WHAT IF Check report

This file was created 2013-12-26 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb4i56.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 : 0.846
CA-only RMS fit for the two chains : 0.553

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.

 755 1CZ   ( 501-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 416 ASP   ( 545-)  B  -
 566 GLU   ( 695-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: 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.

  18 ASP   (  20-)  A    0.50
  22 GLN   (  24-)  A    0.50
 120 GLN   ( 122-)  A    0.50
 133 LYS   ( 135-)  A    0.50
 138 GLU   ( 140-)  A    0.50
 142 ARG   ( 144-)  A    0.50
 143 LYS   ( 145-)  A    0.50
 145 GLN   ( 147-)  A    0.50
 157 ILE   ( 159-)  A    0.50
 164 ASP   ( 166-)  A    0.50
 230 GLN   ( 232-)  A    0.50
 310 ASN   ( 312-)  A    0.50
 331 LYS   ( 333-)  A    0.50
 346 LYS   ( 348-)  A    0.50
 367 MET   ( 369-)  A    0.50
 368 ARG   ( 370-)  A    0.80
 373 GLU   ( 375-)  A    0.50
 382 ARG   ( 511-)  B    0.50
 391 ASP   ( 520-)  B    0.50
 402 ASP   ( 531-)  B    0.50
 409 ASN   ( 538-)  B    0.50
 416 ASP   ( 545-)  B    0.50
 417 ILE   ( 546-)  B    0.50
 444 ARG   ( 573-)  B    0.50
 446 VAL   ( 575-)  B    0.50
 449 PRO   ( 578-)  B    0.50
 456 SER   ( 585-)  B    0.50
 475 THR   ( 604-)  B    0.50
 493 GLN   ( 622-)  B    0.50
 517 ASP   ( 646-)  B    0.50
 531 GLU   ( 660-)  B    0.80
 537 ASP   ( 666-)  B    0.50
 538 THR   ( 667-)  B    0.80
 556 MET   ( 685-)  B    0.50
 559 ASN   ( 688-)  B    0.50
 566 GLU   ( 695-)  B    0.50
 579 GLN   ( 708-)  B    0.50
 595 ARG   ( 724-)  B    0.50
 606 GLU   ( 735-)  B    0.50
 617 GLU   ( 746-)  B    0.50
 704 LYS   ( 833-)  B    0.50
 722 GLN   ( 851-)  B    0.50
 735 GLN   ( 864-)  B    0.50
 741 ARG   ( 870-)  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: 0

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.

 283 ARG   ( 285-)  A
 595 ARG   ( 724-)  B
 656 ARG   ( 785-)  B

Warning: Tyrosine convention problem

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

  60 TYR   (  62-)  A
 258 TYR   ( 260-)  A
 299 TYR   ( 301-)  A
 631 TYR   ( 760-)  B
 672 TYR   ( 801-)  B

Warning: Phenylalanine convention problem

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

  56 PHE   (  58-)  A
 162 PHE   ( 164-)  A
 429 PHE   ( 558-)  B
 535 PHE   ( 664-)  B
 610 PHE   ( 739-)  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.

  43 ASP   (  45-)  A
 164 ASP   ( 166-)  A
 217 ASP   ( 219-)  A
 590 ASP   ( 719-)  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.

  50 GLU   (  52-)  A
  57 GLU   (  59-)  A
 135 GLU   ( 137-)  A
 240 GLU   ( 242-)  A
 423 GLU   ( 552-)  B
 508 GLU   ( 637-)  B
 606 GLU   ( 735-)  B
 609 GLU   ( 738-)  B
 746 GLU   ( 875-)  B

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

   4 ARG   (   6-)  A      CA   C     1.61    4.2
   9 ARG   (  11-)  A      N    CA    1.38   -4.2
 296 SER   ( 298-)  A      N    CA    1.55    4.8
 330 THR   ( 332-)  A      CB   OG1   1.51    4.7
 416 ASP   ( 545-)  B      CB   CG    1.84   12.8

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

 |  0.998123  0.006984  0.002530|
 |  0.006984  1.000038 -0.000788|
 |  0.002530 -0.000788  0.999408|
Proposed new scale matrix

 |  0.004432 -0.000031 -0.000011|
 | -0.000031  0.004423  0.000004|
 | -0.000011  0.000004  0.004426|
With corresponding cell

    A    = 225.673  B   = 226.105  C    = 225.958
    Alpha=  90.089  Beta=  89.710  Gamma=  89.199

The CRYST1 cell dimensions

    A    = 226.082  B   = 226.082  C    = 226.082
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 345.212
(Under-)estimated Z-score: 13.693

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.

 160 HIS   ( 162-)  A      CG   ND1  CE1 110.08    4.5
 174 HIS   ( 176-)  A      CG   ND1  CE1 110.46    4.9
 290 HIS   ( 292-)  A      CG   ND1  CE1 110.10    4.5
 416 ASP   ( 545-)  B      CA   CB   CG   94.86  -17.7
 416 ASP   ( 545-)  B      CB   CG   OD2 107.54   -4.7
 416 ASP   ( 545-)  B      CB   CG   OD1 128.61    4.4
 533 HIS   ( 662-)  B      CG   ND1  CE1 109.63    4.0
 547 HIS   ( 676-)  B      CG   ND1  CE1 110.28    4.7
 636 HIS   ( 765-)  B      CG   ND1  CE1 109.96    4.4
 668 ARG   ( 797-)  B      CB   CG   CD  105.99   -4.1

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.

  43 ASP   (  45-)  A
  50 GLU   (  52-)  A
  57 GLU   (  59-)  A
 135 GLU   ( 137-)  A
 164 ASP   ( 166-)  A
 217 ASP   ( 219-)  A
 240 GLU   ( 242-)  A
 283 ARG   ( 285-)  A
 423 GLU   ( 552-)  B
 508 GLU   ( 637-)  B
 590 ASP   ( 719-)  B
 595 ARG   ( 724-)  B
 606 GLU   ( 735-)  B
 609 GLU   ( 738-)  B
 656 ARG   ( 785-)  B
 746 GLU   ( 875-)  B

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.

 526 GLY   ( 655-)  B      C      6.5     8.64     0.06
 528 ARG   ( 657-)  B      C     -6.1    -9.19     0.13
 535 PHE   ( 664-)  B      C     -6.2    -9.83     0.23
The average deviation= 1.762

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.

 484 HIS   ( 613-)  B    8.42
 362 GLN   ( 364-)  A    8.09
 621 ASP   ( 750-)  B    7.43
 433 TYR   ( 562-)  B    7.12
  67 GLN   (  69-)  A    6.88
 518 GLN   ( 647-)  B    6.31
 391 ASP   ( 520-)  B    6.31
 186 ASN   ( 188-)  A    6.09
 419 ASN   ( 548-)  B    5.89
 416 ASP   ( 545-)  B    5.73
 111 HIS   ( 113-)  A    5.21
 486 GLN   ( 615-)  B    5.19
 318 GLU   ( 320-)  A    5.08
 685 HIS   ( 814-)  B    4.92
 113 GLN   ( 115-)  A    4.74
 124 ASN   ( 126-)  A    4.59
  51 ASN   (  53-)  A    4.41
  46 ASN   (  48-)  A    4.27
 174 HIS   ( 176-)  A    4.21
 424 ASN   ( 553-)  B    4.12
  69 ASN   (  71-)  A    4.02

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 322 PRO   ( 324-)  A    -2.6
 584 ILE   ( 713-)  B    -2.5
 695 PRO   ( 824-)  B    -2.5
 211 ILE   ( 213-)  A    -2.5
  79 VAL   (  81-)  A    -2.5
 452 VAL   ( 581-)  B    -2.4

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.

   7 ALA   (   9-)  A  Poor phi/psi
  51 ASN   (  53-)  A  Poor phi/psi
  57 GLU   (  59-)  A  omega poor
  65 ASN   (  67-)  A  Poor phi/psi
  80 GLU   (  82-)  A  omega poor
  83 SER   (  85-)  A  Poor phi/psi
 174 HIS   ( 176-)  A  omega poor
 180 ARG   ( 182-)  A  Poor phi/psi
 182 ALA   ( 184-)  A  omega poor
 203 THR   ( 205-)  A  omega poor
 208 ARG   ( 210-)  A  Poor phi/psi
 210 ARG   ( 212-)  A  omega poor
 212 LEU   ( 214-)  A  omega poor
 215 LEU   ( 217-)  A  omega poor
 296 SER   ( 298-)  A  omega poor
 303 THR   ( 305-)  A  omega poor
 324 GLY   ( 326-)  A  omega poor
 380 ALA   ( 509-)  B  Poor phi/psi
 424 ASN   ( 553-)  B  Poor phi/psi
 430 GLU   ( 559-)  B  omega poor
 438 ASN   ( 567-)  B  Poor phi/psi
 453 GLU   ( 582-)  B  omega poor
 456 SER   ( 585-)  B  Poor phi/psi
 484 HIS   ( 613-)  B  omega poor
 515 ARG   ( 644-)  B  omega poor
 530 ILE   ( 659-)  B  omega poor
 535 PHE   ( 664-)  B  omega poor
 547 HIS   ( 676-)  B  omega poor
 549 ILE   ( 678-)  B  omega poor
 553 ARG   ( 682-)  B  Poor phi/psi
 579 GLN   ( 708-)  B  omega poor
 581 ARG   ( 710-)  B  Poor phi/psi
 583 ARG   ( 712-)  B  omega poor
 585 LEU   ( 714-)  B  omega poor
 588 LEU   ( 717-)  B  omega poor
 609 GLU   ( 738-)  B  omega poor
 676 THR   ( 805-)  B  omega poor
 689 THR   ( 818-)  B  omega poor
 697 GLY   ( 826-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -0.506

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.

 501 SER   ( 630-)  B    0.37
 339 SER   ( 341-)  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!

   3 SER   (   5-)  A      0
   5 LEU   (   7-)  A      0
   6 PRO   (   8-)  A      0
   7 ALA   (   9-)  A      0
  28 HIS   (  30-)  A      0
  35 ALA   (  37-)  A      0
  36 ASN   (  38-)  A      0
  37 ALA   (  39-)  A      0
  42 MET   (  44-)  A      0
  48 MET   (  50-)  A      0
  49 ILE   (  51-)  A      0
  50 GLU   (  52-)  A      0
  52 VAL   (  54-)  A      0
  53 ILE   (  55-)  A      0
  64 SER   (  66-)  A      0
  65 ASN   (  67-)  A      0
  66 PHE   (  68-)  A      0
  78 VAL   (  80-)  A      0
  79 VAL   (  81-)  A      0
  80 GLU   (  82-)  A      0
  82 PRO   (  84-)  A      0
  83 SER   (  85-)  A      0
  98 ASN   ( 100-)  A      0
 101 PHE   ( 103-)  A      0
 104 SER   ( 106-)  A      0
And so on for a total of 214 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!

 700 GLY   ( 829-)  B   2.28   18

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]

  41 PRO   (  43-)  A    0.11 LOW
  76 PRO   (  78-)  A    0.15 LOW
 197 PRO   ( 199-)  A    0.20 LOW
 229 PRO   ( 231-)  A    0.16 LOW
 602 PRO   ( 731-)  B    0.15 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].

 379 PRO   ( 508-)  B  -112.5 envelop C-gamma (-108 degrees)
 570 PRO   ( 699-)  B  -128.1 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.

 208 ARG   ( 210-)  A    A NH1 <->  621 ASP   ( 750-)  B      OD2    0.44    2.26  INTRA
 374 LEU   ( 503-)  B      N   <->  757 HOH   (1462 )  B      O      0.39    2.31  INTRA
 358 VAL   ( 360-)  A      CG1 <->  756 HOH   ( 954 )  A      O      0.39    2.41  INTRA
   5 LEU   (   7-)  A      N   <->  756 HOH   ( 970 )  A      O      0.37    2.33  INTRA
 528 ARG   ( 657-)  B      NH1 <->  757 HOH   (1459 )  B      O      0.34    2.36  INTRA
 537 ASP   ( 666-)  B      CA  <->  757 HOH   (1467 )  B      O      0.27    2.53  INTRA BF
 164 ASP   ( 166-)  A      N   <->  756 HOH   ( 883 )  A      O      0.26    2.44  INTRA BF
 628 VAL   ( 757-)  B      CG1 <->  757 HOH   (1455 )  B      O      0.26    2.54  INTRA
 294 CYS   ( 296-)  A    A SG  <->  667 CYS   ( 796-)  B    A SG     0.25    3.20  INTRA
 444 ARG   ( 573-)  B      NE  <->  757 HOH   (1193 )  B      O      0.24    2.46  INTRA
 295 ARG   ( 297-)  A      NH1 <->  756 HOH   ( 963 )  A      O      0.24    2.46  INTRA
 538 THR   ( 667-)  B      N   <->  757 HOH   (1467 )  B      O      0.24    2.46  INTRA
 159 VAL   ( 161-)  A      CG1 <->  171 LEU   ( 173-)  A      CD1    0.22    2.98  INTRA
 409 ASN   ( 538-)  B      ND2 <->  757 HOH   (1417 )  B      O      0.20    2.50  INTRA
 504 ARG   ( 633-)  B      NE  <->  757 HOH   (1410 )  B    B O      0.20    2.50  INTRA
 755 1CZ   ( 501-)  A      P3' <->  756 HOH   ( 964 )  A      O      0.18    2.82  INTRA
 595 ARG   ( 724-)  B      NH2 <->  757 HOH   (1447 )  B      O      0.17    2.53  INTRA
 668 ARG   ( 797-)  B      NH1 <->  757 HOH   (1260 )  B      O      0.16    2.54  INTRA
 167 ARG   ( 169-)  A      NH2 <->  617 GLU   ( 746-)  B      OE1    0.15    2.55  INTRA
 516 LYS   ( 645-)  B      CD  <->  757 HOH   (1450 )  B      O      0.12    2.68  INTRA BF
 272 ASP   ( 274-)  A      N   <->  273 PRO   ( 275-)  A      CD     0.11    2.89  INTRA BL
 749 GLN   ( 878-)  B      OE1 <->  757 HOH   (1434 )  B      O      0.11    2.29  INTRA BF
 408 ALA   ( 537-)  B      C   <->  409 ASN   ( 538-)  B      OD1    0.11    2.59  INTRA
 340 LEU   ( 342-)  A      CD1 <->  756 HOH   ( 951 )  A      O      0.10    2.70  INTRA
 477 SER   ( 606-)  B      OG  <->  595 ARG   ( 724-)  B      NE     0.09    2.61  INTRA
And so on for a total of 51 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.

 493 GLN   ( 622-)  B      -7.03
 120 GLN   ( 122-)  A      -6.92
 668 ARG   ( 797-)  B      -6.38
 295 ARG   ( 297-)  A      -6.34
 167 ARG   ( 169-)  A      -6.26
 540 ARG   ( 669-)  B      -5.97
 346 LYS   ( 348-)  A      -5.64
 377 ARG   ( 506-)  B      -5.62
 528 ARG   ( 657-)  B      -5.61
   4 ARG   (   6-)  A      -5.58
 719 LYS   ( 848-)  B      -5.56
 155 ARG   ( 157-)  A      -5.52
 383 ASN   ( 512-)  B      -5.33
  10 ASN   (  12-)  A      -5.28
 748 ILE   ( 877-)  B      -5.17
 682 ASN   ( 811-)  B      -5.04

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.

 671 HIS   ( 800-)  B   -2.77
 298 HIS   ( 300-)  A   -2.75
 747 GLY   ( 876-)  B   -2.72
 211 ILE   ( 213-)  A   -2.56

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 757 HOH   (1261 )  B      O    118.20  113.92  130.45

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.

  50 GLU   (  52-)  A      N
  79 VAL   (  81-)  A      N
  81 GLU   (  83-)  A      N
  84 ILE   (  86-)  A      N
 208 ARG   ( 210-)  A    A NH1
 259 ARG   ( 261-)  A      NH1
 259 ARG   ( 261-)  A      NH2
 269 ASN   ( 271-)  A      ND2
 282 TRP   ( 284-)  A      N
 283 ARG   ( 285-)  A      NH1
 305 TRP   ( 307-)  A      N
 323 VAL   ( 325-)  A      N
 345 VAL   ( 347-)  A      N
 363 ASN   ( 365-)  A      ND2
 423 GLU   ( 552-)  B      N
 454 GLU   ( 583-)  B      N
 457 ILE   ( 586-)  B      N
 488 GLN   ( 617-)  B      NE2
 632 ARG   ( 761-)  B      NH1
 655 TRP   ( 784-)  B      N
 656 ARG   ( 785-)  B      NH1
 678 TRP   ( 807-)  B      N
 696 VAL   ( 825-)  B      N
 718 VAL   ( 847-)  B      N
 735 GLN   ( 864-)  B    A NE2
 751 GOL   ( 503-)  A      O3

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.

 272 ASP   ( 274-)  A      OD1
 424 ASN   ( 553-)  B      OD1
 645 ASP   ( 774-)  B      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 756 HOH   ( 617 )  A      O  1.05  K  4
 756 HOH   ( 626 )  A      O  1.15  K  4 (or NA *2)
 756 HOH   ( 642 )  A      O  0.98  K  4
 756 HOH   ( 663 )  A      O  1.02  K  4
 756 HOH   ( 669 )  A      O  0.98  K  4
 756 HOH   ( 681 )  A      O  0.87  K  4
 756 HOH   ( 695 )  A      O  0.89  K  4
 756 HOH   ( 731 )  A      O  0.94  K  4
 756 HOH   ( 786 )  A      O  1.04  K  5 Ion-B
 756 HOH   ( 789 )  A      O  1.09  K  4 Ion-B
 757 HOH   (1114 )  B      O  0.98  K  5
 757 HOH   (1144 )  B      O  0.85  K  4
 757 HOH   (1151 )  B      O  0.92  K  4
 757 HOH   (1152 )  B      O  1.00  K  4
 757 HOH   (1164 )  B      O  1.10  K  4
 757 HOH   (1233 )  B      O  0.85  K  5
 757 HOH   (1324 )  B      O  1.00  K  5 Ion-B

Warning: Possible wrong residue type

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

  81 GLU   (  83-)  A   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 373 GLU   ( 375-)  A   H-bonding suggests Gln
 454 GLU   ( 583-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact

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 :   0.319
  2nd generation packing quality :  -0.802
  Ramachandran plot appearance   :   0.580
  chi-1/chi-2 rotamer normality  :  -0.506
  Backbone conformation          :   0.914

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.936
  Bond angles                    :   0.891
  Omega angle restraints         :   1.145
  Side chain planarity           :   2.481 (loose)
  Improper dihedral distribution :   1.556 (loose)
  B-factor distribution          :   0.818
  Inside/Outside distribution    :   0.961

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 : 1.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.936
  Bond angles                    :   0.891
  Omega angle restraints         :   1.145
  Side chain planarity           :   2.481 (loose)
  Improper dihedral distribution :   1.556 (loose)
  B-factor distribution          :   0.818
  Inside/Outside distribution    :   0.961
==============

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.