WHAT IF Check report

This file was created 2014-06-26 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 pdb1kh9.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 : 0.565
CA-only RMS fit for the two chains : 0.285

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 PO4   ( 453-)  A  -
 897 PO4   ( 453-)  B  -

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: Missing atoms

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

   1 VAL   (   6-)  A      CG1
   1 VAL   (   6-)  A      CG2
   3 GLU   (   8-)  A      CG
   3 GLU   (   8-)  A      CD
   3 GLU   (   8-)  A      OE1
   3 GLU   (   8-)  A      OE2
 148 ASP   ( 153-)  A      CB
 148 ASP   ( 153-)  A      CG
 148 ASP   ( 153-)  A      OD1
 148 ASP   ( 153-)  A      OD2
 444 LYS   ( 449-)  A      CG
 444 LYS   ( 449-)  A      CD
 444 LYS   ( 449-)  A      CE
 444 LYS   ( 449-)  A      NZ
 445 VAL   (   6-)  B      CG1
 445 VAL   (   6-)  B      CG2
 447 GLU   (   8-)  B      CG
 447 GLU   (   8-)  B      CD
 447 GLU   (   8-)  B      OE1
 447 GLU   (   8-)  B      OE2
 592 ASP   ( 153-)  B      CB
 592 ASP   ( 153-)  B      CG
 592 ASP   ( 153-)  B      OD1
 592 ASP   ( 153-)  B      OD2
 888 LYS   ( 449-)  B      CG
 888 LYS   ( 449-)  B      CD
 888 LYS   ( 449-)  B      CE
 888 LYS   ( 449-)  B      NZ

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) :292.000

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 4.83

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: Arginine nomenclature problem

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

 605 ARG   ( 166-)  B
 706 ARG   ( 267-)  B

Warning: Tyrosine convention problem

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

  82 TYR   (  87-)  A
 164 TYR   ( 169-)  A
 229 TYR   ( 234-)  A
 397 TYR   ( 402-)  A
 673 TYR   ( 234-)  B
 841 TYR   ( 402-)  B

Warning: Phenylalanine convention problem

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

  66 PHE   (  71-)  A
 312 PHE   ( 317-)  A
 350 PHE   ( 355-)  A
 434 PHE   ( 439-)  A
 510 PHE   (  71-)  B
 756 PHE   ( 317-)  B
 794 PHE   ( 355-)  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.

  23 ASP   (  28-)  A
  46 ASP   (  51-)  A
  50 ASP   (  55-)  A
  96 ASP   ( 101-)  A
 234 ASP   ( 239-)  A
 299 ASP   ( 304-)  A
 322 ASP   ( 327-)  A
 364 ASP   ( 369-)  A
 467 ASP   (  28-)  B
 494 ASP   (  55-)  B
 540 ASP   ( 101-)  B
 640 ASP   ( 201-)  B
 719 ASP   ( 280-)  B
 733 ASP   ( 294-)  B
 743 ASP   ( 304-)  B
 847 ASP   ( 408-)  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.

  61 GLU   (  66-)  A
 145 GLU   ( 150-)  A
 179 GLU   ( 184-)  A
 188 GLU   ( 193-)  A
 243 GLU   ( 248-)  A
 303 GLU   ( 308-)  A
 309 GLU   ( 314-)  A
 349 GLU   ( 354-)  A
 402 GLU   ( 407-)  A
 505 GLU   (  66-)  B
 623 GLU   ( 184-)  B
 632 GLU   ( 193-)  B
 687 GLU   ( 248-)  B
 747 GLU   ( 308-)  B
 793 GLU   ( 354-)  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.

  97 SER   ( 102-)  A      CA   C     1.71    8.7
  97 SER   ( 102-)  A      N   -C     1.24   -4.6

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 HIS   (  86-)  A      CG   ND1  CE1 109.66    4.1
  92 ASP   (  97-)  A      N    CA   C    97.64   -4.8
  97 SER   ( 102-)  A     -O   -C    N   129.44    4.0
 318 GLY   ( 323-)  A      N    CA   C    99.98   -4.3
 320 SER   ( 325-)  A      N    CA   C   122.66    4.1
 377 LYS   ( 382-)  A      N    CA   C    99.53   -4.2
 536 ASP   (  97-)  B      N    CA   C    95.12   -5.7
 762 GLY   ( 323-)  B      N    CA   C   100.29   -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.

  23 ASP   (  28-)  A
  46 ASP   (  51-)  A
  50 ASP   (  55-)  A
  61 GLU   (  66-)  A
  96 ASP   ( 101-)  A
 145 GLU   ( 150-)  A
 179 GLU   ( 184-)  A
 188 GLU   ( 193-)  A
 234 ASP   ( 239-)  A
 243 GLU   ( 248-)  A
 299 ASP   ( 304-)  A
 303 GLU   ( 308-)  A
 309 GLU   ( 314-)  A
 322 ASP   ( 327-)  A
 349 GLU   ( 354-)  A
 364 ASP   ( 369-)  A
 402 GLU   ( 407-)  A
 467 ASP   (  28-)  B
 494 ASP   (  55-)  B
 505 GLU   (  66-)  B
 540 ASP   ( 101-)  B
 605 ARG   ( 166-)  B
 623 GLU   ( 184-)  B
 632 GLU   ( 193-)  B
 640 ASP   ( 201-)  B
 687 GLU   ( 248-)  B
 706 ARG   ( 267-)  B
 719 ASP   ( 280-)  B
 733 ASP   ( 294-)  B
 743 ASP   ( 304-)  B
 747 GLU   ( 308-)  B
 793 GLU   ( 354-)  B
 847 ASP   ( 408-)  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.

 320 SER   ( 325-)  A    6.90
 764 SER   ( 325-)  B    6.25
 155 VAL   ( 160-)  A    6.20
 171 GLN   ( 176-)  A    5.69
 321 ILE   ( 326-)  A    5.52
 149 ALA   ( 154-)  A    5.26
 615 GLN   ( 176-)  B    5.21
 536 ASP   (  97-)  B    5.19
 765 ILE   ( 326-)  B    5.09
 318 GLY   ( 323-)  A    5.00
 762 GLY   ( 323-)  B    4.87
 377 LYS   ( 382-)  A    4.53
 812 ALA   ( 373-)  B    4.50
 275 ASP   ( 280-)  A    4.30
  92 ASP   (  97-)  A    4.25
 504 ALA   (  65-)  B    4.10
 763 ALA   ( 324-)  B    4.03
 128 LEU   ( 133-)  A    4.02

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.619

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.

 362 THR   ( 367-)  A    -3.3
 806 THR   ( 367-)  B    -3.2
 811 HIS   ( 372-)  B    -2.7
 110 THR   ( 115-)  A    -2.6
 412 LEU   ( 417-)  A    -2.6
 856 LEU   ( 417-)  B    -2.6
 554 THR   ( 115-)  B    -2.5
 367 HIS   ( 372-)  A    -2.4
 708 LEU   ( 269-)  B    -2.4
 774 PRO   ( 335-)  B    -2.3
 166 PRO   ( 171-)  A    -2.3
  66 PHE   (  71-)  A    -2.3
 424 VAL   ( 429-)  A    -2.2
 671 ARG   ( 232-)  B    -2.2
 610 PRO   ( 171-)  B    -2.1
  79 TYR   (  84-)  A    -2.1
 692 LYS   ( 253-)  B    -2.1
 594 THR   ( 155-)  B    -2.0
 510 PHE   (  71-)  B    -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.

  66 PHE   (  71-)  A  Poor phi/psi
 121 GLU   ( 126-)  A  Poor phi/psi
 163 CYS   ( 168-)  A  Poor phi/psi
 194 ARG   ( 199-)  A  Poor phi/psi
 271 HIS   ( 276-)  A  Poor phi/psi
 328 ALA   ( 333-)  A  Poor phi/psi
 420 HIS   ( 425-)  A  Poor phi/psi
 565 GLU   ( 126-)  B  Poor phi/psi
 616 LYS   ( 177-)  B  Poor phi/psi
 656 ALA   ( 217-)  B  Poor phi/psi
 715 HIS   ( 276-)  B  Poor phi/psi
 750 SER   ( 311-)  B  Poor phi/psi
 806 THR   ( 367-)  B  Poor phi/psi
 811 HIS   ( 372-)  B  Poor phi/psi
 864 HIS   ( 425-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.968

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.968

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 GLU   (   8-)  A      0
   4 ASN   (   9-)  A      0
   5 ARG   (  10-)  A      0
   8 GLN   (  13-)  A      0
  10 ASN   (  15-)  A      0
  13 ALA   (  18-)  A      0
  14 PRO   (  19-)  A      0
  21 THR   (  26-)  A      0
  23 ASP   (  28-)  A      0
  38 LYS   (  43-)  A      0
  39 ASN   (  44-)  A      0
  46 ASP   (  51-)  A      0
  48 MET   (  53-)  A      0
  66 PHE   (  71-)  A      0
  72 ALA   (  77-)  A      0
  81 HIS   (  86-)  A      0
  88 THR   (  93-)  A      0
  93 TYR   (  98-)  A      0
 109 LYS   ( 114-)  A      0
 111 TYR   ( 116-)  A      0
 112 ASN   ( 117-)  A      0
 115 LEU   ( 120-)  A      0
 119 ILE   ( 124-)  A      0
 121 GLU   ( 126-)  A      0
 144 ALA   ( 149-)  A      0
And so on for a total of 329 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 : 1.544

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!

 818 PRO   ( 379-)  B   1.53   17

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]

 174 PRO   ( 179-)  A    0.46 HIGH
 277 PRO   ( 282-)  A    0.45 HIGH
 283 PRO   ( 288-)  A    0.46 HIGH
 374 PRO   ( 379-)  A    0.45 HIGH

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].

 151 PRO   ( 156-)  A  -112.3 envelop C-gamma (-108 degrees)
 166 PRO   ( 171-)  A  -119.0 half-chair C-delta/C-gamma (-126 degrees)
 260 PRO   ( 265-)  A    44.5 envelop C-delta (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.

  97 SER   ( 102-)  A      OG  <->  896 PO4   ( 453-)  A      P      1.00    1.60  INTRA BF
 407 HIS   ( 412-)  A      CE1 <->  896 PO4   ( 453-)  A      O1     0.64    2.16  INTRA BF
 541 SER   ( 102-)  B      OG  <->  897 PO4   ( 453-)  B      P      0.57    2.03  INTRA BF
 407 HIS   ( 412-)  A      NE2 <->  896 PO4   ( 453-)  A      O1     0.47    2.23  INTRA BF
  97 SER   ( 102-)  A      CB  <->  896 PO4   ( 453-)  A      P      0.42    2.98  INTRA BF
 449 ARG   (  10-)  B      NH2 <->  468 GLN   (  29-)  B      OE1    0.28    2.42  INTRA
 194 ARG   ( 199-)  A      NH2 <->  227 ARG   ( 232-)  A      O      0.26    2.44  INTRA
 584 ASN   ( 145-)  B      ND2 <->  899 HOH   (1033 )  B      O      0.23    2.47  INTRA
 770 HIS   ( 331-)  B      NE2 <->  851 HIS   ( 412-)  B      NE2    0.23    2.77  INTRA BL
 329 ASN   ( 334-)  A      ND2 <->  898 HOH   (1047 )  A      O      0.20    2.50  INTRA
 809 HIS   ( 370-)  B      CE1 <->  851 HIS   ( 412-)  B      CD2    0.19    3.01  INTRA BL
 809 HIS   ( 370-)  B      CE1 <->  851 HIS   ( 412-)  B      CG     0.19    3.01  INTRA BL
   1 VAL   (   6-)  A      N   <->   24 GLN   (  29-)  A      CG     0.18    2.92  INTRA BF
 731 ARG   ( 292-)  B      NH2 <->  736 PRO   ( 297-)  B      O      0.18    2.52  INTRA
 427 LEU   ( 432-)  A      N   <->  898 HOH   (1124 )  A      O      0.17    2.53  INTRA
 770 HIS   ( 331-)  B      ND1 <->  849 GLN   ( 410-)  B      O      0.16    2.54  INTRA
 326 HIS   ( 331-)  A      ND1 <->  405 GLN   ( 410-)  A      O      0.15    2.55  INTRA
 194 ARG   ( 199-)  A      NH1 <->  246 GLN   ( 251-)  A      O      0.15    2.55  INTRA
   5 ARG   (  10-)  A      NH2 <->   24 GLN   (  29-)  A      CD     0.14    2.96  INTRA
 814 GLN   ( 375-)  B      NE2 <->  899 HOH   (1028 )  B      O      0.14    2.56  INTRA BL
 163 CYS   ( 168-)  A      SG  <->  172 LYS   ( 177-)  A      CB     0.14    3.26  INTRA
 365 HIS   ( 370-)  A      CE1 <->  407 HIS   ( 412-)  A      CE1    0.14    3.06  INTRA BL
 241 VAL   ( 246-)  A      O   <->  300 LYS   ( 305-)  A      NZ     0.14    2.56  INTRA
 669 GLU   ( 230-)  B      O   <->  672 GLY   ( 233-)  B      N      0.13    2.57  INTRA
 235 ALA   ( 240-)  A      N   <->  290 SER   ( 295-)  A      O      0.13    2.57  INTRA
And so on for a total of 132 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.

 714 TYR   ( 275-)  B      -6.58
 270 TYR   ( 275-)  A      -6.35
 691 GLN   ( 252-)  B      -6.01
  87 LYS   (  92-)  A      -5.86
 247 GLN   ( 252-)  A      -5.86
 531 LYS   (  92-)  B      -5.82
 624 LYS   ( 185-)  B      -5.22
 183 LYS   ( 188-)  A      -5.17
 615 GLN   ( 176-)  B      -5.08
 798 GLU   ( 359-)  B      -5.03
 354 GLU   ( 359-)  A      -5.01
 706 ARG   ( 267-)  B      -5.00

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.

 120 HIS   ( 125-)  A   -2.89
 763 ALA   ( 324-)  B   -2.60
 564 HIS   ( 125-)  B   -2.58
 319 ALA   ( 324-)  A   -2.58
 412 LEU   ( 417-)  A   -2.51

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.

 596 ALA   ( 157-)  B     -  599 VAL   ( 160-)  B        -1.57

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: 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.

 898 HOH   (1072 )  A      O
 899 HOH   (1070 )  B      O
 899 HOH   (1100 )  B      O
Metal-coordinating Histidine residue 326 fixed to   1
Metal-coordinating Histidine residue 407 fixed to   1
Metal-coordinating Histidine residue 365 fixed to   1
Metal-coordinating Histidine residue 770 fixed to   1
Metal-coordinating Histidine residue 851 fixed to   1
Metal-coordinating Histidine residue 809 fixed to   1

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.

 124 HIS   ( 129-)  A
 216 GLN   ( 221-)  A
 230 GLN   ( 235-)  A
 271 HIS   ( 276-)  A
 329 ASN   ( 334-)  A
 430 GLN   ( 435-)  A
 674 GLN   ( 235-)  B
 773 ASN   ( 334-)  B
 814 GLN   ( 375-)  B
 827 GLN   ( 388-)  B
 849 GLN   ( 410-)  B
 874 GLN   ( 435-)  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.

   5 ARG   (  10-)  A      N
   6 ALA   (  11-)  A      N
   8 GLN   (  13-)  A      NE2
  24 GLN   (  29-)  A      NE2
  73 LEU   (  78-)  A      N
  76 THR   (  81-)  A      N
  97 SER   ( 102-)  A      N
  98 ALA   ( 103-)  A      N
 106 THR   ( 111-)  A      OG1
 108 VAL   ( 113-)  A      N
 117 VAL   ( 122-)  A      N
 128 LEU   ( 133-)  A      N
 140 ASN   ( 145-)  A      ND2
 145 GLU   ( 150-)  A      N
 147 GLN   ( 152-)  A      N
 150 THR   ( 155-)  A      OG1
 212 ALA   ( 217-)  A      N
 215 TRP   ( 220-)  A      N
 227 ARG   ( 232-)  A      NH2
 234 ASP   ( 239-)  A      N
 243 GLU   ( 248-)  A      N
 245 ASN   ( 250-)  A      N
 258 ASN   ( 263-)  A      ND2
 262 ARG   ( 267-)  A      NH1
 271 HIS   ( 276-)  A      N
And so on for a total of 72 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.

  78 GLN   (  83-)  A      OE1
 339 ASP   ( 344-)  A      OD1
 383 GLN   ( 388-)  A      OE1
 490 ASP   (  51-)  B      OD1
 522 GLN   (  83-)  B      OE1
 525 HIS   (  86-)  B      ND1
 591 GLN   ( 152-)  B      OE1
 783 ASP   ( 344-)  B      OD1
 845 GLU   ( 406-)  B      OE1

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+.

 893  MG   ( 452-)  A   -.-  -.-  Part of ionic cluster
 893  MG   ( 452-)  A   -.-  -.-  Too few ligands (3)

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.

  52 GLU   (  57-)  A   H-bonding suggests Gln
 118 ASP   ( 123-)  A   H-bonding suggests Asn; but Alt-Rotamer
 640 ASP   ( 201-)  B   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.605
  2nd generation packing quality :  -1.426
  Ramachandran plot appearance   :  -1.900
  chi-1/chi-2 rotamer normality  :  -3.968 (poor)
  Backbone conformation          :  -0.048

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.485 (tight)
  Bond angles                    :   0.761
  Omega angle restraints         :   0.281 (tight)
  Side chain planarity           :   0.584 (tight)
  Improper dihedral distribution :   0.929
  B-factor distribution          :   1.472
  Inside/Outside distribution    :   0.940

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 :   0.3
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.485 (tight)
  Bond angles                    :   0.761
  Omega angle restraints         :   0.281 (tight)
  Side chain planarity           :   0.584 (tight)
  Improper dihedral distribution :   0.929
  B-factor distribution          :   1.472
  Inside/Outside distribution    :   0.940
==============

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.