WHAT IF Check report

This file was created 2011-12-15 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 pdb2f61.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 : 0.982
CA-only RMS fit for the two chains : 0.555

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.

1005 NDG   (1001-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

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

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

 995 NAG   (1001-)  B  -   O4  bound to  996 NAG   (1002-)  B  -   C1

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: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  57 GLN   (  57-)  A    0.50
  73 GLN   (  73-)  A    0.50
 151 GLU   ( 151-)  A    0.50
 358 ASP   ( 358-)  A    0.50
 388 GLU   ( 388-)  A    0.50
 570 GLN   (  73-)  B    0.50
 599 ASN   ( 102-)  B    0.50
 608 GLU   ( 111-)  B    0.50
 609 GLU   ( 112-)  B    0.50
 708 ARG   ( 211-)  B    0.50
 767 ASN   ( 270-)  B    0.50
 855 ASP   ( 358-)  B    0.50

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: Arginine nomenclature problem

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

 541 ARG   (  44-)  B

Warning: Tyrosine convention problem

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

  11 TYR   (  11-)  A
  22 TYR   (  22-)  A
 108 TYR   ( 108-)  A
 116 TYR   ( 116-)  A
 135 TYR   ( 135-)  A
 205 TYR   ( 205-)  A
 212 TYR   ( 212-)  A
 304 TYR   ( 304-)  A
 412 TYR   ( 412-)  A
 487 TYR   ( 487-)  A
 519 TYR   (  22-)  B
 605 TYR   ( 108-)  B
 613 TYR   ( 116-)  B
 632 TYR   ( 135-)  B
 702 TYR   ( 205-)  B
 709 TYR   ( 212-)  B
 801 TYR   ( 304-)  B
 909 TYR   ( 412-)  B
 915 TYR   ( 418-)  B
 984 TYR   ( 487-)  B

Warning: Phenylalanine convention problem

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

  26 PHE   (  26-)  A
 147 PHE   ( 147-)  A
 246 PHE   ( 246-)  A
 347 PHE   ( 347-)  A
 397 PHE   ( 397-)  A
 417 PHE   ( 417-)  A
 426 PHE   ( 426-)  A
 523 PHE   (  26-)  B
 528 PHE   (  31-)  B
 639 PHE   ( 142-)  B
 644 PHE   ( 147-)  B
 748 PHE   ( 251-)  B
 813 PHE   ( 316-)  B
 828 PHE   ( 331-)  B
 894 PHE   ( 397-)  B
 908 PHE   ( 411-)  B
 923 PHE   ( 426-)  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.

 358 ASP   ( 358-)  A
 779 ASP   ( 282-)  B
 855 ASP   ( 358-)  B

Warning: Glutamic acid convention problem

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

 885 GLU   ( 388-)  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.

 115 GLY   ( 115-)  A      N    CA   C   124.82    4.2

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.

 358 ASP   ( 358-)  A
 541 ARG   (  44-)  B
 779 ASP   ( 282-)  B
 855 ASP   ( 358-)  B
 885 GLU   ( 388-)  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.

 109 PHE   ( 109-)  A    4.61
 296 LEU   ( 296-)  A    4.22
 115 GLY   ( 115-)  A    4.04

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.

 560 THR   (  63-)  B    -3.1
 482 THR   ( 482-)  A    -2.9
 319 PRO   ( 319-)  A    -2.8
 786 PRO   ( 289-)  B    -2.8
 979 THR   ( 482-)  B    -2.5
 732 GLU   ( 235-)  B    -2.4
 967 LEU   ( 470-)  B    -2.4
 316 PHE   ( 316-)  A    -2.3
 379 THR   ( 379-)  A    -2.3
 343 VAL   ( 343-)  A    -2.3
 612 GLY   ( 115-)  B    -2.2
 595 PRO   (  98-)  B    -2.2
 924 ILE   ( 427-)  B    -2.2
 528 PHE   (  31-)  B    -2.1
  19 ASN   (  19-)  A    -2.1
  13 SER   (  13-)  A    -2.1
 895 VAL   ( 398-)  B    -2.1
 686 GLY   ( 189-)  B    -2.1
 449 LEU   ( 449-)  A    -2.1
 873 VAL   ( 376-)  B    -2.1
 413 LYS   ( 413-)  A    -2.0
 447 VAL   ( 447-)  A    -2.0
 289 PRO   ( 289-)  A    -2.0
 381 TRP   ( 381-)  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.

  19 ASN   (  19-)  A  Poor phi/psi
  75 PHE   (  75-)  A  Poor phi/psi
 124 ALA   ( 124-)  A  Poor phi/psi
 133 TYR   ( 133-)  A  Poor phi/psi
 156 LEU   ( 156-)  A  Poor phi/psi
 192 ASN   ( 192-)  A  Poor phi/psi
 224 LYS   ( 224-)  A  Poor phi/psi
 233 GLU   ( 233-)  A  Poor phi/psi
 281 LEU   ( 281-)  A  Poor phi/psi
 288 LEU   ( 288-)  A  PRO omega poor
 311 HIS   ( 311-)  A  Poor phi/psi
 312 TRP   ( 312-)  A  Poor phi/psi
 313 TYR   ( 313-)  A  Poor phi/psi
 374 HIS   ( 374-)  A  Poor phi/psi
 381 TRP   ( 381-)  A  Poor phi/psi
 390 GLY   ( 390-)  A  PRO omega poor
 395 ARG   ( 395-)  A  Poor phi/psi
 397 PHE   ( 397-)  A  Poor phi/psi
 516 ASN   (  19-)  B  Poor phi/psi
 572 PHE   (  75-)  B  Poor phi/psi
 612 GLY   ( 115-)  B  Poor phi/psi
 621 ALA   ( 124-)  B  Poor phi/psi
 623 CYS   ( 126-)  B  Poor phi/psi
 628 ARG   ( 131-)  B  Poor phi/psi
 641 LEU   ( 144-)  B  Poor phi/psi
 686 GLY   ( 189-)  B  Poor phi/psi
 689 ASN   ( 192-)  B  Poor phi/psi
 721 LYS   ( 224-)  B  Poor phi/psi
 730 GLU   ( 233-)  B  Poor phi/psi
 732 GLU   ( 235-)  B  Poor phi/psi
 778 LEU   ( 281-)  B  Poor phi/psi
 779 ASP   ( 282-)  B  Poor phi/psi
 785 LEU   ( 288-)  B  PRO omega poor
 820 THR   ( 323-)  B  Poor phi/psi
 845 TRP   ( 348-)  B  Poor phi/psi
 871 HIS   ( 374-)  B  Poor phi/psi
 878 TRP   ( 381-)  B  Poor phi/psi
 887 GLY   ( 390-)  B  PRO omega poor
 892 ARG   ( 395-)  B  Poor phi/psi
 893 ASN   ( 396-)  B  Poor phi/psi
 984 TYR   ( 487-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.251

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.

 863 SER   ( 366-)  B    0.36
 604 SER   ( 107-)  B    0.39

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!

   6 PRO   (   6-)  A      0
   9 PHE   (   9-)  A      0
  11 TYR   (  11-)  A      0
  12 SER   (  12-)  A      0
  18 CYS   (  18-)  A      0
  19 ASN   (  19-)  A      0
  22 TYR   (  22-)  A      0
  23 CYS   (  23-)  A      0
  24 ASP   (  24-)  A      0
  34 LEU   (  34-)  A      0
  45 SER   (  45-)  A      0
  47 ARG   (  47-)  A      0
  48 ARG   (  48-)  A      0
  49 MET   (  49-)  A      0
  57 GLN   (  57-)  A      0
  65 LEU   (  65-)  A      0
  70 GLN   (  70-)  A      0
  73 GLN   (  73-)  A      0
  75 PHE   (  75-)  A      0
  79 LYS   (  79-)  A      0
  81 PHE   (  81-)  A      0
  85 MET   (  85-)  A      0
 108 TYR   ( 108-)  A      0
 114 ILE   ( 114-)  A      0
 123 MET   ( 123-)  A      0
And so on for a total of 412 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 : 1.282

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!

  46 GLY   (  46-)  A   1.54   60

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]

  55 PRO   (  55-)  A    0.45 HIGH

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.

  19 ASN   (  19-)  A      ND2 <-> 1005 NDG   (1001-)  A      C1     1.24    1.46  INTRA B3
  19 ASN   (  19-)  A      CG  <-> 1005 NDG   (1001-)  A      C1     0.72    2.48  INTRA
 285 ARG   ( 285-)  A      N   <->  312 TRP   ( 312-)  A      CD1    0.39    2.71  INTRA BF
 541 ARG   (  44-)  B      NH2 <->  984 TYR   ( 487-)  B      CE2    0.30    2.80  INTRA
 186 LYS   ( 186-)  A      NZ  <-> 1006 HOH   (1558 )  A      O      0.26    2.44  INTRA BL
 207 GLN   ( 207-)  A      NE2 <->  263 ASP   ( 263-)  A      OD1    0.25    2.45  INTRA
  75 PHE   (  75-)  A      CG  <->  433 ARG   ( 433-)  A      NH1    0.24    2.86  INTRA
 871 HIS   ( 374-)  B      ND1 <-> 1007 HOH   (1662 )  B      O      0.24    2.46  INTRA BL
 226 GLN   ( 226-)  A      NE2 <-> 1006 HOH   (1660 )  A      O      0.23    2.47  INTRA
 426 PHE   ( 426-)  A      O   <->  451 HIS   ( 451-)  A      NE2    0.23    2.47  INTRA
 386 ASN   ( 386-)  A      ND2 <->  390 GLY   ( 390-)  A      C      0.23    2.87  INTRA BL
 771 HIS   ( 274-)  B      ND1 <-> 1007 HOH   (1523 )  B      O      0.22    2.48  INTRA
 703 HIS   ( 206-)  B      NE2 <->  752 HIS   ( 255-)  B      CE1    0.21    2.89  INTRA BL
 408 LYS   ( 408-)  A      O   <->  410 THR   ( 410-)  A      CG2    0.20    2.60  INTRA BL
 358 ASP   ( 358-)  A      CB  <-> 1006 HOH   (1552 )  A      O      0.20    2.60  INTRA BL
 541 ARG   (  44-)  B      NH2 <->  984 TYR   ( 487-)  B      CD2    0.20    2.90  INTRA
  57 GLN   (  57-)  A      O   <->  479 PHE   ( 479-)  A      N      0.19    2.51  INTRA BL
 782 ARG   ( 285-)  B      NH2 <->  815 ALA   ( 318-)  B      C      0.19    2.91  INTRA BF
 495 HIS   ( 495-)  A      N   <-> 1006 HOH   (1565 )  A      O      0.19    2.51  INTRA BL
 782 ARG   ( 285-)  B      NH1 <->  809 TRP   ( 312-)  B      CZ3    0.19    2.91  INTRA BF
 141 ASP   ( 141-)  A      O   <->  144 LEU   ( 144-)  A      N      0.18    2.52  INTRA BF
 544 ARG   (  47-)  B      NH1 <-> 1007 HOH   (1596 )  B      O      0.18    2.52  INTRA BF
 862 HIS   ( 365-)  B      CD2 <->  960 ARG   ( 463-)  B      CZ     0.18    3.02  INTRA
  44 ARG   (  44-)  A      NH2 <->  487 TYR   ( 487-)  A      CE2    0.18    2.92  INTRA
 206 HIS   ( 206-)  A      NE2 <->  255 HIS   ( 255-)  A      NE2    0.18    2.82  INTRA
And so on for a total of 179 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.

 814 LEU   ( 317-)  B      -6.94
 666 GLN   ( 169-)  B      -6.81
 844 PHE   ( 347-)  B      -6.76
 938 LYS   ( 441-)  B      -6.68
 317 LEU   ( 317-)  A      -6.61
 441 LYS   ( 441-)  A      -6.55
  31 PHE   (  31-)  A      -6.24
 697 GLN   ( 200-)  B      -6.23
 200 GLN   ( 200-)  A      -6.08
 347 PHE   ( 347-)  A      -5.85
 759 ARG   ( 262-)  B      -5.69
 169 GLN   ( 169-)  A      -5.65
 993 ARG   ( 496-)  B      -5.63
 262 ARG   ( 262-)  A      -5.49
 496 ARG   ( 496-)  A      -5.30
 528 PHE   (  31-)  B      -5.27
 608 GLU   ( 111-)  B      -5.21
 627 ILE   ( 130-)  B      -5.19
 194 LYS   ( 194-)  A      -5.19
 313 TYR   ( 313-)  A      -5.16
 130 ILE   ( 130-)  A      -5.07
 123 MET   ( 123-)  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.

 557 HIS   (  60-)  B       560 - THR     63- ( B)         -4.65

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.

  62 GLY   (  62-)  A   -2.76
 170 ARG   ( 170-)  A   -2.58

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

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.

1006 HOH   (1619 )  A      O     44.02  106.17   23.96
1006 HOH   (1685 )  A      O     -0.54   72.65   18.97
1007 HOH   (1682 )  B      O      9.44   39.22  -19.66
1007 HOH   (1695 )  B      O     29.64   51.58  -22.64

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.

1006 HOH   (1589 )  A      O
1007 HOH   (1696 )  B      O
Bound group on Asn; dont flip   19 ASN  (  19-) A
Bound to: 1005 NDG  (1001-) A
Bound group on Asn; dont flip  516 ASN  (  19-) B
Bound to:  995 NAG  (1001-) B

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.

 274 HIS   ( 274-)  A
 362 GLN   ( 362-)  A
 752 HIS   ( 255-)  B
 859 GLN   ( 362-)  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.

  43 THR   (  43-)  A      OG1
  45 SER   (  45-)  A      N
 131 ARG   ( 131-)  A      N
 135 TYR   ( 135-)  A      OH
 140 ASP   ( 140-)  A      N
 141 ASP   ( 141-)  A      N
 147 PHE   ( 147-)  A      N
 151 GLU   ( 151-)  A      N
 184 TRP   ( 184-)  A      N
 227 PHE   ( 227-)  A      N
 233 GLU   ( 233-)  A      N
 246 PHE   ( 246-)  A      N
 254 GLU   ( 254-)  A      N
 285 ARG   ( 285-)  A      N
 285 ARG   ( 285-)  A      NE
 286 LEU   ( 286-)  A      N
 312 TRP   ( 312-)  A      NE1
 313 TYR   ( 313-)  A      N
 314 LEU   ( 314-)  A      N
 315 ASP   ( 315-)  A      N
 316 PHE   ( 316-)  A      N
 348 TRP   ( 348-)  A      N
 350 GLN   ( 350-)  A      N
 382 ASN   ( 382-)  A      ND2
 384 ALA   ( 384-)  A      N
And so on for a total of 61 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

 273 HIS   ( 273-)  A      ND1
 419 HIS   ( 419-)  A      NE2
 451 HIS   ( 451-)  A      NE2
 584 ASP   (  87-)  B      OD1
 648 GLU   ( 151-)  B      OE2
 803 HIS   ( 306-)  B      ND1
 916 HIS   ( 419-)  B      NE2

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.

1006 HOH   (1624 )  A      O  0.98  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.

 137 ASP   ( 137-)  A   H-bonding suggests Asn
 203 ASP   ( 203-)  A   H-bonding suggests Asn
 218 ASP   ( 218-)  A   H-bonding suggests Asn; but Alt-Rotamer
 233 GLU   ( 233-)  A   H-bonding suggests Gln
 380 ASP   ( 380-)  A   H-bonding suggests Asn; but Alt-Rotamer
 399 ASP   ( 399-)  A   H-bonding suggests Asn
 634 ASP   ( 137-)  B   H-bonding suggests Asn
 700 ASP   ( 203-)  B   H-bonding suggests Asn
 715 ASP   ( 218-)  B   H-bonding suggests Asn; but Alt-Rotamer
 730 GLU   ( 233-)  B   H-bonding suggests Gln
 877 ASP   ( 380-)  B   H-bonding suggests Asn; but Alt-Rotamer
 896 ASP   ( 399-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.466
  2nd generation packing quality :  -1.523
  Ramachandran plot appearance   :  -1.947
  chi-1/chi-2 rotamer normality  :  -2.251
  Backbone conformation          :  -0.466

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.284 (tight)
  Bond angles                    :   0.639 (tight)
  Omega angle restraints         :   0.233 (tight)
  Side chain planarity           :   0.241 (tight)
  Improper dihedral distribution :   0.589
  B-factor distribution          :   0.546
  Inside/Outside distribution    :   1.038

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.284 (tight)
  Bond angles                    :   0.639 (tight)
  Omega angle restraints         :   0.233 (tight)
  Side chain planarity           :   0.241 (tight)
  Improper dihedral distribution :   0.589
  B-factor distribution          :   0.546
  Inside/Outside distribution    :   1.038
==============

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.