WHAT IF Check report

This file was created 2012-01-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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

Verification log for pdb1vai.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 : 0.702
CA-only RMS fit for the two chains : 0.394

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

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 340 MCM   (   6-)  C  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 333 ALA   (   2-)  C  -   N   bound to  339 ACE   (   1-)  C  -   C

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'.

   2 LYS   (   2-)  A      CG
   2 LYS   (   2-)  A      CD
   2 LYS   (   2-)  A      CE
   2 LYS   (   2-)  A      NZ
   4 ASP   (   4-)  A      CG
   4 ASP   (   4-)  A      OD1
   4 ASP   (   4-)  A      OD2
  65 GLN   (  65-)  A      CG
  65 GLN   (  65-)  A      CD
  65 GLN   (  65-)  A      OE1
  65 GLN   (  65-)  A      NE2
  68 LYS   (  68-)  A      CG
  68 LYS   (  68-)  A      CD
  68 LYS   (  68-)  A      CE
  68 LYS   (  68-)  A      NZ
 168 LYS   (   2-)  B      CG
 168 LYS   (   2-)  B      CD
 168 LYS   (   2-)  B      CE
 168 LYS   (   2-)  B      NZ
 189 GLN   (  23-)  B      CG
 189 GLN   (  23-)  B      CD
 189 GLN   (  23-)  B      OE1
 189 GLN   (  23-)  B      NE2
 196 GLN   (  30-)  B      CG
 196 GLN   (  30-)  B      CD
And so on for a total of 66 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :293.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  85 ARG   (  85-)  A
  92 ARG   (  92-)  A
 251 ARG   (  85-)  B
 258 ARG   (  92-)  B

Warning: Tyrosine convention problem

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

 149 TYR   ( 149-)  A
 315 TYR   ( 149-)  B

Warning: Phenylalanine convention problem

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

  32 PHE   (  32-)  A
  46 PHE   (  46-)  A
  60 PHE   (  60-)  A
 104 PHE   ( 104-)  A
 112 PHE   ( 112-)  A
 198 PHE   (  32-)  B
 226 PHE   (  60-)  B
 270 PHE   ( 104-)  B
 291 PHE   ( 125-)  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.

  21 ASP   (  21-)  A
  34 ASP   (  34-)  A
  95 ASP   (  95-)  A
 133 ASP   ( 133-)  A
 136 ASP   ( 136-)  A
 200 ASP   (  34-)  B
 261 ASP   (  95-)  B
 299 ASP   ( 133-)  B
 302 ASP   ( 136-)  B
 311 ASP   ( 145-)  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.

  19 GLU   (  19-)  A
  76 GLU   (  76-)  A
 242 GLU   (  76-)  B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.303
RMS-deviation in bond distances: 0.007

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.

  46 PHE   (  46-)  A      N    CA   C    97.21   -5.0
 212 PHE   (  46-)  B      N    CA   C    97.04   -5.1
 323 VAL   ( 157-)  B      N    CA   C    99.36   -4.2

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.617
RMS-deviation in bond angles: 1.398

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.

  19 GLU   (  19-)  A
  21 ASP   (  21-)  A
  34 ASP   (  34-)  A
  76 GLU   (  76-)  A
  85 ARG   (  85-)  A
  92 ARG   (  92-)  A
  95 ASP   (  95-)  A
 133 ASP   ( 133-)  A
 136 ASP   ( 136-)  A
 200 ASP   (  34-)  B
 242 GLU   (  76-)  B
 251 ARG   (  85-)  B
 258 ARG   (  92-)  B
 261 ASP   (  95-)  B
 299 ASP   ( 133-)  B
 302 ASP   ( 136-)  B
 311 ASP   ( 145-)  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.

 212 PHE   (  46-)  B    5.47
  46 PHE   (  46-)  A    5.40
 321 LYS   ( 155-)  B    4.16
 323 VAL   ( 157-)  B    4.12
 324 VAL   ( 158-)  B    4.08

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.

  69 PRO   (  69-)  A    -2.6
 144 HIS   ( 144-)  A    -2.5
  54 MET   (  54-)  A    -2.4
 220 MET   (  54-)  B    -2.4
 235 PRO   (  69-)  B    -2.3
 230 MET   (  64-)  B    -2.3
 163 THR   ( 163-)  A    -2.3
 127 LYS   ( 127-)  A    -2.3
  53 PHE   (  53-)  A    -2.2
 148 PRO   ( 148-)  A    -2.2
  82 ARG   (  82-)  A    -2.2
 313 GLY   ( 147-)  B    -2.1
 170 ASP   (   4-)  B    -2.1
 329 THR   ( 163-)  B    -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.

   3 GLY   (   3-)  A  Poor phi/psi
   4 ASP   (   4-)  A  Poor phi/psi
  43 ASN   (  43-)  A  Poor phi/psi
  53 PHE   (  53-)  A  Poor phi/psi
  59 GLY   (  59-)  A  Poor phi/psi
  64 MET   (  64-)  A  Poor phi/psi
  83 ASN   (  83-)  A  Poor phi/psi
  93 THR   (  93-)  A  Poor phi/psi
 100 THR   ( 100-)  A  Poor phi/psi
 151 ASN   ( 151-)  A  Poor phi/psi
 209 ASN   (  43-)  B  Poor phi/psi
 219 PHE   (  53-)  B  Poor phi/psi
 225 GLY   (  59-)  B  Poor phi/psi
 230 MET   (  64-)  B  Poor phi/psi
 249 ASN   (  83-)  B  Poor phi/psi
 259 THR   (  93-)  B  Poor phi/psi
 266 THR   ( 100-)  B  Poor phi/psi
 313 GLY   ( 147-)  B  Poor phi/psi
 317 ASN   ( 151-)  B  Poor phi/psi
 334 ALA   (   3-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.962

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   5 PRO   (   5-)  A      0
  13 ALA   (  13-)  A      0
  15 ASN   (  15-)  A      0
  22 LYS   (  22-)  A      0
  25 ALA   (  25-)  A      0
  38 SER   (  38-)  A      0
  42 ASN   (  42-)  A      0
  43 ASN   (  43-)  A      0
  46 PHE   (  46-)  A      0
  47 HIS   (  47-)  A      0
  48 ARG   (  48-)  A      0
  51 PRO   (  51-)  A      0
  53 PHE   (  53-)  A      0
  54 MET   (  54-)  A      0
  56 GLN   (  56-)  A      0
  64 MET   (  64-)  A      0
  70 ASN   (  70-)  A      0
  78 ASP   (  78-)  A      0
  79 ASN   (  79-)  A      0
  83 ASN   (  83-)  A      0
  84 THR   (  84-)  A      0
  85 ARG   (  85-)  A      0
  90 MET   (  90-)  A      0
  91 ALA   (  91-)  A      0
  93 THR   (  93-)  A      0
And so on for a total of 146 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 : 1.464

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].

  69 PRO   (  69-)  A   -50.7 half-chair C-beta/C-alpha (-54 degrees)
 148 PRO   ( 148-)  A   -63.3 envelop C-beta (-72 degrees)
 235 PRO   (  69-)  B   -57.8 half-chair C-beta/C-alpha (-54 degrees)
 335 PRO   (   4-)  C  -117.4 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 336 ALA   (   5-)  C      C   <->  340 MCM   (   6-)  C      N      1.36    1.34  INTRA B3
 336 ALA   (   5-)  C      CA  <->  340 MCM   (   6-)  C      N      0.70    2.40  INTRA
 258 ARG   (  92-)  B      N   <->  333 ALA   (   2-)  C      CB     0.42    2.68  INTRA
 336 ALA   (   5-)  C      O   <->  340 MCM   (   6-)  C      N      0.40    2.30  INTRA
  85 ARG   (  85-)  A      NH2 <->  136 ASP   ( 136-)  A      OD1    0.36    2.34  INTRA
 333 ALA   (   2-)  C      CB  <->  339 ACE   (   1-)  C      CH3    0.32    2.88  INTRA
 312 VAL   ( 146-)  B      N   <->  315 TYR   ( 149-)  B      O      0.31    2.39  INTRA BF
  82 ARG   (  82-)  A      NH1 <->  341 HOH   ( 254 )  A      O      0.23    2.47  INTRA
  85 ARG   (  85-)  A      NH2 <->  136 ASP   ( 136-)  A      CG     0.20    2.90  INTRA
  36 VAL   (  36-)  A      CG2 <->   37 ASN   (  37-)  A      N      0.19    2.81  INTRA
 257 ALA   (  91-)  B      C   <->  333 ALA   (   2-)  C      CB     0.16    3.04  INTRA
 167 ALA   (   1-)  B      C   <->  169 GLY   (   3-)  B      N      0.16    2.74  INTRA BF
 206 PHE   (  40-)  B      O   <->  233 LYS   (  67-)  B      NZ     0.15    2.55  INTRA BL
 168 LYS   (   2-)  B      CA  <->  185 GLU   (  19-)  B      CD     0.14    3.06  INTRA BF
  19 GLU   (  19-)  A      OE1 <->  127 LYS   ( 127-)  A      NZ     0.13    2.57  INTRA
   3 GLY   (   3-)  A      N   <->   21 ASP   (  21-)  A      CA     0.13    2.97  INTRA
 168 LYS   (   2-)  B      CB  <->  293 LYS   ( 127-)  B      NZ     0.12    2.98  INTRA BF
   3 GLY   (   3-)  A      CA  <->   22 LYS   (  22-)  A      N      0.12    2.98  INTRA
 167 ALA   (   1-)  B      CB  <->  185 GLU   (  19-)  B      O      0.12    2.68  INTRA
 257 ALA   (  91-)  B      CB  <->  333 ALA   (   2-)  C      CB     0.12    3.08  INTRA
 258 ARG   (  92-)  B      CA  <->  333 ALA   (   2-)  C      CB     0.10    3.10  INTRA
  97 ASP   (  97-)  A      N   <->  341 HOH   ( 270 )  A      O      0.10    2.60  INTRA
  70 ASN   (  70-)  A      ND2 <->  341 HOH   ( 189 )  A      O      0.09    2.61  INTRA
 183 GLU   (  17-)  B      OE1 <->  296 LYS   ( 130-)  B      NZ     0.09    2.61  INTRA
 251 ARG   (  85-)  B      NH2 <->  302 ASP   ( 136-)  B      OD2    0.09    2.61  INTRA BL
And so on for a total of 54 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.

 118 ARG   ( 118-)  A      -8.17
  63 GLN   (  63-)  A      -6.62
 315 TYR   ( 149-)  B      -6.53
 321 LYS   ( 155-)  B      -5.77
 117 GLN   ( 117-)  A      -5.68
 155 LYS   ( 155-)  A      -5.58
 236 ASN   (  70-)  B      -5.43
  70 ASN   (  70-)  A      -5.39
 306 GLN   ( 140-)  B      -5.29
 203 ASN   (  37-)  B      -5.15
  37 ASN   (  37-)  A      -5.13
 245 ASN   (  79-)  B      -5.13
  79 ASN   (  79-)  A      -5.13
 232 GLN   (  66-)  B      -5.02

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.

 283 GLN   ( 117-)  B   -3.01
 284 ARG   ( 118-)  B   -2.98
 229 GLN   (  63-)  B   -2.81
 246 GLY   (  80-)  B   -2.72

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.

 244 ASP   (  78-)  B     -  247 LEU   (  81-)  B        -1.73
 276 ASN   ( 110-)  B     -  279 LEU   ( 113-)  B        -1.15
 282 GLY   ( 116-)  B     -  285 ASP   ( 119-)  B        -2.34

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.

 341 HOH   ( 220 )  A      O    -17.74   34.66   11.77
 341 HOH   ( 262 )  A      O     55.44   31.95   12.54
 342 HOH   ( 199 )  B      O     66.02   39.93   -2.45
 342 HOH   ( 211 )  B      O     65.42   40.68    0.08

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.

 341 HOH   ( 219 )  A      O
 341 HOH   ( 220 )  A      O
 341 HOH   ( 261 )  A      O
 341 HOH   ( 271 )  A      O
 342 HOH   ( 205 )  B      O
 342 HOH   ( 209 )  B      O
 342 HOH   ( 222 )  B      O
 342 HOH   ( 233 )  B      O
 342 HOH   ( 238 )  B      O
 342 HOH   ( 241 )  B      O
 342 HOH   ( 242 )  B      O
 342 HOH   ( 246 )  B      O
 342 HOH   ( 247 )  B      O
Unrecognized bound group for 336
  Bound atom=  340 MCM  (   6-) C      N

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.

  47 HIS   (  47-)  A
 150 GLN   ( 150-)  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.

 108 ALA   ( 108-)  A      N
 112 PHE   ( 112-)  A      N
 118 ARG   ( 118-)  A      N
 168 LYS   (   2-)  B      N
 169 GLY   (   3-)  B      N
 211 THR   (  45-)  B      OG1
 246 GLY   (  80-)  B      N
 258 ARG   (  92-)  B      N
 274 ALA   ( 108-)  B      N
 287 GLY   ( 121-)  B      N

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.

 187 ASP   (  21-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.408
  2nd generation packing quality :  -0.502
  Ramachandran plot appearance   :  -1.014
  chi-1/chi-2 rotamer normality  :  -1.962
  Backbone conformation          :  -0.808

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.303 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   0.266 (tight)
  Side chain planarity           :   0.111 (tight)
  Improper dihedral distribution :   0.589
  B-factor distribution          :   0.831
  Inside/Outside distribution    :   0.956

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :  -1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.303 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   0.266 (tight)
  Side chain planarity           :   0.111 (tight)
  Improper dihedral distribution :   0.589
  B-factor distribution          :   0.831
  Inside/Outside distribution    :   0.956
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
    D.Cremer and J.A.Pople,
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Quality Control
    G.Vriend and C.Sander,
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      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.