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 pdb3s0z.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 : 0.863
CA-only RMS fit for the two chains : 0.598

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: 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'.

  16 THR   (  62-)  A      CG2
  64 ASN   ( 110-)  A      CG
  64 ASN   ( 110-)  A      OD1
  64 ASN   ( 110-)  A      ND2
 236 THR   (  62-)  B      CG2
 284 ASN   ( 110-)  B      CG
 284 ASN   ( 110-)  B      OD1
 284 ASN   ( 110-)  B      ND2

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

  94 TYR   ( 140-)  A
 179 TYR   ( 229-)  A

Warning: Phenylalanine convention problem

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

   5 PHE   (  51-)  A
  24 PHE   (  70-)  A
 244 PHE   (  70-)  B
 347 PHE   ( 177-)  B
 406 PHE   ( 236-)  B
 410 PHE   ( 240-)  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.

  20 ASP   (  66-)  A
  44 ASP   (  90-)  A
  49 ASP   (  95-)  A
 162 ASP   ( 212-)  A
 217 ASP   ( 267-)  A
 240 ASP   (  66-)  B
 264 ASP   (  90-)  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

 |  0.996886 -0.000245  0.000127|
 | -0.000245  0.997044 -0.000486|
 |  0.000127 -0.000486  0.996382|
Proposed new scale matrix

 |  0.024652  0.014235  0.000004|
 |  0.000007  0.028458  0.000014|
 |  0.000000  0.000002  0.004662|
With corresponding cell

    A    =  40.570  B   =  40.583  C    = 214.506
    Alpha=  90.051  Beta=  89.994  Gamma= 120.018

The CRYST1 cell dimensions

    A    =  40.696  B   =  40.696  C    = 215.292
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 146.663
(Under-)estimated Z-score: 8.925

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.

 113 HIS   ( 159-)  A      CG   ND1  CE1 109.80    4.2
 190 PHE   ( 240-)  A      N    CA   C    98.97   -4.4
 247 VAL   (  73-)  B      C    CA   CB  101.72   -4.4
 261 LEU   (  87-)  B      CA   CB   CG  131.84    4.4
 392 GLY   ( 222-)  B      N    CA   C   125.13    4.4
 420 HIS   ( 250-)  B      CG   ND1  CE1 109.69    4.1

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.

  20 ASP   (  66-)  A
  44 ASP   (  90-)  A
  49 ASP   (  95-)  A
 162 ASP   ( 212-)  A
 217 ASP   ( 267-)  A
 240 ASP   (  66-)  B
 264 ASP   (  90-)  B

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.

 317 ALA   ( 143-)  B    4.93
 190 PHE   ( 240-)  A    4.72
  31 GLY   (  77-)  A    4.37
 185 ALA   ( 235-)  A    4.24
 392 GLY   ( 222-)  B    4.15

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -5.562

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.

 116 THR   ( 162-)  A    -3.4
 432 THR   ( 262-)  B    -3.2
 135 PRO   ( 185-)  A    -3.0
 345 PRO   ( 175-)  B    -3.0
 129 PRO   ( 179-)  A    -2.8
 261 LEU   (  87-)  B    -2.7
 127 PHE   ( 177-)  A    -2.7
 104 PRO   ( 150-)  A    -2.7
 347 PHE   ( 177-)  B    -2.7
 349 PRO   ( 179-)  B    -2.6
  24 PHE   (  70-)  A    -2.6
 336 THR   ( 162-)  B    -2.5
  81 GLY   ( 127-)  A    -2.4
 421 SER   ( 251-)  B    -2.4
 161 LYS   ( 211-)  A    -2.4
 125 PRO   ( 175-)  A    -2.4
 392 GLY   ( 222-)  B    -2.4
  65 LEU   ( 111-)  A    -2.4
 239 LEU   (  65-)  B    -2.3
 328 MET   ( 154-)  B    -2.3
 285 LEU   ( 111-)  B    -2.3
 425 SER   ( 255-)  B    -2.3
 289 LEU   ( 115-)  B    -2.3
 265 THR   (  91-)  B    -2.2
 418 MET   ( 248-)  B    -2.2
  15 HIS   (  61-)  A    -2.2
  69 LEU   ( 115-)  A    -2.2
 243 GLY   (  69-)  B    -2.2
 138 GLY   ( 188-)  A    -2.2
 198 MET   ( 248-)  A    -2.2
   8 LEU   (  54-)  A    -2.1
 296 HIS   ( 122-)  B    -2.1
 358 GLY   ( 188-)  B    -2.1
 384 LYS   ( 214-)  B    -2.1
  44 ASP   (  90-)  A    -2.1
 205 SER   ( 255-)  A    -2.1
 348 GLY   ( 178-)  B    -2.1
  40 VAL   (  86-)  A    -2.0
 357 PRO   ( 187-)  B    -2.0
 171 LEU   ( 221-)  A    -2.0
 190 PHE   ( 240-)  A    -2.0
 143 ASN   ( 193-)  A    -2.0
 337 PHE   ( 163-)  B    -2.0
 264 ASP   (  90-)  B    -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.

   2 ASP   (  48-)  A  omega poor
   9 ALA   (  55-)  A  Poor phi/psi
  11 ASN   (  57-)  A  Poor phi/psi, omega poor
  17 SER   (  63-)  A  omega poor
  18 TYR   (  64-)  A  omega poor
  21 MET   (  67-)  A  Poor phi/psi
  22 PRO   (  68-)  A  Poor phi/psi
  23 GLY   (  69-)  A  Poor phi/psi
  24 PHE   (  70-)  A  Poor phi/psi
  30 ASN   (  76-)  A  omega poor
  38 GLY   (  84-)  A  omega poor
  39 ARG   (  85-)  A  Poor phi/psi
  40 VAL   (  86-)  A  omega poor
  42 VAL   (  88-)  A  omega poor
  44 ASP   (  90-)  A  Poor phi/psi
  46 ALA   (  92-)  A  Poor phi/psi
  52 THR   (  98-)  A  omega poor
  62 GLU   ( 108-)  A  Poor phi/psi
  64 ASN   ( 110-)  A  Poor phi/psi
  68 ALA   ( 114-)  A  omega poor
  69 LEU   ( 115-)  A  Poor phi/psi
  74 HIS   ( 120-)  A  Poor phi/psi
  75 ALA   ( 121-)  A  Poor phi/psi
  80 MET   ( 126-)  A  Poor phi/psi
  81 GLY   ( 127-)  A  Poor phi/psi
And so on for a total of 88 lines.

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 : -5.738

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!

   7 GLN   (  53-)  A      0
   8 LEU   (  54-)  A      0
   9 ALA   (  55-)  A      0
  10 PRO   (  56-)  A      0
  19 LEU   (  65-)  A      0
  21 MET   (  67-)  A      0
  22 PRO   (  68-)  A      0
  24 PHE   (  70-)  A      0
  26 ALA   (  72-)  A      0
  30 ASN   (  76-)  A      0
  36 ASP   (  82-)  A      0
  39 ARG   (  85-)  A      0
  43 VAL   (  89-)  A      0
  44 ASP   (  90-)  A      0
  46 ALA   (  92-)  A      0
  47 TRP   (  93-)  A      0
  62 GLU   ( 108-)  A      0
  63 ILE   ( 109-)  A      0
  64 ASN   ( 110-)  A      0
  65 LEU   ( 111-)  A      0
  68 ALA   ( 114-)  A      0
  69 LEU   ( 115-)  A      0
  73 THR   ( 119-)  A      0
  74 HIS   ( 120-)  A      0
  75 ALA   ( 121-)  A      0
And so on for a total of 199 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 : 9.166

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!

  81 GLY   ( 127-)  A   3.19   14

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].

 104 PRO   ( 150-)  A   -13.3 half-chair C-alpha/N (-18 degrees)
 121 PRO   ( 171-)  A   137.9 envelop C-alpha (144 degrees)
 129 PRO   ( 179-)  A   -51.8 half-chair C-beta/C-alpha (-54 degrees)
 135 PRO   ( 185-)  A   -28.1 envelop C-alpha (-36 degrees)
 203 PRO   ( 253-)  A   163.2 half-chair C-alpha/N (162 degrees)
 230 PRO   (  56-)  B  -113.4 envelop C-gamma (-108 degrees)
 324 PRO   ( 150-)  B  -135.5 envelop C-delta (-144 degrees)
 341 PRO   ( 171-)  B   154.9 half-chair C-alpha/N (162 degrees)
 345 PRO   ( 175-)  B   -32.6 envelop C-alpha (-36 degrees)
 349 PRO   ( 179-)  B   -40.4 envelop C-alpha (-36 degrees)
 357 PRO   ( 187-)  B    44.8 envelop C-delta (36 degrees)
 411 PRO   ( 241-)  B    47.9 half-chair C-delta/C-gamma (54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 234 GLN   (  60-)  B      OE1 <->  250 ASN   (  76-)  B      CB     0.80    2.00  INTRA
 234 GLN   (  60-)  B      OE1 <->  250 ASN   (  76-)  B      CG     0.80    2.00  INTRA
 234 GLN   (  60-)  B      OE1 <->  250 ASN   (  76-)  B      ND2    0.51    2.19  INTRA
 406 PHE   ( 236-)  B      C   <->  408 ALA   ( 238-)  B      N      0.49    2.41  INTRA
 116 THR   ( 162-)  A      OG1 <->  117 PHE   ( 163-)  A      N      0.46    2.14  INTRA BL
  69 LEU   ( 115-)  A      CD2 <->   94 TYR   ( 140-)  A      CE2    0.46    2.74  INTRA BL
 116 THR   ( 162-)  A      C   <->  118 ALA   ( 164-)  A      N      0.44    2.46  INTRA BL
 139 HIS   ( 189-)  A      CE1 <->  170 ASN   ( 220-)  A      O      0.44    2.36  INTRA
  23 GLY   (  69-)  A      N   <->   27 VAL   (  73-)  A      CG2    0.43    2.67  INTRA
 279 ILE   ( 105-)  B      O   <->  284 ASN   ( 110-)  B      N      0.40    2.30  INTRA BL
  11 ASN   (  57-)  A      OD1 <->   35 ARG   (  81-)  A      NH2    0.40    2.30  INTRA
  59 ILE   ( 105-)  A      O   <->   64 ASN   ( 110-)  A      N      0.36    2.34  INTRA
 231 ASN   (  57-)  B      OD1 <->  255 ARG   (  81-)  B      NE     0.35    2.35  INTRA
 225 PHE   (  51-)  B      CE2 <->  278 TRP   ( 104-)  B      CG     0.35    2.85  INTRA
  21 MET   (  67-)  A      CB  <->   22 PRO   (  68-)  A      CD     0.34    2.76  INTRA
 145 THR   ( 195-)  A      CG2 <->  186 PHE   ( 236-)  A      CE1    0.33    2.87  INTRA
 225 PHE   (  51-)  B      CE2 <->  278 TRP   ( 104-)  B      CD1    0.32    2.88  INTRA
 100 ASN   ( 146-)  A      C   <->  101 GLN   ( 147-)  A      CG     0.32    2.78  INTRA BL
 296 HIS   ( 122-)  B      CB  <->  444  ZN   (1002-)  B     ZN      0.31    2.89  INTRA
 299 LYS   ( 125-)  B      CE  <->  419 SER   ( 249-)  B      OG     0.31    2.49  INTRA
  10 PRO   (  56-)  A      C   <->   11 ASN   (  57-)  A      ND2    0.31    2.69  INTRA BL
 307 HIS   ( 133-)  B      CE1 <->  313 THR   ( 139-)  B      OG1    0.29    2.51  INTRA
 121 PRO   ( 171-)  A      CB  <->  136 GLY   ( 186-)  A      CA     0.29    2.91  INTRA
 336 THR   ( 162-)  B      C   <->  338 ALA   ( 164-)  B      N      0.28    2.62  INTRA
  19 LEU   (  65-)  A      N   <->   47 TRP   (  93-)  A      CZ3    0.28    2.82  INTRA BL
And so on for a total of 211 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 166 LYS   ( 216-)  A      -6.27
 386 LYS   ( 216-)  B      -6.18
 117 PHE   ( 163-)  A      -5.79
 285 LEU   ( 111-)  B      -5.64
  21 MET   (  67-)  A      -5.61
  35 ARG   (  81-)  A      -5.56
 325 GLN   ( 151-)  B      -5.54
 337 PHE   ( 163-)  B      -5.44
 105 GLN   ( 151-)  A      -5.42
 244 PHE   (  70-)  B      -5.39
  24 PHE   (  70-)  A      -5.38
 241 MET   (  67-)  B      -5.30
  65 LEU   ( 111-)  A      -5.23
 346 ASN   ( 176-)  B      -5.06
  39 ARG   (  85-)  A      -5.04

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 166 LYS   ( 216-)  A       168 - LEU    218- ( A)         -4.80

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.

 164 LYS   ( 214-)  A   -2.63

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.

 445 HOH   (  32 )  A      O      2.49   29.44   19.70
 445 HOH   ( 312 )  A      O      1.90  -14.11   20.21
 445 HOH   ( 343 )  A      O     20.46   14.52    0.14
 445 HOH   ( 344 )  A      O      1.76   -8.87   -1.09
 446 HOH   (  16 )  B      O     33.65   17.29  -21.00
 446 HOH   ( 347 )  B      O    -13.86    9.13   24.85

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.

 445 HOH   (  15 )  A      O
 445 HOH   (  31 )  A      O
 445 HOH   ( 281 )  A      O
 445 HOH   ( 284 )  A      O
 445 HOH   ( 288 )  A      O
 445 HOH   ( 313 )  A      O
 445 HOH   ( 314 )  A      O
 445 HOH   ( 315 )  A      O
 445 HOH   ( 320 )  A      O
 445 HOH   ( 321 )  A      O
 445 HOH   ( 324 )  A      O
 445 HOH   ( 328 )  A      O
 445 HOH   ( 329 )  A      O
 445 HOH   ( 331 )  A      O
 445 HOH   ( 334 )  A      O
 445 HOH   ( 336 )  A      O
 445 HOH   ( 337 )  A      O
 445 HOH   ( 339 )  A      O
 445 HOH   ( 342 )  A      O
 445 HOH   ( 343 )  A      O
 445 HOH   ( 345 )  A      O
 445 HOH   ( 359 )  A      O
 445 HOH   ( 360 )  A      O
 445 HOH   ( 363 )  A      O
 445 HOH   ( 365 )  A      O
 445 HOH   ( 366 )  A      O
 446 HOH   (   5 )  B      O
 446 HOH   ( 271 )  B      O
 446 HOH   ( 275 )  B      O
 446 HOH   ( 287 )  B      O
 446 HOH   ( 302 )  B      O
 446 HOH   ( 307 )  B      O
 446 HOH   ( 308 )  B      O
 446 HOH   ( 310 )  B      O
 446 HOH   ( 311 )  B      O
 446 HOH   ( 312 )  B      O
 446 HOH   ( 316 )  B      O
 446 HOH   ( 317 )  B      O
 446 HOH   ( 320 )  B      O
 446 HOH   ( 322 )  B      O
 446 HOH   ( 323 )  B      O
 446 HOH   ( 330 )  B      O
 446 HOH   ( 332 )  B      O
 446 HOH   ( 339 )  B      O
 446 HOH   ( 344 )  B      O
 446 HOH   ( 349 )  B      O
 446 HOH   ( 351 )  B      O
 446 HOH   ( 353 )  B      O
Metal-coordinating Histidine residue 139 fixed to   1
Metal-coordinating Histidine residue 294 fixed to   1
Metal-coordinating Histidine residue 296 fixed to   1
Metal-coordinating Histidine residue 359 fixed to   1

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.

  11 ASN   (  57-)  A
  15 HIS   (  61-)  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.

  21 MET   (  67-)  A      N
  23 GLY   (  69-)  A      N
  29 SER   (  75-)  A      N
  38 GLY   (  84-)  A      N
  39 ARG   (  85-)  A      N
  48 THR   (  94-)  A      N
  52 THR   (  98-)  A      N
  53 ALA   (  99-)  A      N
  59 ILE   ( 105-)  A      N
  69 LEU   ( 115-)  A      N
  74 HIS   ( 120-)  A      N
  77 GLN   ( 123-)  A      N
  84 ASP   ( 130-)  A      N
  93 THR   ( 139-)  A      OG1
  96 ASN   ( 142-)  A      ND2
 100 ASN   ( 146-)  A      N
 100 ASN   ( 146-)  A      ND2
 105 GLN   ( 151-)  A      N
 113 HIS   ( 159-)  A      N
 118 ALA   ( 164-)  A      N
 119 ALA   ( 165-)  A      N
 127 PHE   ( 177-)  A      N
 132 VAL   ( 182-)  A      N
 136 GLY   ( 186-)  A      N
 152 ASP   ( 202-)  A      N
And so on for a total of 90 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  15 HIS   (  61-)  A      ND1
  74 HIS   ( 120-)  A      NE2
  78 ASP   ( 124-)  A      OD2
 149 ASP   ( 199-)  A      OD1
 162 ASP   ( 212-)  A      OD2
 234 GLN   (  60-)  B      OE1
 235 HIS   (  61-)  B      ND1
 320 ASN   ( 146-)  B      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.

  44 ASP   (  90-)  A   H-bonding suggests Asn; but Alt-Rotamer
  62 GLU   ( 108-)  A   H-bonding suggests Gln
 149 ASP   ( 199-)  A   H-bonding suggests Asn
 162 ASP   ( 212-)  A   H-bonding suggests Asn
 204 ASP   ( 254-)  A   H-bonding suggests Asn; but Alt-Rotamer
 217 ASP   ( 267-)  A   H-bonding suggests Asn
 264 ASP   (  90-)  B   H-bonding suggests Asn; but Alt-Rotamer
 382 ASP   ( 212-)  B   H-bonding suggests Asn; but Alt-Rotamer
 424 ASP   ( 254-)  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 :  -2.214
  2nd generation packing quality :  -3.322 (poor)
  Ramachandran plot appearance   :  -5.562 (bad)
  chi-1/chi-2 rotamer normality  :  -5.738 (bad)
  Backbone conformation          :  -1.201

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.706
  Bond angles                    :   0.889
  Omega angle restraints         :   1.667 (loose)
  Side chain planarity           :   0.692
  Improper dihedral distribution :   0.922
  B-factor distribution          :   0.510
  Inside/Outside distribution    :   1.012

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.4
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -2.8
  chi-1/chi-2 rotamer normality  :  -3.5 (poor)
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.706
  Bond angles                    :   0.889
  Omega angle restraints         :   1.667 (loose)
  Side chain planarity           :   0.692
  Improper dihedral distribution :   0.922
  B-factor distribution          :   0.510
  Inside/Outside distribution    :   1.012
==============

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

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Bond lengths and angles, DNA/RNA
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    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
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    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      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.