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 pdb1usr.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 : 0.487
CA-only RMS fit for the two chains : 0.251

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.

 896 DAN   (1572-)  A  -
 897 NDG   (1573-)  A  -
 900 A10   (1572-)  B  -
 901 NDG   (1571-)  B  -
 902 DAN   (1570-)  B  -
 903 WIA   (1578-)  A  -
 904 SIA   (1571-)  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

Note: Ramachandran plot

Chain identifier: B

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

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 895 GLY   ( 570-)  B
 448 VAL   ( 571-)  A

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

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

 586 TYR   ( 262-)  B
 865 TYR   ( 541-)  B

Warning: Phenylalanine convention problem

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

 289 PHE   ( 412-)  A
 736 PHE   ( 412-)  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.

 666 ASP   ( 342-)  B

Geometric checks

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.

  81 GLN   ( 204-)  A      CG   CD   NE2 126.55    6.8
  81 GLN   ( 204-)  A      NE2  CD   OE1 112.61  -10.0
 528 GLN   ( 204-)  B      CG   CD   NE2 126.82    6.9
 528 GLN   ( 204-)  B      NE2  CD   OE1 111.53  -11.1

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

 666 ASP   ( 342-)  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.

 474 SER   ( 150-)  B    4.77
  27 SER   ( 150-)  A    4.62

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.

 344 THR   ( 467-)  A    -3.0
 791 THR   ( 467-)  B    -2.9
 499 ILE   ( 175-)  B    -2.7
  52 ILE   ( 175-)  A    -2.6
 778 PRO   ( 454-)  B    -2.6
 331 PRO   ( 454-)  A    -2.6
  89 ARG   ( 212-)  A    -2.4
 771 PHE   ( 447-)  B    -2.4
 536 ARG   ( 212-)  B    -2.4
 664 TYR   ( 340-)  B    -2.4
 217 TYR   ( 340-)  A    -2.4
 884 PRO   ( 560-)  B    -2.4
 324 PHE   ( 447-)  A    -2.3
 797 PRO   ( 473-)  B    -2.3
 350 PRO   ( 473-)  A    -2.3
 561 SER   ( 237-)  B    -2.3
  65 THR   ( 188-)  A    -2.3
 721 LEU   ( 397-)  B    -2.3
 274 LEU   ( 397-)  A    -2.3
 543 ILE   ( 219-)  B    -2.3
 340 ASN   ( 463-)  A    -2.3
 346 VAL   ( 469-)  A    -2.2
 369 LEU   ( 492-)  A    -2.2
 580 GLU   ( 256-)  B    -2.2
 326 ARG   ( 449-)  A    -2.2
 437 PRO   ( 560-)  A    -2.2
 793 VAL   ( 469-)  B    -2.2
 816 LEU   ( 492-)  B    -2.2
 521 ARG   ( 197-)  B    -2.2
 512 THR   ( 188-)  B    -2.2
 692 ARG   ( 368-)  B    -2.2
 114 SER   ( 237-)  A    -2.1
 881 ARG   ( 557-)  B    -2.1
 622 ASN   ( 298-)  B    -2.1
 787 ASN   ( 463-)  B    -2.1
 175 ASN   ( 298-)  A    -2.1
 868 SER   ( 544-)  B    -2.1
 434 ARG   ( 557-)  A    -2.1
 421 SER   ( 544-)  A    -2.0
 445 ASN   ( 568-)  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.

  21 ASN   ( 144-)  A  Poor phi/psi
  52 ILE   ( 175-)  A  Poor phi/psi
 108 ASP   ( 231-)  A  Poor phi/psi
 178 GLY   ( 301-)  A  Poor phi/psi
 179 VAL   ( 302-)  A  Poor phi/psi
 200 ASN   ( 323-)  A  Poor phi/psi
 296 SER   ( 419-)  A  Poor phi/psi
 310 ASN   ( 433-)  A  Poor phi/psi
 330 ILE   ( 453-)  A  PRO omega poor
 337 ARG   ( 460-)  A  Poor phi/psi
 344 THR   ( 467-)  A  Poor phi/psi
 359 HIS   ( 482-)  A  Poor phi/psi
 370 ASP   ( 493-)  A  Poor phi/psi
 402 ALA   ( 525-)  A  Poor phi/psi
 429 LEU   ( 552-)  A  Poor phi/psi
 499 ILE   ( 175-)  B  Poor phi/psi
 555 ASP   ( 231-)  B  Poor phi/psi
 626 VAL   ( 302-)  B  Poor phi/psi
 647 ASN   ( 323-)  B  Poor phi/psi
 664 TYR   ( 340-)  B  Poor phi/psi
 743 SER   ( 419-)  B  Poor phi/psi
 757 ASN   ( 433-)  B  Poor phi/psi
 777 ILE   ( 453-)  B  PRO omega poor
 791 THR   ( 467-)  B  Poor phi/psi
 806 HIS   ( 482-)  B  Poor phi/psi
 817 ASP   ( 493-)  B  Poor phi/psi
 833 THR   ( 509-)  B  Poor phi/psi
 849 ALA   ( 525-)  B  Poor phi/psi
 876 LEU   ( 552-)  B  Poor phi/psi
 892 ASN   ( 568-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.652

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.

 203 SER   ( 326-)  A    0.36
 650 SER   ( 326-)  B    0.36

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!

  10 ILE   ( 133-)  A      0
  13 ILE   ( 136-)  A      0
  17 LEU   ( 140-)  A      0
  20 ASP   ( 143-)  A      0
  21 ASN   ( 144-)  A      0
  32 ALA   ( 155-)  A      0
  36 HIS   ( 159-)  A      0
  37 LEU   ( 160-)  A      0
  39 PHE   ( 162-)  A      0
  51 ARG   ( 174-)  A      0
  52 ILE   ( 175-)  A      0
  66 HIS   ( 189-)  A      0
  71 SER   ( 194-)  A      0
  77 SER   ( 200-)  A      0
  78 HIS   ( 201-)  A      0
  93 THR   ( 216-)  A      0
 101 LEU   ( 224-)  A      0
 107 ASP   ( 230-)  A      0
 108 ASP   ( 231-)  A      0
 109 THR   ( 232-)  A      0
 113 LYS   ( 236-)  A      0
 114 SER   ( 237-)  A      0
 115 CYS   ( 238-)  A      0
 122 LEU   ( 245-)  A      0
 124 CYS   ( 247-)  A      0
And so on for a total of 390 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 : 1.733

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!

  48 GLY   ( 171-)  A   1.59   14
 123 GLY   ( 246-)  A   1.57   19
 495 GLY   ( 171-)  B   1.56   11
 570 GLY   ( 246-)  B   1.53   21

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 376 LEU   ( 499-)  A   1.53

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].

 318 PRO   ( 441-)  A   -32.3 envelop C-alpha (-36 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.

 901 WIA   (1578-)  A      S1  <->  902 SIA   (1571-)  A      C2     1.24    1.76  INTRA BL
 562 CYS   ( 238-)  B      SG  <->  575 CYS   ( 251-)  B      SG     0.68    2.77  INTRA BL
 358 ASN   ( 481-)  A      ND2 <->  895 NDG   (1573-)  A      C1     0.62    2.48  INTRA
 805 ASN   ( 481-)  B      ND2 <->  899 NDG   (1571-)  B      C1     0.62    2.48  INTRA
 901 WIA   (1578-)  A      C6  <->  902 SIA   (1571-)  A      C2     0.56    2.64  INTRA BL
 562 CYS   ( 238-)  B      SG  <->  575 CYS   ( 251-)  B      CB     0.47    2.93  INTRA BL
 895 NDG   (1573-)  A      C7  <->  903 HOH   (2448 )  A      O      0.36    2.44  INTRA BF
 805 ASN   ( 481-)  B      CG  <->  899 NDG   (1571-)  B      C1     0.33    2.87  INTRA
 557 GLN   ( 233-)  B      NE2 <->  577 LYS   ( 253-)  B      NZ     0.31    2.54  INTRA
 149 HIS   ( 272-)  A      ND1 <->  260 GLY   ( 383-)  A      N      0.29    2.71  INTRA
 360 THR   ( 483-)  A      CB  <->  895 NDG   (1573-)  A      O1L    0.27    2.53  INTRA
 358 ASN   ( 481-)  A      CG  <->  895 NDG   (1573-)  A      C1     0.25    2.95  INTRA
 577 LYS   ( 253-)  B      NZ  <->  607 GLU   ( 283-)  B      OE2    0.24    2.46  INTRA
 110 GLN   ( 233-)  A      NE2 <->  130 LYS   ( 253-)  A      NZ     0.22    2.63  INTRA
 326 ARG   ( 449-)  A      NH2 <->  332 CYS   ( 455-)  A      O      0.22    2.48  INTRA
 170 GLU   ( 293-)  A      O   <->  198 LYS   ( 321-)  A      NZ     0.22    2.48  INTRA
 248 GLN   ( 371-)  A      NE2 <->  277 ALA   ( 400-)  A      N      0.18    2.67  INTRA
 110 GLN   ( 233-)  A      CD  <->  130 LYS   ( 253-)  A      NZ     0.17    2.93  INTRA
  81 GLN   ( 204-)  A      NE2 <->  903 HOH   (2099 )  A      O      0.17    2.53  INTRA BL
 178 GLY   ( 301-)  A      O   <->  179 VAL   ( 302-)  A      CG2    0.16    2.54  INTRA
  70 LEU   ( 193-)  A      CD1 <->  542 ARG   ( 218-)  B      NH2    0.16    2.94  INTRA
  67 ASN   ( 190-)  A      ND2 <->   81 GLN   ( 204-)  A      NE2    0.15    2.70  INTRA BL
 528 GLN   ( 204-)  B      NE2 <->  904 HOH   (2094 )  B      O      0.15    2.55  INTRA BL
 596 HIS   ( 272-)  B      ND1 <->  707 GLY   ( 383-)  B      N      0.15    2.85  INTRA
 536 ARG   ( 212-)  B      NH2 <->  904 HOH   (2105 )  B      O      0.15    2.55  INTRA
And so on for a total of 155 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.

 390 ARG   ( 513-)  A      -6.48
 217 TYR   ( 340-)  A      -6.43
  74 ARG   ( 197-)  A      -6.27
 521 ARG   ( 197-)  B      -5.82
 337 ARG   ( 460-)  A      -5.76
 687 ARG   ( 363-)  B      -5.70
 240 ARG   ( 363-)  A      -5.68
 664 TYR   ( 340-)  B      -5.63
 837 ARG   ( 513-)  B      -5.50
 784 ARG   ( 460-)  B      -5.40
 326 ARG   ( 449-)  A      -5.12
 601 PHE   ( 277-)  B      -5.09
 154 PHE   ( 277-)  A      -5.08

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.

 445 ASN   ( 568-)  A       447 - GLY    570- ( A)         -4.62

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.

 517 LEU   ( 193-)  B   -2.99
 206 VAL   ( 329-)  A   -2.61
 358 ASN   ( 481-)  A   -2.51

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.

 903 HOH   (2063 )  A      O    130.59   88.06   42.07
 903 HOH   (2131 )  A      O    132.00   65.79   36.85
 903 HOH   (2165 )  A      O     85.69   53.97   43.59

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.

 903 HOH   (2001 )  A      O
 903 HOH   (2007 )  A      O
 903 HOH   (2013 )  A      O
 903 HOH   (2054 )  A      O
 903 HOH   (2063 )  A      O
 903 HOH   (2076 )  A      O
 903 HOH   (2093 )  A      O
 903 HOH   (2105 )  A      O
 903 HOH   (2135 )  A      O
 903 HOH   (2147 )  A      O
 903 HOH   (2165 )  A      O
 903 HOH   (2179 )  A      O
 903 HOH   (2196 )  A      O
 903 HOH   (2234 )  A      O
 903 HOH   (2298 )  A      O
 903 HOH   (2318 )  A      O
 903 HOH   (2323 )  A      O
 903 HOH   (2324 )  A      O
 903 HOH   (2373 )  A      O
 903 HOH   (2377 )  A      O
 903 HOH   (2436 )  A      O
 903 HOH   (2454 )  A      O
 904 HOH   (2089 )  B      O
 904 HOH   (2140 )  B      O
 904 HOH   (2146 )  B      O
 904 HOH   (2198 )  B      O
 904 HOH   (2230 )  B      O
 904 HOH   (2268 )  B      O
 904 HOH   (2295 )  B      O
 904 HOH   (2298 )  B      O
 904 HOH   (2343 )  B      O
 904 HOH   (2418 )  B      O

Error: HIS, ASN, GLN side chain flips

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

  34 GLN   ( 157-)  A
  80 HIS   ( 203-)  A
  81 GLN   ( 204-)  A
 110 GLN   ( 233-)  A
 175 ASN   ( 298-)  A
 248 GLN   ( 371-)  A
 333 GLN   ( 456-)  A
 340 ASN   ( 463-)  A
 481 GLN   ( 157-)  B
 527 HIS   ( 203-)  B
 528 GLN   ( 204-)  B
 622 ASN   ( 298-)  B
 695 GLN   ( 371-)  B
 780 GLN   ( 456-)  B

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  33 PHE   ( 156-)  A      N
  51 ARG   ( 174-)  A      NH2
  62 TYR   ( 185-)  A      OH
  72 GLY   ( 195-)  A      N
  79 SER   ( 202-)  A      N
 105 SER   ( 228-)  A      N
 136 GLU   ( 259-)  A      N
 147 MET   ( 270-)  A      N
 218 ASN   ( 341-)  A      N
 220 THR   ( 343-)  A      N
 230 ARG   ( 353-)  A      NE
 245 ARG   ( 368-)  A      NH2
 326 ARG   ( 449-)  A      NH1
 340 ASN   ( 463-)  A      N
 346 VAL   ( 469-)  A      N
 347 TYR   ( 470-)  A      N
 362 ARG   ( 485-)  A      NE
 387 SER   ( 510-)  A      OG
 390 ARG   ( 513-)  A      NH1
 393 ARG   ( 516-)  A      N
 393 ARG   ( 516-)  A      NH2
 408 CYS   ( 531-)  A      N
 412 VAL   ( 535-)  A      N
 413 LYS   ( 536-)  A      N
 472 VAL   ( 148-)  B      N
 480 PHE   ( 156-)  B      N
 493 GLY   ( 169-)  B      N
 498 ARG   ( 174-)  B      NH2
 509 TYR   ( 185-)  B      OH
 511 TYR   ( 187-)  B      OH
 513 HIS   ( 189-)  B      ND1
 519 GLY   ( 195-)  B      N
 521 ARG   ( 197-)  B      N
 552 SER   ( 228-)  B      N
 559 ARG   ( 235-)  B      NH2
 583 GLU   ( 259-)  B      N
 594 MET   ( 270-)  B      N
 658 TYR   ( 334-)  B      N
 688 PHE   ( 364-)  B      N
 777 ILE   ( 453-)  B      N
 787 ASN   ( 463-)  B      N
 793 VAL   ( 469-)  B      N
 794 TYR   ( 470-)  B      N
 827 SER   ( 503-)  B      OG
 840 ARG   ( 516-)  B      N
 855 CYS   ( 531-)  B      N
 893 ASP   ( 569-)  B      N
Only metal coordination for  585 ASP  ( 261-) B      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 896  CA   (1574-)  A     0.84   1.07 Scores about as good as NA
 897  CA   (1573-)  B     0.80   1.05 Scores about as good as NA

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.

 904 HOH   (2460 )  B      O  0.90  K  4 Ion-B

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.

  56 ASP   ( 179-)  A   H-bonding suggests Asn; but Alt-Rotamer
 503 ASP   ( 179-)  B   H-bonding suggests Asn
 582 GLU   ( 258-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact

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 :  -0.358
  2nd generation packing quality :  -1.767
  Ramachandran plot appearance   :  -1.778
  chi-1/chi-2 rotamer normality  :  -1.652
  Backbone conformation          :  -0.543

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.290 (tight)
  Bond angles                    :   0.680
  Omega angle restraints         :   0.315 (tight)
  Side chain planarity           :   0.235 (tight)
  Improper dihedral distribution :   0.608
  B-factor distribution          :   0.510
  Inside/Outside distribution    :   1.011

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -1.1
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.290 (tight)
  Bond angles                    :   0.680
  Omega angle restraints         :   0.315 (tight)
  Side chain planarity           :   0.235 (tight)
  Improper dihedral distribution :   0.608
  B-factor distribution          :   0.510
  Inside/Outside distribution    :   1.011
==============

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.