WHAT IF Check report

This file was created 2012-01-05 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 pdb1od0.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  94.313  B   =  94.547  C    = 113.064
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  94.313  B   =  94.547  C    = 113.064
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  94.547  B   =  94.313  C    = 113.064
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000 -1.000000  0.000000|
 |  1.000000  0.000000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: P 21 21 21

Bravais type of conventional cell is: P

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
but NCS matrices (but not the unitary matrix) are found labeled `dont use`: 1
SEQRES multiplicity agrees with number of MTRIX matrices labeled `dont use`
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Missing atoms

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

   3 LYS   (   5-)  A      CE
   3 LYS   (   5-)  A      NZ
  68 LYS   (  70-)  A      CE
  68 LYS   (  70-)  A      NZ
 146 ARG   ( 148-)  A      CZ
 146 ARG   ( 148-)  A      NH1
 146 ARG   ( 148-)  A      NH2
 183 ARG   ( 185-)  A      CZ
 183 ARG   ( 185-)  A      NH1
 183 ARG   ( 185-)  A      NH2
 263 GLU   ( 270-)  A      CD
 263 GLU   ( 270-)  A      OE1
 263 GLU   ( 270-)  A      OE2
 294 LYS   ( 301-)  A      CG
 294 LYS   ( 301-)  A      CD
 294 LYS   ( 301-)  A      CE
 294 LYS   ( 301-)  A      NZ
 299 LYS   ( 309-)  A      CD
 299 LYS   ( 309-)  A      CE
 299 LYS   ( 309-)  A      NZ
 329 LYS   ( 339-)  A      CD
 329 LYS   ( 339-)  A      CE
 329 LYS   ( 339-)  A      NZ
 383 LYS   ( 393-)  A      CE
 383 LYS   ( 393-)  A      NZ
And so on for a total of 95 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.

 719 GLU   ( 282-)  B    0.50

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Phenylalanine convention problem

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

 282 PHE   ( 289-)  A
 404 PHE   ( 414-)  A

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.

 435 GLU   ( 445-)  A
 711 GLU   ( 274-)  B

Geometric checks

Warning: Unusual bond lengths

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

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

 267 GLU   ( 274-)  A      C    O     1.14   -4.5

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

 |  0.998747 -0.000186 -0.000309|
 | -0.000186  0.998191 -0.000371|
 | -0.000309 -0.000371  0.998065|
Proposed new scale matrix

 |  0.010616  0.000002  0.000003|
 |  0.000002  0.010596  0.000004|
 |  0.000003  0.000003  0.008861|
With corresponding cell

    A    =  94.195  B   =  94.374  C    = 112.852
    Alpha=  90.043  Beta=  90.035  Gamma=  90.021

The CRYST1 cell dimensions

    A    =  94.313  B   =  94.547  C    = 113.064
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 87.720
(Under-)estimated Z-score: 6.903

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.

 193 HIS   ( 195-)  A      CG   ND1  CE1 109.62    4.0
 268 ASN   ( 275-)  A     -CA  -C    N   124.55    4.2
 474 HIS   (  36-)  B      CG   ND1  CE1 109.65    4.1
 712 ASN   ( 275-)  B     -CA  -C    N   124.86    4.3

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.

 435 GLU   ( 445-)  A
 711 GLU   ( 274-)  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.

 261 ALA   ( 268-)  A    4.29

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.

 180 PRO   ( 182-)  A    -2.4
 620 PRO   ( 182-)  B    -2.4
 217 ILE   ( 219-)  A    -2.4
   9 LEU   (  11-)  A    -2.2
 755 LYS   ( 319-)  B    -2.2
 786 THR   ( 350-)  B    -2.1
 355 ARG   ( 365-)  A    -2.1
 119 HIS   ( 121-)  A    -2.1
 462 SER   (  24-)  B    -2.1
 340 THR   ( 350-)  A    -2.0
 559 HIS   ( 121-)  B    -2.0
 577 ILE   ( 139-)  B    -2.0
 829 LYS   ( 393-)  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.

  11 GLY   (  13-)  A  omega poor
  20 GLU   (  22-)  A  omega poor
  45 ASN   (  47-)  A  Poor phi/psi
  52 ALA   (  54-)  A  Poor phi/psi
 119 HIS   ( 121-)  A  omega poor
 120 TRP   ( 122-)  A  Poor phi/psi
 179 ALA   ( 181-)  A  PRO omega poor
 228 SER   ( 230-)  A  omega poor
 260 PHE   ( 267-)  A  omega poor
 288 TYR   ( 295-)  A  omega poor
 299 LYS   ( 309-)  A  Poor phi/psi
 306 ASP   ( 316-)  A  Poor phi/psi
 307 LEU   ( 317-)  A  Poor phi/psi
 338 TYR   ( 348-)  A  omega poor
 381 PRO   ( 391-)  A  Poor phi/psi
 388 TRP   ( 398-)  A  omega poor
 391 LEU   ( 401-)  A  omega poor
 396 TRP   ( 406-)  A  Poor phi/psi
 405 GLY   ( 415-)  A  omega poor
 414 GLN   ( 424-)  A  Poor phi/psi
 451 GLY   (  13-)  B  omega poor
 459 ILE   (  21-)  B  omega poor
 485 ASN   (  47-)  B  Poor phi/psi
 492 ALA   (  54-)  B  Poor phi/psi
 559 HIS   ( 121-)  B  omega poor
 560 TRP   ( 122-)  B  Poor phi/psi
 619 ALA   ( 181-)  B  PRO omega poor
 704 PHE   ( 267-)  B  omega poor
 712 ASN   ( 275-)  B  Poor phi/psi
 745 LYS   ( 309-)  B  Poor phi/psi
 752 ASP   ( 316-)  B  Poor phi/psi
 753 LEU   ( 317-)  B  Poor phi/psi
 784 TYR   ( 348-)  B  omega poor
 827 PRO   ( 391-)  B  Poor phi/psi
 833 VAL   ( 397-)  B  omega poor
 834 TRP   ( 398-)  B  omega poor
 837 LEU   ( 401-)  B  omega poor
 842 TRP   ( 406-)  B  Poor phi/psi
 851 GLY   ( 415-)  B  omega poor
 860 GLN   ( 424-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.057

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.

 585 SER   ( 147-)  B    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!

   6 GLU   (   8-)  A      0
  20 GLU   (  22-)  A      0
  22 SER   (  24-)  A      0
  25 ALA   (  27-)  A      0
  26 ASP   (  28-)  A      0
  38 HIS   (  40-)  A      0
  40 PRO   (  42-)  A      0
  42 ASN   (  44-)  A      0
  44 LYS   (  46-)  A      0
  45 ASN   (  47-)  A      0
  47 ASP   (  49-)  A      0
  50 ASP   (  52-)  A      0
  51 VAL   (  53-)  A      0
  52 ALA   (  54-)  A      0
  53 CYS   (  55-)  A      0
  54 ASP   (  56-)  A      0
  55 HIS   (  57-)  A      0
  57 ASN   (  59-)  A      0
  72 LYS   (  74-)  A      0
  80 TRP   (  82-)  A      0
  86 GLU   (  88-)  A      0
  88 THR   (  90-)  A      0
 109 LYS   ( 111-)  A      0
 117 ILE   ( 119-)  A      0
 119 HIS   ( 121-)  A      0
And so on for a total of 336 lines.

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]

 254 PRO   ( 261-)  A    0.04 LOW
 710 PRO   ( 273-)  B    0.04 LOW
 781 PRO   ( 345-)  B    0.19 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].

 226 PRO   ( 228-)  A   -65.3 envelop C-beta (-72 degrees)
 297 PRO   ( 304-)  A    45.8 half-chair C-delta/C-gamma (54 degrees)
 308 PRO   ( 318-)  A  -114.6 envelop C-gamma (-108 degrees)
 525 PRO   (  87-)  B  -129.0 half-chair C-delta/C-gamma (-126 degrees)
 620 PRO   ( 182-)  B   -63.1 envelop C-beta (-72 degrees)
 665 PRO   ( 228-)  B   -62.6 half-chair C-beta/C-alpha (-54 degrees)
 741 PRO   ( 304-)  B    47.4 half-chair C-delta/C-gamma (54 degrees)
 754 PRO   ( 318-)  B  -116.9 envelop C-gamma (-108 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.

 240 ASN   ( 247-)  A      C   <->  242 PRO   ( 249-)  A      CD     0.33    2.87  INTRA BL
 684 ASN   ( 247-)  B      C   <->  686 PRO   ( 249-)  B      CD     0.30    2.90  INTRA BL
 799 ASP   ( 363-)  B      OD2 <->  803 HIS   ( 367-)  B      NE2    0.25    2.45  INTRA BF
 139 ASP   ( 141-)  A      OD1 <->  201 ARG   ( 203-)  A      NH1    0.22    2.48  INTRA
  72 LYS   (  74-)  A      NZ  <->  882 HOH   (2090 )  A      O      0.19    2.51  INTRA BF
 410 ASP   ( 420-)  A      O   <->  414 GLN   ( 424-)  A      N      0.18    2.52  INTRA BF
 291 HIS   ( 298-)  A      ND1 <->  882 HOH   (2215 )  A      O      0.18    2.52  INTRA BF
 100 ASN   ( 102-)  A      ND2 <->  882 HOH   (2114 )  A      O      0.18    2.52  INTRA
 856 ASP   ( 420-)  B      O   <->  860 GLN   ( 424-)  B      N      0.17    2.53  INTRA BF
 593 GLY   ( 155-)  B      O   <->  597 LYS   ( 159-)  B      NZ     0.17    2.53  INTRA
 736 LEU   ( 299-)  B      CD2 <->  749 VAL   ( 313-)  B      CG2    0.16    3.04  INTRA BF
 520 TRP   (  82-)  B      N   <->  521 PRO   (  83-)  B      CD     0.15    2.85  INTRA BL
 193 HIS   ( 195-)  A      NE2 <->  272 ASP   ( 279-)  A      OD2    0.13    2.57  INTRA BL
 630 ARG   ( 192-)  B      NH1 <->  708 TYR   ( 271-)  B      O      0.13    2.57  INTRA BL
 436 HIS   (  -2-)  B      CE1 <->  883 HOH   (2001 )  B      O      0.13    2.67  INTRA BF
 779 ASN   ( 343-)  B      N   <->  780 PRO   ( 344-)  B      CD     0.13    2.87  INTRA
 238 PHE   ( 245-)  A      CD2 <->  239 ASN   ( 246-)  A      ND2    0.13    2.97  INTRA
 491 VAL   (  53-)  B      N   <->  883 HOH   (2054 )  B      O      0.12    2.58  INTRA
 723 LYS   ( 286-)  B      CG  <->  883 HOH   (2204 )  B      O      0.12    2.68  INTRA BF
 364 TYR   ( 374-)  A      O   <->  368 HIS   ( 378-)  A      ND1    0.12    2.58  INTRA
 685 TYR   ( 248-)  B      N   <->  686 PRO   ( 249-)  B      CD     0.12    2.88  INTRA BL
 711 GLU   ( 274-)  B      CG  <->  883 HOH   (2184 )  B      O      0.12    2.68  INTRA BF
 666 ALA   ( 229-)  B      CA  <->  736 LEU   ( 299-)  B      CD1    0.12    3.08  INTRA BF
 694 ARG   ( 257-)  B      NE  <->  883 HOH   (2168 )  B      O      0.11    2.59  INTRA BF
 462 SER   (  24-)  B      N   <->  463 PRO   (  25-)  B      CD     0.11    2.89  INTRA BL
And so on for a total of 91 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 295 PHE   ( 302-)  A      -7.12
 250 ARG   ( 257-)  A      -5.71
 694 ARG   ( 257-)  B      -5.62
 739 PHE   ( 302-)  B      -5.57
 352 GLU   ( 362-)  A      -5.56
 823 GLN   ( 387-)  B      -5.56
 377 GLN   ( 387-)  A      -5.51
  45 ASN   (  47-)  A      -5.31
 485 ASN   (  47-)  B      -5.30
 151 ASN   ( 153-)  A      -5.14
 591 ASN   ( 153-)  B      -5.13
 211 LYS   ( 213-)  A      -5.12
 683 ASN   ( 246-)  B      -5.11
 239 ASN   ( 246-)  A      -5.08
 880 LEU   ( 444-)  B      -5.04

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

  51 VAL   (  53-)  A   -2.68

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.

 883 HOH   (2066 )  B      O     23.08   12.07   -1.92

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.

 882 HOH   (2002 )  A      O
 882 HOH   (2007 )  A      O
 882 HOH   (2055 )  A      O
 882 HOH   (2057 )  A      O
 882 HOH   (2071 )  A      O
 882 HOH   (2077 )  A      O
 882 HOH   (2078 )  A      O
 882 HOH   (2176 )  A      O
 882 HOH   (2177 )  A      O
 882 HOH   (2276 )  A      O
 883 HOH   (2009 )  B      O
 883 HOH   (2087 )  B      O
 883 HOH   (2104 )  B      O
 883 HOH   (2149 )  B      O
 883 HOH   (2213 )  B      O
 883 HOH   (2221 )  B      O
 883 HOH   (2223 )  B      O

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.

 371 GLN   ( 381-)  A
 377 GLN   ( 387-)  A
 393 ASN   ( 403-)  A
 440 ASN   (   2-)  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.

  10 TRP   (  12-)  A      N
  15 ALA   (  17-)  A      N
  88 THR   (  90-)  A      N
 116 THR   ( 118-)  A      OG1
 120 TRP   ( 122-)  A      N
 122 LEU   ( 124-)  A      N
 166 TRP   ( 168-)  A      NE1
 179 ALA   ( 181-)  A      N
 201 ARG   ( 203-)  A      NE
 228 SER   ( 230-)  A      N
 322 TYR   ( 332-)  A      N
 336 GLU   ( 346-)  A      N
 342 ASN   ( 352-)  A      ND2
 343 GLY   ( 353-)  A      N
 384 GLY   ( 394-)  A      N
 402 LYS   ( 412-)  A      N
 424 TRP   ( 434-)  A      NE1
 441 VAL   (   3-)  B      N
 455 ALA   (  17-)  B      N
 458 GLN   (  20-)  B      NE2
 500 LYS   (  62-)  B      N
 522 ARG   (  84-)  B      NH1
 556 THR   ( 118-)  B      OG1
 560 TRP   ( 122-)  B      N
 562 LEU   ( 124-)  B      N
 567 GLN   ( 129-)  B      NE2
 606 TRP   ( 168-)  B      NE1
 619 ALA   ( 181-)  B      N
 641 ARG   ( 203-)  B    A NH1
 671 GLU   ( 234-)  B      N
 746 VAL   ( 310-)  B      N
 768 TYR   ( 332-)  B      N
 782 GLU   ( 346-)  B      N
 789 GLY   ( 353-)  B      N
 830 GLY   ( 394-)  B      N
 839 ASN   ( 403-)  B      ND2
 842 TRP   ( 406-)  B      N
 848 LYS   ( 412-)  B      N

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.

 882 HOH   (2209 )  A      O  1.11  K  4
 883 HOH   (2027 )  B      O  1.07  K  4
 883 HOH   (2118 )  B      O  0.89  K  4
 883 HOH   (2126 )  B      O  0.97  K  4
 883 HOH   (2196 )  B      O  1.04 NA  5 (or CA)

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.

 296 ASP   ( 303-)  A   H-bonding suggests Asn
 420 ASP   ( 430-)  A   H-bonding suggests Asn; but Alt-Rotamer
 537 ASP   (  99-)  B   H-bonding suggests Asn
 804 ASP   ( 368-)  B   H-bonding suggests Asn
 809 ASP   ( 373-)  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 :  -0.477
  2nd generation packing quality :  -0.558
  Ramachandran plot appearance   :  -1.353
  chi-1/chi-2 rotamer normality  :  -2.057
  Backbone conformation          :  -0.550

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.441 (tight)
  Bond angles                    :   0.671
  Omega angle restraints         :   1.049
  Side chain planarity           :   0.498 (tight)
  Improper dihedral distribution :   0.698
  B-factor distribution          :   0.401
  Inside/Outside distribution    :   0.990

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 : 2.11


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.441 (tight)
  Bond angles                    :   0.671
  Omega angle restraints         :   1.049
  Side chain planarity           :   0.498 (tight)
  Improper dihedral distribution :   0.698
  B-factor distribution          :   0.401
  Inside/Outside distribution    :   0.990
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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
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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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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
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      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      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.