WHAT IF Check report

This file was created 2012-01-05 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 pdb1qb4.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 117.750  B   = 248.410  C    =  83.470
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 117.750  B   = 143.649  C    = 143.649
    Alpha= 119.684  Beta= 114.196  Gamma= 114.196

Dimensions of the conventional cell

    A    =  83.470  B   = 117.750  C    = 248.410
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  0.000000  1.000000|
 | -1.000000  0.000000  0.000000|
 |  0.000000 -1.000000  0.000000|

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 699 LYS   ( 702-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

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

Warning: 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 GLN   (   4-)  A      CG
   1 GLN   (   4-)  A      CD
   1 GLN   (   4-)  A      OE1
   1 GLN   (   4-)  A      NE2
  21 LYS   (  24-)  A      CG
  21 LYS   (  24-)  A      CD
  21 LYS   (  24-)  A      CE
  21 LYS   (  24-)  A      NZ
  91 LYS   (  94-)  A      CG
  91 LYS   (  94-)  A      CD
  91 LYS   (  94-)  A      CE
  91 LYS   (  94-)  A      NZ
 117 ASP   ( 120-)  A      CG
 117 ASP   ( 120-)  A      OD1
 117 ASP   ( 120-)  A      OD2
 161 LYS   ( 164-)  A      CG
 161 LYS   ( 164-)  A      CD
 161 LYS   ( 164-)  A      CE
 161 LYS   ( 164-)  A      NZ
 291 GLU   ( 294-)  A      CG
 291 GLU   ( 294-)  A      CD
 291 GLU   ( 294-)  A      OE1
 291 GLU   ( 294-)  A      OE2
 302 GLU   ( 305-)  A      CG
 302 GLU   ( 305-)  A      CD
And so on for a total of 54 lines.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 699 LYS   ( 702-)  A

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) :293.000

Note: B-factor plot

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

Chain identifier: A

Nomenclature related problems

Warning: Tyrosine convention problem

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

 166 TYR   ( 169-)  A
 217 TYR   ( 220-)  A
 309 TYR   ( 312-)  A
 311 TYR   ( 314-)  A
 357 TYR   ( 360-)  A
 469 TYR   ( 472-)  A
 555 TYR   ( 558-)  A
 618 TYR   ( 621-)  A
 631 TYR   ( 634-)  A
 668 TYR   ( 671-)  A
 825 TYR   ( 835-)  A

Warning: Phenylalanine convention problem

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

  72 PHE   (  75-)  A
  75 PHE   (  78-)  A
 203 PHE   ( 206-)  A
 276 PHE   ( 279-)  A
 383 PHE   ( 386-)  A
 494 PHE   ( 497-)  A
 502 PHE   ( 505-)  A
 616 PHE   ( 619-)  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.

  22 ASP   (  25-)  A
  47 ASP   (  50-)  A
 165 ASP   ( 168-)  A
 186 ASP   ( 189-)  A
 249 ASP   ( 252-)  A
 540 ASP   ( 543-)  A
 851 ASP   ( 861-)  A

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.

  83 GLU   (  86-)  A
 124 GLU   ( 127-)  A
 129 GLU   ( 132-)  A
 167 GLU   ( 170-)  A
 207 GLU   ( 210-)  A
 223 GLU   ( 226-)  A
 227 GLU   ( 230-)  A
 348 GLU   ( 351-)  A
 351 GLU   ( 354-)  A
 405 GLU   ( 408-)  A
 460 GLU   ( 463-)  A
 503 GLU   ( 506-)  A
 622 GLU   ( 625-)  A
 637 GLU   ( 640-)  A
 645 GLU   ( 648-)  A
 648 GLU   ( 651-)  A
 656 GLU   ( 659-)  A
 793 GLU   ( 803-)  A

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.

 393 ARG   ( 396-)  A      CD   NE    1.38   -4.6
 578 ARG   ( 581-)  A      N    CA    1.37   -4.8
 694 GLY   ( 697-)  A      N    CA    1.52    4.0
 696 ARG   ( 699-)  A      NE   CZ    1.27   -4.3

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.

   6 ARG   (   9-)  A      CD   NE   CZ  134.83    7.3
   9 VAL   (  12-)  A      N    CA   CB  118.70    4.8
  16 LEU   (  19-)  A     -CA  -C    N   126.26    5.0
  22 ASP   (  25-)  A      CA   CB   CG  118.96    6.4
  25 GLY   (  28-)  A     -C    N    CA  113.15   -4.4
  27 HIS   (  30-)  A      CG   ND1  CE1 110.30    4.7
  30 GLU   (  33-)  A      CA   C    O   113.54   -4.3
  31 ARG   (  34-)  A     -C    N    CA  130.40    4.8
  43 ARG   (  46-)  A      CB   CG   CD  103.94   -5.1
  46 ASN   (  49-)  A      CA   CB   CG  116.75    4.1
  48 ALA   (  51-)  A     -CA  -C    N   124.32    4.1
  63 ASP   (  66-)  A      C    CA   CB  118.30    4.3
  63 ASP   (  66-)  A      CA   CB   CG  105.83   -6.8
  64 GLU   (  67-)  A      CB   CG   CD  121.03    5.0
  69 ALA   (  72-)  A      C    CA   CB  104.37   -4.1
  73 SER   (  76-)  A      CA   CB   OG  101.77   -4.7
  80 ASN   (  83-)  A     -O   -C    N   115.97   -4.4
  84 GLN   (  87-)  A     -O   -C    N   115.68   -4.6
  86 HIS   (  89-)  A     -O   -C    N   115.10   -4.9
  86 HIS   (  89-)  A     -C    N    CA  130.15    4.7
  86 HIS   (  89-)  A      CG   ND1  CE1 110.11    4.5
  87 SER   (  90-)  A      CA   CB   OG  100.72   -5.2
  92 GLY   (  95-)  A     -C    N    CA  129.66    5.3
  93 GLU   (  96-)  A      C    CA   CB  121.47    6.0
  94 ALA   (  97-)  A     -O   -C    N   114.41   -5.4
And so on for a total of 234 lines.

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.

  22 ASP   (  25-)  A
  47 ASP   (  50-)  A
  83 GLU   (  86-)  A
 124 GLU   ( 127-)  A
 129 GLU   ( 132-)  A
 165 ASP   ( 168-)  A
 167 GLU   ( 170-)  A
 186 ASP   ( 189-)  A
 207 GLU   ( 210-)  A
 223 GLU   ( 226-)  A
 227 GLU   ( 230-)  A
 249 ASP   ( 252-)  A
 348 GLU   ( 351-)  A
 351 GLU   ( 354-)  A
 405 GLU   ( 408-)  A
 460 GLU   ( 463-)  A
 503 GLU   ( 506-)  A
 540 ASP   ( 543-)  A
 622 GLU   ( 625-)  A
 637 GLU   ( 640-)  A
 645 GLU   ( 648-)  A
 648 GLU   ( 651-)  A
 656 GLU   ( 659-)  A
 793 GLU   ( 803-)  A
 851 ASP   ( 861-)  A

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.

  93 GLU   (  96-)  A      CA    -7.3    22.06    33.96
 163 ILE   ( 166-)  A      CA    -6.1    24.06    33.24
 483 VAL   ( 486-)  A      CA    -6.6    23.64    33.23
 483 VAL   ( 486-)  A      CB     6.3   -24.72   -32.96
 545 ALA   ( 548-)  A      CA     6.3    42.15    34.09
The average deviation= 1.565

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.

 545 ALA   ( 548-)  A    6.96
 547 VAL   ( 550-)  A    6.05
 746 ASP   ( 756-)  A    5.89
  23 ALA   (  26-)  A    5.77
  82 ALA   (  85-)  A    5.46
 720 ALA   ( 730-)  A    4.99
  65 LEU   (  68-)  A    4.85
 294 PRO   ( 297-)  A    4.83
 404 GLY   ( 407-)  A    4.82
 586 GLY   ( 589-)  A    4.65
 682 ALA   ( 685-)  A    4.51
 372 ASP   ( 375-)  A    4.26
 517 GLN   ( 520-)  A    4.23
 592 ALA   ( 595-)  A    4.19
 139 ILE   ( 142-)  A    4.16
  21 LYS   (  24-)  A    4.15
  94 ALA   (  97-)  A    4.13
 351 GLU   ( 354-)  A    4.04
  14 LYS   (  17-)  A    4.04

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 : 1.730

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.

 722 LEU   ( 732-)  A    -2.8
 145 ILE   ( 148-)  A    -2.7
 718 LEU   ( 728-)  A    -2.6
 608 THR   ( 611-)  A    -2.6
 139 ILE   ( 142-)  A    -2.5
  24 LEU   (  27-)  A    -2.4
 684 PRO   ( 687-)  A    -2.4
 702 LEU   ( 712-)  A    -2.4
 705 ILE   ( 715-)  A    -2.4
 301 GLY   ( 304-)  A    -2.4
 336 LEU   ( 339-)  A    -2.4
 847 GLY   ( 857-)  A    -2.4
 434 LYS   ( 437-)  A    -2.4
 307 GLU   ( 310-)  A    -2.3
 250 ARG   ( 253-)  A    -2.3
 504 THR   ( 507-)  A    -2.3
 736 LYS   ( 746-)  A    -2.3
 443 GLN   ( 446-)  A    -2.3
 181 GLN   ( 184-)  A    -2.2
  88 ILE   (  91-)  A    -2.2
 351 GLU   ( 354-)  A    -2.2
 127 SER   ( 130-)  A    -2.2
 387 LEU   ( 390-)  A    -2.1
 190 LYS   ( 193-)  A    -2.1
 584 ARG   ( 587-)  A    -2.1
 294 PRO   ( 297-)  A    -2.1
 397 THR   ( 400-)  A    -2.1
 338 LYS   ( 341-)  A    -2.1
 717 MET   ( 727-)  A    -2.1
 191 LEU   ( 194-)  A    -2.1
 388 VAL   ( 391-)  A    -2.1
 620 LEU   ( 623-)  A    -2.1
 390 ILE   ( 393-)  A    -2.0
 137 THR   ( 140-)  A    -2.0
 492 ILE   ( 495-)  A    -2.0
 111 GLN   ( 114-)  A    -2.0
 435 ARG   ( 438-)  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.

  23 ALA   (  26-)  A  Poor phi/psi
  24 LEU   (  27-)  A  Poor phi/psi
  98 PRO   ( 101-)  A  Poor phi/psi
 113 GLU   ( 116-)  A  Poor phi/psi
 162 ASP   ( 165-)  A  Poor phi/psi
 248 GLY   ( 251-)  A  Poor phi/psi
 301 GLY   ( 304-)  A  Poor phi/psi
 302 GLU   ( 305-)  A  Poor phi/psi
 303 GLU   ( 306-)  A  Poor phi/psi
 344 THR   ( 347-)  A  Poor phi/psi
 384 GLY   ( 387-)  A  Poor phi/psi
 387 LEU   ( 390-)  A  Poor phi/psi
 417 SER   ( 420-)  A  Poor phi/psi
 437 LEU   ( 440-)  A  Poor phi/psi
 473 MET   ( 476-)  A  Poor phi/psi
 692 PRO   ( 695-)  A  Poor phi/psi
 715 ARG   ( 725-)  A  Poor phi/psi
 717 MET   ( 727-)  A  Poor phi/psi
 722 LEU   ( 732-)  A  Poor phi/psi
 733 GLU   ( 743-)  A  Poor phi/psi
 804 ASN   ( 814-)  A  Poor phi/psi
 845 LYS   ( 855-)  A  Poor phi/psi
 847 GLY   ( 857-)  A  Poor phi/psi
 870 ARG   ( 880-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.815

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 : -4.815

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.

 182 SER   ( 185-)  A    0.36
 285 SER   ( 288-)  A    0.36
 318 SER   ( 321-)  A    0.36
 268 SER   ( 271-)  A    0.37
 818 SER   ( 828-)  A    0.37
  42 SER   (  45-)  A    0.39
 658 SER   ( 661-)  A    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!

  23 ALA   (  26-)  A      0
  24 LEU   (  27-)  A      0
  26 GLU   (  29-)  A      0
  46 ASN   (  49-)  A      0
  47 ASP   (  50-)  A      0
  65 LEU   (  68-)  A      0
  88 ILE   (  91-)  A      0
  91 LYS   (  94-)  A      0
  93 GLU   (  96-)  A      0
  97 ASN   ( 100-)  A      0
 110 ASN   ( 113-)  A      0
 112 PRO   ( 115-)  A      0
 113 GLU   ( 116-)  A      0
 126 LEU   ( 129-)  A      0
 137 THR   ( 140-)  A      0
 139 ILE   ( 142-)  A      0
 142 ARG   ( 145-)  A      0
 160 ASN   ( 163-)  A      0
 184 HIS   ( 187-)  A      0
 185 THR   ( 188-)  A      0
 186 ASP   ( 189-)  A      0
 187 GLU   ( 190-)  A      0
 189 ARG   ( 192-)  A      0
 190 LYS   ( 193-)  A      0
 208 ASN   ( 211-)  A      0
And so on for a total of 210 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 : 1.774

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!

 491 GLY   ( 494-)  A   1.73   38
 585 GLY   ( 588-)  A   1.57   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]

  67 PRO   (  70-)  A    0.13 LOW
  90 PRO   (  93-)  A    0.09 LOW
 112 PRO   ( 115-)  A    0.08 LOW
 234 PRO   ( 237-)  A    0.14 LOW
 254 PRO   ( 257-)  A    0.10 LOW
 308 PRO   ( 311-)  A    0.18 LOW
 339 PRO   ( 342-)  A    0.13 LOW
 352 PRO   ( 355-)  A    0.13 LOW
 386 PRO   ( 389-)  A    0.17 LOW
 444 PRO   ( 447-)  A    0.15 LOW
 462 PRO   ( 465-)  A    0.17 LOW
 500 PRO   ( 503-)  A    0.12 LOW
 642 PRO   ( 645-)  A    0.07 LOW
 646 PRO   ( 649-)  A    0.11 LOW
 677 PRO   ( 680-)  A    0.18 LOW
 706 PRO   ( 716-)  A    0.06 LOW
 852 PRO   ( 862-)  A    0.11 LOW

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].

 136 PRO   ( 139-)  A    45.0 half-chair C-delta/C-gamma (54 degrees)
 337 PRO   ( 340-)  A   100.5 envelop C-beta (108 degrees)
 597 PRO   ( 600-)  A   100.0 envelop C-beta (108 degrees)
 719 PRO   ( 729-)  A   112.6 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.

 566 GLU   ( 569-)  A      OE2 <->  602 LYS   ( 605-)  A      NZ     0.40    2.30  INTRA BF
 251 ASP   ( 254-)  A      O   <->  696 ARG   ( 699-)  A      NH1    0.38    2.32  INTRA BF
 844 GLU   ( 854-)  A      O   <->  846 GLU   ( 856-)  A      N      0.36    2.34  INTRA BF
 181 GLN   ( 184-)  A      O   <->  185 THR   ( 188-)  A      N      0.32    2.38  INTRA BF
  43 ARG   (  46-)  A      NH2 <->  765 ASP   ( 775-)  A      OD2    0.31    2.39  INTRA BF
  99 GLU   ( 102-)  A      OE2 <->  106 ARG   ( 109-)  A      NH2    0.31    2.39  INTRA BF
 297 LEU   ( 300-)  A      O   <->  301 GLY   ( 304-)  A      N      0.30    2.40  INTRA BF
 651 ARG   ( 654-)  A      NH1 <->  878 HOH   ( 952 )  A      O      0.26    2.44  INTRA BF
 714 ASN   ( 724-)  A      ND2 <->  878 HOH   ( 957 )  A      O      0.26    2.44  INTRA BF
  43 ARG   (  46-)  A      NH2 <->  765 ASP   ( 775-)  A      CG     0.24    2.86  INTRA
  60 LEU   (  63-)  A      O   <->  839 ARG   ( 849-)  A      NH2    0.24    2.46  INTRA BF
 391 ASP   ( 394-)  A      OD2 <->  606 ARG   ( 609-)  A      NH2    0.23    2.47  INTRA BL
 456 GLN   ( 459-)  A      NE2 <->  460 GLU   ( 463-)  A      OE1    0.23    2.47  INTRA BF
 822 ARG   ( 832-)  A      NH1 <->  874 ASP   ( 884-)  A      OD2    0.23    2.47  INTRA BL
 160 ASN   ( 163-)  A      ND2 <->  161 LYS   ( 164-)  A      O      0.22    2.38  INTRA BF
  99 GLU   ( 102-)  A      O   <->  103 ARG   ( 106-)  A      N      0.20    2.50  INTRA BF
 251 ASP   ( 254-)  A      CG  <->  703 ARG   ( 713-)  A      NH2    0.20    2.90  INTRA
 506 ASP   ( 509-)  A      O   <->  510 ASN   ( 513-)  A      N      0.19    2.51  INTRA BL
  26 GLU   (  29-)  A      N   <->   27 HIS   (  30-)  A      N      0.19    2.41  INTRA BF
 576 HIS   ( 579-)  A      CE1 <->  596 GLN   ( 599-)  A      NE2    0.19    2.91  INTRA BF
  46 ASN   (  49-)  A      ND2 <->   48 ALA   (  51-)  A      N      0.18    2.67  INTRA BF
 449 ARG   ( 452-)  A      O   <->  453 ASP   ( 456-)  A      N      0.18    2.52  INTRA BL
 805 ASP   ( 815-)  A      OD1 <->  806 SER   ( 816-)  A      N      0.18    2.42  INTRA BF
 399 HIS   ( 402-)  A      NE2 <->  469 TYR   ( 472-)  A      OH     0.18    2.52  INTRA BL
 200 LYS   ( 203-)  A      NZ  <->  267 LEU   ( 270-)  A      CD1    0.18    2.92  INTRA
And so on for a total of 171 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 578 ARG   ( 581-)  A      -7.51
 435 ARG   ( 438-)  A      -6.83
 434 LYS   ( 437-)  A      -6.14
 191 LEU   ( 194-)  A      -6.12
 338 LYS   ( 341-)  A      -5.99
 602 LYS   ( 605-)  A      -5.67
 443 GLN   ( 446-)  A      -5.64
 584 ARG   ( 587-)  A      -5.51
  43 ARG   (  46-)  A      -5.36
 441 ASN   ( 444-)  A      -5.28
 330 ARG   ( 333-)  A      -5.27
 141 ARG   ( 144-)  A      -5.27
 184 HIS   ( 187-)  A      -5.26
 190 LYS   ( 193-)  A      -5.22
 432 ASN   ( 435-)  A      -5.19
 208 ASN   ( 211-)  A      -5.16
 189 ARG   ( 192-)  A      -5.14
 142 ARG   ( 145-)  A      -5.11
 460 GLU   ( 463-)  A      -5.03
 303 GLU   ( 306-)  A      -5.02

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 189 ARG   ( 192-)  A       191 - LEU    194- ( A)         -5.49

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 848 GLN   ( 858-)  A   -2.95
 161 LYS   ( 164-)  A   -2.67

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

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.

  46 ASN   (  49-)  A
  84 GLN   (  87-)  A
 110 ASN   ( 113-)  A
 253 ASN   ( 256-)  A
 346 ASN   ( 349-)  A
 554 GLN   ( 557-)  A
 558 GLN   ( 561-)  A
 590 HIS   ( 593-)  A
 596 GLN   ( 599-)  A
 823 ASN   ( 833-)  A
 833 GLN   ( 843-)  A

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.

  19 THR   (  22-)  A      OG1
  28 ILE   (  31-)  A      N
  29 LEU   (  32-)  A      N
  66 LEU   (  69-)  A      N
  93 GLU   (  96-)  A      N
 101 ILE   ( 104-)  A      N
 133 THR   ( 136-)  A      N
 138 GLU   ( 141-)  A      N
 141 ARG   ( 144-)  A      N
 142 ARG   ( 145-)  A      N
 145 ILE   ( 148-)  A      N
 166 TYR   ( 169-)  A      N
 174 ARG   ( 177-)  A      NH1
 190 LYS   ( 193-)  A      N
 191 LEU   ( 194-)  A      N
 212 GLN   ( 215-)  A      N
 233 LEU   ( 236-)  A      N
 236 GLU   ( 239-)  A      N
 240 VAL   ( 243-)  A      N
 306 ALA   ( 309-)  A      N
 309 TYR   ( 312-)  A      N
 310 ARG   ( 313-)  A      N
 343 LEU   ( 346-)  A      N
 393 ARG   ( 396-)  A      NE
 393 ARG   ( 396-)  A      NH2
And so on for a total of 62 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.

  49 ASN   (  52-)  A      OD1
  86 HIS   (  89-)  A      ND1
 181 GLN   ( 184-)  A      OE1
 792 GLN   ( 802-)  A      OE1
 817 GLU   ( 827-)  A      OE1
 823 ASN   ( 833-)  A      OD1

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.

 187 GLU   ( 190-)  A   H-bonding suggests Gln; but Alt-Rotamer
 655 ASP   ( 658-)  A   H-bonding suggests Asn
 734 ASP   ( 744-)  A   H-bonding suggests Asn
 795 ASP   ( 805-)  A   H-bonding suggests Asn
 846 GLU   ( 856-)  A   H-bonding suggests Gln

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 :  -0.226
  2nd generation packing quality :  -1.503
  Ramachandran plot appearance   :  -2.329
  chi-1/chi-2 rotamer normality  :  -4.815 (bad)
  Backbone conformation          :   0.701

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.799
  Bond angles                    :   1.646
  Omega angle restraints         :   0.323 (tight)
  Side chain planarity           :   0.588 (tight)
  Improper dihedral distribution :   1.364
  B-factor distribution          :   0.549
  Inside/Outside distribution    :   0.974

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :   1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.799
  Bond angles                    :   1.646
  Omega angle restraints         :   0.323 (tight)
  Side chain planarity           :   0.588 (tight)
  Improper dihedral distribution :   1.364
  B-factor distribution          :   0.549
  Inside/Outside distribution    :   0.974
==============

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.