WHAT IF Check report

This file was created 2012-01-30 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 pdb3k3p.ent

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 375 SER   (  60-)  B  -   OG

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

   1 LYS   (   3-)  A    0.40
  14 GLU   (  16-)  A    0.30
  16 ASP   (  18-)  A    0.50
  17 VAL   (  19-)  A    0.50
  27 ARG   (  29-)  A    0.50
  43 GLN   (  45-)  A    0.50
  56 GLN   (  58-)  A    0.50
  60 LYS   (  64-)  A    0.50
  91 GLY   (  95-)  A    0.50
 160 GLU   ( 164-)  A    0.50
 169 LYS   ( 173-)  A    0.50
 172 ASN   ( 176-)  A    0.50
 203 ASP   ( 213-)  A    0.50
 218 LYS   ( 228-)  A    0.50
 226 VAL   ( 236-)  A    0.70
 235 ASP   ( 262-)  A    0.50
 240 GLU   ( 267-)  A    0.50
 267 GLU   ( 294-)  A    0.50
 268 ASP   ( 295-)  A    0.50
 270 LYS   ( 297-)  A    0.50
 283 THR   ( 310-)  A    0.40
 317 SER   ( 346-)  A    0.50
 318 LYS   (   3-)  B    0.40
 331 GLU   (  16-)  B    0.30
 333 ASP   (  18-)  B    0.50
 360 GLN   (  45-)  B    0.50
 377 LYS   (  64-)  B    0.50
 408 GLY   (  95-)  B    0.50
 410 MET   (  97-)  B    0.50
 477 GLU   ( 164-)  B    0.50
 486 LYS   ( 173-)  B    0.50
 497 ARG   ( 189-)  B    0.50
 534 ASP   ( 226-)  B    0.50
 536 LYS   ( 228-)  B    0.50
 544 VAL   ( 236-)  B    0.70
 553 ASP   ( 262-)  B    0.50
 558 GLU   ( 267-)  B    0.50
 585 GLU   ( 294-)  B    0.50
 586 ASP   ( 295-)  B    0.50
 588 LYS   ( 297-)  B    0.50
 601 THR   ( 310-)  B    0.50
 635 SER   ( 346-)  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) :110.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 328 ARG   (  13-)  B

Warning: Tyrosine convention problem

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

   8 TYR   (  10-)  A
  31 TYR   (  33-)  A
  39 TYR   (  41-)  A
 272 TYR   ( 299-)  A
 325 TYR   (  10-)  B
 348 TYR   (  33-)  B
 356 TYR   (  41-)  B
 510 TYR   ( 202-)  B
 590 TYR   ( 299-)  B

Warning: Phenylalanine convention problem

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

  47 PHE   (  49-)  A
 167 PHE   ( 171-)  A
 250 PHE   ( 277-)  A
 264 PHE   ( 291-)  A
 282 PHE   ( 309-)  A
 364 PHE   (  49-)  B
 484 PHE   ( 171-)  B
 582 PHE   ( 291-)  B
 600 PHE   ( 309-)  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.

 268 ASP   ( 295-)  A
 376 ASP   (  63-)  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.

   2 GLU   (   4-)  A
 319 GLU   (   4-)  B
 398 GLU   (  85-)  B
 634 GLU   ( 345-)  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.

  58 SER   (  60-)  A      N   -C     1.25   -4.0
 174 SER   ( 184-)  A      N   -C     1.23   -5.0
 552 ILE   ( 261-)  B      CA   CB    1.64    5.4

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

 |  0.997988 -0.000404 -0.000121|
 | -0.000404  0.997625  0.000676|
 | -0.000121  0.000676  0.996573|
Proposed new scale matrix

 |  0.012606  0.007284 -0.000003|
 |  0.000006  0.014559 -0.000010|
 |  0.000001 -0.000006  0.009172|
With corresponding cell

    A    =  79.344  B   =  79.349  C    = 109.022
    Alpha=  89.926  Beta=  90.014  Gamma= 120.044

The CRYST1 cell dimensions

    A    =  79.502  B   =  79.502  C    = 109.400
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 142.228
(Under-)estimated Z-score: 8.789

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.

  50 THR   (  52-)  A      C    CA   CB  102.24   -4.1
 277 ASN   ( 304-)  A      N    CA   CB  103.49   -4.1
 328 ARG   (  13-)  B      CB   CG   CD  105.27   -4.4
 344 ARG   (  29-)  B      CB   CG   CD  105.85   -4.1
 367 THR   (  52-)  B      C    CA   CB  100.04   -5.3
 368 GLN   (  53-)  B      N    CA   C   122.84    4.2

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   (   4-)  A
 268 ASP   ( 295-)  A
 319 GLU   (   4-)  B
 328 ARG   (  13-)  B
 376 ASP   (  63-)  B
 398 GLU   (  85-)  B
 634 GLU   ( 345-)  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.

 368 GLN   (  53-)  B    5.47
  51 GLN   (  53-)  A    5.17
 134 ALA   ( 138-)  A    4.70
 603 MET   ( 314-)  B    4.39
 497 ARG   ( 189-)  B    4.24

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.

 404 PRO   (  91-)  B    -2.5
  86 PHE   (  90-)  A    -2.2
  87 PRO   (  91-)  A    -2.2
  93 MET   (  97-)  A    -2.2
 403 PHE   (  90-)  B    -2.2
 452 THR   ( 139-)  B    -2.2
 374 PRO   (  59-)  B    -2.1
 315 ARG   ( 344-)  A    -2.1
 398 GLU   (  85-)  B    -2.1
 383 THR   (  70-)  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.

  34 PHE   (  36-)  A  omega poor
  51 GLN   (  53-)  A  omega poor
  73 ILE   (  77-)  A  omega poor
  77 ASP   (  81-)  A  omega poor
  82 GLU   (  86-)  A  Poor phi/psi
  93 MET   (  97-)  A  Poor phi/psi, omega poor
  94 GLY   (  98-)  A  Poor phi/psi
 107 LYS   ( 111-)  A  Poor phi/psi
 111 VAL   ( 115-)  A  omega poor
 147 GLU   ( 151-)  A  omega poor
 164 TYR   ( 168-)  A  PRO omega poor
 220 THR   ( 230-)  A  omega poor
 230 ILE   ( 257-)  A  PRO omega poor
 263 PHE   ( 290-)  A  omega poor
 281 GLY   ( 308-)  A  omega poor
 285 MET   ( 314-)  A  omega poor
 351 PHE   (  36-)  B  omega poor
 367 THR   (  52-)  B  omega poor
 390 ILE   (  77-)  B  omega poor
 399 GLU   (  86-)  B  Poor phi/psi
 410 MET   (  97-)  B  Poor phi/psi
 411 GLY   (  98-)  B  Poor phi/psi
 412 GLU   (  99-)  B  omega poor
 424 LYS   ( 111-)  B  Poor phi/psi
 428 VAL   ( 115-)  B  omega poor
 464 GLU   ( 151-)  B  omega poor
 481 TYR   ( 168-)  B  PRO omega poor
 538 THR   ( 230-)  B  omega poor
 546 MET   ( 255-)  B  omega poor
 548 ILE   ( 257-)  B  PRO omega poor
 581 PHE   ( 290-)  B  omega poor
 593 GLU   ( 302-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -2.346

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.

 338 SER   (  23-)  B    0.36
  24 SER   (  26-)  A    0.36
  21 SER   (  23-)  A    0.37
 616 SER   ( 327-)  B    0.37
 119 SER   ( 123-)  A    0.38
 435 SER   ( 122-)  B    0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   8 TYR   (  10-)  A      0
  11 ARG   (  13-)  A      0
  31 TYR   (  33-)  A      0
  33 ASN   (  35-)  A      0
  50 THR   (  52-)  A      0
  51 GLN   (  53-)  A      0
  53 PHE   (  55-)  A      0
  57 PRO   (  59-)  A      0
  58 SER   (  60-)  A      0
  59 ASP   (  63-)  A      0
  60 LYS   (  64-)  A      0
  62 MET   (  66-)  A      0
  66 THR   (  70-)  A      0
  67 ILE   (  71-)  A      0
  77 ASP   (  81-)  A      0
  78 ILE   (  82-)  A      0
  81 GLU   (  85-)  A      0
  82 GLU   (  86-)  A      0
  87 PRO   (  91-)  A      0
  88 VAL   (  92-)  A      0
  89 LEU   (  93-)  A      0
  90 HIS   (  94-)  A      0
  92 PRO   (  96-)  A      0
  93 MET   (  97-)  A      0
  95 GLU   (  99-)  A      0
And so on for a total of 222 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]

  57 PRO   (  59-)  A    0.19 LOW
  87 PRO   (  91-)  A    0.19 LOW
 222 PRO   ( 232-)  A    0.46 HIGH
 487 PRO   ( 174-)  B    0.17 LOW
 549 PRO   ( 258-)  B    0.47 HIGH
 605 PRO   ( 316-)  B    0.12 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].

  92 PRO   (  96-)  A   102.8 envelop C-beta (108 degrees)
 150 PRO   ( 154-)  A  -124.9 half-chair C-delta/C-gamma (-126 degrees)
 236 PRO   ( 263-)  A   102.9 envelop C-beta (108 degrees)
 404 PRO   (  91-)  B   -33.6 envelop C-alpha (-36 degrees)
 409 PRO   (  96-)  B   129.5 half-chair C-beta/C-alpha (126 degrees)
 467 PRO   ( 154-)  B  -129.6 half-chair C-delta/C-gamma (-126 degrees)
 554 PRO   ( 263-)  B   101.1 envelop C-beta (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.

 579 CYS   ( 288-)  B      SG  <->  594 LEU   ( 303-)  B      CD1    0.65    2.75  INTRA
 261 CYS   ( 288-)  A      SG  <->  276 LEU   ( 303-)  A      CD1    0.44    2.96  INTRA
 368 GLN   (  53-)  B      NE2 <->  377 LYS   (  64-)  B      O      0.30    2.40  INTRA
 225 ILE   ( 235-)  A      O   <->  226 VAL   ( 236-)  A      CG1    0.27    2.43  INTRA BF
 366 LYS   (  51-)  B      NZ  <->  369 GLU   (  54-)  B      OE2    0.26    2.44  INTRA
 578 ARG   ( 287-)  B      NH2 <->  580 ASP   ( 289-)  B      OD2    0.22    2.48  INTRA BL
 329 SER   (  14-)  B      O   <->  332 ARG   (  17-)  B      NH1    0.20    2.50  INTRA BF
 416 ILE   ( 103-)  B      CG2 <->  417 GLN   ( 104-)  B      N      0.20    2.80  INTRA BL
  12 SER   (  14-)  A      O   <->   15 ARG   (  17-)  A      NH1    0.20    2.50  INTRA
  23 GLU   (  25-)  A      OE2 <->   61 LEU   (  65-)  A      N      0.19    2.51  INTRA
 416 ILE   ( 103-)  B      CG2 <->  417 GLN   ( 104-)  B      CD     0.18    3.02  INTRA BL
 146 ILE   ( 150-)  A      N   <->  149 GLU   ( 153-)  A      OE1    0.17    2.53  INTRA
  37 LYS   (  39-)  A      NZ  <->   80 GLU   (  84-)  A      OE1    0.17    2.53  INTRA
  37 LYS   (  39-)  A      NZ  <->  636 HOH   ( 414 )  A      O      0.14    2.56  INTRA
 633 ARG   ( 344-)  B      NH2 <->  637 HOH   ( 425 )  B      O      0.14    2.56  INTRA
 441 LYS   ( 128-)  B      NZ  <->  517 GLU   ( 209-)  B      OE2    0.14    2.56  INTRA BL
 636 HOH   ( 362 )  A      O   <->  637 HOH   ( 371 )  B      O      0.13    2.27  INTRA BL
 551 GLU   ( 260-)  B      N   <->  637 HOH   ( 362 )  B      O      0.13    2.57  INTRA BL
 408 GLY   (  95-)  B      O   <->  412 GLU   (  99-)  B      N      0.12    2.58  INTRA BF
 416 ILE   ( 103-)  B      CG2 <->  417 GLN   ( 104-)  B      NE2    0.12    2.98  INTRA BL
  49 LYS   (  51-)  A      NZ  <->   52 GLU   (  54-)  A      OE2    0.11    2.59  INTRA
 260 ARG   ( 287-)  A      NH2 <->  262 ASP   ( 289-)  A      OD2    0.11    2.59  INTRA BL
 489 ASN   ( 176-)  B      N   <->  511 ASP   ( 203-)  B      OD2    0.11    2.59  INTRA
   2 GLU   (   4-)  A      OE2 <->  309 LYS   ( 338-)  A      NZ     0.10    2.60  INTRA BF
 466 GLU   ( 153-)  B      CD  <->  471 LYS   ( 158-)  B      CE     0.10    3.10  INTRA
And so on for a total of 66 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.

 373 GLN   (  58-)  B      -5.72
 585 GLU   ( 294-)  B      -5.57
 551 GLU   ( 260-)  B      -5.53
 221 LEU   ( 231-)  A      -5.51
 539 LEU   ( 231-)  B      -5.48
 233 GLU   ( 260-)  A      -5.43
  43 GLN   (  45-)  A      -5.43
 267 GLU   ( 294-)  A      -5.38
 163 ILE   ( 167-)  A      -5.34
 480 ILE   ( 167-)  B      -5.32
 360 GLN   (  45-)  B      -5.27
  56 GLN   (  58-)  A      -5.27
 388 GLN   (  75-)  B      -5.18
 292 ASN   ( 321-)  A      -5.14
  71 GLN   (  75-)  A      -5.13
 610 ASN   ( 321-)  B      -5.13
 377 LYS   (  64-)  B      -5.09

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.

  58 SER   (  60-)  A   -2.83
 140 VAL   ( 144-)  A   -2.79
 457 VAL   ( 144-)  B   -2.78

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

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   (  68-)  A
  71 GLN   (  75-)  A
 381 ASN   (  68-)  B
 388 GLN   (  75-)  B
 489 ASN   ( 176-)  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.

  16 ASP   (  18-)  A      N
  68 ILE   (  72-)  A      N
  76 SER   (  80-)  A      OG
  80 GLU   (  84-)  A      N
  93 MET   (  97-)  A      N
 114 ASN   ( 118-)  A      N
 139 GLN   ( 143-)  A      NE2
 178 ASN   ( 188-)  A      N
 195 ARG   ( 205-)  A      N
 214 ASN   ( 224-)  A      ND2
 256 CYS   ( 283-)  A      N
 266 THR   ( 293-)  A      OG1
 268 ASP   ( 295-)  A      N
 284 SER   ( 313-)  A      OG
 290 TRP   ( 319-)  A      NE1
 372 SER   (  57-)  B      N
 382 ASP   (  69-)  B      N
 385 ILE   (  72-)  B      N
 397 GLU   (  84-)  B      N
 410 MET   (  97-)  B      N
 431 ASN   ( 118-)  B      N
 456 GLN   ( 143-)  B      NE2
 496 ASN   ( 188-)  B      N
 513 ARG   ( 205-)  B      N
 532 ASN   ( 224-)  B      ND2
 574 CYS   ( 283-)  B      N
 602 SER   ( 313-)  B      OG
 608 TRP   ( 319-)  B      NE1

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.

 489 ASN   ( 176-)  B      OD1

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 :   0.930
  2nd generation packing quality :  -0.188
  Ramachandran plot appearance   :   0.333
  chi-1/chi-2 rotamer normality  :  -2.346
  Backbone conformation          :   0.875

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.959
  Bond angles                    :   0.913
  Omega angle restraints         :   1.214
  Side chain planarity           :   0.814
  Improper dihedral distribution :   1.072
  B-factor distribution          :   0.614
  Inside/Outside distribution    :   0.996

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 : 2.23


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.4
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   1.4
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.959
  Bond angles                    :   0.913
  Omega angle restraints         :   1.214
  Side chain planarity           :   0.814
  Improper dihedral distribution :   1.072
  B-factor distribution          :   0.614
  Inside/Outside distribution    :   0.996
==============

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.