WHAT IF Check report

This file was created 2011-12-17 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 pdb3pxj.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 : 0.981
CA-only RMS fit for the two chains : 0.399

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

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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'.

 476 GLU   ( 114-)  C      CG
 476 GLU   ( 114-)  C      CD
 476 GLU   ( 114-)  C      OE1
 476 GLU   ( 114-)  C      OE2

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 ALA   (  32-)  A    High
   2 ALA   (  33-)  A    High
   3 HIS   (  34-)  A    High
  29 ARG   (  60-)  A    High
  31 ASP   (  62-)  A    High
  46 SER   (  77-)  A    High
  47 GLY   (  78-)  A    High
  48 THR   (  79-)  A    High
  49 GLN   (  80-)  A    High
  50 SER   (  81-)  A    High
  56 GLU   (  87-)  A    High
  58 PRO   (  89-)  A    High
  59 GLY   (  90-)  A    High
  73 ARG   ( 104-)  A    High
  79 GLU   ( 110-)  A    High
  83 GLU   ( 114-)  A    High
  88 ASP   ( 119-)  A    High
  93 ASP   ( 124-)  A    High
 100 GLU   ( 131-)  A    High
 102 ASP   ( 133-)  A    High
 103 LYS   ( 134-)  A    High
 113 GLN   ( 144-)  A    High
 121 GLU   ( 152-)  A    High
 130 CYS   ( 161-)  A    High
 160 ASP   ( 191-)  A    High
And so on for a total of 98 lines.

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 8

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.619 over 5001 bonds
Average difference in B over a bond : 5.94
RMS difference in B over a bond : 7.72

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Tyrosine convention problem

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

  78 TYR   ( 109-)  A
  99 TYR   ( 130-)  A
 141 TYR   ( 172-)  A
 176 TYR   ( 207-)  A
 195 TYR   ( 226-)  A
 277 TYR   ( 109-)  B
 298 TYR   ( 130-)  B
 375 TYR   ( 207-)  B
 394 TYR   ( 226-)  B
 445 TYR   (  83-)  C
 527 TYR   ( 172-)  C
 562 TYR   ( 207-)  C
 581 TYR   ( 226-)  C
 660 TYR   ( 109-)  D
 681 TYR   ( 130-)  D
 721 TYR   ( 172-)  D
 756 TYR   ( 207-)  D
 775 TYR   ( 226-)  D

Warning: Phenylalanine convention problem

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

  24 PHE   (  55-)  A
 108 PHE   ( 139-)  A

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.

  88 ASP   ( 119-)  A
 160 ASP   ( 191-)  A
 481 ASP   ( 124-)  C
 670 ASP   ( 119-)  D

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.

  56 GLU   (  87-)  A
  79 GLU   ( 110-)  A
 170 GLU   ( 201-)  A
 177 GLU   ( 208-)  A
 255 GLU   (  87-)  B
 278 GLU   ( 110-)  B
 299 GLU   ( 131-)  B
 320 GLU   ( 152-)  B
 376 GLU   ( 208-)  B
 552 GLU   ( 197-)  C
 567 GLU   ( 212-)  C
 638 GLU   (  87-)  D
 661 GLU   ( 110-)  D
 665 GLU   ( 114-)  D
 746 GLU   ( 197-)  D

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.

 283 ASN   ( 115-)  B      N   -C     1.50    8.3
 284 GLY   ( 116-)  B      N   -C     1.44    5.6
 312 GLN   ( 144-)  B      N   -C     1.24   -4.6
 313 GLY   ( 145-)  B      N   -C     1.21   -5.8
 643 ILE   (  92-)  D      N   -C     1.20   -6.2
 683 LYS   ( 134-)  D      N   -C     2.33   50.1
 758 CYS   ( 209-)  D      N   -C     1.55   11.0
  26 CYS   (  57-)  A      SG  -SG*   2.25    5.4
  80 CYS   ( 111-)  A      SG  -SG*   2.25    5.4
 225 CYS   (  57-)  B      SG  -SG*   2.21    4.3
 279 CYS   ( 111-)  B      SG  -SG*   2.21    4.3
 423 CYS   (  57-)  C      SG  -SG*   2.28    6.0
 473 CYS   ( 111-)  C      SG  -SG*   2.28    6.0
 516 CYS   ( 161-)  C      SG  -SG*   2.32    7.0
 564 CYS   ( 209-)  C      SG  -SG*   2.32    7.0
 610 CYS   (  57-)  D      SG  -SG*   2.22    4.6
 662 CYS   ( 111-)  D      SG  -SG*   2.22    4.6
 710 CYS   ( 161-)  D      SG  -SG*   2.20    4.1
 758 CYS   ( 209-)  D      SG  -SG*   2.20    4.1

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

 |  1.012790  0.000426 -0.000290|
 |  0.000426  1.014217  0.000196|
 | -0.000290  0.000196  1.013150|
Proposed new scale matrix

 |  0.013535 -0.000006  0.002652|
 | -0.000005  0.012720 -0.000002|
 |  0.000004 -0.000002  0.012306|
With corresponding cell

    A    =  73.889  B   =  78.615  C    =  82.810
    Alpha=  89.988  Beta= 101.103  Gamma=  89.952

The CRYST1 cell dimensions

    A    =  72.957  B   =  77.513  C    =  81.726
    Alpha=  90.000  Beta= 101.080  Gamma=  90.000

Variance: 4527.228
(Under-)estimated Z-score: 49.589

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.

 283 ASN   ( 115-)  B     -O   -C    N   132.55    6.0
 283 ASN   ( 115-)  B     -CA  -C    N   105.90   -5.1
 283 ASN   ( 115-)  B     -C    N    CA  103.73  -10.0
 284 GLY   ( 116-)  B     -O   -C    N   132.01    5.6
 284 GLY   ( 116-)  B     -CA  -C    N   106.33   -4.9
 312 GLN   ( 144-)  B     -O   -C    N   115.31   -4.8
 312 GLN   ( 144-)  B     -CA  -C    N   124.48    4.1
 312 GLN   ( 144-)  B     -C    N    CA  130.59    4.9
 313 GLY   ( 145-)  B     -C    N    CA  130.24    5.7
 387 HIS   ( 219-)  B      CG   ND1  CE1 109.71    4.1
 521 ASN   ( 166-)  C      N    CA   CB  118.09    4.5
 683 LYS   ( 134-)  D     -CA  -C    N   100.78   -7.7
 683 LYS   ( 134-)  D     -C    N    CA   85.17  -20.3
 695 PRO   ( 146-)  D      C    CA   CB  119.72    5.1
 759 VAL   ( 210-)  D     -O   -C    N   130.63    4.8
 759 VAL   ( 210-)  D     -CA  -C    N   107.80   -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.

  56 GLU   (  87-)  A
  79 GLU   ( 110-)  A
  88 ASP   ( 119-)  A
 160 ASP   ( 191-)  A
 170 GLU   ( 201-)  A
 177 GLU   ( 208-)  A
 255 GLU   (  87-)  B
 278 GLU   ( 110-)  B
 299 GLU   ( 131-)  B
 320 GLU   ( 152-)  B
 376 GLU   ( 208-)  B
 481 ASP   ( 124-)  C
 552 GLU   ( 197-)  C
 567 GLU   ( 212-)  C
 638 GLU   (  87-)  D
 661 GLU   ( 110-)  D
 665 GLU   ( 114-)  D
 670 ASP   ( 119-)  D
 746 GLU   ( 197-)  D

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 257 PRO   (  89-)  B      N     -8.9   -31.75    -2.48
 695 PRO   ( 146-)  D      N     -7.0   -25.48    -2.48
The average deviation= 1.235

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.

 526 ILE   ( 171-)  C    4.25
 695 PRO   ( 146-)  D    4.17
 761 GLU   ( 212-)  D    4.09
 130 CYS   ( 161-)  A    4.06

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 264 ARG   (  96-)  B    4.79

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.

 692 THR   ( 143-)  D    -3.6
 238 ARG   (  70-)  B    -2.6
 207 ILE   (  39-)  B    -2.5
  39 ARG   (  70-)  A    -2.5
   8 ILE   (  39-)  A    -2.5
 159 LYS   ( 190-)  A    -2.5
 449 GLU   (  87-)  C    -2.5
 485 THR   ( 128-)  C    -2.4
  77 PRO   ( 108-)  A    -2.4
 404 ILE   (  38-)  C    -2.4
 118 ARG   ( 149-)  A    -2.4
 133 ILE   ( 164-)  A    -2.4
 228 ARG   (  60-)  B    -2.3
 506 ILE   ( 151-)  C    -2.3
 698 ARG   ( 149-)  D    -2.3
 319 ILE   ( 151-)  B    -2.3
 497 ILE   ( 142-)  C    -2.3
 120 ILE   ( 151-)  A    -2.3
  43 LYS   (  74-)  A    -2.2
 276 PRO   ( 108-)  B    -2.2
 516 CYS   ( 161-)  C    -2.2
 198 VAL   ( 229-)  A    -2.2
 317 ARG   ( 149-)  B    -2.2
 778 VAL   ( 229-)  D    -2.2
 440 LYS   (  74-)  C    -2.1
 405 ILE   (  39-)  C    -2.1
 302 LYS   ( 134-)  B    -2.1
 695 PRO   ( 146-)  D    -2.1
 513 LEU   ( 158-)  C    -2.1
 448 LEU   (  86-)  C    -2.1
  83 GLU   ( 114-)  A    -2.1
 567 GLU   ( 212-)  C    -2.1
 160 ASP   ( 191-)  A    -2.0
 127 LEU   ( 158-)  A    -2.0
 682 GLU   ( 131-)  D    -2.0
 169 ARG   ( 200-)  A    -2.0
 192 THR   ( 223-)  A    -2.0
 332 ILE   ( 164-)  B    -2.0
  16 VAL   (  47-)  A    -2.0
 381 ASN   ( 213-)  B    -2.0
 700 ILE   ( 151-)  D    -2.0
 707 LEU   ( 158-)  D    -2.0
 584 VAL   ( 229-)  C    -2.0
 326 LEU   ( 158-)  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.

   8 ILE   (  39-)  A  omega poor
  30 GLY   (  61-)  A  omega poor
  31 ASP   (  62-)  A  PRO omega poor
  34 PRO   (  65-)  A  omega poor
  41 ASN   (  72-)  A  Poor phi/psi
  45 VAL   (  76-)  A  omega poor
  48 THR   (  79-)  A  omega poor
  58 PRO   (  89-)  A  omega poor
  67 GLU   (  98-)  A  PRO omega poor
  73 ARG   ( 104-)  A  omega poor
 129 THR   ( 160-)  A  omega poor
 135 ASN   ( 166-)  A  PRO omega poor
 138 PRO   ( 169-)  A  omega poor
 145 ASN   ( 176-)  A  Poor phi/psi
 146 GLN   ( 177-)  A  Poor phi/psi
 159 LYS   ( 190-)  A  Poor phi/psi
 167 ASN   ( 198-)  A  omega poor
 198 VAL   ( 229-)  A  omega poor
 207 ILE   (  39-)  B  omega poor
 230 ASP   (  62-)  B  PRO omega poor
 233 PRO   (  65-)  B  omega poor
 245 SER   (  77-)  B  omega poor
 248 GLN   (  80-)  B  omega poor
 266 GLU   (  98-)  B  PRO omega poor
 286 GLY   ( 118-)  B  omega poor
 302 LYS   ( 134-)  B  Poor phi/psi
 334 ASN   ( 166-)  B  PRO omega poor
 344 ASN   ( 176-)  B  Poor phi/psi
 345 GLN   ( 177-)  B  Poor phi/psi
 359 ASP   ( 191-)  B  Poor phi/psi
 366 ASN   ( 198-)  B  omega poor
 427 GLY   (  61-)  C  omega poor
 428 ASP   (  62-)  C  PRO omega poor
 460 GLU   (  98-)  C  PRO omega poor
 520 GLY   ( 165-)  C  omega poor
 521 ASN   ( 166-)  C  PRO omega poor
 532 GLN   ( 177-)  C  Poor phi/psi
 615 ASP   (  62-)  D  PRO omega poor
 649 GLU   (  98-)  D  PRO omega poor
 682 GLU   ( 131-)  D  omega poor
 692 THR   ( 143-)  D  Poor phi/psi
 715 ASN   ( 166-)  D  PRO omega poor
 718 PRO   ( 169-)  D  omega poor
 726 GLN   ( 177-)  D  Poor phi/psi
 740 ASP   ( 191-)  D  Poor phi/psi
 761 GLU   ( 212-)  D  omega poor
 773 ASN   ( 224-)  D  omega poor
 chi-1/chi-2 correlation Z-score : -4.612

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 : -4.612

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 HIS   (  34-)  A      0
   8 ILE   (  39-)  A      0
   9 ARG   (  40-)  A      0
  18 VAL   (  49-)  A      0
  29 ARG   (  60-)  A      0
  31 ASP   (  62-)  A      0
  32 PRO   (  63-)  A      0
  33 PRO   (  64-)  A      0
  52 TYR   (  83-)  A      0
  58 PRO   (  89-)  A      0
  67 GLU   (  98-)  A      0
  75 ASP   ( 106-)  A      0
  84 ASN   ( 115-)  A      0
  86 VAL   ( 117-)  A      0
  88 ASP   ( 119-)  A      0
 100 GLU   ( 131-)  A      0
 102 ASP   ( 133-)  A      0
 103 LYS   ( 134-)  A      0
 106 ALA   ( 137-)  A      0
 108 PHE   ( 139-)  A      0
 113 GLN   ( 144-)  A      0
 117 THR   ( 148-)  A      0
 122 VAL   ( 153-)  A      0
 133 ILE   ( 164-)  A      0
 135 ASN   ( 166-)  A      0
And so on for a total of 320 lines.

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!

 654 GLY   ( 103-)  D   1.64   25
  72 GLY   ( 103-)  A   1.61   23
 271 GLY   ( 103-)  B   1.61   15

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].

   4 PRO   (  35-)  A    46.3 half-chair C-delta/C-gamma (54 degrees)
   5 PRO   (  36-)  A   -63.0 half-chair C-beta/C-alpha (-54 degrees)
  77 PRO   ( 108-)  A    14.0 half-chair N/C-delta (18 degrees)
 154 PRO   ( 185-)  A  -125.9 half-chair C-delta/C-gamma (-126 degrees)
 210 PRO   (  42-)  B  -144.3 envelop C-delta (-144 degrees)
 257 PRO   (  89-)  B   146.2 envelop C-alpha (144 degrees)
 276 PRO   ( 108-)  B    31.0 envelop C-delta (36 degrees)
 304 PRO   ( 136-)  B  -129.5 half-chair C-delta/C-gamma (-126 degrees)
 308 PRO   ( 140-)  B    51.1 half-chair C-delta/C-gamma (54 degrees)
 337 PRO   ( 169-)  B  -122.9 half-chair C-delta/C-gamma (-126 degrees)
 353 PRO   ( 185-)  B   162.9 half-chair C-alpha/N (162 degrees)
 408 PRO   (  42-)  C   139.7 envelop C-alpha (144 degrees)
 429 PRO   (  63-)  C    23.8 half-chair N/C-delta (18 degrees)
 430 PRO   (  64-)  C   -62.5 half-chair C-beta/C-alpha (-54 degrees)
 431 PRO   (  65-)  C    49.6 half-chair C-delta/C-gamma (54 degrees)
 451 PRO   (  89-)  C    36.7 envelop C-delta (36 degrees)
 470 PRO   ( 108-)  C   -64.9 envelop C-beta (-72 degrees)
 491 PRO   ( 136-)  C   117.0 envelop C-beta (108 degrees)
 524 PRO   ( 169-)  C    41.4 envelop C-delta (36 degrees)
 595 PRO   (  42-)  D  -127.3 half-chair C-delta/C-gamma (-126 degrees)
 617 PRO   (  64-)  D  -124.8 half-chair C-delta/C-gamma (-126 degrees)
 618 PRO   (  65-)  D    22.5 half-chair N/C-delta (18 degrees)
 659 PRO   ( 108-)  D    21.7 half-chair N/C-delta (18 degrees)
 685 PRO   ( 136-)  D   104.3 envelop C-beta (108 degrees)
 718 PRO   ( 169-)  D    22.8 half-chair N/C-delta (18 degrees)
 734 PRO   ( 185-)  D  -121.9 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.

 450 GLN   (  88-)  C      NE2 <->  456 ILE   (  94-)  C      CD1    0.82    2.28  INTRA BF
 487 TYR   ( 130-)  C      CE1 <->  491 PRO   ( 136-)  C      CD     0.82    2.38  INTRA BF
 397 VAL   ( 229-)  B      CG1 <->  398 ARG   ( 230-)  B      N      0.71    2.29  INTRA BF
 198 VAL   ( 229-)  A      CG1 <->  199 ARG   ( 230-)  A      N      0.70    2.30  INTRA BF
 584 VAL   ( 229-)  C      CG1 <->  585 ARG   ( 230-)  C      N      0.69    2.31  INTRA BF
 248 GLN   (  80-)  B      NE2 <->  272 ARG   ( 104-)  B      NH2    0.65    2.20  INTRA BF
 121 GLU   ( 152-)  A      CG  <->  124 HIS   ( 155-)  A      ND1    0.56    2.54  INTRA BF
 376 GLU   ( 208-)  B      OE2 <->  387 HIS   ( 219-)  B      CD2    0.51    2.29  INTRA BL
 536 ASP   ( 181-)  C      OD1 <->  538 SER   ( 183-)  C      CB     0.51    2.29  INTRA BF
 177 GLU   ( 208-)  A      OE2 <->  188 HIS   ( 219-)  A      CD2    0.48    2.32  INTRA BF
 254 LEU   (  86-)  B      C   <->  255 GLU   (  87-)  B      OE1    0.46    2.24  INTRA BF
  40 LYS   (  71-)  A      NZ  <->   52 TYR   (  83-)  A      OH     0.45    2.25  INTRA BF
 354 ARG   ( 186-)  B      NH2 <->  371 ASP   ( 203-)  B      OD2    0.45    2.25  INTRA BL
 403 GLU   (  37-)  C      OE1 <->  426 ARG   (  60-)  C      NH2    0.44    2.26  INTRA BF
 521 ASN   ( 166-)  C      CA  <->  522 PRO   ( 167-)  C      C      0.42    2.58  INTRA BF
 202 HIS   (  34-)  B      O   <->  283 ASN   ( 115-)  B      ND2    0.42    2.28  INTRA BF
 666 ASN   ( 115-)  D      OD1 <->  668 VAL   ( 117-)  D      N      0.41    2.29  INTRA BF
 773 ASN   ( 224-)  D      ND2 <->  775 TYR   ( 226-)  D      OH     0.41    2.29  INTRA BF
 248 GLN   (  80-)  B      NE2 <->  272 ARG   ( 104-)  B      CZ     0.41    2.69  INTRA BF
  65 ARG   (  96-)  A      NH1 <->   67 GLU   (  98-)  A      OE1    0.40    2.30  INTRA BF
  57 GLN   (  88-)  A      NE2 <->  147 THR   ( 178-)  A      CG2    0.37    2.73  INTRA BF
  12 GLN   (  43-)  A      NE2 <->  739 LYS   ( 190-)  D      NZ     0.36    2.49  INTRA BF
 296 THR   ( 128-)  B      CG2 <->  781 HOH   (  10 )  B      O      0.36    2.44  INTRA BF
   3 HIS   (  34-)  A      ND1 <->   31 ASP   (  62-)  A      OD2    0.36    2.34  INTRA BF
 487 TYR   ( 130-)  C      CD1 <->  491 PRO   ( 136-)  C      CD     0.36    2.84  INTRA BF
And so on for a total of 189 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 683 LYS   ( 134-)  D      -6.06
  29 ARG   (  60-)  A      -6.05
 228 ARG   (  60-)  B      -5.99
 613 ARG   (  60-)  D      -5.76
 184 MET   ( 215-)  A      -5.71
 639 GLN   (  88-)  D      -5.69
 715 ASN   ( 166-)  D      -5.55
 334 ASN   ( 166-)  B      -5.53
 383 MET   ( 215-)  B      -5.53
 441 LYS   (  75-)  C      -5.40
 135 ASN   ( 166-)  A      -5.38
  17 ARG   (  48-)  A      -5.29
 400 HIS   (  34-)  C      -5.28
 584 VAL   ( 229-)  C      -5.27
 198 VAL   ( 229-)  A      -5.26
 426 ARG   (  60-)  C      -5.18
 397 VAL   ( 229-)  B      -5.18
 521 ASN   ( 166-)  C      -5.17
 256 GLN   (  88-)  B      -5.14
 601 ARG   (  48-)  D      -5.07
 216 ARG   (  48-)  B      -5.07
 450 GLN   (  88-)  C      -5.01

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.

 283 ASN   ( 115-)  B       285 - VAL    117- ( B)         -4.08

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

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: C

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: D

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

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

 780 HOH   ( 244 )  A      O
 781 HOH   (  11 )  B      O
 781 HOH   (  13 )  B      O
 781 HOH   ( 249 )  B      O
 782 HOH   ( 255 )  C      O
 783 HOH   ( 248 )  D      O
ERROR. Strange cone in HB2INI
Affected atom  683 LYS  ( 134-) D      N
Expected ambiguity-2 in FILL1HARR 0 82 584

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.

  12 GLN   (  43-)  A
  14 GLN   (  45-)  A
 167 ASN   ( 198-)  A
 193 ASN   ( 224-)  A
 202 HIS   (  34-)  B
 213 GLN   (  45-)  B
 345 GLN   ( 177-)  B
 392 ASN   ( 224-)  B
 574 HIS   ( 219-)  C
 596 GLN   (  43-)  D
 598 GLN   (  45-)  D
 753 GLN   ( 204-)  D
 768 HIS   ( 219-)  D

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.

  85 GLY   ( 116-)  A      N
 121 GLU   ( 152-)  A      N
 129 THR   ( 160-)  A      N
 129 THR   ( 160-)  A      OG1
 130 CYS   ( 161-)  A      N
 160 ASP   ( 191-)  A      N
 162 PHE   ( 193-)  A      N
 171 GLU   ( 202-)  A      N
 182 ASN   ( 213-)  A      ND2
 184 MET   ( 215-)  A      N
 185 GLY   ( 216-)  A      N
 196 VAL   ( 227-)  A      N
 235 ILE   (  67-)  B      N
 248 GLN   (  80-)  B      NE2
 283 ASN   ( 115-)  B      N
 283 ASN   ( 115-)  B      ND2
 285 VAL   ( 117-)  B      N
 286 GLY   ( 118-)  B      N
 301 ASP   ( 133-)  B      N
 303 THR   ( 135-)  B      OG1
 328 THR   ( 160-)  B      OG1
 329 CYS   ( 161-)  B      N
 370 GLU   ( 202-)  B      N
 387 HIS   ( 219-)  B      ND1
 391 THR   ( 223-)  B      OG1
 425 ALA   (  59-)  C      N
 445 TYR   (  83-)  C      N
 450 GLN   (  88-)  C      NE2
 454 ILE   (  92-)  C      N
 488 GLU   ( 131-)  C      N
 516 CYS   ( 161-)  C      N
 541 ARG   ( 186-)  C      NH2
 569 SER   ( 214-)  C      N
 571 GLY   ( 216-)  C      N
 612 ALA   (  59-)  D      N
 634 TYR   (  83-)  D      N
 635 THR   (  84-)  D      OG1
 643 ILE   (  92-)  D      N
 647 ARG   (  96-)  D      NH2
 709 THR   ( 160-)  D      N
 710 CYS   ( 161-)  D      N
 726 GLN   ( 177-)  D      N
 741 GLY   ( 192-)  D      N
 765 GLY   ( 216-)  D      N

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.

 188 HIS   ( 219-)  A      ND1
 255 GLU   (  87-)  B      OE1
 283 ASN   ( 115-)  B      OD1
 376 GLU   ( 208-)  B      OE2
 757 GLU   ( 208-)  D      OE2

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.

 255 GLU   (  87-)  B   H-bonding suggests Gln
 428 ASP   (  62-)  C   H-bonding suggests Asn; but Alt-Rotamer
 468 ASP   ( 106-)  C   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 :  -1.287
  2nd generation packing quality :  -1.212
  Ramachandran plot appearance   :   2.596
  chi-1/chi-2 rotamer normality  :  -4.612 (bad)
  Backbone conformation          :   1.028

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.174
  Bond angles                    :   0.801
  Omega angle restraints         :   1.203
  Side chain planarity           :   0.557 (tight)
  Improper dihedral distribution :   1.028
  B-factor distribution          :   1.619 (loose)
  Inside/Outside distribution    :   1.002

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :   3.4
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.174
  Bond angles                    :   0.801
  Omega angle restraints         :   1.203
  Side chain planarity           :   0.557 (tight)
  Improper dihedral distribution :   1.028
  B-factor distribution          :   1.619 (loose)
  Inside/Outside distribution    :   1.002
==============

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.