WHAT IF Check report

This file was created 2011-12-13 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 pdb2cwx.ent

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

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

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

 414 ALA   ( 424-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: E

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'.

 414 ALA   ( 424-)  A      O

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: E

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.

 227 ARG   ( 237-)  A
 351 ARG   ( 361-)  A
 642 ARG   ( 237-)  E

Warning: Tyrosine convention problem

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

   4 TYR   (  11-)  A
  12 TYR   (  19-)  A
  24 TYR   (  31-)  A
  64 TYR   (  74-)  A
  72 TYR   (  82-)  A
  78 TYR   (  88-)  A
 165 TYR   ( 175-)  A
 197 TYR   ( 207-)  A
 238 TYR   ( 248-)  A
 313 TYR   ( 323-)  A
 416 TYR   (  11-)  E
 424 TYR   (  19-)  E
 436 TYR   (  31-)  E
 479 TYR   (  74-)  E
 487 TYR   (  82-)  E
 493 TYR   (  88-)  E
 534 TYR   ( 129-)  E
 580 TYR   ( 175-)  E
 612 TYR   ( 207-)  E
 653 TYR   ( 248-)  E
 728 TYR   ( 323-)  E

Warning: Phenylalanine convention problem

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

   7 PHE   (  14-)  A
  63 PHE   (  73-)  A
 100 PHE   ( 110-)  A
 113 PHE   ( 123-)  A
 136 PHE   ( 146-)  A
 181 PHE   ( 191-)  A
 184 PHE   ( 194-)  A
 334 PHE   ( 344-)  A
 353 PHE   ( 363-)  A
 419 PHE   (  14-)  E
 478 PHE   (  73-)  E
 515 PHE   ( 110-)  E
 528 PHE   ( 123-)  E
 538 PHE   ( 133-)  E
 551 PHE   ( 146-)  E
 596 PHE   ( 191-)  E
 599 PHE   ( 194-)  E
 749 PHE   ( 344-)  E
 768 PHE   ( 363-)  E

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.

   9 ASP   (  16-)  A
  17 ASP   (  24-)  A
 178 ASP   ( 188-)  A
 201 ASP   ( 211-)  A
 321 ASP   ( 331-)  A
 370 ASP   ( 380-)  A
 418 ASP   (  13-)  E
 421 ASP   (  16-)  E
 429 ASP   (  24-)  E
 556 ASP   ( 151-)  E
 593 ASP   ( 188-)  E
 616 ASP   ( 211-)  E
 736 ASP   ( 331-)  E
 785 ASP   ( 380-)  E

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.

   2 GLU   (   9-)  A
  18 GLU   (  25-)  A
  22 GLU   (  29-)  A
  34 GLU   (  41-)  A
  53 GLU   (  63-)  A
  70 GLU   (  80-)  A
 118 GLU   ( 128-)  A
 166 GLU   ( 176-)  A
 179 GLU   ( 189-)  A
 190 GLU   ( 200-)  A
 191 GLU   ( 201-)  A
 234 GLU   ( 244-)  A
 256 GLU   ( 266-)  A
 388 GLU   ( 398-)  A
 401 GLU   ( 411-)  A
 446 GLU   (  41-)  E
 454 GLU   (  49-)  E
 468 GLU   (  63-)  E
 485 GLU   (  80-)  E
 533 GLU   ( 128-)  E
 573 GLU   ( 168-)  E
 581 GLU   ( 176-)  E
 605 GLU   ( 200-)  E
 649 GLU   ( 244-)  E
 816 GLU   ( 411-)  E

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

 |  0.998684 -0.000701 -0.000270|
 | -0.000701  0.998324 -0.000124|
 | -0.000270 -0.000124  0.998709|
Proposed new scale matrix

 |  0.006954  0.000005  0.000002|
 |  0.000005  0.006957  0.000000|
 |  0.000003  0.000001  0.009873|
With corresponding cell

    A    = 143.799  B   = 143.747  C    = 101.289
    Alpha=  90.008  Beta=  90.031  Gamma=  90.080

The CRYST1 cell dimensions

    A    = 143.992  B   = 143.992  C    = 101.417
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 60.049
(Under-)estimated Z-score: 5.711

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.

 192 ARG   ( 202-)  A      CG   CD   NE  118.23    4.5
 221 VAL   ( 231-)  A      N    CA   CB  117.81    4.3
 221 VAL   ( 231-)  A      C    CA   CB   99.87   -5.4
 238 TYR   ( 248-)  A      CA   CB   CG  122.38    4.6
 460 TRP   (  55-)  E      N    CA   C   123.08    4.2
 687 HIS   ( 282-)  E      CG   ND1  CE1 109.64    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.

   2 GLU   (   9-)  A
   9 ASP   (  16-)  A
  17 ASP   (  24-)  A
  18 GLU   (  25-)  A
  22 GLU   (  29-)  A
  34 GLU   (  41-)  A
  53 GLU   (  63-)  A
  70 GLU   (  80-)  A
 118 GLU   ( 128-)  A
 166 GLU   ( 176-)  A
 178 ASP   ( 188-)  A
 179 GLU   ( 189-)  A
 190 GLU   ( 200-)  A
 191 GLU   ( 201-)  A
 201 ASP   ( 211-)  A
 227 ARG   ( 237-)  A
 234 GLU   ( 244-)  A
 256 GLU   ( 266-)  A
 321 ASP   ( 331-)  A
 351 ARG   ( 361-)  A
 370 ASP   ( 380-)  A
 388 GLU   ( 398-)  A
 401 GLU   ( 411-)  A
 418 ASP   (  13-)  E
 421 ASP   (  16-)  E
 429 ASP   (  24-)  E
 446 GLU   (  41-)  E
 454 GLU   (  49-)  E
 468 GLU   (  63-)  E
 485 GLU   (  80-)  E
 533 GLU   ( 128-)  E
 556 ASP   ( 151-)  E
 573 GLU   ( 168-)  E
 581 GLU   ( 176-)  E
 593 ASP   ( 188-)  E
 605 GLU   ( 200-)  E
 616 ASP   ( 211-)  E
 642 ARG   ( 237-)  E
 649 GLU   ( 244-)  E
 736 ASP   ( 331-)  E
 785 ASP   ( 380-)  E
 816 GLU   ( 411-)  E

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.

 614 VAL   ( 209-)  E      CA    -6.1    24.42    33.23
The average deviation= 1.069

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.

 460 TRP   (  55-)  E    4.49
 658 ILE   ( 253-)  E    4.05

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.

 299 GLN   ( 309-)  A    4.15

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.

 461 THR   (  56-)  E    -3.0
 463 LEU   (  58-)  E    -2.8
 721 VAL   ( 316-)  E    -2.6
 399 SER   ( 409-)  A    -2.3
 464 TRP   (  59-)  E    -2.2
 754 GLY   ( 349-)  E    -2.2
 568 MET   ( 163-)  E    -2.1
 567 LYS   ( 162-)  E    -2.1
 327 TRP   ( 337-)  A    -2.1
 460 TRP   (  55-)  E    -2.1
 711 GLY   ( 306-)  E    -2.0
  95 VAL   ( 105-)  A    -2.0
 510 VAL   ( 105-)  E    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  23 TYR   (  30-)  A  omega poor
  44 SER   (  51-)  A  Poor phi/psi
  82 LEU   (  92-)  A  omega poor
 139 VAL   ( 149-)  A  omega poor
 150 LYS   ( 160-)  A  PRO omega poor
 153 MET   ( 163-)  A  omega poor
 155 TRP   ( 165-)  A  omega poor
 182 THR   ( 192-)  A  Poor phi/psi
 220 PRO   ( 230-)  A  omega poor
 238 TYR   ( 248-)  A  omega poor
 242 ASP   ( 252-)  A  omega poor
 271 MET   ( 281-)  A  Poor phi/psi
 296 GLY   ( 306-)  A  omega poor
 305 ALA   ( 315-)  A  omega poor
 306 VAL   ( 316-)  A  omega poor
 309 MET   ( 319-)  A  omega poor
 328 GLU   ( 338-)  A  Poor phi/psi
 357 LEU   ( 367-)  A  omega poor
 435 TYR   (  30-)  E  omega poor
 456 SER   (  51-)  E  Poor phi/psi
 459 THR   (  54-)  E  omega poor
 460 TRP   (  55-)  E  Poor phi/psi, omega poor
 462 THR   (  57-)  E  Poor phi/psi
 463 LEU   (  58-)  E  omega poor
 464 TRP   (  59-)  E  Poor phi/psi
 465 LYS   (  60-)  E  Poor phi/psi, omega poor
 467 PRO   (  62-)  E  omega poor
 497 LEU   (  92-)  E  omega poor
 554 VAL   ( 149-)  E  omega poor
 565 LYS   ( 160-)  E  PRO omega poor
 570 TRP   ( 165-)  E  omega poor
 586 GLY   ( 181-)  E  Poor phi/psi
 589 LEU   ( 184-)  E  omega poor
 597 THR   ( 192-)  E  Poor phi/psi
 635 PRO   ( 230-)  E  omega poor
 653 TYR   ( 248-)  E  omega poor
 686 MET   ( 281-)  E  Poor phi/psi
 711 GLY   ( 306-)  E  omega poor
 721 VAL   ( 316-)  E  Poor phi/psi, omega poor
 722 GLY   ( 317-)  E  Poor phi/psi
 723 LYS   ( 318-)  E  omega poor
 725 ALA   ( 320-)  E  Poor phi/psi
 727 ASN   ( 322-)  E  omega poor
 743 GLU   ( 338-)  E  Poor phi/psi
 772 LEU   ( 367-)  E  omega poor
 782 GLY   ( 377-)  E  Poor phi/psi
 810 LYS   ( 405-)  E  omega poor
 821 LEU   ( 416-)  E  omega poor
 chi-1/chi-2 correlation Z-score : -1.334

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.

 249 SER   ( 259-)  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!

   8 VAL   (  15-)  A      0
   9 ASP   (  16-)  A      0
  10 LEU   (  17-)  A      0
  25 PHE   (  32-)  A      0
  28 ASN   (  35-)  A      0
  43 SER   (  50-)  A      0
  44 SER   (  51-)  A      0
  45 ILE   (  52-)  A      0
  46 GLY   (  53-)  A      0
  47 THR   (  54-)  A      0
  48 LEU   (  58-)  A      0
  49 TRP   (  59-)  A      0
  59 MET   (  69-)  A      0
  63 PHE   (  73-)  A      0
  66 GLU   (  76-)  A      0
  70 GLU   (  80-)  A      0
  85 GLU   (  95-)  A      0
  96 ALA   ( 106-)  A      0
  98 ASN   ( 108-)  A      0
 102 MET   ( 112-)  A      0
 107 ASN   ( 117-)  A      0
 112 ASP   ( 122-)  A      0
 122 HIS   ( 132-)  A      0
 123 PHE   ( 133-)  A      0
 126 PRO   ( 136-)  A      0
And so on for a total of 269 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!

 754 GLY   ( 349-)  E   2.71   10
 307 GLY   ( 317-)  A   1.78   11
  32 PRO   (  39-)  A   1.54   11

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]

  52 PRO   (  62-)  A    0.19 LOW
 115 PRO   ( 125-)  A    0.19 LOW
 143 PRO   ( 153-)  A    0.04 LOW
 185 PRO   ( 195-)  A    0.07 LOW
 279 PRO   ( 289-)  A    0.20 LOW
 372 PRO   ( 382-)  A    0.14 LOW
 426 PRO   (  21-)  E    0.07 LOW
 787 PRO   ( 382-)  E    0.05 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].

 467 PRO   (  62-)  E    49.8 half-chair C-delta/C-gamma (54 degrees)
 750 PRO   ( 345-)  E    52.3 half-chair C-delta/C-gamma (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.

 568 MET   ( 163-)  E      SD  <->  595 ASN   ( 190-)  E      ND2    0.70    2.60  INTRA BF
 593 ASP   ( 188-)  E      OD2 <->  595 ASN   ( 190-)  E      ND2    0.49    2.21  INTRA
 446 GLU   (  41-)  E      OE2 <->  450 ARG   (  45-)  E      NH1    0.39    2.31  INTRA BF
 268 HIS   ( 278-)  A      CD2 <->  301 HIS   ( 311-)  A      CE1    0.32    2.88  INTRA BF
 238 TYR   ( 248-)  A      OH  <->  299 GLN   ( 309-)  A      NE2    0.31    2.39  INTRA BL
 500 GLU   (  95-)  E      O   <->  824 HOH   ( 585 )  E      O      0.29    2.11  INTRA
 653 TYR   ( 248-)  E      OH  <->  714 GLN   ( 309-)  E      NE2    0.29    2.41  INTRA BL
  34 GLU   (  41-)  A      OE2 <->   38 ARG   (  45-)  A      NH1    0.27    2.43  INTRA BF
 468 GLU   (  63-)  E      O   <->  824 HOH   ( 535 )  E      O      0.26    2.14  INTRA BF
 394 GLU   ( 404-)  A      OE2 <->  397 LYS   ( 407-)  A      NZ     0.22    2.48  INTRA
 608 VAL   ( 203-)  E      CG1 <->  649 GLU   ( 244-)  E      CG     0.18    3.02  INTRA
 306 VAL   ( 316-)  A      CG1 <->  307 GLY   ( 317-)  A      N      0.15    2.85  INTRA BF
 304 THR   ( 314-)  A      CG2 <->  338 SER   ( 348-)  A      N      0.15    2.95  INTRA BF
 222 ASN   ( 232-)  A      ND2 <->  824 HOH   ( 605 )  E      O      0.15    2.55  INTRA
 209 GLU   ( 219-)  A      OE1 <->  823 HOH   ( 633 )  A      O      0.15    2.25  INTRA BF
 518 LYS   ( 113-)  E      NZ  <->  824 HOH   ( 586 )  E      O      0.14    2.56  INTRA BF
 460 TRP   (  55-)  E      CZ3 <->  463 LEU   (  58-)  E      O      0.14    2.66  INTRA BF
 317 LYS   ( 327-)  A      NZ  <->  321 ASP   ( 331-)  A      OD1    0.13    2.57  INTRA
 631 ASN   ( 226-)  E      ND2 <->  633 THR   ( 228-)  E      CB     0.13    2.97  INTRA BL
 761 MET   ( 356-)  E      N   <->  762 PRO   ( 357-)  E      CD     0.13    2.87  INTRA
 814 SER   ( 409-)  E      OG  <->  824 HOH   ( 600 )  E      O      0.12    2.28  INTRA BF
 823 HOH   ( 568 )  A      O   <->  824 HOH   ( 532 )  E      O      0.11    2.29  INTRA BF
 346 MET   ( 356-)  A      N   <->  347 PRO   ( 357-)  A      CD     0.10    2.90  INTRA BL
 216 ASN   ( 226-)  A      ND2 <->  218 THR   ( 228-)  A      OG1    0.10    2.60  INTRA BL
 687 HIS   ( 282-)  E      CG  <->  688 ALA   ( 283-)  E      N      0.10    2.90  INTRA
And so on for a total of 54 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: E

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.

 724 MET   ( 319-)  E      -6.31
 413 LYS   ( 423-)  A      -6.26
  16 ARG   (  23-)  A      -6.16
  50 LYS   (  60-)  A      -6.06
 277 ARG   ( 287-)  A      -5.98
 463 LEU   (  58-)  E      -5.95
 428 ARG   (  23-)  E      -5.91
 692 ARG   ( 287-)  E      -5.89
 425 GLU   (  20-)  E      -5.81
 326 LYS   ( 336-)  A      -5.80
  13 GLU   (  20-)  A      -5.68
 465 LYS   (  60-)  E      -5.60
 741 LYS   ( 336-)  E      -5.39
 309 MET   ( 319-)  A      -5.32
 482 LYS   (  77-)  E      -5.29
 124 LYS   ( 134-)  A      -5.26
 555 LYS   ( 150-)  E      -5.22
 723 LYS   ( 318-)  E      -5.18
  67 LYS   (  77-)  A      -5.09
 233 ASN   ( 243-)  A      -5.08
 648 ASN   ( 243-)  E      -5.08
 140 LYS   ( 150-)  A      -5.07
 388 GLU   ( 398-)  A      -5.05
 565 LYS   ( 160-)  E      -5.00

Warning: Abnormal packing environment for sequential residues

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

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

 168 TRP   ( 178-)  A       170 - GLY    180- ( A)         -4.21
 462 THR   (  57-)  E       466 - LEU     61- ( E)         -4.88
 583 TRP   ( 178-)  E       585 - GLY    180- ( E)         -4.17

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: E

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.

 273 ALA   ( 283-)  A   -2.82
 497 LEU   (  92-)  E   -2.81
 688 ALA   ( 283-)  E   -2.78
  82 LEU   (  92-)  A   -2.66

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: E

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.

 823 HOH   ( 591 )  A      O     61.90   53.45   62.32
 823 HOH   ( 649 )  A      O    104.65   31.61   44.01
 823 HOH   ( 666 )  A      O     88.72   14.52   46.62
 824 HOH   ( 432 )  E      O     51.60   19.20   32.02
 824 HOH   ( 464 )  E      O     40.70   25.46   33.26
 824 HOH   ( 544 )  E      O     89.32   23.18   20.46
 824 HOH   ( 556 )  E      O     39.98   46.67    8.69
 824 HOH   ( 629 )  E      O     55.58   13.64   22.27

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.

 823 HOH   ( 439 )  A      O
 823 HOH   ( 480 )  A      O
 823 HOH   ( 483 )  A      O
 823 HOH   ( 484 )  A      O
 823 HOH   ( 491 )  A      O
 823 HOH   ( 495 )  A      O
 823 HOH   ( 500 )  A      O
 823 HOH   ( 520 )  A      O
 823 HOH   ( 522 )  A      O
 823 HOH   ( 533 )  A      O
 823 HOH   ( 535 )  A      O
 823 HOH   ( 548 )  A      O
 823 HOH   ( 550 )  A      O
 823 HOH   ( 558 )  A      O
 823 HOH   ( 559 )  A      O
 823 HOH   ( 569 )  A      O
 823 HOH   ( 572 )  A      O
 823 HOH   ( 578 )  A      O
 823 HOH   ( 584 )  A      O
 823 HOH   ( 586 )  A      O
 823 HOH   ( 591 )  A      O
 823 HOH   ( 594 )  A      O
 823 HOH   ( 602 )  A      O
 823 HOH   ( 603 )  A      O
 823 HOH   ( 612 )  A      O
And so on for a total of 60 lines.

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.

  28 ASN   (  35-)  A
  90 GLN   ( 100-)  A
 114 HIS   ( 124-)  A
 122 HIS   ( 132-)  A
 216 ASN   ( 226-)  A
 233 ASN   ( 243-)  A
 440 ASN   (  35-)  E
 505 GLN   ( 100-)  E
 529 HIS   ( 124-)  E
 537 HIS   ( 132-)  E
 631 ASN   ( 226-)  E
 648 ASN   ( 243-)  E
 696 HIS   ( 291-)  E
 727 ASN   ( 322-)  E

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.

   4 TYR   (  11-)  A      N
  30 VAL   (  37-)  A      N
 108 LEU   ( 118-)  A      N
 150 LYS   ( 160-)  A      N
 153 MET   ( 163-)  A      N
 155 TRP   ( 165-)  A      N
 186 PHE   ( 196-)  A      N
 187 ASN   ( 197-)  A      ND2
 197 TYR   ( 207-)  A      OH
 219 GLY   ( 229-)  A      N
 238 TYR   ( 248-)  A      OH
 299 GLN   ( 309-)  A      NE2
 305 ALA   ( 315-)  A      N
 311 GLY   ( 321-)  A      N
 315 GLU   ( 325-)  A      N
 320 ASN   ( 330-)  A      ND2
 339 GLY   ( 349-)  A      N
 342 HIS   ( 352-)  A      N
 402 LEU   ( 412-)  A      N
 442 VAL   (  37-)  E      N
 460 TRP   (  55-)  E      N
 462 THR   (  57-)  E      OG1
 532 TYR   ( 127-)  E      OH
 565 LYS   ( 160-)  E      N
 568 MET   ( 163-)  E      N
 569 GLY   ( 164-)  E      N
 570 TRP   ( 165-)  E      N
 595 ASN   ( 190-)  E      ND2
 601 PHE   ( 196-)  E      N
 602 ASN   ( 197-)  E      ND2
 603 ARG   ( 198-)  E      NE
 634 GLY   ( 229-)  E      N
 637 ASN   ( 232-)  E      ND2
 653 TYR   ( 248-)  E      OH
 714 GLN   ( 309-)  E      NE2
 720 ALA   ( 315-)  E      N
 724 MET   ( 319-)  E      N
 725 ALA   ( 320-)  E      N
 735 ASN   ( 330-)  E      ND2
 753 SER   ( 348-)  E      N
 757 HIS   ( 352-)  E      N
 795 ARG   ( 390-)  E      NH1

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.

 242 ASP   ( 252-)  A      OD1
 360 GLN   ( 370-)  A      OE1
 500 GLU   (  95-)  E      OE2
 606 GLU   ( 201-)  E      OE2
 657 ASP   ( 252-)  E      OD1
 657 ASP   ( 252-)  E      OD2

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.

 823 HOH   ( 541 )  A      O  0.99  K  5
 823 HOH   ( 595 )  A      O  1.01  K  4 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.

   6 ASP   (  13-)  A   H-bonding suggests Asn
 201 ASP   ( 211-)  A   H-bonding suggests Asn; but Alt-Rotamer
 204 GLU   ( 214-)  A   H-bonding suggests Gln; but Alt-Rotamer
 242 ASP   ( 252-)  A   H-bonding suggests Asn
 657 ASP   ( 252-)  E   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.088
  2nd generation packing quality :  -0.580
  Ramachandran plot appearance   :  -0.628
  chi-1/chi-2 rotamer normality  :  -1.334
  Backbone conformation          :   0.027

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.651 (tight)
  Bond angles                    :   0.796
  Omega angle restraints         :   1.182
  Side chain planarity           :   0.859
  Improper dihedral distribution :   0.917
  B-factor distribution          :   0.476
  Inside/Outside distribution    :   0.984

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.651 (tight)
  Bond angles                    :   0.796
  Omega angle restraints         :   1.182
  Side chain planarity           :   0.859
  Improper dihedral distribution :   0.917
  B-factor distribution          :   0.476
  Inside/Outside distribution    :   0.984
==============

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.