212-)  A
 221 GLU   ( 221-)  A
 240 ASP   (  17-)  B
 249 GLU   (  26-)  B
 250 GLU   (  27-)  B
 255 GLU   (  32-)  B
 281 ASP   (  58-)  B
 286 GLU   (  63-)  B
 291 GLU   (  68-)  B
 294 GLU   (  71-)  B
 370 GLU   ( 147-)  B
 373 ASP   ( 150-)  B
 426 GLU   ( 203-)  B
 433 ASP   ( 210-)  B
 441 GLU   ( 218-)  B

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.

 123 SER   ( 123-)  A    -2.6
 332 ILE   ( 109-)  B    -2.5
  23 THR   (  23-)  A    -2.5
 109 ILE   ( 109-)  A    -2.4
 193 ILE   ( 193-)  A    -2.3
 246 THR   (  23-)  B    -2.2
 330 LEU   ( 107-)  B    -2.2
 331 THR   ( 108-)  B    -2.2
 143 ILE   ( 143-)  A    -2.1

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   (  17-)  A  Poor phi/psi
  18 GLY   (  18-)  A  Poor phi/psi
  31 LYS   (  31-)  A  omega poor
  79 ALA   (  79-)  A  Poor phi/psi
 112 ASP   ( 112-)  A  Poor phi/psi
 123 SER   ( 123-)  A  Poor phi/psi
 141 TYR   ( 141-)  A  omega poor
 167 LEU   ( 167-)  A  Poor phi/psi
 176 ASN   ( 176-)  A  Poor phi/psi
 264 TYR   (  41-)  B  Poor phi/psi
 269 ILE   (  46-)  B  omega poor
 290 GLY   (  67-)  B  Poor phi/psi
 302 ALA   (  79-)  B  Poor phi/psi
 335 ASP   ( 112-)  B  Poor phi/psi
 354 ASN   ( 131-)  B  omega poor
 364 TYR   ( 141-)  B  omega poor
 372 VAL   ( 149-)  B  omega poor
 390 LEU   ( 167-)  B  Poor phi/psi
 415 ASN   ( 192-)  B  Poor phi/psi
 445 ARG   ( 222-)  B  omega poor
 446 LYS   ( 223-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.337

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 LYS   (   4-)  A      0
  11 SER   (  11-)  A      0
  16 VAL   (  16-)  A      0
  22 ASP   (  22-)  A      0
  32 GLU   (  32-)  A      0
  34 ILE   (  34-)  A      0
  41 TYR   (  41-)  A      0
  43 PRO   (  43-)  A      0
  48 ALA   (  48-)  A      0
  50 GLU   (  50-)  A      0
  52 GLN   (  52-)  A      0
  53 VAL   (  53-)  A      0
  54 LEU   (  54-)  A      0
  66 VAL   (  66-)  A      0
  78 LYS   (  78-)  A      0
  79 ALA   (  79-)  A      0
  80 PHE   (  80-)  A      0
 105 LYS   ( 105-)  A      0
 112 ASP   ( 112-)  A      0
 120 SER   ( 120-)  A      0
 122 ASN   ( 122-)  A      0
 123 SER   ( 123-)  A      0
 132 HIS   ( 132-)  A      0
 146 GLU   ( 146-)  A      0
 147 GLU   ( 147-)  A      0
And so on for a total of 147 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 336 GLY   ( 113-)  B   1.57   75

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].

  76 PRO   (  76-)  A  -122.5 half-chair C-delta/C-gamma (-126 degrees)
 165 PRO   ( 165-)  A   100.7 envelop C-beta (108 degrees)
 191 PRO   ( 191-)  A  -136.3 envelop C-delta (-144 degrees)
 260 PRO   (  37-)  B  -116.7 envelop C-gamma (-108 degrees)
 299 PRO   (  76-)  B  -139.9 envelop C-delta (-144 degrees)
 338 PRO   ( 115-)  B   -61.2 half-chair C-beta/C-alpha (-54 degrees)
 411 PRO   ( 188-)  B  -112.9 envelop C-gamma (-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.

 365 ARG   ( 142-)  B      NH2 <->  449 HOH   ( 295 )  B      O      0.64    2.06  INTRA BF
 198 MET   ( 198-)  A      SD  <->  412 PHE   ( 189-)  B      CE2    0.38    3.02  INTRA BF
 189 PHE   ( 189-)  A      CE1 <->  421 MET   ( 198-)  B      SD     0.33    3.07  INTRA BF
 194 GLN   ( 194-)  A      OE1 <->  197 LYS   ( 197-)  A      NZ     0.21    2.49  INTRA BL
 355 HIS   ( 132-)  B      CD2 <->  357 LEU   ( 134-)  B      N      0.21    2.89  INTRA BF
 291 GLU   (  68-)  B      OE2 <->  293 ARG   (  70-)  B      NH2    0.20    2.50  INTRA BF
 420 LYS   ( 197-)  B      NZ  <->  448 HOH   ( 331 )  A      O      0.20    2.50  INTRA
 222 ARG   ( 222-)  A      NH2 <->  428 LEU   ( 205-)  B      O      0.19    2.51  INTRA BF
 132 HIS   ( 132-)  A      CD2 <->  134 LEU   ( 134-)  A      N      0.16    2.94  INTRA BL
  91 ILE   (  91-)  A      CD1 <->  111 ILE   ( 111-)  A      CD1    0.16    3.04  INTRA BF
 295 VAL   (  72-)  B      CG1 <->  449 HOH   ( 299 )  B      O      0.15    2.65  INTRA BF
  70 ARG   (  70-)  A      N   <->  143 ILE   ( 143-)  A      O      0.11    2.59  INTRA BF
  95 GLU   (  95-)  A      OE1 <->   99 ARG   (  99-)  A      NH1    0.11    2.59  INTRA BL
  15 TYR   (  15-)  A      N   <->  140 LYS   ( 140-)  A      O      0.10    2.60  INTRA BF
 386 TYR   ( 163-)  B      OH  <->  426 GLU   ( 203-)  B      OE1    0.10    2.30  INTRA BL
 401 THR   ( 178-)  B      OG1 <->  436 LYS   ( 213-)  B      CE     0.09    2.71  INTRA BF
 247 THR   (  24-)  B      O   <->  265 GLY   (  42-)  B      N      0.09    2.61  INTRA BF
 329 GLY   ( 106-)  B      N   <->  341 ILE   ( 118-)  B      O      0.09    2.61  INTRA BF
  70 ARG   (  70-)  A      O   <->  143 ILE   ( 143-)  A      N      0.09    2.61  INTRA BL
 187 ALA   ( 187-)  A      N   <->  188 PRO   ( 188-)  A      CD     0.08    2.92  INTRA BL
 224 MET   (   1-)  B      N   <->  288 ASP   (  65-)  B      OD1    0.08    2.62  INTRA BF
 169 ASP   ( 169-)  A      N   <->  448 HOH   ( 276 )  A      O      0.08    2.62  INTRA BF
 297 LEU   (  74-)  B      N   <->  362 VAL   ( 139-)  B      O      0.07    2.63  INTRA BF
 232 LYS   (   9-)  B      NZ  <->  449 HOH   ( 245 )  B      O      0.07    2.63  INTRA BF
 274 GLY   (  51-)  B      N   <->  281 ASP   (  58-)  B      OD2    0.07    2.63  INTRA BL
  66 VAL   (  66-)  A      CG2 <->  148 VAL   ( 148-)  A      CG2    0.06    3.14  INTRA BL
 296 VAL   (  73-)  B      O   <->  449 HOH   ( 299 )  B      O      0.06    2.34  INTRA BF
 400 GLY   ( 177-)  B      O   <->  435 GLU   ( 212-)  B      N      0.06    2.64  INTRA BF
  24 THR   (  24-)  A      O   <->   42 GLY   (  42-)  A      N      0.05    2.65  INTRA BL
 344 ILE   ( 121-)  B      N   <->  449 HOH   ( 274 )  B      O      0.04    2.66  INTRA BF
 216 PHE   ( 216-)  A      N   <->  441 GLU   ( 218-)  B      O      0.04    2.66  INTRA BL
  68 GLU   (  68-)  A      OE2 <->  448 HOH   ( 303 )  A      O      0.04    2.36  INTRA BF
 340 LYS   ( 117-)  B      O   <->  352 ASP   ( 129-)  B      N      0.04    2.66  INTRA BF
 314 ILE   (  91-)  B      N   <->  349 VAL   ( 126-)  B      O      0.03    2.67  INTRA BF
 410 ALA   ( 187-)  B      N   <->  411 PRO   ( 188-)  B      CD     0.03    2.97  INTRA BL
 177 GLY   ( 177-)  A      O   <->  212 GLU   ( 212-)  A      N      0.03    2.67  INTRA BL
 290 GLY   (  67-)  B      N   <->  368 ILE   ( 145-)  B      O      0.02    2.68  INTRA BL
 433 ASP   ( 210-)  B      N   <->  449 HOH   ( 272 )  B      O      0.02    2.68  INTRA BF
  11 SER   (  11-)  A      OG  <->  146 GLU   ( 146-)  A      OE2    0.02    2.38  INTRA BL
   5 GLY   (   5-)  A      O   <->  448 HOH   ( 279 )  A      O      0.02    2.38  INTRA BL
  52 GLN   (  52-)  A      NE2 <->  162 MET   ( 162-)  A      SD     0.02    3.28  INTRA BL
 314 ILE   (  91-)  B      O   <->  349 VAL   ( 126-)  B      N      0.02    2.68  INTRA BF
  81 GLY   (  81-)  A      O   <->  136 GLY   ( 136-)  A      N      0.02    2.68  INTRA BL
  87 LYS   (  87-)  A      O   <->  130 PHE   ( 130-)  A      N      0.01    2.69  INTRA BL
 282 GLU   (  59-)  B      OE2 <->  301 LYS   (  78-)  B      NZ     0.01    2.69  INTRA BF
 195 THR   ( 195-)  A      CA  <->  198 MET   ( 198-)  A      CE     0.01    3.19  INTRA BF
 404 ILE   ( 181-)  B      N   <->  438 SER   ( 215-)  B      O      0.01    2.69  INTRA BL
 420 LYS   ( 197-)  B      NZ  <->  441 GLU   ( 218-)  B      CD     0.01    3.09  INTRA BL
 226 GLU   (   3-)  B      N   <->  449 HOH   ( 289 )  B      O      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: 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.

 306 ARG   (  83-)  B      -6.90
 222 ARG   ( 222-)  A      -6.71
 445 ARG   ( 222-)  B      -6.59
 398 ARG   ( 175-)  B      -6.27
 175 ARG   ( 175-)  A      -6.17
 258 TYR   (  35-)  B      -5.92
  35 TYR   (  35-)  A      -5.68
  83 ARG   (  83-)  A      -5.65
  40 ILE   (  40-)  A      -5.62
  52 GLN   (  52-)  A      -5.62
 275 GLN   (  52-)  B      -5.51
 263 ILE   (  40-)  B      -5.41
 412 PHE   ( 189-)  B      -5.12
 189 PHE   ( 189-)  A      -5.09

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: 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

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.

 448 HOH   ( 329 )  A      O     10.00   -0.39   21.22
 449 HOH   ( 309 )  B      O     29.13   -5.39   48.15

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.

 448 HOH   ( 273 )  A      O
 449 HOH   ( 279 )  B      O
 449 HOH   ( 295 )  B      O
 449 HOH   ( 307 )  B      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.

 355 HIS   ( 132-)  B
 425 ASN   ( 202-)  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.

  53 VAL   (  53-)  A      N
  70 ARG   (  70-)  A      NH1
 104 ILE   ( 104-)  A      N
 123 SER   ( 123-)  A      OG
 125 ARG   ( 125-)  A      NH1
 134 LEU   ( 134-)  A      N
 153 LYS   ( 153-)  A      NZ
 157 LYS   ( 157-)  A      NZ
 166 ARG   ( 166-)  A      N
 172 VAL   ( 172-)  A      N
 186 PHE   ( 186-)  A      N
 264 TYR   (  41-)  B      N
 275 GLN   (  52-)  B      NE2
 276 VAL   (  53-)  B      N
 292 GLU   (  69-)  B      N
 300 GLU   (  77-)  B      N
 337 ILE   ( 114-)  B      N
 341 ILE   ( 118-)  B      N

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.

 218 GLU   ( 218-)  A      OE2
 441 GLU   ( 218-)  B      OE2

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.

 449 HOH   ( 241 )  B      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.

  13 ASP   (  13-)  A   H-bonding suggests Asn; but Alt-Rotamer
 236 ASP   (  13-)  B   H-bonding suggests Asn; but Alt-Rotamer

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 :   0.083
  2nd generation packing quality :   0.298
  Ramachandran plot appearance   :  -0.137
  chi-1/chi-2 rotamer normality  :  -2.337
  Backbone conformation          :   1.311

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.566 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   0.978
  Side chain planarity           :   0.418 (tight)
  Improper dihedral distribution :   0.641
  B-factor distribution          :   0.380
  Inside/Outside distribution    :   0.988

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.566 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   0.978
  Side chain planarity           :   0.418 (tight)
  Improper dihedral distribution :   0.641
  B-factor distribution          :   0.380
  Inside/Outside distribution    :   0.988
==============

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Quality Control
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Checking checks
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