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 pdb1ht8.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 : 0.297
CA-only RMS fit for the two chains : 0.246

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: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 128131.125
Volume of the Unit Cell V= 4597111.5
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.485
Vm by authors and this calculated Vm agree remarkably well
Matthews coefficient read from REMARK 280 Vm= 4.520

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.

1111 BOG   (1802-)  A  -
1112 BOG   (1801-)  B  -
1113 34C   (1701-)  A  -
1116 34C   (2701-)  B  -
1117 BOG   (2802-)  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: 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) :120.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 148 ARG   ( 180-)  A
 427 ARG   ( 459-)  A
 699 ARG   ( 180-)  B
 978 ARG   ( 459-)  B

Warning: Tyrosine convention problem

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

   6 TYR   (  38-)  A
  98 TYR   ( 130-)  A
 210 TYR   ( 242-)  A
 230 TYR   ( 262-)  A
 323 TYR   ( 355-)  A
 341 TYR   ( 373-)  A
 353 TYR   ( 385-)  A
 372 TYR   ( 404-)  A
 385 TYR   ( 417-)  A
 443 TYR   ( 475-)  A
 463 TYR   ( 495-)  A
 512 TYR   ( 544-)  A
 557 TYR   (  38-)  B
 649 TYR   ( 130-)  B
 761 TYR   ( 242-)  B
 773 TYR   ( 254-)  B
 781 TYR   ( 262-)  B
 874 TYR   ( 355-)  B
 892 TYR   ( 373-)  B
 904 TYR   ( 385-)  B
 923 TYR   ( 404-)  B
 994 TYR   ( 475-)  B
1014 TYR   ( 495-)  B
1063 TYR   ( 544-)  B

Warning: Phenylalanine convention problem

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

  56 PHE   (  88-)  A
  70 PHE   ( 102-)  A
  75 PHE   ( 107-)  A
 155 PHE   ( 187-)  A
 169 PHE   ( 201-)  A
 177 PHE   ( 209-)  A
 188 PHE   ( 220-)  A
 215 PHE   ( 247-)  A
 335 PHE   ( 367-)  A
 446 PHE   ( 478-)  A
 486 PHE   ( 518-)  A
 497 PHE   ( 529-)  A
 518 PHE   ( 550-)  A
 548 PHE   ( 580-)  A
 607 PHE   (  88-)  B
 621 PHE   ( 102-)  B
 700 PHE   ( 181-)  B
 706 PHE   ( 187-)  B
 720 PHE   ( 201-)  B
 728 PHE   ( 209-)  B
 739 PHE   ( 220-)  B
 766 PHE   ( 247-)  B
 886 PHE   ( 367-)  B
 997 PHE   ( 478-)  B
1037 PHE   ( 518-)  B
1048 PHE   ( 529-)  B
1069 PHE   ( 550-)  B
1099 PHE   ( 580-)  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.

  21 ASP   (  53-)  A
 217 ASP   ( 249-)  A
 282 ASP   ( 314-)  A
 361 ASP   ( 393-)  A
 465 ASP   ( 497-)  A
 572 ASP   (  53-)  B
 768 ASP   ( 249-)  B
 833 ASP   ( 314-)  B
 912 ASP   ( 393-)  B
1016 ASP   ( 497-)  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.

  41 GLU   (  73-)  A
 143 GLU   ( 175-)  A
 207 GLU   ( 239-)  A
 236 GLU   ( 268-)  A
 276 GLU   ( 308-)  A
 287 GLU   ( 319-)  A
 307 GLU   ( 339-)  A
 332 GLU   ( 364-)  A
 373 GLU   ( 405-)  A
 422 GLU   ( 454-)  A
 448 GLU   ( 480-)  A
 478 GLU   ( 510-)  A
 488 GLU   ( 520-)  A
 521 GLU   ( 553-)  A
 592 GLU   (  73-)  B
 694 GLU   ( 175-)  B
 758 GLU   ( 239-)  B
 787 GLU   ( 268-)  B
 827 GLU   ( 308-)  B
 838 GLU   ( 319-)  B
 858 GLU   ( 339-)  B
 866 GLU   ( 347-)  B
 883 GLU   ( 364-)  B
 924 GLU   ( 405-)  B
 973 GLU   ( 454-)  B
 999 GLU   ( 480-)  B
1003 GLU   ( 484-)  B
1029 GLU   ( 510-)  B
1039 GLU   ( 520-)  B
1072 GLU   ( 553-)  B

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.998461 -0.000052 -0.000075|
 | -0.000052  0.999002  0.000057|
 | -0.000075  0.000057  0.999233|
Proposed new scale matrix

 |  0.010102  0.000000  0.000000|
 |  0.000000  0.004802  0.000000|
 |  0.000000  0.000000  0.004499|
With corresponding cell

    A    =  98.995  B   = 208.256  C    = 222.249
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    =  99.149  B   = 208.450  C    = 222.399
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 48.828
(Under-)estimated Z-score: 5.150

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.

 116 TYR   ( 148-)  A      N    CA   C    96.92   -5.1
 192 LEU   ( 224-)  A      N    CA   C    98.40   -4.6
 667 TYR   ( 148-)  B      N    CA   C    98.89   -4.4
 743 LEU   ( 224-)  B      N    CA   C    99.31   -4.2
 806 VAL   ( 287-)  B      N    CA   C   122.62    4.1
 927 LEU   ( 408-)  B      N    CA   C   122.91    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.

  21 ASP   (  53-)  A
  41 GLU   (  73-)  A
 143 GLU   ( 175-)  A
 148 ARG   ( 180-)  A
 207 GLU   ( 239-)  A
 217 ASP   ( 249-)  A
 236 GLU   ( 268-)  A
 276 GLU   ( 308-)  A
 282 ASP   ( 314-)  A
 287 GLU   ( 319-)  A
 307 GLU   ( 339-)  A
 332 GLU   ( 364-)  A
 361 ASP   ( 393-)  A
 373 GLU   ( 405-)  A
 422 GLU   ( 454-)  A
 427 ARG   ( 459-)  A
 448 GLU   ( 480-)  A
 465 ASP   ( 497-)  A
 478 GLU   ( 510-)  A
 488 GLU   ( 520-)  A
 521 GLU   ( 553-)  A
 572 ASP   (  53-)  B
 592 GLU   (  73-)  B
 694 GLU   ( 175-)  B
 699 ARG   ( 180-)  B
 758 GLU   ( 239-)  B
 768 ASP   ( 249-)  B
 787 GLU   ( 268-)  B
 827 GLU   ( 308-)  B
 833 ASP   ( 314-)  B
 838 GLU   ( 319-)  B
 858 GLU   ( 339-)  B
 866 GLU   ( 347-)  B
 883 GLU   ( 364-)  B
 912 ASP   ( 393-)  B
 924 GLU   ( 405-)  B
 973 GLU   ( 454-)  B
 978 ARG   ( 459-)  B
 999 GLU   ( 480-)  B
1003 GLU   ( 484-)  B
1016 ASP   ( 497-)  B
1029 GLU   ( 510-)  B
1039 GLU   ( 520-)  B
1072 GLU   ( 553-)  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.

 314 GLU   ( 346-)  A    5.71
 865 GLU   ( 346-)  B    5.56
 116 TYR   ( 148-)  A    5.45
1088 CYS   ( 569-)  B    5.35
 192 LEU   ( 224-)  A    5.22
 537 CYS   ( 569-)  A    4.93
 806 VAL   ( 287-)  B    4.86
 743 LEU   ( 224-)  B    4.85
 927 LEU   ( 408-)  B    4.72
 667 TYR   ( 148-)  B    4.69
 255 VAL   ( 287-)  A    4.49
 149 PHE   ( 181-)  A    4.37
 700 PHE   ( 181-)  B    4.28
 811 PHE   ( 292-)  B    4.25
 376 LEU   ( 408-)  A    4.18
 545 TYR   ( 577-)  A    4.04
 260 PHE   ( 292-)  A    4.02

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.

1037 PHE   ( 518-)  B    -3.4
 486 PHE   ( 518-)  A    -3.2
 482 PRO   ( 514-)  A    -3.1
1033 PRO   ( 514-)  B    -3.1
 544 PRO   ( 576-)  A    -2.7
 904 TYR   ( 385-)  B    -2.5
1082 THR   ( 563-)  B    -2.5
 198 LEU   ( 230-)  A    -2.5
   7 TYR   (  39-)  A    -2.5
1095 PRO   ( 576-)  B    -2.5
 353 TYR   ( 385-)  A    -2.5
 531 THR   ( 563-)  A    -2.5
 558 TYR   (  39-)  B    -2.4
 562 HIS   (  43-)  B    -2.4
 651 ILE   ( 132-)  B    -2.4
1003 GLU   ( 484-)  B    -2.4
  17 ARG   (  49-)  A    -2.4
 466 ILE   ( 498-)  A    -2.4
 452 GLU   ( 484-)  A    -2.4
 895 ARG   ( 376-)  B    -2.3
 669 ARG   ( 150-)  B    -2.3
 344 ARG   ( 376-)  A    -2.3
 810 VAL   ( 291-)  B    -2.2
 668 THR   ( 149-)  B    -2.2
 259 VAL   ( 291-)  A    -2.2
 222 TYR   ( 254-)  A    -2.2
 376 LEU   ( 408-)  A    -2.2
 749 LEU   ( 230-)  B    -2.2
 588 CYS   (  69-)  B    -2.2
 538 LEU   ( 570-)  A    -2.2
 568 ARG   (  49-)  B    -2.1
 118 ARG   ( 150-)  A    -2.1
  37 CYS   (  69-)  A    -2.1
 649 TYR   ( 130-)  B    -2.1
1017 ILE   ( 498-)  B    -2.1
 132 GLY   ( 164-)  A    -2.1
  11 HIS   (  43-)  A    -2.1
 212 LEU   ( 244-)  A    -2.1
 683 GLY   ( 164-)  B    -2.1
 771 LEU   ( 252-)  B    -2.0
 220 LEU   ( 252-)  A    -2.0
 117 THR   ( 149-)  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.

  12 GLN   (  44-)  A  Poor phi/psi
  21 ASP   (  53-)  A  Poor phi/psi
  37 CYS   (  69-)  A  Poor phi/psi
  94 SER   ( 126-)  A  PRO omega poor
  97 THR   ( 129-)  A  Poor phi/psi
 133 THR   ( 165-)  A  Poor phi/psi
 191 ALA   ( 223-)  A  Poor phi/psi
 198 LEU   ( 230-)  A  Poor phi/psi
 215 PHE   ( 247-)  A  Poor phi/psi
 217 ASP   ( 249-)  A  Poor phi/psi
 226 ASN   ( 258-)  A  Poor phi/psi
 238 PRO   ( 270-)  A  Poor phi/psi
 482 PRO   ( 514-)  A  Poor phi/psi
 513 TRP   ( 545-)  A  Poor phi/psi
 547 SER   ( 579-)  A  Poor phi/psi
 563 GLN   (  44-)  B  Poor phi/psi
 588 CYS   (  69-)  B  Poor phi/psi
 645 SER   ( 126-)  B  PRO omega poor
 648 THR   ( 129-)  B  Poor phi/psi
 684 THR   ( 165-)  B  Poor phi/psi
 742 ALA   ( 223-)  B  Poor phi/psi
 749 LEU   ( 230-)  B  Poor phi/psi
 766 PHE   ( 247-)  B  Poor phi/psi
 768 ASP   ( 249-)  B  Poor phi/psi
 806 VAL   ( 287-)  B  Poor phi/psi
 892 TYR   ( 373-)  B  Poor phi/psi
 931 SER   ( 412-)  B  Poor phi/psi
 978 ARG   ( 459-)  B  Poor phi/psi
1003 GLU   ( 484-)  B  Poor phi/psi
1004 LYS   ( 485-)  B  Poor phi/psi
1022 PHE   ( 503-)  B  Poor phi/psi
1033 PRO   ( 514-)  B  Poor phi/psi
1064 TRP   ( 545-)  B  Poor phi/psi
1098 SER   ( 579-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.229

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.

 660 SER   ( 141-)  B    0.36
 697 SER   ( 178-)  B    0.36
1049 SER   ( 530-)  B    0.38
 974 SER   ( 455-)  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!

   4 CYS   (  36-)  A      0
   5 CYS   (  37-)  A      0
   8 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  11 HIS   (  43-)  A      0
  12 GLN   (  44-)  A      0
  18 PHE   (  50-)  A      0
  20 LEU   (  52-)  A      0
  21 ASP   (  53-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  32 TYR   (  64-)  A      0
  33 SER   (  65-)  A      0
  35 PRO   (  67-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  73 ALA   ( 105-)  A      0
  91 LEU   ( 123-)  A      0
  93 PRO   ( 125-)  A      0
  94 SER   ( 126-)  A      0
And so on for a total of 414 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 : 1.330

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!

 681 PRO   ( 162-)  B   1.58   10

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]

 544 PRO   ( 576-)  A    0.45 HIGH
 591 PRO   (  72-)  B    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].

 482 PRO   ( 514-)  A   112.0 envelop C-beta (108 degrees)
1033 PRO   ( 514-)  B   104.1 envelop C-beta (108 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.

 112 ASN   ( 144-)  A      ND2 <-> 1104 NAG   (1671-)  A      C1     0.74    2.36  INTRA BL
 663 ASN   ( 144-)  B      ND2 <-> 1108 NAG   (2671-)  B      C1     0.61    2.49  INTRA BL
 587 ASN   (  68-)  B      ND2 <-> 1107 NAG   (2661-)  B      C1     0.49    2.61  INTRA
  36 ASN   (  68-)  A      ND2 <-> 1103 NAG   (1661-)  A      C1     0.47    2.63  INTRA BF
 378 ASN   ( 410-)  A      ND2 <-> 1106 NAG   (1681-)  A      C1     0.47    2.63  INTRA BF
 153 ARG   ( 185-)  A      NH2 <->  406 ARG   ( 438-)  A      NH1    0.44    2.41  INTRA BF
 929 ASN   ( 410-)  B      ND2 <-> 1110 NAG   (2681-)  B      C1     0.41    2.69  INTRA BF
 704 ARG   ( 185-)  B      NH2 <->  957 ARG   ( 438-)  B      NH1    0.39    2.46  INTRA BF
 663 ASN   ( 144-)  B      CG  <-> 1108 NAG   (2671-)  B      C1     0.38    2.82  INTRA BL
 699 ARG   ( 180-)  B      O   <->  957 ARG   ( 438-)  B      NH1    0.38    2.32  INTRA
 670 ILE   ( 151-)  B      CG2 <->  988 ARG   ( 469-)  B      NH1    0.36    2.74  INTRA BL
 112 ASN   ( 144-)  A      CG  <-> 1104 NAG   (1671-)  A      C1     0.36    2.84  INTRA BL
 148 ARG   ( 180-)  A      NH1 <->  458 GLU   ( 490-)  A      OE1    0.32    2.38  INTRA
 262 LEU   ( 294-)  A      CD2 <->  377 PHE   ( 409-)  A      CE2    0.29    2.91  INTRA
 907 HIS   ( 388-)  B      N   <->  908 PRO   ( 389-)  B      CD     0.28    2.72  INTRA BL
 108 GLU   ( 140-)  A      OE2 <->  112 ASN   ( 144-)  A      ND2    0.27    2.43  INTRA BL
 999 GLU   ( 480-)  B      O   <-> 1030 LYS   ( 511-)  B      NZ     0.27    2.43  INTRA
1082 THR   ( 563-)  B      CG2 <-> 1085 LYS   ( 566-)  B      N      0.27    2.83  INTRA BL
 663 ASN   ( 144-)  B      ND2 <-> 1108 NAG   (2671-)  B      C2     0.27    2.83  INTRA BL
 714 ASN   ( 195-)  B      ND2 <-> 1098 SER   ( 579-)  B      O      0.26    2.44  INTRA
 663 ASN   ( 144-)  B      ND2 <-> 1108 NAG   (2671-)  B      N2     0.25    2.75  INTRA BL
 208 ARG   ( 240-)  A      NH1 <->  239 VAL   ( 271-)  A      CG1    0.25    2.85  INTRA
 148 ARG   ( 180-)  A      O   <->  406 ARG   ( 438-)  A      NH1    0.23    2.47  INTRA
 176 GLN   ( 208-)  A      NE2 <->  198 LEU   ( 230-)  A      N      0.23    2.62  INTRA BL
 356 HIS   ( 388-)  A      N   <->  357 PRO   ( 389-)  A      CD     0.22    2.78  INTRA BL
And so on for a total of 191 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.

 245 ARG   ( 277-)  A      -7.95
 796 ARG   ( 277-)  B      -7.71
 689 GLN   ( 170-)  B      -7.21
 138 GLN   ( 170-)  A      -7.04
  29 ARG   (  61-)  A      -6.95
 580 ARG   (  61-)  B      -6.74
 571 LEU   (  52-)  B      -6.24
  20 LEU   (  52-)  A      -6.23
 704 ARG   ( 185-)  B      -6.13
 893 ARG   ( 374-)  B      -5.97
 183 LYS   ( 215-)  A      -5.97
 342 ARG   ( 374-)  A      -5.94
 734 LYS   ( 215-)  B      -5.84
 155 PHE   ( 187-)  A      -5.73
 706 PHE   ( 187-)  B      -5.72
 153 ARG   ( 185-)  A      -5.52
 401 ARG   ( 433-)  A      -5.42
 396 ARG   ( 428-)  A      -5.36
 947 ARG   ( 428-)  B      -5.30
  22 ARG   (  54-)  A      -5.30
 411 HIS   ( 443-)  A      -5.25
 148 ARG   ( 180-)  A      -5.21
 338 GLN   ( 370-)  A      -5.19
 437 ARG   ( 469-)  A      -5.18
 952 ARG   ( 433-)  B      -5.18
 688 LYS   ( 169-)  B      -5.16
 988 ARG   ( 469-)  B      -5.13
 137 LYS   ( 169-)  A      -5.08
 699 ARG   ( 180-)  B      -5.02
 573 ARG   (  54-)  B      -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.

 137 LYS   ( 169-)  A       139 - LEU    171- ( A)         -5.51
 152 ARG   ( 184-)  A       155 - PHE    187- ( A)         -4.90
 688 LYS   ( 169-)  B       690 - LEU    171- ( B)         -5.65

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

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.

 655 TYR   ( 136-)  B   -2.82
 333 LEU   ( 365-)  A   -2.61
 963 ILE   ( 444-)  B   -2.61
 104 TYR   ( 136-)  A   -2.51

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

  10 GLN   (  42-)  A
  63 HIS   (  95-)  A
 102 HIS   ( 134-)  A
 172 HIS   ( 204-)  A
 176 GLN   ( 208-)  A
 205 ASN   ( 237-)  A
 209 GLN   ( 241-)  A
 343 ASN   ( 375-)  A
 368 GLN   ( 400-)  A
 410 HIS   ( 442-)  A
 411 HIS   ( 443-)  A
 447 GLN   ( 479-)  A
 561 GLN   (  42-)  B
 653 HIS   ( 134-)  B
 727 GLN   ( 208-)  B
 756 ASN   ( 237-)  B
 760 GLN   ( 241-)  B
 919 GLN   ( 400-)  B
 962 HIS   ( 443-)  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 TRP   (  75-)  A      N
  88 ARG   ( 120-)  A      NE
 104 TYR   ( 136-)  A      N
 133 THR   ( 165-)  A      OG1
 143 GLU   ( 175-)  A      N
 171 GLN   ( 203-)  A      NE2
 176 GLN   ( 208-)  A      NE2
 181 SER   ( 213-)  A      OG
 208 ARG   ( 240-)  A      NE
 208 ARG   ( 240-)  A      NH2
 216 LYS   ( 248-)  A      N
 250 GLN   ( 282-)  A      N
 256 GLY   ( 288-)  A      N
 257 GLN   ( 289-)  A      N
 258 GLU   ( 290-)  A      N
 261 GLY   ( 293-)  A      N
 265 GLY   ( 297-)  A      N
 316 TYR   ( 348-)  A      OH
 318 GLN   ( 350-)  A      N
 325 LEU   ( 357-)  A      N
 342 ARG   ( 374-)  A      N
 349 PHE   ( 381-)  A      N
 350 ASN   ( 382-)  A      ND2
 356 HIS   ( 388-)  A      N
 372 TYR   ( 404-)  A      N
And so on for a total of 79 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.

 288 HIS   ( 320-)  A      NE2
 351 GLN   ( 383-)  A      OE1
 447 GLN   ( 479-)  A      OE1
 481 HIS   ( 513-)  A      ND1
 723 HIS   ( 204-)  B      NE2
 839 HIS   ( 320-)  B      NE2
1032 HIS   ( 513-)  B      ND1
1043 GLU   ( 524-)  B      OE1

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.

1118 HOH   (1899 )  A      O  1.17  K  4 *2 ION-B
1119 HOH   (2865 )  B      O  1.13  K  5 *2 ION-B

Warning: Possible wrong residue type

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

  69 ASP   ( 101-)  A   H-bonding suggests Asn
 384 ASP   ( 416-)  A   H-bonding suggests Asn
 620 ASP   ( 101-)  B   H-bonding suggests Asn; but Alt-Rotamer
 935 ASP   ( 416-)  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 :  -1.606
  2nd generation packing quality :  -1.668
  Ramachandran plot appearance   :  -1.888
  chi-1/chi-2 rotamer normality  :  -2.229
  Backbone conformation          :  -0.907

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.668
  Omega angle restraints         :   0.242 (tight)
  Side chain planarity           :   0.250 (tight)
  Improper dihedral distribution :   0.616
  B-factor distribution          :   0.413
  Inside/Outside distribution    :   1.099

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 : 2.69


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :   0.0
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.668
  Omega angle restraints         :   0.242 (tight)
  Side chain planarity           :   0.250 (tight)
  Improper dihedral distribution :   0.616
  B-factor distribution          :   0.413
  Inside/Outside distribution    :   1.099
==============

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.