WHAT IF Check report

This file was created 2011-12-18 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 pdb1y7w.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 : 0.468
CA-only RMS fit for the two chains : 0.259

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.

 553 ACY   ( 279-)  A  -
 557 ACY   ( 280-)  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.

 299 LYS   (  27-)  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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :120.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  50 ARG   (  52-)  A
 222 ARG   ( 224-)  A
 232 ARG   ( 234-)  A
 236 ARG   ( 238-)  A
 324 ARG   (  52-)  B
 496 ARG   ( 224-)  B
 506 ARG   ( 234-)  B
 510 ARG   ( 238-)  B

Warning: Tyrosine convention problem

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

 128 TYR   ( 130-)  A
 207 TYR   ( 209-)  A
 274 TYR   ( 276-)  A
 402 TYR   ( 130-)  B
 432 TYR   ( 160-)  B
 481 TYR   ( 209-)  B

Warning: Phenylalanine convention problem

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

 107 PHE   ( 109-)  A
 165 PHE   ( 167-)  A
 228 PHE   ( 230-)  A
 242 PHE   ( 244-)  A
 287 PHE   (  15-)  B
 362 PHE   (  90-)  B
 388 PHE   ( 116-)  B
 439 PHE   ( 167-)  B
 502 PHE   ( 230-)  B
 516 PHE   ( 244-)  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.

  89 ASP   (  91-)  A
 143 ASP   ( 145-)  A
 186 ASP   ( 188-)  A
 211 ASP   ( 213-)  A
 244 ASP   ( 246-)  A
 266 ASP   ( 268-)  A
 278 ASP   (   6-)  B
 281 ASP   (   9-)  B
 312 ASP   (  40-)  B
 338 ASP   (  66-)  B
 363 ASP   (  91-)  B
 460 ASP   ( 188-)  B
 485 ASP   ( 213-)  B
 518 ASP   ( 246-)  B
 540 ASP   ( 268-)  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.

 160 GLU   ( 162-)  A
 174 GLU   ( 176-)  A
 221 GLU   ( 223-)  A
 233 GLU   ( 235-)  A
 294 GLU   (  22-)  B
 412 GLU   ( 140-)  B
 448 GLU   ( 176-)  B
 495 GLU   ( 223-)  B
 507 GLU   ( 235-)  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

 |  0.996132 -0.000511 -0.000878|
 | -0.000511  0.995945 -0.001338|
 | -0.000878 -0.001338  0.996234|
Proposed new scale matrix

 |  0.021351  0.000013  0.001717|
 |  0.000004  0.008379  0.000011|
 |  0.000015  0.000023  0.017230|
With corresponding cell

    A    =  46.839  B   = 119.346  C    =  58.230
    Alpha=  90.149  Beta=  94.649  Gamma=  90.059

The CRYST1 cell dimensions

    A    =  47.022  B   = 119.835  C    =  58.442
    Alpha=  90.000  Beta=  94.550  Gamma=  90.000

Variance: 279.941
(Under-)estimated Z-score: 12.331

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.

  25 LYS   (  27-)  A      CB   CG   CD  102.03   -4.0
  57 SER   (  59-)  A      N    CA   C    99.84   -4.1
 115 HIS   ( 117-)  A      N    CA   C    97.55   -4.9
 115 HIS   ( 117-)  A      CG   ND1  CE1 109.71    4.1
 116 HIS   ( 118-)  A      CG   ND1  CE1 109.74    4.1
 389 HIS   ( 117-)  B      N    CA   C    98.29   -4.6
 390 HIS   ( 118-)  B      CG   ND1  CE1 109.85    4.2
 408 ILE   ( 136-)  B      N    CA   C    98.94   -4.4
 524 HIS   ( 252-)  B      CG   ND1  CE1 109.65    4.0

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.

  50 ARG   (  52-)  A
  89 ASP   (  91-)  A
 143 ASP   ( 145-)  A
 160 GLU   ( 162-)  A
 174 GLU   ( 176-)  A
 186 ASP   ( 188-)  A
 211 ASP   ( 213-)  A
 221 GLU   ( 223-)  A
 222 ARG   ( 224-)  A
 232 ARG   ( 234-)  A
 233 GLU   ( 235-)  A
 236 ARG   ( 238-)  A
 244 ASP   ( 246-)  A
 266 ASP   ( 268-)  A
 278 ASP   (   6-)  B
 281 ASP   (   9-)  B
 294 GLU   (  22-)  B
 312 ASP   (  40-)  B
 324 ARG   (  52-)  B
 338 ASP   (  66-)  B
 363 ASP   (  91-)  B
 412 GLU   ( 140-)  B
 448 GLU   ( 176-)  B
 460 ASP   ( 188-)  B
 485 ASP   ( 213-)  B
 495 GLU   ( 223-)  B
 496 ARG   ( 224-)  B
 506 ARG   ( 234-)  B
 507 GLU   ( 235-)  B
 510 ARG   ( 238-)  B
 518 ASP   ( 246-)  B
 540 ASP   ( 268-)  B

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 115 HIS   ( 117-)  A    5.25
 389 HIS   ( 117-)  B    4.92
  57 SER   (  59-)  A    4.49
 408 ILE   ( 136-)  B    4.32
 199 GLN   ( 201-)  A    4.12
 506 ARG   ( 234-)  B    4.06

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 : 1.545

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 285 HIS   (  13-)  B      CB   5.40
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.444

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.

  88 PHE   (  90-)  A    -2.5
 111 GLN   ( 113-)  A    -2.1
 385 GLN   ( 113-)  B    -2.1
 415 PRO   ( 143-)  B    -2.1
 234 VAL   ( 236-)  A    -2.1
 508 VAL   ( 236-)  B    -2.1

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.

  35 SER   (  37-)  A  PRO omega poor
  59 ASN   (  61-)  A  Poor phi/psi
  75 ASN   (  77-)  A  Poor phi/psi
  94 ASN   (  96-)  A  Poor phi/psi
 111 GLN   ( 113-)  A  Poor phi/psi
 117 PHE   ( 119-)  A  Poor phi/psi
 217 PRO   ( 219-)  A  omega poor
 218 GLY   ( 220-)  A  Poor phi/psi
 219 CYS   ( 221-)  A  Poor phi/psi
 273 ASN   ( 275-)  A  Poor phi/psi
 278 ASP   (   6-)  B  Poor phi/psi
 309 SER   (  37-)  B  PRO omega poor
 333 ASN   (  61-)  B  Poor phi/psi
 368 ASN   (  96-)  B  Poor phi/psi
 391 PHE   ( 119-)  B  Poor phi/psi
 414 ASP   ( 142-)  B  Poor phi/psi
 491 PRO   ( 219-)  B  omega poor
 493 CYS   ( 221-)  B  Poor phi/psi
 547 ASN   ( 275-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.629

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.

 240 LYS   ( 242-)  A    0.33
 168 SER   ( 170-)  A    0.38

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   (   5-)  A      0
   8 TYR   (  10-)  A      0
  11 HIS   (  13-)  A      0
  20 GLU   (  22-)  A      0
  29 CYS   (  31-)  A      0
  33 ASN   (  35-)  A      0
  35 SER   (  37-)  A      0
  50 ARG   (  52-)  A      0
  51 SER   (  53-)  A      0
  58 LEU   (  60-)  A      0
  59 ASN   (  61-)  A      0
  69 ASP   (  71-)  A      0
  75 ASN   (  77-)  A      0
  76 ALA   (  78-)  A      0
  80 LEU   (  82-)  A      0
  81 GLU   (  83-)  A      0
  82 GLN   (  84-)  A      0
  84 MET   (  86-)  A      0
  88 PHE   (  90-)  A      0
  89 ASP   (  91-)  A      0
  91 PRO   (  93-)  A      0
  92 ALA   (  94-)  A      0
  93 ALA   (  95-)  A      0
  94 ASN   (  96-)  A      0
 111 GLN   ( 113-)  A      0
And so on for a total of 227 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 : 2.825

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!

 295 GLY   (  23-)  B   1.51   12

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]

 310 PRO   (  38-)  B    0.47 HIGH
 365 PRO   (  93-)  B    0.45 HIGH
 383 PRO   ( 111-)  B    0.46 HIGH
 491 PRO   ( 219-)  B    0.48 HIGH

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 521 MET   ( 249-)  B      CG   <->   559 HOH   ( 383 )  B      O    0.47    2.33  INTRA
 247 MET   ( 249-)  A    A SD   <->   255 VAL   ( 257-)  A      CG2  0.38    3.02  INTRA
 534 MET   ( 262-)  B    A SD   <->   559 HOH   ( 377 )  B      O    0.37    2.63  INTRA
 392 LEU   ( 120-)  B      CD1  <->   559 HOH   ( 540 )  B      O    0.30    2.50  INTRA
 275 ASN   (   3-)  B      N    <->   276 PRO   (   4-)  B      CD   0.25    2.75  INTRA BF
 528 ASP   ( 256-)  B      OD2  <->   559 HOH   ( 313 )  B      O    0.24    2.16  INTRA
   1 ASN   (   3-)  A      N    <->     2 PRO   (   4-)  A      CD   0.23    2.77  INTRA BF
 357 GLY   (  85-)  B      N    <->   390 HIS   ( 118-)  B      CE1  0.21    2.89  INTRA BL
 364 GLN   (  92-)  B      CG   <->   382 VAL   ( 110-)  B      CG1  0.20    3.00  INTRA
 197 LYS   ( 199-)  A      CE   <->   558 HOH   ( 486 )  A      O    0.17    2.63  INTRA BF
 266 ASP   ( 268-)  A      OD1  <->   558 HOH   ( 548 )  A      O    0.16    2.24  INTRA BF
  83 GLY   (  85-)  A      N    <->   116 HIS   ( 118-)  A      NE2  0.16    2.84  INTRA BL
 349 ASN   (  77-)  B      ND2  <->   363 ASP   (  91-)  B      OD2  0.15    2.55  INTRA
 160 GLU   ( 162-)  A      N    <->   558 HOH   ( 387 )  A      O    0.14    2.56  INTRA
 366 ALA   (  94-)  B      N    <->   559 HOH   ( 386 )  B      O    0.14    2.56  INTRA
 131 GLU   ( 133-)  A      OE2  <->   133 HIS   ( 135-)  A      NE2  0.13    2.57  INTRA BL
 336 ASN   (  64-)  B      OD1  <->   471 LYS   ( 199-)  B      NZ   0.12    2.58  INTRA
 320 GLU   (  48-)  B      OE2  <->   545 LYS   ( 273-)  B      NZ   0.10    2.60  INTRA BF
 115 HIS   ( 117-)  A      CD2  <->   133 HIS   ( 135-)  A      CE1  0.09    3.11  INTRA BL
  90 GLN   (  92-)  A      CG   <->   558 HOH   ( 494 )  A      O    0.08    2.72  INTRA
 260 MET   ( 262-)  A      SD   <->   558 HOH   ( 545 )  A      O    0.08    2.92  INTRA
 413 GLN   ( 141-)  B      O    <->   414 ASP   ( 142-)  B      C    0.08    2.52  INTRA
 471 LYS   ( 199-)  B      NZ   <->   559 HOH   ( 507 )  B      O    0.06    2.64  INTRA
 278 ASP   (   6-)  B      CB   <->   279 GLY   (   7-)  B      N    0.06    2.64  INTRA BF
 395 HIS   ( 123-)  B      NE2  <->   484 TYR   ( 212-)  B      OH   0.05    2.65  INTRA BL
 391 PHE   ( 119-)  B      CZ   <->   517 VAL   ( 245-)  B      CG2  0.05    3.15  INTRA
 139 GLN   ( 141-)  A      O    <->   140 ASP   ( 142-)  A      C    0.05    2.55  INTRA
 320 GLU   (  48-)  B      OE2  <->   545 LYS   ( 273-)  B      CE   0.04    2.76  INTRA BF
  80 LEU   (  82-)  A      O    <->   185 GLY   ( 187-)  A      N    0.04    2.66  INTRA BL
 390 HIS   ( 118-)  B      CD2  <->   529 VAL   ( 257-)  B    A O    0.04    2.76  INTRA BL
   8 TYR   (  10-)  A      OH   <->   558 HOH   ( 450 )  A      O    0.04    2.36  INTRA
 160 GLU   ( 162-)  A      OE1  <->   558 HOH   ( 387 )  A      O    0.04    2.36  INTRA BF
 558 HOH   ( 390 )  A      O    <->   558 HOH   ( 426 )  A      O    0.03    2.17  INTRA
 481 TYR   ( 209-)  B      CE1  <->   546 TYR   ( 274-)  B      CD1  0.03    3.17  INTRA BL
 224 LYS   ( 226-)  A      NZ   <->   558 HOH   ( 376 )  A      O    0.03    2.67  INTRA
  15 TRP   (  17-)  A      N    <->    16 PRO   (  18-)  A      CD   0.03    2.97  INTRA BL
 559 HOH   ( 448 )  B      O    <->   559 HOH   ( 543 )  B      O    0.03    2.17  INTRA BF
 394 GLU   ( 122-)  B      N    <->   405 GLU   ( 133-)  B      OE1  0.03    2.67  INTRA BL
 356 GLN   (  84-)  B      NE2  <->   528 ASP   ( 256-)  B      O    0.02    2.68  INTRA
 163 ASP   ( 165-)  A      OD1  <->   232 ARG   ( 234-)  A      NH1  0.02    2.68  INTRA
 240 LYS   ( 242-)  A      NZ   <->   244 ASP   ( 246-)  A      OD2  0.01    2.69  INTRA
 330 VAL   (  58-)  B      O    <->   559 HOH   ( 474 )  B      O    0.01    2.39  INTRA
 374 ILE   ( 102-)  B      N    <->   377 THR   ( 105-)  B      O    0.01    2.69  INTRA
 411 GLN   ( 139-)  B      NE2  <->   559 HOH   ( 451 )  B      O    0.01    2.69  INTRA

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   ( 141-)  A      -5.79
 413 GLN   ( 141-)  B      -5.76
 160 GLU   ( 162-)  A      -5.58
 434 GLU   ( 162-)  B      -5.53
  43 GLN   (  45-)  A      -5.31
 317 GLN   (  45-)  B      -5.18
 283 MET   (  11-)  B      -5.13
 324 ARG   (  52-)  B      -5.09
 473 GLN   ( 201-)  B      -5.08
 199 GLN   ( 201-)  A      -5.07
  82 GLN   (  84-)  A      -5.05
  50 ARG   (  52-)  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.

 332 LEU   (  60-)  B   -2.69
  81 GLU   (  83-)  A   -2.67
   8 TYR   (  10-)  A   -2.60

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.

 558 HOH   ( 506 )  A      O     45.99   16.01   12.14
 559 HOH   ( 412 )  B      O     11.92  -24.32    9.69
 559 HOH   ( 433 )  B      O      5.32    9.82   23.50
 559 HOH   ( 472 )  B      O     12.35  -15.49   30.12

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.

 558 HOH   ( 522 )  A      O
 559 HOH   ( 383 )  B      O
 559 HOH   ( 531 )  B      O
Metal-coordinating Histidine residue 113 fixed to   1
Metal-coordinating Histidine residue 115 fixed to   1
Metal-coordinating Histidine residue 133 fixed to   1
Metal-coordinating Histidine residue 387 fixed to   1
Metal-coordinating Histidine residue 389 fixed to   1
Metal-coordinating Histidine residue 407 fixed to   1
Metal-coordinating Histidine residue  11 fixed to   1
Metal-coordinating Histidine residue 285 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.

  82 GLN   (  84-)  A
 195 ASN   ( 197-)  A
 316 ASN   (  44-)  B
 341 GLN   (  69-)  B
 390 HIS   ( 118-)  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.

   3 ASN   (   5-)  A      N
  23 THR   (  25-)  A      N
  35 SER   (  37-)  A      OG
  37 ILE   (  39-)  A      N
 118 LEU   ( 120-)  A      N
 130 LEU   ( 132-)  A      N
 204 SER   ( 206-)  A      N
 216 THR   ( 218-)  A      N
 272 TYR   ( 274-)  A      OH
 277 ASN   (   5-)  B      N
 277 ASN   (   5-)  B      ND2
 311 ILE   (  39-)  B      N
 318 LEU   (  46-)  B      N
 392 LEU   ( 120-)  B      N
 404 LEU   ( 132-)  B      N
 478 SER   ( 206-)  B      N
Only metal coordination for   11 HIS  (  13-) A      NE2
Only metal coordination for  115 HIS  ( 117-) A      NE2
Only metal coordination for  133 HIS  ( 135-) A      ND1
Only metal coordination for  285 HIS  (  13-) B      NE2
Only metal coordination for  389 HIS  ( 117-) B      NE2
Only metal coordination for  407 HIS  ( 135-) B      ND1

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.

 250 HIS   ( 252-)  A      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 551  NA   ( 281-)  A     1.27   1.03 Scores about as good as CA

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.

 558 HOH   ( 297 )  A      O  0.98  K  4
 559 HOH   ( 315 )  B      O  0.97  K  5
 559 HOH   ( 375 )  B      O  1.00  K  4
 559 HOH   ( 392 )  B      O  1.09  K  4 NCS 1/1

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.

  38 ASP   (  40-)  A   H-bonding suggests Asn
 179 ASP   ( 181-)  A   H-bonding suggests Asn; but Alt-Rotamer
 233 GLU   ( 235-)  A   H-bonding suggests Gln
 373 GLU   ( 101-)  B   H-bonding suggests Gln; but Alt-Rotamer
 453 ASP   ( 181-)  B   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.594
  2nd generation packing quality :  -1.128
  Ramachandran plot appearance   :  -0.444
  chi-1/chi-2 rotamer normality  :  -0.629
  Backbone conformation          :  -0.565

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.773
  Bond angles                    :   0.922
  Omega angle restraints         :   0.514 (tight)
  Side chain planarity           :   0.697
  Improper dihedral distribution :   0.976
  B-factor distribution          :   0.572
  Inside/Outside distribution    :   0.962

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 : 1.86


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.773
  Bond angles                    :   0.922
  Omega angle restraints         :   0.514 (tight)
  Side chain planarity           :   0.697
  Improper dihedral distribution :   0.976
  B-factor distribution          :   0.572
  Inside/Outside distribution    :   0.962
==============

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.