WHAT IF Check report

This file was created 2013-12-10 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 pdb4fpe.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.

 659 DMS   ( 702-)  A  -
 660 DMS   ( 703-)  A  -
 661 0H9   ( 701-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 234 LYS   ( 272-)  A  -
 286 SER   ( 324-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 234 LYS   ( 272-)  A  -
 286 SER   ( 324-)  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: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

 315 ASN   ( 353-)  A    High

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

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   (  48-)  A
 122 TYR   ( 160-)  A
 212 TYR   ( 250-)  A
 345 TYR   ( 383-)  A
 384 TYR   ( 422-)  A
 420 TYR   ( 458-)  A
 471 TYR   ( 509-)  A
 633 TYR   ( 671-)  A

Warning: Phenylalanine convention problem

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

  38 PHE   (  76-)  A
  67 PHE   ( 105-)  A
 173 PHE   ( 211-)  A
 191 PHE   ( 229-)  A
 324 PHE   ( 362-)  A
 343 PHE   ( 381-)  A
 407 PHE   ( 445-)  A
 497 PHE   ( 535-)  A
 518 PHE   ( 556-)  A
 630 PHE   ( 668-)  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.

  25 ASP   (  63-)  A
 387 ASP   ( 425-)  A
 651 ASP   ( 689-)  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.

  77 GLU   ( 115-)  A
 105 GLU   ( 143-)  A
 326 GLU   ( 364-)  A
 445 GLU   ( 483-)  A
 503 GLU   ( 541-)  A

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

 |  0.997341  0.000131 -0.000099|
 |  0.000131  0.997433 -0.000312|
 | -0.000099 -0.000312  0.997347|
Proposed new scale matrix

 |  0.013153 -0.000002  0.000001|
 | -0.000002  0.012155  0.000004|
 |  0.000000  0.000003  0.008625|
With corresponding cell

    A    =  76.028  B   =  82.269  C    = 115.944
    Alpha=  90.036  Beta=  90.006  Gamma=  89.985

The CRYST1 cell dimensions

    A    =  76.229  B   =  82.480  C    = 116.248
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 148.181
(Under-)estimated Z-score: 8.971

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.

  25 ASP   (  63-)  A
  77 GLU   ( 115-)  A
 105 GLU   ( 143-)  A
 326 GLU   ( 364-)  A
 387 ASP   ( 425-)  A
 445 GLU   ( 483-)  A
 503 GLU   ( 541-)  A
 651 ASP   ( 689-)  A

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.

 472 THR   ( 510-)  A    -2.9
 161 TYR   ( 199-)  A    -2.9
 642 HIS   ( 680-)  A    -2.8
 633 TYR   ( 671-)  A    -2.7
 208 ILE   ( 246-)  A    -2.6
 574 THR   ( 612-)  A    -2.5
 312 ILE   ( 350-)  A    -2.4
 418 THR   ( 456-)  A    -2.3
 484 SER   ( 522-)  A    -2.3
   9 SER   (  47-)  A    -2.3
 619 THR   ( 657-)  A    -2.3
 293 VAL   ( 331-)  A    -2.3
 235 SER   ( 273-)  A    -2.2
 348 ARG   ( 386-)  A    -2.2
  74 ILE   ( 112-)  A    -2.1
 196 GLN   ( 234-)  A    -2.1
 396 ARG   ( 434-)  A    -2.1
 455 GLY   ( 493-)  A    -2.1
 190 PRO   ( 228-)  A    -2.1
 172 LEU   ( 210-)  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.

  14 ASN   (  52-)  A  Poor phi/psi
  53 SER   (  91-)  A  omega poor
  63 TYR   ( 101-)  A  omega poor
  65 SER   ( 103-)  A  omega poor
  76 VAL   ( 114-)  A  omega poor
  95 LEU   ( 133-)  A  omega poor
 100 LYS   ( 138-)  A  Poor phi/psi
 101 GLY   ( 139-)  A  Poor phi/psi
 124 ASN   ( 162-)  A  Poor phi/psi
 161 TYR   ( 199-)  A  Poor phi/psi
 202 GLN   ( 240-)  A  Poor phi/psi
 208 ILE   ( 246-)  A  Poor phi/psi
 232 ASP   ( 270-)  A  omega poor
 233 SER   ( 271-)  A  Poor phi/psi, omega poor
 235 SER   ( 273-)  A  omega poor
 247 ASN   ( 285-)  A  Poor phi/psi
 289 ASP   ( 327-)  A  Poor phi/psi
 315 ASN   ( 353-)  A  Poor phi/psi
 316 ASN   ( 354-)  A  Poor phi/psi
 317 ALA   ( 355-)  A  omega poor
 318 ASN   ( 356-)  A  omega poor
 320 ALA   ( 358-)  A  Poor phi/psi
 328 ASN   ( 366-)  A  Poor phi/psi
 348 ARG   ( 386-)  A  Poor phi/psi
 359 ASN   ( 397-)  A  Poor phi/psi
 370 TYR   ( 408-)  A  Poor phi/psi
 429 ARG   ( 467-)  A  Poor phi/psi
 456 GLN   ( 494-)  A  omega poor
 475 GLU   ( 513-)  A  omega poor
 484 SER   ( 522-)  A  Poor phi/psi
 496 PRO   ( 534-)  A  Poor phi/psi
 585 GLN   ( 623-)  A  omega poor
 596 ASP   ( 634-)  A  Poor phi/psi
 600 TRP   ( 638-)  A  omega poor
 614 ALA   ( 652-)  A  Poor phi/psi
 624 HIS   ( 662-)  A  Poor phi/psi
 642 HIS   ( 680-)  A  Poor phi/psi
 645 ASN   ( 683-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.176

Warning: Unusual rotamers

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

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

  21 SER   (  59-)  A    0.37

Warning: Unusual backbone conformations

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

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

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

   4 ILE   (  42-)  A      0
   5 PHE   (  43-)  A      0
   6 GLN   (  44-)  A      0
   9 SER   (  47-)  A      0
  10 TYR   (  48-)  A      0
  13 ASN   (  51-)  A      0
  14 ASN   (  52-)  A      0
  19 ILE   (  57-)  A      0
  23 LEU   (  61-)  A      0
  30 GLU   (  68-)  A      0
  31 SER   (  69-)  A      0
  40 ALA   (  78-)  A      0
  41 ASP   (  79-)  A      0
  42 LYS   (  80-)  A      0
  45 SER   (  83-)  A      0
  46 LEU   (  84-)  A      0
  50 PHE   (  88-)  A      0
  54 ASN   (  92-)  A      0
  55 SER   (  93-)  A      0
  57 ALA   (  95-)  A      0
  59 PHE   (  97-)  A      0
  62 ASN   ( 100-)  A      0
  63 TYR   ( 101-)  A      0
  71 SER   ( 109-)  A      0
  79 ARG   ( 117-)  A      0
And so on for a total of 305 lines.

Warning: Backbone oxygen evaluation

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

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

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

  20 SER   (  58-)  A   2.12   14
 584 GLY   ( 622-)  A   1.65   10

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.

 196 GLN   ( 234-)  A      NE2 <->  662 HOH   (1141 )  A      O      0.36    2.34  INTRA
 350 ASN   ( 388-)  A      ND2 <->  662 HOH   (1187 )  A      O      0.36    2.34  INTRA BF
  13 ASN   (  51-)  A      OD1 <->  164 LYS   ( 202-)  A      NZ     0.33    2.37  INTRA BF
 593 LYS   ( 631-)  A      NZ  <->  662 HOH   (1044 )  A      O      0.32    2.38  INTRA BF
 147 LYS   ( 185-)  A      NZ  <->  662 HOH   (1106 )  A      O      0.30    2.40  INTRA
 259 LYS   ( 297-)  A      NZ  <->  261 ASN   ( 299-)  A      OD1    0.29    2.41  INTRA BL
 489 LYS   ( 527-)  A      NZ  <->  662 HOH   (1127 )  A      O      0.24    2.46  INTRA
 234 LYS   ( 272-)  A    A N   <->  280 GLN   ( 318-)  A      OE1    0.22    2.48  INTRA
  91 ARG   ( 129-)  A      NH1 <->  660 DMS   ( 703-)  A      O      0.22    2.48  INTRA BL
 638 ARG   ( 676-)  A      NH2 <->  662 HOH   ( 955 )  A      O      0.20    2.50  INTRA
 346 THR   ( 384-)  A      OG1 <->  356 GLU   ( 394-)  A      OE2    0.19    2.21  INTRA BF
 100 LYS   ( 138-)  A      NZ  <->  662 HOH   ( 893 )  A      O      0.19    2.51  INTRA
 661 0H9   ( 701-)  A      NAL <->  662 HOH   (1077 )  A      O      0.15    2.55  INTRA
 605 ASP   ( 643-)  A      OD2 <->  662 HOH   (1062 )  A      O      0.14    2.26  INTRA BF
 300 LYS   ( 338-)  A      NZ  <->  662 HOH   ( 984 )  A      O      0.14    2.56  INTRA
 607 ASP   ( 645-)  A      OD2 <->  632 LYS   ( 670-)  A      NZ     0.13    2.57  INTRA BL
 272 ARG   ( 310-)  A      NH2 <->  639 ASN   ( 677-)  A      O      0.12    2.58  INTRA BL
 358 THR   ( 396-)  A      C   <->  360 LYS   ( 398-)  A      N      0.12    2.78  INTRA BF
 321 ASP   ( 359-)  A      OD2 <->  662 HOH   (1236 )  A      O      0.12    2.28  INTRA BF
 545 GLY   ( 583-)  A      O   <->  662 HOH   (1125 )  A      O      0.12    2.28  INTRA
 442 PHE   ( 480-)  A      N   <->  662 HOH   (1175 )  A      O      0.11    2.59  INTRA
 292 ILE   ( 330-)  A      O   <->  457 GLY   ( 495-)  A      N      0.09    2.61  INTRA BL
 465 ARG   ( 503-)  A      NH2 <->  482 ASP   ( 520-)  A      OD2    0.09    2.61  INTRA
 266 GLN   ( 304-)  A      OE1 <->  386 VAL   ( 424-)  A      N      0.09    2.61  INTRA
 355 ASN   ( 393-)  A      O   <->  359 ASN   ( 397-)  A      N      0.09    2.61  INTRA BF
And so on for a total of 63 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.

 269 TYR   ( 307-)  A      -7.74
 578 ARG   ( 616-)  A      -6.17
 551 TYR   ( 589-)  A      -6.17
 314 ASN   ( 352-)  A      -5.65
 350 ASN   ( 388-)  A      -5.31
  82 GLN   ( 120-)  A      -5.21
 341 ASN   ( 379-)  A      -5.20
 155 ARG   ( 193-)  A      -5.05
 510 ARG   ( 548-)  A      -5.00

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.

 314 ASN   ( 352-)  A       316 - ASN    354- ( A)         -5.14

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: 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: 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.

 196 GLN   ( 234-)  A
 427 GLN   ( 465-)  A
 447 HIS   ( 485-)  A
 639 ASN   ( 677-)  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.

  91 ARG   ( 129-)  A      NH1
 142 ILE   ( 180-)  A      N
 152 ALA   ( 190-)  A      N
 175 LYS   ( 213-)  A      N
 191 PHE   ( 229-)  A      N
 204 ASN   ( 242-)  A      ND2
 207 ARG   ( 245-)  A      NH2
 231 HIS   ( 269-)  A      N
 233 SER   ( 271-)  A      N
 237 ILE   ( 275-)  A      N
 296 LYS   ( 334-)  A      N
 297 LYS   ( 335-)  A      N
 301 THR   ( 339-)  A      OG1
 313 GLY   ( 351-)  A      N
 317 ALA   ( 355-)  A      N
 323 GLY   ( 361-)  A      N
 330 HIS   ( 368-)  A      N
 341 ASN   ( 379-)  A      N
 342 ASP   ( 380-)  A      N
 405 ASN   ( 443-)  A      N
 456 GLN   ( 494-)  A      NE2
 516 THR   ( 554-)  A      OG1
 546 ILE   ( 584-)  A      N
 554 GLN   ( 592-)  A      N
 562 GLN   ( 600-)  A      N
 581 ARG   ( 619-)  A      NH1
 581 ARG   ( 619-)  A      NH2
 644 SER   ( 682-)  A      N

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

 330 HIS   ( 368-)  A      ND1

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.

 662 HOH   ( 990 )  A      O  1.04  K  4
 662 HOH   ( 996 )  A      O  1.13  K  4
 662 HOH   (1030 )  A      O  0.98  K  4 Ion-B
 662 HOH   (1034 )  A      O  0.92  K  5
 662 HOH   (1068 )  A      O  0.86  K  5
 662 HOH   (1116 )  A      O  1.15  K  4
 662 HOH   (1147 )  A      O  1.10  K  4

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  18 ASP   (  56-)  A   H-bonding suggests Asn; but Alt-Rotamer
 146 ASP   ( 184-)  A   H-bonding suggests Asn
 199 ASP   ( 237-)  A   H-bonding suggests Asn; but Alt-Rotamer
 246 ASP   ( 284-)  A   H-bonding suggests Asn; but Alt-Rotamer
 342 ASP   ( 380-)  A   H-bonding suggests Asn
 483 ASP   ( 521-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.374
  2nd generation packing quality :  -1.000
  Ramachandran plot appearance   :  -0.110
  chi-1/chi-2 rotamer normality  :  -1.176
  Backbone conformation          :  -0.287

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.346 (tight)
  Bond angles                    :   0.536 (tight)
  Omega angle restraints         :   1.112
  Side chain planarity           :   0.349 (tight)
  Improper dihedral distribution :   0.566
  B-factor distribution          :   1.259
  Inside/Outside distribution    :   0.962

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 : 2.18


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :   1.0
  chi-1/chi-2 rotamer normality  :   0.0
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.346 (tight)
  Bond angles                    :   0.536 (tight)
  Omega angle restraints         :   1.112
  Side chain planarity           :   0.349 (tight)
  Improper dihedral distribution :   0.566
  B-factor distribution          :   1.259
  Inside/Outside distribution    :   0.962
==============

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.