WHAT IF Check report

This file was created 2011-12-16 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 pdb1ivc.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.

 796 BMA   ( 480-)  A  -
 797 MAN   ( 482-)  A  -
 798 MAN   ( 483-)  A  -
 799 BMA   ( 476-)  B  -
 800 BMA   ( 480-)  B  -
 801 MAN   ( 481-)  B  -
 802 MAN   ( 482-)  B  -
 803 MAN   ( 483-)  B  -
 806 ST2   ( 471-)  B  -
 807 BMA   ( 476-)  A  -
 808 FUL   ( 477-)  A  -
 809 MAN   ( 481-)  A  -
 810 ST2   ( 471-)  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.

 777 NAG   ( 472-)  A  -   O4  bound to  778 NAG   ( 473-)  A  -   C1
 779 NAG   ( 474-)  A  -   O4  bound to  780 NAG   ( 475-)  A  -   C1
 780 NAG   ( 475-)  A  -   O4  bound to  807 BMA   ( 476-)  A  -   C1
 781 NAG   ( 478-)  A  -   O4  bound to  782 NAG   ( 479-)  A  -   C1
 782 NAG   ( 479-)  A  -   O4  bound to  796 BMA   ( 480-)  A  -   C1
 783 NAG   ( 484-)  A  -   O4  bound to  784 NAG   ( 485-)  A  -   C1
 785 NAG   ( 472-)  B  -   O4  bound to  786 NAG   ( 473-)  B  -   C1
 787 NAG   ( 474-)  B  -   O4  bound to  788 NAG   ( 475-)  B  -   C1
 788 NAG   ( 475-)  B  -   O4  bound to  799 BMA   ( 476-)  B  -   C1
 790 NAG   ( 478-)  B  -   O4  bound to  791 NAG   ( 479-)  B  -   C1
 791 NAG   ( 479-)  B  -   O4  bound to  800 BMA   ( 480-)  B  -   C1
 792 NAG   ( 484-)  B  -   O4  bound to  793 NAG   ( 485-)  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

Note: Ramachandran plot

Chain identifier: B

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

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 6.95

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

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 121 THR   ( 202-)  A      CA   CB    1.61    4.1
 509 THR   ( 202-)  B      CA   CB    1.61    4.1

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.

  10 GLN   (  91-)  A      N    CA   C    99.55   -4.2
  74 HIS   ( 155-)  A      CG   ND1  CE1 109.81    4.2
 145 GLN   ( 226-)  A      N    CA   C   124.27    4.7
 202 ARG   ( 283-)  A      N    CA   C    97.78   -4.8
 264 GLY   ( 345-)  A      N    CA   C   125.97    4.6
 349 ARG   ( 430-)  A      N    CA   C   126.28    5.4
 350 LYS   ( 431-)  A     -CA  -C    N   106.53   -4.8
 350 LYS   ( 431-)  A     -C    N    CA  129.95    4.6
 363 VAL   ( 444-)  A      N    CA   C    99.97   -4.0
 398 GLN   (  91-)  B      N    CA   C    99.55   -4.2
 462 HIS   ( 155-)  B      CG   ND1  CE1 109.81    4.2
 533 GLN   ( 226-)  B      N    CA   C   124.27    4.7
 590 ARG   ( 283-)  B      N    CA   C    97.78   -4.8
 652 GLY   ( 345-)  B      N    CA   C   125.97    4.6
 737 ARG   ( 430-)  B      N    CA   C   126.28    5.4
 738 LYS   ( 431-)  B     -CA  -C    N   106.53   -4.8
 738 LYS   ( 431-)  B     -C    N    CA  129.95    4.6
 751 VAL   ( 444-)  B      N    CA   C    99.97   -4.0
 777 NAG   ( 472-)  A      N2   C2   C1   99.74   -4.5
 782 NAG   ( 479-)  A      N2   C2   C1  100.92   -4.2
 785 NAG   ( 472-)  B      N2   C2   C1   99.74   -4.5
 791 NAG   ( 479-)  B      N2   C2   C1  100.92   -4.2

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.

 349 ARG   ( 430-)  A    5.60
 737 ARG   ( 430-)  B    5.60
 202 ARG   ( 283-)  A    5.40
 590 ARG   ( 283-)  B    5.40
 145 GLN   ( 226-)  A    5.07
 533 GLN   ( 226-)  B    5.07
  10 GLN   (  91-)  A    4.64
 398 GLN   (  91-)  B    4.64
  93 VAL   ( 174-)  A    4.50
 481 VAL   ( 174-)  B    4.50
 264 GLY   ( 345-)  A    4.45
 652 GLY   ( 345-)  B    4.45
 182 VAL   ( 263-)  A    4.38
 570 VAL   ( 263-)  B    4.38
 350 LYS   ( 431-)  A    4.35
 738 LYS   ( 431-)  B    4.35
  99 SER   ( 180-)  A    4.22
 487 SER   ( 180-)  B    4.22
  24 SER   ( 105-)  A    4.13
 412 SER   ( 105-)  B    4.13

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.754

Error: Connections to aromatic rings out of plane

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

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

 659 TRP   ( 352-)  B      CB   4.14
 271 TRP   ( 352-)  A      CB   4.14
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.582

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.582

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.

  57 THR   ( 138-)  A    -3.0
 445 THR   ( 138-)  B    -3.0
 383 ILE   ( 464-)  A    -2.7
 771 ILE   ( 464-)  B    -2.7
 425 ARG   ( 118-)  B    -2.7
  37 ARG   ( 118-)  A    -2.7
 738 LYS   ( 431-)  B    -2.6
 350 LYS   ( 431-)  A    -2.6
 204 PRO   ( 285-)  A    -2.6
 592 PRO   ( 285-)  B    -2.6
 532 THR   ( 225-)  B    -2.5
 144 THR   ( 225-)  A    -2.5
 574 PRO   ( 267-)  B    -2.5
 186 PRO   ( 267-)  A    -2.5
 534 GLU   ( 227-)  B    -2.5
 146 GLU   ( 227-)  A    -2.5
 256 CYS   ( 337-)  A    -2.4
 644 CYS   ( 337-)  B    -2.4
 234 SER   ( 315-)  A    -2.4
 622 SER   ( 315-)  B    -2.4
 694 ASN   ( 387-)  B    -2.3
 306 ASN   ( 387-)  A    -2.3
  67 THR   ( 148-)  A    -2.3
 455 THR   ( 148-)  B    -2.3
 653 THR   ( 346-)  B    -2.2
And so on for a total of 66 lines.

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.

  23 ASN   ( 104-)  A  Poor phi/psi
  37 ARG   ( 118-)  A  Poor phi/psi
  40 TYR   ( 121-)  A  Poor phi/psi
  52 ALA   ( 133-)  A  Poor phi/psi
  66 ASP   ( 147-)  A  Poor phi/psi
  89 GLY   ( 170-)  A  Poor phi/psi
 127 ASP   ( 208-)  A  Poor phi/psi
 146 GLU   ( 227-)  A  Poor phi/psi
 153 ASN   ( 234-)  A  Poor phi/psi
 165 ALA   ( 246-)  A  Poor phi/psi
 166 SER   ( 247-)  A  Poor phi/psi
 178 GLU   ( 259-)  A  Poor phi/psi
 179 GLY   ( 260-)  A  Poor phi/psi
 183 HIS   ( 264-)  A  Poor phi/psi
 203 TYR   ( 284-)  A  PRO omega poor
 210 CYS   ( 291-)  A  Poor phi/psi
 229 TYR   ( 310-)  A  Poor phi/psi
 234 SER   ( 315-)  A  Poor phi/psi
 241 VAL   ( 322-)  A  Poor phi/psi
 244 THR   ( 325-)  A  PRO omega poor
 248 ASP   ( 329-)  A  Poor phi/psi
 249 ASP   ( 330-)  A  Poor phi/psi
 256 CYS   ( 337-)  A  Poor phi/psi
 261 ASN   ( 342-)  A  Poor phi/psi
 263 ARG   ( 344-)  A  Poor phi/psi
And so on for a total of 70 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.441

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!

   3 TYR   (  84-)  A      0
   4 ARG   (  85-)  A      0
   5 ASN   (  86-)  A      0
   6 TRP   (  87-)  A      0
   7 SER   (  88-)  A      0
  11 CYS   (  92-)  A      0
  14 THR   (  95-)  A      0
  20 SER   ( 101-)  A      0
  24 SER   ( 105-)  A      0
  34 TRP   ( 115-)  A      0
  37 ARG   ( 118-)  A      0
  38 GLU   ( 119-)  A      0
  39 PRO   ( 120-)  A      0
  46 VAL   ( 127-)  A      0
  47 LYS   ( 128-)  A      0
  55 GLN   ( 136-)  A      0
  61 ASN   ( 142-)  A      0
  63 HIS   ( 144-)  A      0
  65 ASN   ( 146-)  A      0
  66 ASP   ( 147-)  A      0
  67 THR   ( 148-)  A      0
  68 VAL   ( 149-)  A      0
  70 ASP   ( 151-)  A      0
  72 ILE   ( 153-)  A      0
  75 ARG   ( 156-)  A      0
And so on for a total of 467 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 : 2.077

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!

 267 GLY   ( 348-)  A   1.53   55
 655 GLY   ( 348-)  B   1.53   55

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].

 220 PRO   ( 301-)  A  -118.2 half-chair C-delta/C-gamma (-126 degrees)
 259 PRO   ( 340-)  A  -116.1 envelop C-gamma (-108 degrees)
 305 PRO   ( 386-)  A  -118.5 half-chair C-delta/C-gamma (-126 degrees)
 608 PRO   ( 301-)  B  -118.2 half-chair C-delta/C-gamma (-126 degrees)
 647 PRO   ( 340-)  B  -116.1 envelop C-gamma (-108 degrees)
 693 PRO   ( 386-)  B  -118.5 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 779 NAG   ( 474-)  A      O6  <->  808 FUL   ( 477-)  A      C1     0.92    1.48  INTRA B3
 780 NAG   ( 475-)  A      O4  <->  807 BMA   ( 476-)  A      C1     0.89    1.51  INTRA B3
 796 BMA   ( 480-)  A      O3  <->  809 MAN   ( 481-)  A      C1     0.86    1.54  INTRA B3
 762 THR   ( 455-)  B      CG2 <->  781 NAG   ( 478-)  A      C6     0.75    2.45  INTRA
 780 NAG   ( 475-)  A      C4  <->  807 BMA   ( 476-)  A      C1     0.66    2.54  INTRA
 779 NAG   ( 474-)  A      C6  <->  808 FUL   ( 477-)  A      C1     0.64    2.56  INTRA
 762 THR   ( 455-)  B      CG2 <->  798 MAN   ( 483-)  A      C2     0.56    2.64  INTRA
 796 BMA   ( 480-)  A      C3  <->  809 MAN   ( 481-)  A      C1     0.49    2.71  INTRA
 781 NAG   ( 478-)  A      O6  <->  782 NAG   ( 479-)  A      N2     0.42    2.28  INTRA
 790 NAG   ( 478-)  B      O6  <->  791 NAG   ( 479-)  B      N2     0.42    2.28  INTRA
 443 GLN   ( 136-)  B      CD  <->  463 ARG   ( 156-)  B      NH1    0.41    2.69  INTRA BL
  55 GLN   ( 136-)  A      CD  <->   75 ARG   ( 156-)  A      NH1    0.41    2.69  INTRA BL
 531 ARG   ( 224-)  B      NH2 <->  551 GLY   ( 244-)  B      N      0.36    2.49  INTRA
 143 ARG   ( 224-)  A      NH2 <->  163 GLY   ( 244-)  A      N      0.36    2.49  INTRA
 491 HIS   ( 184-)  B      CD2 <->  493 GLY   ( 186-)  B      N      0.35    2.75  INTRA BL
 103 HIS   ( 184-)  A      CD2 <->  105 GLY   ( 186-)  A      N      0.35    2.75  INTRA BL
 211 ARG   ( 292-)  A      NH1 <->  213 ASN   ( 294-)  A      OD1    0.30    2.40  INTRA
 599 ARG   ( 292-)  B      NH1 <->  601 ASN   ( 294-)  B      OD1    0.30    2.40  INTRA
 800 BMA   ( 480-)  B      O6  <->  803 MAN   ( 483-)  B      C6     0.27    2.53  INTRA
 796 BMA   ( 480-)  A      O6  <->  798 MAN   ( 483-)  A      C6     0.27    2.53  INTRA
 553 ALA   ( 246-)  B      O   <->  581 HIS   ( 274-)  B      NE2    0.27    2.43  INTRA
 165 ALA   ( 246-)  A      O   <->  193 HIS   ( 274-)  A      NE2    0.27    2.43  INTRA
   8 LYS   (  89-)  A      NZ  <->  333 GLY   ( 414-)  A      O      0.26    2.44  INTRA BL
 396 LYS   (  89-)  B      NZ  <->  721 GLY   ( 414-)  B      O      0.26    2.44  INTRA BL
 255 ASN   ( 336-)  A      C   <->  256 CYS   ( 337-)  A      SG     0.26    3.04  INTRA BL
And so on for a total of 262 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.

 556 ARG   ( 249-)  B      -7.79
 168 ARG   ( 249-)  A      -7.79
 372 TYR   ( 453-)  A      -7.26
 590 ARG   ( 283-)  B      -6.71
 202 ARG   ( 283-)  A      -6.71
 203 TYR   ( 284-)  A      -6.23
 591 TYR   ( 284-)  B      -6.23
 654 GLN   ( 347-)  B      -6.14
 266 GLN   ( 347-)  A      -6.14
 334 LYS   ( 415-)  A      -6.10
 722 LYS   ( 415-)  B      -5.80
 760 TYR   ( 453-)  B      -5.58
 257 ARG   ( 338-)  A      -5.25
 645 ARG   ( 338-)  B      -5.19
 459 ARG   ( 152-)  B      -5.02

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.

 371 THR   ( 452-)  A       374 - THR    455- ( A)         -5.30

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.

  65 ASN   ( 146-)  A   -2.85
 453 ASN   ( 146-)  B   -2.85

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

  28 SER   ( 109-)  A     -   31 GLY   ( 112-)  A        -1.66
 416 SER   ( 109-)  B     -  419 GLY   ( 112-)  B        -1.66

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

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.

  23 ASN   ( 104-)  A
  50 GLN   ( 131-)  A
  61 ASN   ( 142-)  A
  69 HIS   ( 150-)  A
  80 ASN   ( 161-)  A
  92 GLN   ( 173-)  A
 145 GLN   ( 226-)  A
 193 HIS   ( 274-)  A
 266 GLN   ( 347-)  A
 411 ASN   ( 104-)  B
 438 GLN   ( 131-)  B
 449 ASN   ( 142-)  B
 457 HIS   ( 150-)  B
 480 GLN   ( 173-)  B
 533 GLN   ( 226-)  B
 581 HIS   ( 274-)  B
 654 GLN   ( 347-)  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.

  21 LYS   ( 102-)  A      NZ
  23 ASN   ( 104-)  A      N
  26 ARG   ( 107-)  A      N
  32 ASP   ( 113-)  A      N
  41 VAL   ( 122-)  A      N
  47 LYS   ( 128-)  A      N
  56 GLY   ( 137-)  A      N
  57 THR   ( 138-)  A      N
  61 ASN   ( 142-)  A      ND2
  63 HIS   ( 144-)  A      NE2
  68 VAL   ( 149-)  A      N
  72 ILE   ( 153-)  A      N
  74 HIS   ( 155-)  A      N
  75 ARG   ( 156-)  A      NE
  75 ARG   ( 156-)  A      NH1
  76 THR   ( 157-)  A      N
  80 ASN   ( 161-)  A      ND2
  86 PHE   ( 167-)  A      N
  94 CYS   ( 175-)  A      N
  98 SER   ( 179-)  A      N
 101 SER   ( 182-)  A      N
 105 GLY   ( 186-)  A      N
 106 LYS   ( 187-)  A      N
 119 ASN   ( 200-)  A      N
 120 ALA   ( 201-)  A      N
And so on for a total of 128 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.

  74 HIS   ( 155-)  A      ND1
 103 HIS   ( 184-)  A      ND1
 104 ASP   ( 185-)  A      OD2
 116 ASP   ( 197-)  A      OD2
 183 HIS   ( 264-)  A      ND1
 243 ASP   ( 324-)  A      OD2
 462 HIS   ( 155-)  B      ND1
 491 HIS   ( 184-)  B      ND1
 492 ASP   ( 185-)  B      OD2
 504 ASP   ( 197-)  B      OD2
 571 HIS   ( 264-)  B      ND1
 631 ASP   ( 324-)  B      OD2

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+.

 804  CA   ( 470-)  A     1.80   0.97 Is perhaps MG
 805  CA   ( 470-)  B     1.80   0.97 Is perhaps MG
Since there are no waters, the water check has been skipped.

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.

  44 ASP   ( 125-)  A   H-bonding suggests Asn
 104 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 116 ASP   ( 197-)  A   H-bonding suggests Asn
 146 GLU   ( 227-)  A   H-bonding suggests Gln; but Alt-Rotamer
 162 ASP   ( 243-)  A   H-bonding suggests Asn; but Alt-Rotamer
 227 GLU   ( 308-)  A   H-bonding suggests Gln; but Alt-Rotamer
 262 GLU   ( 343-)  A   H-bonding suggests Gln; but Alt-Rotamer
 432 ASP   ( 125-)  B   H-bonding suggests Asn
 492 ASP   ( 185-)  B   H-bonding suggests Asn; but Alt-Rotamer
 504 ASP   ( 197-)  B   H-bonding suggests Asn
 534 GLU   ( 227-)  B   H-bonding suggests Gln; but Alt-Rotamer
 550 ASP   ( 243-)  B   H-bonding suggests Asn; but Alt-Rotamer
 615 GLU   ( 308-)  B   H-bonding suggests Gln; but Alt-Rotamer
 650 GLU   ( 343-)  B   H-bonding suggests Gln; 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 :  -0.982
  2nd generation packing quality :  -1.581
  Ramachandran plot appearance   :  -3.582 (poor)
  chi-1/chi-2 rotamer normality  :  -4.441 (bad)
  Backbone conformation          :  -1.156

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.626 (tight)
  Bond angles                    :   0.936
  Omega angle restraints         :   0.378 (tight)
  Side chain planarity           :   0.638 (tight)
  Improper dihedral distribution :   1.254
  Inside/Outside distribution    :   1.056

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.626 (tight)
  Bond angles                    :   0.936
  Omega angle restraints         :   0.378 (tight)
  Side chain planarity           :   0.638 (tight)
  Improper dihedral distribution :   1.254
  Inside/Outside distribution    :   1.056
==============

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.