WHAT IF Check report

This file was created 2012-01-19 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 pdb2cfm.ent

Checks that need to be done early-on in validation

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.

 564 AMP   (1563-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   2 ARG   (   2-)  A      CB
   2 ARG   (   2-)  A      CG
   2 ARG   (   2-)  A      CD
   2 ARG   (   2-)  A      NE
   2 ARG   (   2-)  A      CZ
   2 ARG   (   2-)  A      NH1
   2 ARG   (   2-)  A      NH2
  99 LYS   (  99-)  A      CG
  99 LYS   (  99-)  A      CD
  99 LYS   (  99-)  A      CE
  99 LYS   (  99-)  A      NZ
 103 GLN   ( 103-)  A      CG
 103 GLN   ( 103-)  A      CD
 103 GLN   ( 103-)  A      OE1
 103 GLN   ( 103-)  A      NE2
 104 LYS   ( 104-)  A      CG
 104 LYS   ( 104-)  A      CD
 104 LYS   ( 104-)  A      CE
 104 LYS   ( 104-)  A      NZ
 127 THR   ( 127-)  A      OG1
 127 THR   ( 127-)  A      CG2
 129 GLU   ( 129-)  A      CG
 129 GLU   ( 129-)  A      CD
 129 GLU   ( 129-)  A      OE1
 129 GLU   ( 129-)  A      OE2
And so on for a total of 67 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) :100.000

Note: B-factor plot

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

Chain identifier: A

Nomenclature related problems

Warning: Tyrosine convention problem

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

  10 TYR   (  10-)  A
  43 TYR   (  43-)  A
 138 TYR   ( 138-)  A
 153 TYR   ( 153-)  A
 250 TYR   ( 250-)  A
 267 TYR   ( 267-)  A
 343 TYR   ( 343-)  A

Warning: Phenylalanine convention problem

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

  50 PHE   (  50-)  A
 107 PHE   ( 107-)  A
 143 PHE   ( 143-)  A
 179 PHE   ( 179-)  A
 196 PHE   ( 196-)  A
 246 PHE   ( 246-)  A
 319 PHE   ( 319-)  A
 446 PHE   ( 446-)  A
 479 PHE   ( 479-)  A
 520 PHE   ( 520-)  A

Warning: Aspartic acid convention problem

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

 474 ASP   ( 474-)  A

Warning: Glutamic acid convention problem

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

  62 GLU   (  62-)  A
  79 GLU   (  79-)  A
 280 GLU   ( 280-)  A
 297 GLU   ( 297-)  A
 335 GLU   ( 335-)  A
 363 GLU   ( 363-)  A
 537 GLU   ( 537-)  A

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: 0.421
RMS-deviation in bond distances: 0.015

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.

  54 ASP   (  54-)  A      N    CA   C   122.51    4.0
 109 GLN   ( 109-)  A      N    CA   C    94.05   -6.1
 147 GLU   ( 147-)  A      N    CA   C    99.65   -4.1
 358 ARG   ( 358-)  A      CA   CB   CG  103.22   -5.4
 366 LYS   ( 366-)  A      N    CA   C    99.80   -4.1
 514 PRO   ( 514-)  A      N    CA   CB  110.13    6.5

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.

  62 GLU   (  62-)  A
  79 GLU   (  79-)  A
 280 GLU   ( 280-)  A
 297 GLU   ( 297-)  A
 335 GLU   ( 335-)  A
 363 GLU   ( 363-)  A
 474 ASP   ( 474-)  A
 537 GLU   ( 537-)  A

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.

 109 GLN   ( 109-)  A    6.80
 364 ILE   ( 364-)  A    5.60
 366 LYS   ( 366-)  A    4.43
 106 PHE   ( 106-)  A    4.12
 147 GLU   ( 147-)  A    4.02

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.550

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

  43 TYR   (  43-)  A      CB   4.16
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : 0.085

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.

 524 PHE   ( 524-)  A    -2.7
 442 ARG   ( 442-)  A    -2.3
 110 PRO   ( 110-)  A    -2.1
 439 GLU   ( 439-)  A    -2.1
 379 THR   ( 379-)  A    -2.1
 180 HIS   ( 180-)  A    -2.1
 526 ARG   ( 526-)  A    -2.0
  41 ILE   (  41-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  55 GLU   (  55-)  A  Poor phi/psi
 128 GLY   ( 128-)  A  Poor phi/psi
 129 GLU   ( 129-)  A  Poor phi/psi
 194 SER   ( 194-)  A  Poor phi/psi
 271 LEU   ( 271-)  A  Poor phi/psi
 500 LYS   ( 500-)  A  Poor phi/psi
 560 GLU   ( 560-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.485

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!

  16 THR   (  16-)  A      0
  17 THR   (  17-)  A      0
  18 MSE   (  18-)  A      0
  33 VAL   (  33-)  A      0
  46 LEU   (  46-)  A      0
  49 VAL   (  49-)  A      0
  53 TRP   (  53-)  A      0
  55 GLU   (  55-)  A      0
  56 ARG   (  56-)  A      0
  71 MSE   (  71-)  A      0
 104 LYS   ( 104-)  A      0
 106 PHE   ( 106-)  A      0
 107 PHE   ( 107-)  A      0
 126 THR   ( 126-)  A      0
 127 THR   ( 127-)  A      0
 129 GLU   ( 129-)  A      0
 144 MSE   ( 144-)  A      0
 161 THR   ( 161-)  A      0
 162 MSE   ( 162-)  A      0
 177 MSE   ( 177-)  A      0
 180 HIS   ( 180-)  A      0
 191 MSE   ( 191-)  A      0
 196 PHE   ( 196-)  A      0
 208 ASN   ( 208-)  A      0
 215 GLN   ( 215-)  A      0
And so on for a total of 177 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 : 1.903

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  42 PRO   (  42-)  A    0.46 HIGH
 514 PRO   ( 514-)  A    0.00 LOW

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.

 458 THR   ( 458-)  A      CG2 <->  460 GLU   ( 460-)  A      CG     0.38    2.82  INTRA
 256 GLN   ( 256-)  A      NE2 <->  258 HIS   ( 258-)  A      NE2    0.34    2.66  INTRA BL
 391 ARG   ( 391-)  A      C   <->  395 MSE   ( 395-)  A      CE     0.31    2.89  INTRA
 328 MSE   ( 328-)  A      O   <->  332 ILE   ( 332-)  A      N      0.30    2.40  INTRA
 507 TYR   ( 507-)  A      C   <->  526 ARG   ( 526-)  A      NH2    0.27    2.83  INTRA
 320 ARG   ( 320-)  A      NH2 <->  565 HOH   (2265 )  A      O      0.26    2.44  INTRA
 372 LYS   ( 372-)  A      NZ  <->  565 HOH   (2301 )  A      O      0.26    2.44  INTRA
 392 ALA   ( 392-)  A      N   <->  395 MSE   ( 395-)  A      CE     0.25    2.85  INTRA
  31 LYS   (  31-)  A      NZ  <->  565 HOH   (2034 )  A      O      0.25    2.45  INTRA
 558 LYS   ( 558-)  A      NZ  <->  565 HOH   (2443 )  A      O      0.25    2.45  INTRA BF
 558 LYS   ( 558-)  A      NZ  <->  565 HOH   (2442 )  A      O      0.24    2.46  INTRA
 269 ARG   ( 269-)  A      NH2 <->  565 HOH   (2230 )  A      O      0.24    2.46  INTRA
 392 ALA   ( 392-)  A      CA  <->  395 MSE   ( 395-)  A      CE     0.23    2.97  INTRA
 507 TYR   ( 507-)  A      CA  <->  526 ARG   ( 526-)  A      NH2    0.22    2.88  INTRA
 291 PRO   ( 291-)  A      CD  <->  364 ILE   ( 364-)  A      CG2    0.21    2.99  INTRA
  87 THR   (  87-)  A      CG2 <->   89 ASP   (  89-)  A      N      0.19    2.91  INTRA
 439 GLU   ( 439-)  A      N   <->  565 HOH   (2366 )  A      O      0.19    2.51  INTRA
 544 ARG   ( 544-)  A      NH1 <->  565 HOH   (2434 )  A      O      0.18    2.52  INTRA
 249 LYS   ( 249-)  A      NZ  <->  398 GLU   ( 398-)  A      OE1    0.18    2.52  INTRA BL
  87 THR   (  87-)  A      CG2 <->   93 SER   (  93-)  A      OG     0.18    2.62  INTRA
  59 GLY   (  59-)  A      CA  <->  135 LYS   ( 135-)  A      NZ     0.17    2.93  INTRA
 172 ARG   ( 172-)  A      NH2 <->  457 GLU   ( 457-)  A      OE1    0.17    2.53  INTRA
 391 ARG   ( 391-)  A      CG  <->  395 MSE   ( 395-)  A      CE     0.16    3.04  INTRA
  79 GLU   (  79-)  A      OE2 <->  100 LYS   ( 100-)  A      NZ     0.16    2.54  INTRA
 404 ARG   ( 404-)  A      NH2 <->  406 ASP   ( 406-)  A      OD1    0.16    2.54  INTRA
And so on for a total of 124 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

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.

 163 ARG   ( 163-)  A      -8.00
 305 GLU   ( 305-)  A      -6.17
 223 LYS   ( 223-)  A      -6.15
 107 PHE   ( 107-)  A      -5.83
 560 GLU   ( 560-)  A      -5.71
 321 ARG   ( 321-)  A      -5.67
 320 ARG   ( 320-)  A      -5.64
 414 ARG   ( 414-)  A      -5.39
 512 LYS   ( 512-)  A      -5.18
 559 VAL   ( 559-)  A      -5.17
 326 GLU   ( 326-)  A      -5.13
 206 GLU   ( 206-)  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.

 558 LYS   ( 558-)  A       560 - GLU    560- ( A)         -5.06

Note: Quality value plot

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

Chain identifier: A

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 515 LYS   ( 515-)  A   -3.48
 276 ARG   ( 276-)  A   -3.13
 516 TYR   ( 516-)  A   -2.99
 517 ARG   ( 517-)  A   -2.59
   2 ARG   (   2-)  A   -2.56

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.

 100 LYS   ( 100-)  A     -  104 LYS   ( 104-)  A        -1.83
 514 PRO   ( 514-)  A     -  517 ARG   ( 517-)  A        -2.64

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

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.

 565 HOH   (2445 )  A      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 132 GLN   ( 132-)  A
 215 GLN   ( 215-)  A
 217 GLN   ( 217-)  A
 256 GLN   ( 256-)  A
 376 ASN   ( 376-)  A
 552 GLN   ( 552-)  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.

  53 TRP   (  53-)  A      N
  59 GLY   (  59-)  A      N
  89 ASP   (  89-)  A      N
 108 SER   ( 108-)  A      N
 108 SER   ( 108-)  A      OG
 114 LYS   ( 114-)  A      N
 167 ALA   ( 167-)  A      N
 227 ALA   ( 227-)  A      N
 232 SER   ( 232-)  A      N
 243 GLU   ( 243-)  A      N
 250 TYR   ( 250-)  A      N
 251 ASP   ( 251-)  A      N
 254 ARG   ( 254-)  A      NH1
 254 ARG   ( 254-)  A      NH2
 306 ASN   ( 306-)  A      N
 318 ARG   ( 318-)  A      NH2
 322 LYS   ( 322-)  A      N
 337 ASN   ( 337-)  A      ND2
 383 GLU   ( 383-)  A      N
 397 HIS   ( 397-)  A      ND1
 399 GLY   ( 399-)  A      N
 424 THR   ( 424-)  A      N
 448 SER   ( 448-)  A      OG
 458 THR   ( 458-)  A      N
 494 ARG   ( 494-)  A      NE
 544 ARG   ( 544-)  A      NH1

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.

  37 HIS   (  37-)  A      ND1
 245 GLU   ( 245-)  A      OE2
 299 GLU   ( 299-)  A      OE1

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.

 565 HOH   (2064 )  A      O  1.07  K  4 ION-B
 565 HOH   (2130 )  A      O  0.94  K  4
 565 HOH   (2279 )  A      O  1.01  K  5 Ion-B
 565 HOH   (2294 )  A      O  1.06  K  4
 565 HOH   (2314 )  A      O  0.96  K  5
 565 HOH   (2316 )  A      O  0.99  K  5 Ion-B
 565 HOH   (2346 )  A      O  0.94  K  4 Ion-B
 565 HOH   (2355 )  A      O  0.91  K  5
 565 HOH   (2361 )  A      O  0.89  K  4
 565 HOH   (2403 )  A      O  0.99  K  7
 565 HOH   (2431 )  A      O  1.01  K  5

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.

   5 GLU   (   5-)  A   H-bonding suggests Gln; but Alt-Rotamer
 141 ASP   ( 141-)  A   H-bonding suggests Asn
 550 GLU   ( 550-)  A   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.590
  2nd generation packing quality :  -0.915
  Ramachandran plot appearance   :   0.085
  chi-1/chi-2 rotamer normality  :  -0.485
  Backbone conformation          :   0.285

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.421 (tight)
  Bond angles                    :   0.727
  Omega angle restraints         :   0.346 (tight)
  Side chain planarity           :   0.350 (tight)
  Improper dihedral distribution :   0.744
  B-factor distribution          :   0.616
  Inside/Outside distribution    :   0.986

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 :   1.0
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.421 (tight)
  Bond angles                    :   0.727
  Omega angle restraints         :   0.346 (tight)
  Side chain planarity           :   0.350 (tight)
  Improper dihedral distribution :   0.744
  B-factor distribution          :   0.616
  Inside/Outside distribution    :   0.986
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

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

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.