WHAT IF Check report

This file was created 2012-11-04 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 pdb4faa.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 737 HAS   ( 603-)  A  -         Atom types
 738 PEO   ( 604-)  A  -         Size
 739 OLC   ( 605-)  C  -         OK
 740 OLC   ( 606-)  A  -         OK
 741 OLC   ( 614-)  A  -         OK
 742 OLC   ( 616-)  A  -         OK
 743 CUA   ( 201-)  B  -         Atom types
 744 OLC   ( 202-)  B  -         OK
 745 OLC   ( 203-)  C  -         OK
 746 OLC   ( 204-)  B  -         OK
 748 OLC   ( 101-)  C  -         OK
 749 A17   ( 615-)  A  -         OK
 750 A16   ( 613-)  A  -         OK
 751 A15   ( 612-)  A  -         OK
 752 A14   ( 611-)  A  -         OK
 753 A13   ( 610-)  A  -         OK
 754 A12   ( 609-)  A  -         OK
 755 A11   ( 608-)  A  -         OK
 756 A10   ( 607-)  A  -         OK

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

Note: Ramachandran plot

Chain identifier: C

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

Warning: Missing atoms

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

   1 GLU   (  13-)  A      CG
   1 GLU   (  13-)  A      CD
   1 GLU   (  13-)  A      OE1
   1 GLU   (  13-)  A      OE2
  45 ARG   (  57-)  A      CG
  45 ARG   (  57-)  A      CD
  45 ARG   (  57-)  A      NE
  45 ARG   (  57-)  A      CZ
  45 ARG   (  57-)  A      NH1
  45 ARG   (  57-)  A      NH2
 318 ARG   ( 330-)  A      CG
 318 ARG   ( 330-)  A      CD
 318 ARG   ( 330-)  A      NE
 318 ARG   ( 330-)  A      CZ
 318 ARG   ( 330-)  A      NH1
 318 ARG   ( 330-)  A      NH2
 325 ARG   ( 337-)  A      CD
 325 ARG   ( 337-)  A      NE
 325 ARG   ( 337-)  A      CZ
 325 ARG   ( 337-)  A      NH1
 325 ARG   ( 337-)  A      NH2
 477 PHE   ( 489-)  A      CG
 477 PHE   ( 489-)  A      CD1
 477 PHE   ( 489-)  A      CD2
 477 PHE   ( 489-)  A      CE1
And so on for a total of 53 lines.

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.

 380 LEU   ( 392-)  A    0.86
 390 TYR   ( 402-)  A    0.75
 691 GLN   ( 158-)  B    0.80

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

Note: B-factor plot

Chain identifier: C

Nomenclature related problems

Warning: Leucine nomenclature problem

The leucine residues listed in the table below have their C-delta-1 and C-delta-2 swapped.

 327 LEU   ( 339-)  A
 342 LEU   ( 354-)  A
 418 LEU   ( 430-)  A
 427 LEU   ( 439-)  A
 460 LEU   ( 472-)  A
 495 LEU   ( 522-)  A

Warning: Arginine nomenclature problem

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

  83 ARG   (  95-)  A
  88 ARG   ( 100-)  A
 157 ARG   ( 169-)  A
 313 ARG   ( 325-)  A
 315 ARG   ( 327-)  A
 406 ARG   ( 418-)  A
 438 ARG   ( 450-)  A
 499 ARG   ( 526-)  A
 533 ARG   ( 560-)  A
 592 ARG   (  59-)  B
 669 ARG   ( 136-)  B
 731 ARG   (  33-)  C

Warning: Tyrosine convention problem

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

  11 TYR   (  23-)  A
  54 TYR   (  66-)  A
 124 TYR   ( 136-)  A
 134 TYR   ( 146-)  A
 149 TYR   ( 161-)  A
 172 TYR   ( 184-)  A
 232 TYR   ( 244-)  A
 236 TYR   ( 248-)  A
 361 TYR   ( 373-)  A
 440 TYR   ( 452-)  A
 448 TYR   ( 460-)  A
 547 TYR   (  14-)  B
 612 TYR   (  79-)  B
 670 TYR   ( 137-)  B

Warning: Phenylalanine convention problem

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

  12 PHE   (  24-)  A
  17 PHE   (  29-)  A
  26 PHE   (  38-)  A
  49 PHE   (  61-)  A
 123 PHE   ( 135-)  A
 177 PHE   ( 189-)  A
 182 PHE   ( 194-)  A
 201 PHE   ( 213-)  A
 216 PHE   ( 228-)  A
 226 PHE   ( 238-)  A
 260 PHE   ( 272-)  A
 269 PHE   ( 281-)  A
 273 PHE   ( 285-)  A
 292 PHE   ( 304-)  A
 310 PHE   ( 322-)  A
 357 PHE   ( 369-)  A
 417 PHE   ( 429-)  A
 483 PHE   ( 508-)  A
 504 PHE   ( 531-)  A
 523 PHE   ( 550-)  A
 562 PHE   (  29-)  B
 619 PHE   (  86-)  B
 638 PHE   ( 105-)  B
 672 PHE   ( 139-)  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.

  38 ASP   (  50-)  A
 153 ASP   ( 165-)  A
 250 ASP   ( 262-)  A
 275 ASP   ( 287-)  A
 279 ASP   ( 291-)  A
 360 ASP   ( 372-)  A
 403 ASP   ( 415-)  A
 498 ASP   ( 525-)  A
 536 ASP   (   3-)  B
 644 ASP   ( 111-)  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.

  84 GLU   (  96-)  A
 116 GLU   ( 128-)  A
 191 GLU   ( 203-)  A
 309 GLU   ( 321-)  A
 537 GLU   (   4-)  B
 548 GLU   (  15-)  B
 584 GLU   (  51-)  B
 635 GLU   ( 102-)  B
 652 GLU   ( 119-)  B
 701 GLU   ( 168-)  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

 |  0.996470  0.000020  0.000188|
 |  0.000020  0.996920 -0.000096|
 |  0.000188 -0.000096  0.996725|
Proposed new scale matrix

 |  0.007003  0.000000  0.005371|
 |  0.000000  0.010205  0.000000|
 | -0.000003  0.000001  0.013305|
With corresponding cell

    A    = 142.781  B   =  97.987  C    =  94.712
    Alpha=  90.007  Beta= 127.478  Gamma=  89.997

The CRYST1 cell dimensions

    A    = 143.280  B   =  98.290  C    =  95.050
    Alpha=  90.000  Beta= 127.500  Gamma=  90.000

Variance: 266.344
(Under-)estimated Z-score: 12.028

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.

 119 VAL   ( 131-)  A      N    CA   C    95.26   -5.7
 120 LEU   ( 132-)  A     -C    N    CA  113.45   -4.6
 270 HIS   ( 282-)  A      CG   ND1  CE1 109.86    4.3
 271 HIS   ( 283-)  A      CG   ND1  CE1 109.82    4.2
 357 PHE   ( 369-)  A      N    CA   CB  100.98   -5.6
 358 THR   ( 370-)  A     -C    N    CA  129.40    4.3
 374 HIS   ( 386-)  A      CG   ND1  CE1 109.70    4.1
 428 HIS   ( 440-)  A      CG   ND1  CE1 109.65    4.1
 647 HIS   ( 114-)  B      CG   ND1  CE1 109.62    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.

  38 ASP   (  50-)  A
  83 ARG   (  95-)  A
  84 GLU   (  96-)  A
  88 ARG   ( 100-)  A
 116 GLU   ( 128-)  A
 153 ASP   ( 165-)  A
 157 ARG   ( 169-)  A
 191 GLU   ( 203-)  A
 250 ASP   ( 262-)  A
 275 ASP   ( 287-)  A
 279 ASP   ( 291-)  A
 309 GLU   ( 321-)  A
 313 ARG   ( 325-)  A
 315 ARG   ( 327-)  A
 360 ASP   ( 372-)  A
 403 ASP   ( 415-)  A
 406 ARG   ( 418-)  A
 438 ARG   ( 450-)  A
 498 ASP   ( 525-)  A
 499 ARG   ( 526-)  A
 533 ARG   ( 560-)  A
 536 ASP   (   3-)  B
 537 GLU   (   4-)  B
 548 GLU   (  15-)  B
 584 GLU   (  51-)  B
 592 ARG   (  59-)  B
 635 GLU   ( 102-)  B
 644 ASP   ( 111-)  B
 652 GLU   ( 119-)  B
 669 ARG   ( 136-)  B
 701 GLU   ( 168-)  B
 731 ARG   (  33-)  C

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.

 119 VAL   ( 131-)  A    5.71
 491 ARG   ( 518-)  A    4.08

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.416

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.

 643 PRO   ( 110-)  B    -2.8
 627 PRO   (  94-)  B    -2.7
 703 PRO   (   5-)  C    -2.6
 123 PHE   ( 135-)  A    -2.5
  18 LEU   (  30-)  A    -2.3
   4 PRO   (  16-)  A    -2.3
 389 LEU   ( 401-)  A    -2.2
 232 TYR   ( 244-)  A    -2.2
 440 TYR   ( 452-)  A    -2.2
 700 LYS   ( 167-)  B    -2.2
 366 THR   ( 378-)  A    -2.1
 720 PHE   (  22-)  C    -2.1
 487 ILE   ( 512-)  A    -2.1
 585 ARG   (  52-)  B    -2.1
 714 THR   (  16-)  C    -2.1
 674 ARG   ( 141-)  B    -2.1
 419 GLY   ( 431-)  A    -2.1
 394 PRO   ( 406-)  A    -2.1
 582 LYS   (  49-)  B    -2.1
 644 ASP   ( 111-)  B    -2.1
 413 VAL   ( 425-)  A    -2.1
 639 LYS   ( 106-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   4 PRO   (  16-)  A  omega poor
  17 PHE   (  29-)  A  omega poor
  34 TYR   (  46-)  A  omega poor
  36 ASN   (  48-)  A  Poor phi/psi
  52 SER   (  64-)  A  omega poor
  77 MET   (  89-)  A  omega poor
  85 LEU   (  97-)  A  omega poor
 115 ASN   ( 127-)  A  Poor phi/psi
 123 PHE   ( 135-)  A  Poor phi/psi
 125 PRO   ( 137-)  A  PRO omega poor
 136 GLY   ( 148-)  A  Poor phi/psi
 164 GLY   ( 176-)  A  omega poor
 189 VAL   ( 201-)  A  omega poor
 194 LEU   ( 206-)  A  omega poor
 206 GLY   ( 218-)  A  omega poor
 217 TRP   ( 229-)  A  omega poor
 219 THR   ( 231-)  A  omega poor
 228 LEU   ( 240-)  A  omega poor
 236 TYR   ( 248-)  A  omega poor
 262 LEU   ( 274-)  A  omega poor
 267 VAL   ( 279-)  A  omega poor
 270 HIS   ( 282-)  A  omega poor
 318 ARG   ( 330-)  A  omega poor
 319 GLY   ( 331-)  A  omega poor
 328 PRO   ( 340-)  A  Poor phi/psi
And so on for a total of 51 lines.

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.

  97 SER   ( 109-)  A    0.36
 138 SER   ( 150-)  A    0.36

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!

  39 ALA   (  51-)  A      0
  46 LEU   (  58-)  A      0
  47 LEU   (  59-)  A      0
  49 PHE   (  61-)  A      0
  51 GLN   (  63-)  A      0
  87 MET   (  99-)  A      0
  90 ASN   ( 102-)  A      0
  91 MET   ( 103-)  A      0
 117 ALA   ( 129-)  A      0
 118 THR   ( 130-)  A      0
 120 LEU   ( 132-)  A      0
 121 TYR   ( 133-)  A      0
 123 PHE   ( 135-)  A      0
 124 TYR   ( 136-)  A      0
 125 PRO   ( 137-)  A      0
 126 PRO   ( 138-)  A      0
 127 LEU   ( 139-)  A      0
 130 HIS   ( 142-)  A      0
 163 PRO   ( 175-)  A      0
 195 PHE   ( 207-)  A      0
 196 LEU   ( 208-)  A      0
 201 PHE   ( 213-)  A      0
 229 LEU   ( 241-)  A      0
 237 THR   ( 249-)  A      0
 249 SER   ( 261-)  A      0
And so on for a total of 183 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.503

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].

  41 PRO   (  53-)  A   104.4 envelop C-beta (108 degrees)
  81 PRO   (  93-)  A  -117.6 half-chair C-delta/C-gamma (-126 degrees)
 111 PRO   ( 123-)  A  -121.1 half-chair C-delta/C-gamma (-126 degrees)
 126 PRO   ( 138-)  A    50.6 half-chair C-delta/C-gamma (54 degrees)
 222 PRO   ( 234-)  A  -122.6 half-chair C-delta/C-gamma (-126 degrees)
 296 PRO   ( 308-)  A  -124.5 half-chair C-delta/C-gamma (-126 degrees)
 328 PRO   ( 340-)  A    47.5 half-chair C-delta/C-gamma (54 degrees)
 627 PRO   (  94-)  B   -63.1 envelop C-beta (-72 degrees)
 631 PRO   (  98-)  B    49.1 half-chair C-delta/C-gamma (54 degrees)
 643 PRO   ( 110-)  B   -64.9 envelop C-beta (-72 degrees)
 703 PRO   (   5-)  C   -62.4 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 221 HIS   ( 233-)  A      NE2 <->  225 TYR   ( 237-)  A      CE2    1.00    2.10  INTRA BL
 221 HIS   ( 233-)  A      CD2 <->  225 TYR   ( 237-)  A      CE2    0.60    2.60  INTRA BL
 584 GLU   (  51-)  B      OE1 <->  758 HOH   ( 309 )  B      O      0.51    1.89  INTRA
 217 TRP   ( 229-)  A      CE3 <->  271 HIS   ( 283-)  A      CD2    0.39    2.81  INTRA BL
 221 HIS   ( 233-)  A      NE2 <->  225 TYR   ( 237-)  A      CZ     0.37    2.73  INTRA BL
 303 THR   ( 315-)  A      OG1 <->  757 HOH   ( 726 )  A      O      0.36    2.04  INTRA
 641 THR   ( 108-)  B      OG1 <->  758 HOH   ( 314 )  B      O      0.34    2.06  INTRA BL
 242 GLN   ( 254-)  A      NE2 <->  482 PRO   ( 507-)  A      CG     0.29    2.81  INTRA
 757 HOH   ( 722 )  A      O   <->  757 HOH   ( 723 )  A      O      0.28    1.92  INTRA
 491 ARG   ( 518-)  A      N   <->  492 ARG   ( 519-)  A      N      0.28    2.32  INTRA BF
 374 HIS   ( 386-)  A      NE2 <->  747 HEM   ( 602-)  A      NA     0.27    2.73  INTRA BL
 579 PRO   (  46-)  B      O   <->  758 HOH   ( 340 )  B      O      0.24    2.16  INTRA BL
 644 ASP   ( 111-)  B      OD1 <->  645 VAL   ( 112-)  B      N      0.23    2.37  INTRA BL
 279 ASP   ( 291-)  A      N   <->  757 HOH   ( 730 )  A      O      0.23    2.47  INTRA
 279 ASP   ( 291-)  A      CB  <->  757 HOH   ( 730 )  A      O      0.20    2.60  INTRA
  40 TYR   (  52-)  A      N   <->   41 PRO   (  53-)  A      CD     0.19    2.81  INTRA BL
 584 GLU   (  51-)  B      N   <->  664 GLU   ( 131-)  B      OE2    0.18    2.52  INTRA
 374 HIS   ( 386-)  A      CE1 <->  747 HEM   ( 602-)  A      NA     0.18    2.92  INTRA BL
 661 LEU   ( 128-)  B      N   <->  758 HOH   ( 318 )  B      O      0.17    2.53  INTRA BL
 441 ILE   ( 453-)  A      C   <->  443 GLN   ( 455-)  A      N      0.17    2.73  INTRA BL
 265 THR   ( 277-)  A      N   <->  266 PRO   ( 278-)  A      CD     0.17    2.83  INTRA BL
 162 ASN   ( 174-)  A      ND2 <->  757 HOH   ( 742 )  A      O      0.16    2.54  INTRA BF
 221 HIS   ( 233-)  A      CE1 <->  225 TYR   ( 237-)  A      CE2    0.16    3.04  INTRA BL
 628 ILE   (  95-)  B      O   <->  698 VAL   ( 165-)  B      N      0.14    2.56  INTRA BL
 735 GLY   (  34-)  C      O'' <->  759 HOH   ( 201 )  C      O      0.13    2.27  INTRA
And so on for a total of 113 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 674 ARG   ( 141-)  B      -7.26
 592 ARG   (  59-)  B      -6.49
 491 ARG   ( 518-)  A      -6.46
 315 ARG   ( 327-)  A      -6.03
 673 LYS   ( 140-)  B      -5.98
  51 GLN   (  63-)  A      -5.73
 443 GLN   ( 455-)  A      -5.47
 242 GLN   ( 254-)  A      -5.36
 437 ARG   ( 449-)  A      -5.28
 203 LEU   ( 215-)  A      -5.21
 585 ARG   (  52-)  B      -5.18
   3 TYR   (  15-)  A      -5.03
  88 ARG   ( 100-)  A      -5.02

Warning: Abnormal packing environment for sequential residues

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

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

 203 LEU   ( 215-)  A       205 - GLU    217- ( A)         -4.67

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

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: C

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.

 447 ALA   ( 459-)  A   -2.98
 120 LEU   ( 132-)  A   -2.84
 603 ALA   (  70-)  B   -2.53
 529 VAL   ( 556-)  A   -2.52

Warning: Abnormal packing Z-score for sequential residues

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

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

 360 ASP   ( 372-)  A     -  363 VAL   ( 375-)  A        -1.85
 486 VAL   ( 511-)  A     -  489 GLY   ( 514-)  A        -1.72

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

Note: Second generation quality Z-score plot

Chain identifier: C

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.

 758 HOH   ( 307 )  B      O     29.11   -0.16  -36.46

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.

  64 ASN   (  76-)  A
 443 GLN   ( 455-)  A
 655 ASN   ( 122-)  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.

   6 LYS   (  18-)  A      N
  29 PHE   (  41-)  A      N
  30 GLN   (  42-)  A      NE2
  52 SER   (  64-)  A      N
  53 TYR   (  65-)  A      OH
  64 ASN   (  76-)  A      ND2
  90 ASN   ( 102-)  A      N
  98 TRP   ( 110-)  A      NE1
 117 ALA   ( 129-)  A      N
 118 THR   ( 130-)  A      N
 156 ARG   ( 168-)  A      NH1
 187 GLY   ( 199-)  A      N
 225 TYR   ( 237-)  A      OH
 246 LYS   ( 258-)  A      N
 249 SER   ( 261-)  A      N
 273 PHE   ( 285-)  A      N
 278 ILE   ( 290-)  A      N
 297 SER   ( 309-)  A      N
 323 TRP   ( 335-)  A      N
 324 ILE   ( 336-)  A      N
 354 ASN   ( 366-)  A      ND2
 357 PHE   ( 369-)  A      N
 359 LEU   ( 371-)  A      N
 376 GLN   ( 388-)  A      NE2
 379 SER   ( 391-)  A      OG
 414 TRP   ( 426-)  A      NE1
 437 ARG   ( 449-)  A      NH2
 438 ARG   ( 450-)  A      N
 438 ARG   ( 450-)  A      NE
 438 ARG   ( 450-)  A      NH2
 453 VAL   ( 465-)  A      N
 494 VAL   ( 521-)  A      N
 518 THR   ( 545-)  A      N
 534 LEU   ( 561-)  A      N
 535 TRP   ( 562-)  A      N
 592 ARG   (  59-)  B      N
 611 GLN   (  78-)  B      N
 653 GLY   ( 120-)  B      N
 655 ASN   ( 122-)  B      ND2
 674 ARG   ( 141-)  B      NH1
 685 TYR   ( 152-)  B      N
 686 CYS   ( 153-)  B      N
 687 GLY   ( 154-)  B      N
 689 GLY   ( 156-)  B      N
 701 GLU   ( 168-)  B      N
 731 ARG   (  33-)  C      NE
Only metal coordination for   60 HIS  (  72-) A      NE2
Only metal coordination for  221 HIS  ( 233-) A      ND1
Only metal coordination for  270 HIS  ( 282-) A      NE2
Only metal coordination for  271 HIS  ( 283-) A      NE2
Only metal coordination for  372 HIS  ( 384-) A      NE2
Only metal coordination for  374 HIS  ( 386-) A      NE2
Only metal coordination for  647 HIS  ( 114-) B      ND1
Only metal coordination for  690 HIS  ( 157-) 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.

  30 GLN   (  42-)  A      OE1
 191 GLU   ( 203-)  A      OE1
 360 ASP   ( 372-)  A      OD1
 360 ASP   ( 372-)  A      OD2
 364 HIS   ( 376-)  A      ND1
 376 GLN   ( 388-)  A      OE1
 428 HIS   ( 440-)  A      NE2
 458 ASN   ( 470-)  A      OD1
 548 GLU   (  15-)  B      OE1
 655 ASN   ( 122-)  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.

 758 HOH   ( 309 )  B      O  1.00 NA  5 *2 ION-B
 758 HOH   ( 310 )  B      O  1.07 NA  4 *2

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.

 309 GLU   ( 321-)  A   H-bonding suggests Gln; but Alt-Rotamer
 664 GLU   ( 131-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.321
  2nd generation packing quality :  -0.860
  Ramachandran plot appearance   :  -3.416 (poor)
  chi-1/chi-2 rotamer normality  :  -2.783
  Backbone conformation          :   0.645

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.467 (tight)
  Bond angles                    :   0.607 (tight)
  Omega angle restraints         :   1.364 (loose)
  Side chain planarity           :   0.401 (tight)
  Improper dihedral distribution :   0.688
  B-factor distribution          :   0.979
  Inside/Outside distribution    :   1.149

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :   1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.467 (tight)
  Bond angles                    :   0.607 (tight)
  Omega angle restraints         :   1.364 (loose)
  Side chain planarity           :   0.401 (tight)
  Improper dihedral distribution :   0.688
  B-factor distribution          :   0.979
  Inside/Outside distribution    :   1.149
==============

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

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      refinement,
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Bond lengths and angles, DNA/RNA
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DSSP
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      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
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Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.