WHAT IF Check report

This file was created 2011-12-17 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 pdb2q3z.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 661 ACE   (   1-)  X  -
 663 SO4   ( 688-)  A  -
 664 SO4   ( 689-)  A  -
 665 SO4   ( 690-)  A  -
 666 SO4   ( 691-)  A  -
 667 SO4   ( 692-)  A  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 277 CYS   ( 277-)  A  -   SG   657 ONL   (   3-)  X  -   CE

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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.

  28 ARG   (  28-)  A  -   CD
  28 ARG   (  28-)  A  -   NE
  28 ARG   (  28-)  A  -   CZ
  28 ARG   (  28-)  A  -   NH1
  28 ARG   (  28-)  A  -   NH2
  29 GLU   (  29-)  A  -   OE1
  29 GLU   (  29-)  A  -   OE2
  30 LYS   (  30-)  A  -   CE
  30 LYS   (  30-)  A  -   NZ
  70 GLU   (  70-)  A  -   CD
  70 GLU   (  70-)  A  -   OE1
  70 GLU   (  70-)  A  -   OE2
  85 GLU   (  85-)  A  -   CD
  85 GLU   (  85-)  A  -   OE1
  85 GLU   (  85-)  A  -   OE2
  97 ASP   (  97-)  A  -   OD2
 243 ASN   ( 243-)  A  -   CG
 243 ASN   ( 243-)  A  -   OD1
 243 ASN   ( 243-)  A  -   ND2
 315 ARG   ( 317-)  A  -   CD
 315 ARG   ( 317-)  A  -   NE
 315 ARG   ( 317-)  A  -   CZ
 315 ARG   ( 317-)  A  -   NH1
 315 ARG   ( 317-)  A  -   NH2
 318 GLU   ( 329-)  A  -   OE1
And so on for a total of 57 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone 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. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 247 ASP   ( 247-)  A  -   C
 247 ASP   ( 247-)  A  -   O

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

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'.

  97 ASP   (  97-)  A      OD1
 315 ARG   ( 317-)  A      CG
 318 GLU   ( 329-)  A      CD
 407 LYS   ( 425-)  A      NZ
 562 LYS   ( 590-)  A      CD
 633 LEU   ( 661-)  A      CG
 644 LYS   ( 672-)  A      CD

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: 3

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

 168 TYR   ( 168-)  A
 313 TYR   ( 315-)  A
 358 TYR   ( 369-)  A
 377 TYR   ( 388-)  A
 425 TYR   ( 443-)  A
 427 TYR   ( 445-)  A
 475 TYR   ( 503-)  A
 500 TYR   ( 528-)  A

Warning: Phenylalanine convention problem

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

  45 PHE   (  45-)  A
  59 PHE   (  59-)  A
  77 PHE   (  77-)  A
 135 PHE   ( 135-)  A
 166 PHE   ( 166-)  A
 174 PHE   ( 174-)  A
 314 PHE   ( 316-)  A
 323 PHE   ( 334-)  A
 461 PHE   ( 489-)  A
 509 PHE   ( 537-)  A
 594 PHE   ( 622-)  A
 651 PHE   ( 679-)  A
 660 PHE   (   6-)  X

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.

  25 ASP   (  25-)  A
  55 ASP   (  55-)  A
 191 ASP   ( 191-)  A
 210 ASP   ( 210-)  A
 232 ASP   ( 232-)  A
 233 ASP   ( 233-)  A
 242 ASP   ( 242-)  A
 259 ASP   ( 259-)  A
 416 ASP   ( 434-)  A
 553 ASP   ( 581-)  A
 643 ASP   ( 671-)  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.

   4 GLU   (   4-)  A
  29 GLU   (  29-)  A
  84 GLU   (  84-)  A
 153 GLU   ( 153-)  A
 155 GLU   ( 155-)  A
 341 GLU   ( 352-)  A
 352 GLU   ( 363-)  A
 433 GLU   ( 451-)  A
 511 GLU   ( 539-)  A
 529 GLU   ( 557-)  A
 578 GLU   ( 606-)  A
 597 GLU   ( 625-)  A
 615 GLU   ( 643-)  A
 641 GLU   ( 669-)  A

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

 |  0.999431 -0.000080 -0.000421|
 | -0.000080  1.001233 -0.000137|
 | -0.000421 -0.000137  0.995345|
Proposed new scale matrix

 |  0.013961  0.000001  0.000006|
 |  0.000001  0.013936  0.000002|
 |  0.000001  0.000000  0.003251|
With corresponding cell

    A    =  71.628  B   =  71.758  C    = 307.585
    Alpha=  90.010  Beta=  90.048  Gamma=  90.009

The CRYST1 cell dimensions

    A    =  71.671  B   =  71.671  C    = 309.010
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 95.847
(Under-)estimated Z-score: 7.215

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.

  21 HIS   (  21-)  A      CG   ND1  CE1 109.64    4.0
  28 ARG   (  28-)  A      CB   CG   CD  104.36   -4.9
  28 ARG   (  28-)  A      CG   CD   NE  120.27    5.7
  97 ASP   (  97-)  A      CB   CG   OD2 107.70   -4.7
 350 PRO   ( 361-)  A      N    CA   C   122.31    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.

   4 GLU   (   4-)  A
  25 ASP   (  25-)  A
  29 GLU   (  29-)  A
  55 ASP   (  55-)  A
  84 GLU   (  84-)  A
 153 GLU   ( 153-)  A
 155 GLU   ( 155-)  A
 191 ASP   ( 191-)  A
 210 ASP   ( 210-)  A
 232 ASP   ( 232-)  A
 233 ASP   ( 233-)  A
 242 ASP   ( 242-)  A
 259 ASP   ( 259-)  A
 341 GLU   ( 352-)  A
 352 GLU   ( 363-)  A
 416 ASP   ( 434-)  A
 433 GLU   ( 451-)  A
 511 GLU   ( 539-)  A
 529 GLU   ( 557-)  A
 553 ASP   ( 581-)  A
 578 GLU   ( 606-)  A
 597 GLU   ( 625-)  A
 615 GLU   ( 643-)  A
 641 GLU   ( 669-)  A
 643 ASP   ( 671-)  A

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.

 350 PRO   ( 361-)  A    -3.1
 569 PRO   ( 597-)  A    -3.0
 544 ILE   ( 572-)  A    -2.6
 627 VAL   ( 655-)  A    -2.6
 573 ARG   ( 601-)  A    -2.5
 112 ILE   ( 112-)  A    -2.3
 308 ASN   ( 310-)  A    -2.3
 575 LEU   ( 603-)  A    -2.3
 410 THR   ( 428-)  A    -2.3
  65 PRO   (  65-)  A    -2.2
 565 ILE   ( 593-)  A    -2.2
 400 ARG   ( 418-)  A    -2.2
 598 GLY   ( 626-)  A    -2.2
 645 LEU   ( 673-)  A    -2.2
 581 LEU   ( 609-)  A    -2.1
 370 GLU   ( 381-)  A    -2.1
 453 GLN   ( 481-)  A    -2.1
 609 GLU   ( 637-)  A    -2.1
 641 GLU   ( 669-)  A    -2.1
 541 GLU   ( 569-)  A    -2.1
 593 THR   ( 621-)  A    -2.1
 450 ARG   ( 478-)  A    -2.1
 509 PHE   ( 537-)  A    -2.1
 348 PRO   ( 359-)  A    -2.0
 501 LEU   ( 529-)  A    -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.

  22 HIS   (  22-)  A  Poor phi/psi
  29 GLU   (  29-)  A  Poor phi/psi
 158 GLU   ( 158-)  A  omega poor
 160 VAL   ( 160-)  A  omega poor
 169 GLN   ( 169-)  A  Poor phi/psi
 214 ARG   ( 214-)  A  omega poor
 243 ASN   ( 243-)  A  Poor phi/psi
 247 ASP   ( 247-)  A  omega poor
 273 LYS   ( 273-)  A  omega poor
 275 GLY   ( 275-)  A  omega poor
 305 HIS   ( 305-)  A  omega poor
 322 ASN   ( 333-)  A  omega poor
 349 THR   ( 360-)  A  PRO omega poor
 350 PRO   ( 361-)  A  omega poor
 351 GLN   ( 362-)  A  omega poor
 352 GLU   ( 363-)  A  omega poor
 359 CYS   ( 370-)  A  omega poor
 361 GLY   ( 372-)  A  PRO omega poor
 372 ASP   ( 383-)  A  omega poor
 376 LYS   ( 387-)  A  omega poor
 378 ASP   ( 389-)  A  Poor phi/psi
 392 ASP   ( 403-)  A  omega poor
 406 LEU   ( 424-)  A  omega poor
 408 ILE   ( 426-)  A  omega poor
 462 ASP   ( 490-)  A  omega poor
 464 PHE   ( 492-)  A  omega poor
 502 LEU   ( 530-)  A  omega poor
 531 ASN   ( 559-)  A  Poor phi/psi
 545 ASN   ( 573-)  A  Poor phi/psi
 570 LYS   ( 598-)  A  omega poor
 571 GLN   ( 599-)  A  omega poor
 572 LYS   ( 600-)  A  Poor phi/psi, omega poor
 573 ARG   ( 601-)  A  Poor phi/psi
 594 PHE   ( 622-)  A  omega poor
 621 LYS   ( 649-)  A  omega poor
 630 HIS   ( 658-)  A  omega poor
 631 MET   ( 659-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -2.729

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.

 225 SER   ( 225-)  A    0.38

Warning: Unusual backbone conformations

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

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

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

   8 GLU   (   8-)  A      0
  13 GLU   (  13-)  A      0
  22 HIS   (  22-)  A      0
  23 THR   (  23-)  A      0
  27 CYS   (  27-)  A      0
  28 ARG   (  28-)  A      0
  29 GLU   (  29-)  A      0
  35 ARG   (  35-)  A      0
  40 TRP   (  40-)  A      0
  46 GLU   (  46-)  A      0
  48 ARG   (  48-)  A      0
  50 TYR   (  50-)  A      0
  51 GLN   (  51-)  A      0
  54 VAL   (  54-)  A      0
  63 THR   (  63-)  A      0
  66 ALA   (  66-)  A      0
  67 PRO   (  67-)  A      0
  73 THR   (  73-)  A      0
  80 ARG   (  80-)  A      0
  82 ALA   (  82-)  A      0
  85 GLU   (  85-)  A      0
  88 TRP   (  88-)  A      0
  93 VAL   (  93-)  A      0
  94 ASP   (  94-)  A      0
  96 GLN   (  96-)  A      0
And so on for a total of 270 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 : 7.012

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 598 GLY   ( 626-)  A   2.20   27

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 630 HIS   ( 658-)  A   1.77

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]

  38 PRO   (  38-)  A    0.20 LOW
 111 PRO   ( 111-)  A    0.20 LOW
 542 PRO   ( 570-)  A    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].

  65 PRO   (  65-)  A   -50.6 half-chair C-beta/C-alpha (-54 degrees)
  78 PRO   (  78-)  A   -62.0 half-chair C-beta/C-alpha (-54 degrees)
 201 PRO   ( 201-)  A  -118.4 half-chair C-delta/C-gamma (-126 degrees)
 350 PRO   ( 361-)  A   142.9 envelop C-alpha (144 degrees)
 508 PRO   ( 536-)  A  -159.6 half-chair N/C-delta (-162 degrees)
 515 PRO   ( 543-)  A   -57.3 half-chair C-beta/C-alpha (-54 degrees)
 569 PRO   ( 597-)  A   -48.7 half-chair C-beta/C-alpha (-54 degrees)
 611 PRO   ( 639-)  A    51.3 half-chair C-delta/C-gamma (54 degrees)
 656 PRO   (   2-)  X     0.4 envelop N (0 degrees)
 659 PRO   (   5-)  X  -112.6 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 distance; each bump is listed in only one direction,

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

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

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

 606 LYS   ( 634-)  A      CB   <->   624 MET   ( 652-)  A      SD   0.39    3.01  INTRA
 606 LYS   ( 634-)  A      CG   <->   624 MET   ( 652-)  A      SD   0.36    3.04  INTRA BL
 392 ASP   ( 403-)  A      OD2  <->   399 ASN   ( 417-)  A      ND2  0.26    2.44  INTRA BF
 564 ARG   ( 592-)  A      N    <->   578 GLU   ( 606-)  A      O    0.24    2.46  INTRA BF
 517 CYS   ( 545-)  A      SG   <->   519 LEU   ( 547-)  A      CD2  0.23    3.17  INTRA BL
 349 THR   ( 360-)  A      CG2  <->   350 PRO   ( 361-)  A      CD   0.23    2.97  INTRA BF
 262 ARG   ( 262-)  A      O    <->   266 ASN   ( 266-)  A      ND2  0.22    2.48  INTRA BF
 392 ASP   ( 403-)  A      N    <->   397 SER   ( 415-)  A      O    0.20    2.50  INTRA BF
 592 CYS   ( 620-)  A      N    <->   668 HOH   ( 826 )  A      O    0.20    2.50  INTRA BF
 103 GLN   ( 103-)  A      NE2  <->   668 HOH   ( 751 )  A      O    0.19    2.51  INTRA BF
 534 LYS   ( 562-)  A      NZ   <->   553 ASP   ( 581-)  A      OD1  0.19    2.51  INTRA BL
  49 ASN   (  49-)  A      ND2  <->    96 GLN   (  96-)  A      O    0.19    2.51  INTRA BL
 668 HOH   ( 824 )  A      O    <->   668 HOH   ( 912 )  A      O    0.19    2.01  INTRA BF
 322 ASN   ( 333-)  A      N    <->   658 LEU   (   4-)  X      O    0.18    2.52  INTRA BF
 451 VAL   ( 479-)  A      N    <->   667 SO4   ( 692-)  A      O3   0.18    2.52  INTRA BF
 177 ASN   ( 177-)  A      O    <->   668 HOH   ( 939 )  A      O    0.18    2.22  INTRA BF
 531 ASN   ( 559-)  A      ND2  <->   556 LEU   ( 584-)  A      O    0.16    2.54  INTRA BF
 606 LYS   ( 634-)  A      CD   <->   624 MET   ( 652-)  A      SD   0.16    3.24  INTRA BL
  21 HIS   (  21-)  A      ND1  <->    34 ARG   (  34-)  A      N    0.15    2.85  INTRA BL
 495 GLU   ( 523-)  A      OE2  <->   497 GLY   ( 525-)  A      N    0.15    2.55  INTRA BF
 199 VAL   ( 199-)  A      O    <->   234 GLN   ( 234-)  A      NE2  0.15    2.55  INTRA BF
 277 CYS   ( 277-)  A      SG   <->   278 TRP   ( 278-)  A      N    0.15    3.05  INTRA BF
 305 HIS   ( 305-)  A      CD2  <->   403 ILE   ( 421-)  A      CD1  0.15    3.05  INTRA BF
 259 ASP   ( 259-)  A      OD2  <->   263 ARG   ( 263-)  A      NH1  0.14    2.56  INTRA BF
 317 SER   ( 328-)  A      N    <->   351 GLN   ( 362-)  A      NE2  0.14    2.71  INTRA BF
And so on for a total of 81 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

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.

 125 TYR   ( 125-)  A      -8.24
 573 ARG   ( 601-)  A      -7.35
 488 TYR   ( 516-)  A      -7.07
 337 GLN   ( 348-)  A      -6.82
  28 ARG   (  28-)  A      -6.72
 631 MET   ( 659-)  A      -6.26
 629 LEU   ( 657-)  A      -6.25
 377 TYR   ( 388-)  A      -6.00
 630 HIS   ( 658-)  A      -5.98
 355 GLU   ( 366-)  A      -5.74
  21 HIS   (  21-)  A      -5.61
 376 LYS   ( 387-)  A      -5.59
 574 LYS   ( 602-)  A      -5.57
 560 GLU   ( 588-)  A      -5.54
 572 LYS   ( 600-)  A      -5.47
 571 GLN   ( 599-)  A      -5.37
 442 ASN   ( 460-)  A      -5.35
 266 ASN   ( 266-)  A      -5.25
 319 MET   ( 330-)  A      -5.24

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.

 571 GLN   ( 599-)  A       574 - LYS    602- ( A)         -5.94
 629 LEU   ( 657-)  A       631 - MET    659- ( A)         -6.16

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

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.

 632 GLY   ( 660-)  A   -2.73
 423 HIS   ( 441-)  A   -2.61

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

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.

 668 HOH   ( 811 )  A      O      9.56  -24.35   -3.09
 668 HOH   ( 851 )  A      O      7.44   -2.30   88.27
 668 HOH   ( 887 )  A      O      7.39  -14.76   54.99

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.

 668 HOH   ( 874 )  A      O
Unrecognized bound group for 660
  Bound atom=  662 NH2  (   7-) X      N

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.

  44 HIS   (  44-)  A
 126 GLN   ( 126-)  A
 134 HIS   ( 134-)  A
 206 ASN   ( 206-)  A
 456 ASN   ( 484-)  A
 545 ASN   ( 573-)  A
 605 GLN   ( 633-)  A
 634 HIS   ( 662-)  A

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.

  82 ALA   (  82-)  A      N
  99 THR   (  99-)  A      N
 106 THR   ( 106-)  A      N
 152 SER   ( 152-)  A      N
 156 ARG   ( 156-)  A      NH1
 164 GLN   ( 164-)  A      N
 214 ARG   ( 214-)  A      NH1
 222 ARG   ( 222-)  A      NE
 229 ASN   ( 229-)  A      N
 230 CYS   ( 230-)  A      N
 231 ASN   ( 231-)  A      N
 241 TRP   ( 241-)  A      NE1
 247 ASP   ( 247-)  A      N
 254 TRP   ( 254-)  A      N
 258 VAL   ( 258-)  A      N
 260 ILE   ( 260-)  A      N
 276 GLN   ( 276-)  A      N
 277 CYS   ( 277-)  A      N
 278 TRP   ( 278-)  A      N
 310 LEU   ( 312-)  A      N
 311 ILE   ( 313-)  A      N
 320 ILE   ( 331-)  A      N
 322 ASN   ( 333-)  A      ND2
 325 CYS   ( 336-)  A      N
 349 THR   ( 360-)  A      OG1
 358 TYR   ( 369-)  A      N
 402 LEU   ( 420-)  A      N
 451 VAL   ( 479-)  A      N
 452 GLY   ( 480-)  A      N
 456 ASN   ( 484-)  A      N
 491 ILE   ( 519-)  A      N
 507 GLU   ( 535-)  A      N
 521 GLU   ( 549-)  A      N
 527 LEU   ( 555-)  A      N
 532 LEU   ( 560-)  A      N
 544 ILE   ( 572-)  A      N
 563 ILE   ( 591-)  A      N
 587 VAL   ( 615-)  A      N
 612 ASP   ( 640-)  A      N
 615 GLU   ( 643-)  A      N
 629 LEU   ( 657-)  A      N
 639 ASN   ( 667-)  A      ND2
 645 LEU   ( 673-)  A      N

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.

   4 GLU   (   4-)  A      OE1
 229 ASN   ( 229-)  A      OD1
 308 ASN   ( 310-)  A      OD1
 324 HIS   ( 335-)  A      ND1

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.

 668 HOH   ( 909 )  A      O  1.00  K  5

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.

   4 GLU   (   4-)  A   H-bonding suggests Gln; but Alt-Rotamer
  87 ASP   (  87-)  A   H-bonding suggests Asn
 352 GLU   ( 363-)  A   H-bonding suggests Gln
 643 ASP   ( 671-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.578
  2nd generation packing quality :  -1.876
  Ramachandran plot appearance   :  -0.959
  chi-1/chi-2 rotamer normality  :  -2.729
  Backbone conformation          :   0.056

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.551 (tight)
  Bond angles                    :   0.705
  Omega angle restraints         :   1.275 (loose)
  Side chain planarity           :   0.640 (tight)
  Improper dihedral distribution :   0.764
  B-factor distribution          :   0.734
  Inside/Outside distribution    :   1.016

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.551 (tight)
  Bond angles                    :   0.705
  Omega angle restraints         :   1.275 (loose)
  Side chain planarity           :   0.640 (tight)
  Improper dihedral distribution :   0.764
  B-factor distribution          :   0.734
  Inside/Outside distribution    :   1.016
==============

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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      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
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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.