WHAT IF Check report

This file was created 2012-01-30 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 pdb3n8z.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 : 0.662
CA-only RMS fit for the two chains : 0.420

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

1117 BOG   ( 750-)  A  -
1118 BOG   ( 751-)  A  -
1119 FLP   ( 701-)  A  -
1121 BMA   ( 673-)  B  -
1122 BOG   (1750-)  B  -
1123 FLP   (1701-)  B  -
1124 BOG   (1751-)  B  -
1125 MAN   ( 675-)  B  -
1126 BMA   ( 674-)  B  -
1127 A10   ( 752-)  A  -
1128 NDG   ( 662-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1107 NAG   ( 661-)  A  -   O4  bound to 1128 NDG   ( 662-)  A  -   C1
1108 NAG   ( 671-)  A  -   O4  bound to 1109 NAG   ( 672-)  A  -   C1
1110 NAG   ( 681-)  A  -   O4  bound to 1111 NAG   ( 682-)  A  -   C1
1112 NAG   ( 671-)  B  -   O4  bound to 1113 NAG   ( 672-)  B  -   C1
1113 NAG   ( 672-)  B  -   O4  bound to 1121 BMA   ( 673-)  B  -   C1
1114 NAG   ( 681-)  B  -   O4  bound to 1115 NAG   ( 682-)  B  -   C1

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 744 LYS   ( 222-)  B  -   CE
 744 LYS   ( 222-)  B  -   NZ

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Missing atoms

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

  48 ARG   (  79-)  A      CG
  48 ARG   (  79-)  A      CD
  48 ARG   (  79-)  A      NE
  48 ARG   (  79-)  A      CZ
  48 ARG   (  79-)  A      NH1
  48 ARG   (  79-)  A      NH2
 126 ARG   ( 157-)  A      CG
 126 ARG   ( 157-)  A      CD
 126 ARG   ( 157-)  A      NE
 126 ARG   ( 157-)  A      CZ
 126 ARG   ( 157-)  A      NH1
 126 ARG   ( 157-)  A      NH2
 137 LYS   ( 168-)  A      CG
 137 LYS   ( 168-)  A      CD
 137 LYS   ( 168-)  A      CE
 137 LYS   ( 168-)  A      NZ
 138 LYS   ( 169-)  A      CG
 138 LYS   ( 169-)  A      CD
 138 LYS   ( 169-)  A      CE
 138 LYS   ( 169-)  A      NZ
 144 GLU   ( 175-)  A      CG
 144 GLU   ( 175-)  A      CD
 144 GLU   ( 175-)  A      OE1
 144 GLU   ( 175-)  A      OE2
 148 ARG   ( 179-)  A      CG
And so on for a total of 96 lines.

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.

 804 GLN   ( 282-)  B    High
1111 NAG   ( 682-)  A    High
1114 NAG   ( 681-)  B    High
1115 NAG   ( 682-)  B    High

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 591 CYS   (  69-)  B    0.50

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: 2

Crystal temperature (K) :100.000

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.

  52 ARG   (  83-)  A
 149 ARG   ( 180-)  A
 154 ARG   ( 185-)  A
 428 ARG   ( 459-)  A
 702 ARG   ( 180-)  B

Warning: Tyrosine convention problem

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

  24 TYR   (  55-)  A
  99 TYR   ( 130-)  A
 105 TYR   ( 136-)  A
 211 TYR   ( 242-)  A
 223 TYR   ( 254-)  A
 231 TYR   ( 262-)  A
 317 TYR   ( 348-)  A
 324 TYR   ( 355-)  A
 342 TYR   ( 373-)  A
 354 TYR   ( 385-)  A
 373 TYR   ( 404-)  A
 386 TYR   ( 417-)  A
 444 TYR   ( 475-)  A
 464 TYR   ( 495-)  A
 513 TYR   ( 544-)  A
 560 TYR   (  38-)  B
 577 TYR   (  55-)  B
 652 TYR   ( 130-)  B
 658 TYR   ( 136-)  B
 764 TYR   ( 242-)  B
 776 TYR   ( 254-)  B
 784 TYR   ( 262-)  B
 797 TYR   ( 275-)  B
 877 TYR   ( 355-)  B
 895 TYR   ( 373-)  B
 907 TYR   ( 385-)  B
 926 TYR   ( 404-)  B
 939 TYR   ( 417-)  B
 997 TYR   ( 475-)  B
1017 TYR   ( 495-)  B
1066 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.

  19 PHE   (  50-)  A
  57 PHE   (  88-)  A
  71 PHE   ( 102-)  A
  76 PHE   ( 107-)  A
 150 PHE   ( 181-)  A
 156 PHE   ( 187-)  A
 167 PHE   ( 198-)  A
 170 PHE   ( 201-)  A
 178 PHE   ( 209-)  A
 189 PHE   ( 220-)  A
 216 PHE   ( 247-)  A
 336 PHE   ( 367-)  A
 364 PHE   ( 395-)  A
 439 PHE   ( 470-)  A
 487 PHE   ( 518-)  A
 498 PHE   ( 529-)  A
 519 PHE   ( 550-)  A
 549 PHE   ( 580-)  A
 572 PHE   (  50-)  B
 610 PHE   (  88-)  B
 624 PHE   ( 102-)  B
 629 PHE   ( 107-)  B
 703 PHE   ( 181-)  B
 709 PHE   ( 187-)  B
 720 PHE   ( 198-)  B
 723 PHE   ( 201-)  B
 731 PHE   ( 209-)  B
 742 PHE   ( 220-)  B
 769 PHE   ( 247-)  B
 889 PHE   ( 367-)  B
 931 PHE   ( 409-)  B
1000 PHE   ( 478-)  B
1040 PHE   ( 518-)  B
1051 PHE   ( 529-)  B
1072 PHE   ( 550-)  B
1102 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.

  22 ASP   (  53-)  A
  79 ASP   ( 110-)  A
 218 ASP   ( 249-)  A
 283 ASP   ( 314-)  A
 362 ASP   ( 393-)  A
 419 ASP   ( 450-)  A
 466 ASP   ( 497-)  A
 575 ASP   (  53-)  B
 771 ASP   ( 249-)  B
 836 ASP   ( 314-)  B
 915 ASP   ( 393-)  B
 972 ASP   ( 450-)  B
1019 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.

  42 GLU   (  73-)  A
 208 GLU   ( 239-)  A
 236 GLU   ( 267-)  A
 277 GLU   ( 308-)  A
 288 GLU   ( 319-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 374 GLU   ( 405-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 479 GLU   ( 510-)  A
 489 GLU   ( 520-)  A
 522 GLU   ( 553-)  A
 595 GLU   (  73-)  B
 697 GLU   ( 175-)  B
 790 GLU   ( 268-)  B
 830 GLU   ( 308-)  B
 841 GLU   ( 319-)  B
 848 GLU   ( 326-)  B
 861 GLU   ( 339-)  B
 886 GLU   ( 364-)  B
 927 GLU   ( 405-)  B
 976 GLU   ( 454-)  B
1002 GLU   ( 480-)  B
1006 GLU   ( 484-)  B
1032 GLU   ( 510-)  B
1042 GLU   ( 520-)  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

 |  0.997409 -0.000037  0.000044|
 | -0.000037  0.997214  0.000076|
 |  0.000044  0.000076  0.997405|
Proposed new scale matrix

 |  0.005524  0.003190  0.000000|
 |  0.000000  0.006380  0.000000|
 |  0.000000  0.000000  0.009672|
With corresponding cell

    A    = 181.016  B   = 181.003  C    = 103.390
    Alpha=  90.001  Beta=  90.001  Gamma= 120.005

The CRYST1 cell dimensions

    A    = 181.490  B   = 181.490  C    = 103.661
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 270.492
(Under-)estimated Z-score: 12.121

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   (  53-)  A
  42 GLU   (  73-)  A
  52 ARG   (  83-)  A
  79 ASP   ( 110-)  A
 149 ARG   ( 180-)  A
 154 ARG   ( 185-)  A
 208 GLU   ( 239-)  A
 218 ASP   ( 249-)  A
 236 GLU   ( 267-)  A
 277 GLU   ( 308-)  A
 283 ASP   ( 314-)  A
 288 GLU   ( 319-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 362 ASP   ( 393-)  A
 374 GLU   ( 405-)  A
 419 ASP   ( 450-)  A
 428 ARG   ( 459-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 466 ASP   ( 497-)  A
 479 GLU   ( 510-)  A
 489 GLU   ( 520-)  A
 522 GLU   ( 553-)  A
 575 ASP   (  53-)  B
 595 GLU   (  73-)  B
 697 GLU   ( 175-)  B
 702 ARG   ( 180-)  B
 771 ASP   ( 249-)  B
 790 GLU   ( 268-)  B
 830 GLU   ( 308-)  B
 836 ASP   ( 314-)  B
 841 GLU   ( 319-)  B
 848 GLU   ( 326-)  B
 861 GLU   ( 339-)  B
 886 GLU   ( 364-)  B
 915 ASP   ( 393-)  B
 927 GLU   ( 405-)  B
 972 ASP   ( 450-)  B
 976 GLU   ( 454-)  B
1002 GLU   ( 480-)  B
1006 GLU   ( 484-)  B
1019 ASP   ( 497-)  B
1032 GLU   ( 510-)  B
1042 GLU   ( 520-)  B

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.

 487 PHE   ( 518-)  A    -3.1
1040 PHE   ( 518-)  B    -2.9
 483 PRO   ( 514-)  A    -2.8
 931 PHE   ( 409-)  B    -2.7
1098 PRO   ( 576-)  B    -2.7
 907 TYR   ( 385-)  B    -2.6
   8 TYR   (  39-)  A    -2.6
 361 PRO   ( 392-)  A    -2.5
 354 TYR   ( 385-)  A    -2.5
  38 CYS   (  69-)  A    -2.5
 914 PRO   ( 392-)  B    -2.4
 561 TYR   (  39-)  B    -2.3
  98 THR   ( 129-)  A    -2.3
 591 CYS   (  69-)  B    -2.2
 133 GLY   ( 164-)  A    -2.2
 453 GLU   ( 484-)  A    -2.2
 221 LEU   ( 252-)  A    -2.2
 545 PRO   ( 576-)  A    -2.2
 672 ARG   ( 150-)  B    -2.2
 651 THR   ( 129-)  B    -2.2
1006 GLU   ( 484-)  B    -2.1
 532 THR   ( 563-)  A    -2.1
1036 PRO   ( 514-)  B    -2.1
  52 ARG   (  83-)  A    -2.1
 750 VAL   ( 228-)  B    -2.1
 813 VAL   ( 291-)  B    -2.1
 213 LEU   ( 244-)  A    -2.1
  51 LEU   (  82-)  A    -2.1
1092 LEU   ( 570-)  B    -2.0
  18 ARG   (  49-)  A    -2.0
 752 LEU   ( 230-)  B    -2.0
 686 GLY   ( 164-)  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.

  13 GLN   (  44-)  A  Poor phi/psi
  30 ARG   (  61-)  A  Poor phi/psi
  38 CYS   (  69-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
 116 TYR   ( 147-)  A  omega poor
 134 THR   ( 165-)  A  Poor phi/psi
 150 PHE   ( 181-)  A  Poor phi/psi
 154 ARG   ( 185-)  A  Poor phi/psi
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 227 ASN   ( 258-)  A  Poor phi/psi
 378 PHE   ( 409-)  A  Poor phi/psi
 428 ARG   ( 459-)  A  Poor phi/psi
 484 ASN   ( 515-)  A  Poor phi/psi
 514 TRP   ( 545-)  A  Poor phi/psi
 565 HIS   (  43-)  B  Poor phi/psi
 566 GLN   (  44-)  B  Poor phi/psi
 591 CYS   (  69-)  B  Poor phi/psi
 648 SER   ( 126-)  B  PRO omega poor
 651 THR   ( 129-)  B  Poor phi/psi
 669 TYR   ( 147-)  B  omega poor
 703 PHE   ( 181-)  B  Poor phi/psi
 752 LEU   ( 230-)  B  Poor phi/psi
 769 PHE   ( 247-)  B  Poor phi/psi
 771 ASP   ( 249-)  B  Poor phi/psi
 780 ASN   ( 258-)  B  Poor phi/psi
 908 HIS   ( 386-)  B  Poor phi/psi
 931 PHE   ( 409-)  B  Poor phi/psi
1037 ASN   ( 515-)  B  Poor phi/psi
1067 TRP   ( 545-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.973

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.

 663 SER   ( 141-)  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!

   3 ASN   (  34-)  A      0
   5 CYS   (  36-)  A      0
   6 CYS   (  37-)  A      0
   8 TYR   (  39-)  A      0
   9 PRO   (  40-)  A      0
  10 CYS   (  41-)  A      0
  11 GLN   (  42-)  A      0
  12 HIS   (  43-)  A      0
  13 GLN   (  44-)  A      0
  19 PHE   (  50-)  A      0
  21 LEU   (  52-)  A      0
  22 ASP   (  53-)  A      0
  28 CYS   (  59-)  A      0
  29 THR   (  60-)  A      0
  30 ARG   (  61-)  A      0
  31 THR   (  62-)  A      0
  33 TYR   (  64-)  A      0
  34 SER   (  65-)  A      0
  38 CYS   (  69-)  A      0
  39 THR   (  70-)  A      0
  43 ILE   (  74-)  A      0
  63 THR   (  94-)  A      0
  64 HIS   (  95-)  A      0
  66 ARG   (  97-)  A      0
  74 ALA   ( 105-)  A      0
And so on for a total of 426 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!

 131 PRO   ( 162-)  A   1.82   12
 684 PRO   ( 162-)  B   1.68   16

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].

  36 PRO   (  67-)  A  -123.4 half-chair C-delta/C-gamma (-126 degrees)
  41 PRO   (  72-)  A   -65.6 envelop C-beta (-72 degrees)
 131 PRO   ( 162-)  A   115.4 envelop C-beta (108 degrees)
 239 PRO   ( 270-)  A    50.0 half-chair C-delta/C-gamma (54 degrees)
 361 PRO   ( 392-)  A   -22.1 half-chair C-alpha/N (-18 degrees)
 483 PRO   ( 514-)  A   135.6 envelop C-alpha (144 degrees)
 507 PRO   ( 538-)  A  -113.9 envelop C-gamma (-108 degrees)
 594 PRO   (  72-)  B   -49.8 half-chair C-beta/C-alpha (-54 degrees)
 647 PRO   ( 125-)  B  -115.2 envelop C-gamma (-108 degrees)
 649 PRO   ( 127-)  B  -122.0 half-chair C-delta/C-gamma (-126 degrees)
 694 PRO   ( 172-)  B   104.8 envelop C-beta (108 degrees)
 911 PRO   ( 389-)  B   105.1 envelop C-beta (108 degrees)
 914 PRO   ( 392-)  B   -41.0 envelop C-alpha (-36 degrees)
1036 PRO   ( 514-)  B   107.5 envelop C-beta (108 degrees)
1060 PRO   ( 538-)  B  -122.7 half-chair C-delta/C-gamma (-126 degrees)
1098 PRO   ( 576-)  B   -62.6 half-chair C-beta/C-alpha (-54 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.

1121 BMA   ( 673-)  B      O4  <-> 1126 BMA   ( 674-)  B      C1     0.95    1.45  INTRA BF
1107 NAG   ( 661-)  A      O4  <-> 1128 NDG   ( 662-)  A      C1     0.95    1.45  INTRA BF
1121 BMA   ( 673-)  B      C4  <-> 1126 BMA   ( 674-)  B      C1     0.86    2.34  INTRA BF
1107 NAG   ( 661-)  A      C4  <-> 1128 NDG   ( 662-)  A      C1     0.75    2.45  INTRA BF
 114 VAL   ( 145-)  A      O   <->  195 HIS   ( 226-)  A      NE2    0.28    2.42  INTRA BL
 357 HIS   ( 388-)  A      N   <->  358 PRO   ( 389-)  A      CD     0.26    2.74  INTRA BF
 910 HIS   ( 388-)  B      N   <->  911 PRO   ( 389-)  B      CD     0.24    2.76  INTRA BL
 963 ASP   ( 441-)  B      OD2 <->  965 HIS   ( 443-)  B      ND1    0.21    2.49  INTRA BF
1121 BMA   ( 673-)  B      C4  <-> 1126 BMA   ( 674-)  B      O5     0.17    2.63  INTRA BF
 124 VAL   ( 155-)  A      O   <->  428 ARG   ( 459-)  A      NE     0.15    2.55  INTRA BF
 672 ARG   ( 150-)  B      NH2 <->  980 LEU   ( 458-)  B      O      0.15    2.55  INTRA BL
 119 ARG   ( 150-)  A      NH2 <->  348 MET   ( 379-)  A      SD     0.14    3.16  INTRA BL
1066 TYR   ( 544-)  B      O   <-> 1068 LYS   ( 546-)  B      N      0.14    2.56  INTRA BL
 910 HIS   ( 388-)  B      NE2 <-> 1120 HEM   ( 601-)  B      NB     0.14    2.86  INTRA BF
 989 ARG   ( 467-)  B      NH1 <->  994 MET   ( 472-)  B      SD     0.13    3.17  INTRA BL
 119 ARG   ( 150-)  A      NH2 <->  427 LEU   ( 458-)  A      O      0.13    2.57  INTRA BL
  47 LEU   (  78-)  A      C   <-> 1129 HOH   ( 637 )  A      O      0.10    2.70  INTRA BF
 866 VAL   ( 344-)  B      O   <->  871 VAL   ( 349-)  B      N      0.10    2.60  INTRA BL
 997 TYR   ( 475-)  B      N   <-> 1130 HOH   ( 623 )  B      O      0.09    2.61  INTRA BF
1113 NAG   ( 672-)  B      C3  <-> 1121 BMA   ( 673-)  B      C1     0.09    2.71  INTRA BF
  52 ARG   (  83-)  A      NH2 <->  440 GLY   ( 471-)  A      O      0.09    2.61  INTRA BF
 716 THR   ( 194-)  B      O   <->  953 ALA   ( 431-)  B      N      0.08    2.62  INTRA BL
 364 PHE   ( 395-)  A      N   <->  371 TYR   ( 402-)  A      O      0.08    2.62  INTRA BF
 159 ASP   ( 190-)  A      OD2 <->  163 THR   ( 194-)  A      N      0.08    2.62  INTRA BF
 319 GLN   ( 350-)  A      OE1 <->  328 LEU   ( 359-)  A      N      0.08    2.62  INTRA BL
And so on for a total of 72 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.

 139 GLN   ( 170-)  A      -7.62
 583 ARG   (  61-)  B      -6.87
 707 ARG   ( 185-)  B      -6.62
  30 ARG   (  61-)  A      -6.60
 244 TYR   ( 275-)  A      -6.38
 709 PHE   ( 187-)  B      -6.29
 156 PHE   ( 187-)  A      -6.16
 154 ARG   ( 185-)  A      -6.14
 737 LYS   ( 215-)  B      -6.14
 184 LYS   ( 215-)  A      -5.99
 955 ARG   ( 433-)  B      -5.86
  21 LEU   (  52-)  A      -5.83
 574 LEU   (  52-)  B      -5.76
 896 ARG   ( 374-)  B      -5.76
 690 LYS   ( 168-)  B      -5.74
 185 MET   ( 216-)  A      -5.61
 343 ARG   ( 374-)  A      -5.54
 797 TYR   ( 275-)  B      -5.47
 706 ARG   ( 184-)  B      -5.45
  23 ARG   (  54-)  A      -5.39
 892 GLN   ( 370-)  B      -5.36
   2 VAL   (  33-)  A      -5.24
 702 ARG   ( 180-)  B      -5.22
 693 LEU   ( 171-)  B      -5.18
 402 ARG   ( 433-)  A      -5.16
 555 VAL   (  33-)  B      -5.14
 438 ARG   ( 469-)  A      -5.12
 991 ARG   ( 469-)  B      -5.11
  52 ARG   (  83-)  A      -5.10
 688 LYS   ( 166-)  B      -5.09
 149 ARG   ( 180-)  A      -5.07
 769 PHE   ( 247-)  B      -5.03
 251 GLN   ( 282-)  A      -5.02

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.

 770 LYS   ( 248-)  B   -3.37
 981 ARG   ( 459-)  B   -3.13
 246 ARG   ( 277-)  A   -2.95
 692 GLN   ( 170-)  B   -2.93
 137 LYS   ( 168-)  A   -2.86
 155 LYS   ( 186-)  A   -2.70
 334 LEU   ( 365-)  A   -2.69
 708 LYS   ( 186-)  B   -2.66
 469 ALA   ( 500-)  A   -2.56

Warning: Abnormal packing Z-score for sequential residues

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

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

 152 LEU   ( 183-)  A     -  155 LYS   ( 186-)  A        -2.05

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1129 HOH   ( 588 )  A      O
1129 HOH   ( 615 )  A      O
1130 HOH   (   1 )  B      O
1130 HOH   ( 613 )  B      O
1130 HOH   ( 628 )  B      O
1130 HOH   ( 629 )  B      O
Bound group on Asn; dont flip   37 ASN  (  68-) A
Bound to: 1107 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 1108 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 1110 NAG  ( 681-) A
Bound group on Asn; dont flip  666 ASN  ( 144-) B
Bound to: 1112 NAG  ( 671-) B
Marked this atom as acceptor 1119 FLP  ( 701-) A      F
Marked this atom as acceptor 1123 FLP  (1701-) B      F
Metal-coordinating Histidine residue 910 fixed to   1

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  11 GLN   (  42-)  A
  64 HIS   (  95-)  A
 173 HIS   ( 204-)  A
 590 ASN   (  68-)  B
 656 HIS   ( 134-)  B
 759 ASN   ( 237-)  B
 897 ASN   ( 375-)  B
 968 HIS   ( 446-)  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.

  18 ARG   (  49-)  A      NH1
  44 TRP   (  75-)  A      N
  89 ARG   ( 120-)  A      NE
  89 ARG   ( 120-)  A      NH1
 100 ASN   ( 131-)  A      ND2
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      OG
 119 ARG   ( 150-)  A      NE
 119 ARG   ( 150-)  A      NH1
 119 ARG   ( 150-)  A      NH2
 161 GLN   ( 192-)  A      N
 177 GLN   ( 208-)  A      NE2
 180 LYS   ( 211-)  A      NZ
 182 SER   ( 213-)  A      OG
 186 GLY   ( 217-)  A      N
 196 GLY   ( 227-)  A      N
 200 GLY   ( 231-)  A      N
 204 GLY   ( 235-)  A      N
 205 ASP   ( 236-)  A      N
 214 ARG   ( 245-)  A      NH1
 217 LYS   ( 248-)  A      N
 223 TYR   ( 254-)  A      N
 236 GLU   ( 267-)  A      N
 264 LEU   ( 295-)  A      N
 266 GLY   ( 297-)  A      N
And so on for a total of 96 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.

 159 ASP   ( 190-)  A      OD1
 172 GLN   ( 203-)  A      OE1
 243 HIS   ( 274-)  A      ND1
 289 HIS   ( 320-)  A      NE2
 308 GLU   ( 339-)  A      OE1
 357 HIS   ( 388-)  A      ND1
 482 HIS   ( 513-)  A      ND1
 493 GLU   ( 524-)  A      OE1
 725 GLN   ( 203-)  B      OE1
 726 HIS   ( 204-)  B      NE2
 861 GLU   ( 339-)  B      OE1
 904 ASN   ( 382-)  B      OD1
1024 GLU   ( 502-)  B      OE1

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.

 198 ASP   ( 229-)  A   H-bonding suggests Asn; but Alt-Rotamer
 385 ASP   ( 416-)  A   H-bonding suggests Asn
 419 ASP   ( 450-)  A   H-bonding suggests Asn; but Alt-Rotamer
 461 GLU   ( 492-)  A   H-bonding suggests Gln; but Alt-Rotamer
 623 ASP   ( 101-)  B   H-bonding suggests Asn
 751 ASP   ( 229-)  B   H-bonding suggests Asn
 836 ASP   ( 314-)  B   H-bonding suggests Asn
 938 ASP   ( 416-)  B   H-bonding suggests Asn
 972 ASP   ( 450-)  B   H-bonding suggests Asn; but Alt-Rotamer
1014 GLU   ( 492-)  B   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 :  -1.925
  2nd generation packing quality :  -2.190
  Ramachandran plot appearance   :  -1.730
  chi-1/chi-2 rotamer normality  :  -2.973
  Backbone conformation          :  -1.368

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.320 (tight)
  Bond angles                    :   0.509 (tight)
  Omega angle restraints         :   0.738
  Side chain planarity           :   0.216 (tight)
  Improper dihedral distribution :   0.406
  B-factor distribution          :   0.361
  Inside/Outside distribution    :   1.095

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.320 (tight)
  Bond angles                    :   0.509 (tight)
  Omega angle restraints         :   0.738
  Side chain planarity           :   0.216 (tight)
  Improper dihedral distribution :   0.406
  B-factor distribution          :   0.361
  Inside/Outside distribution    :   1.095
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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      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,
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      protein structures
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Matthews' Coefficient
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      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,
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
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      A general definition of ring puckering coordinates
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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.