WHAT IF Check report

This file was created 2013-12-26 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 pdb4brh.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.836
CA-only RMS fit for the two chains : 0.481

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Warning: Topology could not be determined for some ligands

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

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

 721 TMV   (1395-)  A  -         Atom types
 723 MES   (1397-)  A  -         OK
 724 DVT   (1398-)  A  -         Atom types
 726 TMV   (1395-)  B  -         Atom types
 728 DVT   (1398-)  B  -         Atom types
 731 MES   (1397-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 220 ASP   ( 253-)  A  - A OD2 bound to  725  CL   (1399-)  A  -  CL
 579 ASP   ( 253-)  B  - A OD2 bound to  729  CL   (1400-)  B  -  CL

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'.

 362 THR   (  36-)  B      OG1
 362 THR   (  36-)  B      CG2

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: 6

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: 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.

 220 ASP   ( 253-)  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

 |  0.995579  0.000245 -0.000200|
 |  0.000245  0.994927  0.000080|
 | -0.000200  0.000080  0.995815|
Proposed new scale matrix

 |  0.016089 -0.000004  0.004749|
 | -0.000003  0.011720  0.000000|
 |  0.000003 -0.000001  0.014481|
With corresponding cell

    A    =  62.158  B   =  85.321  C    =  72.008
    Alpha=  90.004  Beta= 106.457  Gamma=  89.972

The CRYST1 cell dimensions

    A    =  62.435  B   =  85.759  C    =  72.306
    Alpha=  90.000  Beta= 106.440  Gamma=  90.000

Variance: 506.055
(Under-)estimated Z-score: 16.579

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.

  25 HIS   (  58-)  A      CG   ND1  CE1 109.71    4.1
 201 MET   ( 234-)  A      CG   SD   CE  114.25    6.1
 220 ASP   ( 253-)  A     -C    N    CA  113.15   -4.7
 220 ASP   ( 253-)  A      C    CA   CB  120.81    5.6
 382 ARG   (  56-)  B      CB   CG   CD  104.71   -4.7
 448 ARG   ( 122-)  B      CG   CD   NE  103.59   -4.1
 533 HIS   ( 207-)  B      CG   ND1  CE1 109.63    4.0
 579 ASP   ( 253-)  B     -C    N    CA  113.29   -4.7
 579 ASP   ( 253-)  B      C    CA   CB  120.85    5.7
 718 ARG   ( 392-)  B      CG   CD   NE   99.13   -6.7

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.

 220 ASP   ( 253-)  A

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 586 ASN   ( 260-)  B    6.53
 566 ASN   ( 240-)  B    4.48
 130 ASP   ( 163-)  A    4.43

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.

  50 PRO   (  83-)  A    -2.7
 409 PRO   (  83-)  B    -2.6
 416 PRO   (  90-)  B    -2.6
 642 LEU   ( 316-)  B    -2.6
 398 HIS   (  72-)  B    -2.5
 283 LEU   ( 316-)  A    -2.5
 538 LEU   ( 212-)  B    -2.5
 179 LEU   ( 212-)  A    -2.3
  12 ILE   (  45-)  A    -2.3
 655 ILE   ( 329-)  B    -2.2
  75 ILE   ( 108-)  A    -2.2
 414 ILE   (  88-)  B    -2.1
 476 GLU   ( 150-)  B    -2.1
  57 PRO   (  90-)  A    -2.1
 541 TYR   ( 215-)  B    -2.1

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.

   2 ASP   (  35-)  A  omega poor
   4 ASN   (  37-)  A  Poor phi/psi
  27 TYR   (  60-)  A  omega poor
  32 ASP   (  65-)  A  Poor phi/psi
  35 ASN   (  68-)  A  Poor phi/psi
  39 HIS   (  72-)  A  Poor phi/psi
  49 LYS   (  82-)  A  PRO omega poor
  69 LEU   ( 102-)  A  omega poor
  70 LEU   ( 103-)  A  omega poor
  85 THR   ( 118-)  A  Poor phi/psi, omega poor
 110 GLN   ( 143-)  A  omega poor
 139 ASP   ( 172-)  A  Poor phi/psi
 215 ASP   ( 248-)  A  Poor phi/psi
 225 GLN   ( 258-)  A  omega poor
 280 ASN   ( 313-)  A  Poor phi/psi
 283 LEU   ( 316-)  A  omega poor
 350 ASP   ( 383-)  A  Poor phi/psi
 357 LEU   ( 390-)  A  omega poor
 394 ASN   (  68-)  B  Poor phi/psi
 408 LYS   (  82-)  B  PRO omega poor
 409 PRO   (  83-)  B  Poor phi/psi
 428 LEU   ( 102-)  B  omega poor
 429 LEU   ( 103-)  B  omega poor
 435 HIS   ( 109-)  B  Poor phi/psi
 436 ASN   ( 110-)  B  Poor phi/psi
 444 THR   ( 118-)  B  Poor phi/psi, omega poor
 498 ASP   ( 172-)  B  Poor phi/psi
 505 ASN   ( 179-)  B  omega poor
 574 ASP   ( 248-)  B  Poor phi/psi
 584 GLN   ( 258-)  B  omega poor
 603 LYS   ( 277-)  B  Poor phi/psi
 639 ASN   ( 313-)  B  Poor phi/psi
 642 LEU   ( 316-)  B  omega poor
 709 ASP   ( 383-)  B  Poor phi/psi
 716 LEU   ( 390-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -0.863

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.

 321 SER   ( 354-)  A    0.35
  94 SER   ( 127-)  A    0.40

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!

   3 THR   (  36-)  A      0
   8 LYS   (  41-)  A      0
  20 THR   (  53-)  A      0
  28 SER   (  61-)  A      0
  34 THR   (  67-)  A      0
  35 ASN   (  68-)  A      0
  39 HIS   (  72-)  A      0
  45 ASN   (  78-)  A      0
  49 LYS   (  82-)  A      0
  50 PRO   (  83-)  A      0
  55 ILE   (  88-)  A      0
  57 PRO   (  90-)  A      0
  70 LEU   ( 103-)  A      0
  74 PRO   ( 107-)  A      0
  76 HIS   ( 109-)  A      0
  77 ASN   ( 110-)  A      0
  79 PRO   ( 112-)  A      0
  85 THR   ( 118-)  A      0
  90 LEU   ( 123-)  A      0
 109 GLN   ( 142-)  A      0
 110 GLN   ( 143-)  A      0
 111 SER   ( 144-)  A      0
 112 GLN   ( 145-)  A      0
 113 TRP   ( 146-)  A      0
 117 GLU   ( 150-)  A      0
And so on for a total of 264 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]

  50 PRO   (  83-)  A    0.46 HIGH
  79 PRO   ( 112-)  A    0.18 LOW
 219 PRO   ( 252-)  A    0.07 LOW
 345 PRO   ( 378-)  A    0.16 LOW
 578 PRO   ( 252-)  B    0.18 LOW
 616 PRO   ( 290-)  B    0.08 LOW
 668 PRO   ( 342-)  B    0.47 HIGH

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].

   5 PRO   (  38-)  A  -117.2 half-chair C-delta/C-gamma (-126 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.

 731 MES   (1397-)  A      C7  <->  732 HOH   (2156 )  A      O      0.43    2.37  INTRA
 290 GLN   ( 323-)  A    A NE2 <->  732 HOH   (2224 )  A      O      0.42    2.28  INTRA
  56 GLN   (  89-)  A      NE2 <->  732 HOH   (2054 )  A      O      0.40    2.30  INTRA
 670 ASP   ( 344-)  B      OD2 <->  676 TYR   ( 350-)  B      OH     0.30    2.10  INTRA
 167 LYS   ( 200-)  A      NZ  <->  178 GLU   ( 211-)  A      OE1    0.26    2.44  INTRA BF
 448 ARG   ( 122-)  B    A NH2 <->  485 GLU   ( 159-)  B      OE1    0.24    2.46  INTRA BL
 436 ASN   ( 110-)  B      N   <->  471 GLN   ( 145-)  B      O      0.24    2.46  INTRA
 723 MES   (1397-)  A      C8  <->  732 HOH   (2248 )  A      O      0.20    2.60  INTRA
 670 ASP   ( 344-)  B      CG  <->  676 TYR   ( 350-)  B      OH     0.19    2.61  INTRA
 526 LYS   ( 200-)  B      NZ  <->  537 GLU   ( 211-)  B      OE1    0.18    2.52  INTRA
  31 THR   (  64-)  A      OG1 <->  732 HOH   (2032 )  A      O      0.15    2.25  INTRA
 717 HIS   ( 391-)  B    A ND1 <->  733 HOH   (2188 )  B      O      0.14    2.56  INTRA
 674 TYR   ( 348-)  B      OH  <->  675 GLN   ( 349-)  B      NE2    0.14    2.56  INTRA
 435 HIS   ( 109-)  B      NE2 <->  733 HOH   (2056 )  B      O      0.14    2.56  INTRA BF
 723 MES   (1397-)  A      O2S <->  732 HOH   (2139 )  A      O      0.14    2.26  INTRA
 243 HIS   ( 276-)  A      ND1 <->  723 MES   (1397-)  A      O3S    0.13    2.57  INTRA
  25 HIS   (  58-)  A      NE2 <->  350 ASP   ( 383-)  A      OD2    0.12    2.58  INTRA BL
  46 LYS   (  79-)  A      NZ  <->   68 MET   ( 101-)  A      O      0.11    2.59  INTRA
 232 LYS   ( 265-)  A      NZ  <->  233 GLU   ( 266-)  A      OE2    0.10    2.60  INTRA
 649 GLN   ( 323-)  B    A NE2 <->  733 HOH   (2168 )  B      O      0.10    2.60  INTRA
 490 TRP   ( 164-)  B      CE2 <->  494 ASN   ( 168-)  B      ND2    0.09    3.01  INTRA BL
  76 HIS   ( 109-)  A      ND1 <->  732 HOH   (2067 )  A      O      0.09    2.61  INTRA
 227 ASN   ( 260-)  A      OD1 <->  732 HOH   (2175 )  A      O      0.07    2.33  INTRA
 368 HIS   (  42-)  B      ND1 <->  389 ASP   (  63-)  B      OD1    0.07    2.63  INTRA BL
 290 GLN   ( 323-)  A    A OE1 <->  294 ASN   ( 327-)  A    A ND2    0.07    2.63  INTRA
 609 GLN   ( 283-)  B      N   <->  610 PRO   ( 284-)  B      CD     0.07    2.93  INTRA BL
 295 GLN   ( 328-)  A      CD  <->  732 HOH   (2226 )  A      O      0.07    2.73  INTRA
 123 GLY   ( 156-)  A      N   <->  579 ASP   ( 253-)  B    A OD1    0.07    2.63  INTRA BL
 384 HIS   (  58-)  B      NE2 <->  709 ASP   ( 383-)  B      OD2    0.06    2.64  INTRA BL
 203 HIS   ( 236-)  A      ND1 <->  559 GLU   ( 233-)  B      OE1    0.05    2.65  INTRA BL
 250 GLN   ( 283-)  A      N   <->  251 PRO   ( 284-)  A      CD     0.05    2.95  INTRA BL
   4 ASN   (  37-)  A      N   <->    5 PRO   (  38-)  A      CD     0.05    2.95  INTRA
 277 HIS   ( 310-)  A      ND1 <->  732 HOH   (2213 )  A      O      0.05    2.65  INTRA
  93 GLN   ( 126-)  A      NE2 <->  732 HOH   (2078 )  A      O      0.05    2.65  INTRA
 471 GLN   ( 145-)  B      C   <->  733 HOH   (2058 )  B      O      0.04    2.76  INTRA
 602 HIS   ( 276-)  B      ND1 <->  731 MES   (1397-)  A      O1S    0.04    2.66  INTRA
 250 GLN   ( 283-)  A    A NE2 <->  732 HOH   (2187 )  A      O      0.04    2.66  INTRA
 587 ALA   ( 261-)  B      N   <->  588 PRO   ( 262-)  B      CD     0.03    2.97  INTRA BL
 200 GLU   ( 233-)  A      OE1 <->  562 HIS   ( 236-)  B      ND1    0.03    2.67  INTRA BL
 189 TYR   ( 222-)  A      OH  <->  191 HIS   ( 224-)  A      ND1    0.02    2.68  INTRA BL
 204 GLN   ( 237-)  A      OE1 <->  602 HIS   ( 276-)  B      NE2    0.02    2.68  INTRA BL
 642 LEU   ( 316-)  B      O   <->  699 ILE   ( 373-)  B      N      0.02    2.68  INTRA BL
   2 ASP   (  35-)  A      N   <->  732 HOH   (2001 )  A      O      0.01    2.69  INTRA
 527 ASN   ( 201-)  B      N   <->  535 GLN   ( 209-)  B      OE1    0.01    2.69  INTRA
 207 ASN   ( 240-)  A      ND2 <->  220 ASP   ( 253-)  A    A OD1    0.01    2.69  INTRA BL
 586 ASN   ( 260-)  B      ND2 <->  657 HIS   ( 331-)  B      NE2    0.01    2.99  INTRA

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.

  49 LYS   (  82-)  A      -6.43
 408 LYS   (  82-)  B      -6.41
 367 LYS   (  41-)  B      -5.65
 706 GLN   ( 380-)  B      -5.63
 501 LYS   ( 175-)  B      -5.60
 347 GLN   ( 380-)  A      -5.56
 666 GLN   ( 340-)  B      -5.46
 307 GLN   ( 340-)  A      -5.40
 277 HIS   ( 310-)  A      -5.39
 274 GLN   ( 307-)  A      -5.10
 654 GLN   ( 328-)  B      -5.07

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.

 144 VAL   ( 177-)  A       146 - ASN    179- ( A)         -4.61

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.

 636 HIS   ( 310-)  B   -2.67

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.

 732 HOH   (2103 )  A      O     91.81   -6.72   13.88
 732 HOH   (2225 )  A      O     56.74   16.66   49.33

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.

 114 GLN   ( 147-)  A
 295 GLN   ( 328-)  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.

  19 SER   (  52-)  A      N
  33 ASP   (  66-)  A      N
  45 ASN   (  78-)  A      ND2
  75 ILE   ( 108-)  A      N
 135 ASN   ( 168-)  A      ND2
 143 SER   ( 176-)  A      N
 147 LYS   ( 180-)  A      N
 156 GLY   ( 189-)  A      N
 157 ALA   ( 190-)  A      N
 158 SER   ( 191-)  A      N
 248 GLN   ( 281-)  A      NE2
 267 ILE   ( 300-)  A      N
 285 ASN   ( 318-)  A      ND2
 351 TRP   ( 384-)  A      N
 378 SER   (  52-)  B      N
 434 ILE   ( 108-)  B      N
 437 ILE   ( 111-)  B      N
 483 ASN   ( 157-)  B      N
 494 ASN   ( 168-)  B      ND2
 506 LYS   ( 180-)  B      N
 515 GLY   ( 189-)  B      N
 516 ALA   ( 190-)  B      N
 517 SER   ( 191-)  B      N
 553 LEU   ( 227-)  B      N
 581 GLU   ( 255-)  B      N
 607 GLN   ( 281-)  B      NE2
 626 ILE   ( 300-)  B      N
 649 GLN   ( 323-)  B    A NE2
 710 TRP   ( 384-)  B      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.

 130 ASP   ( 163-)  A      OD1
 285 ASN   ( 318-)  A      OD1
 358 HIS   ( 391-)  A      ND1
 489 ASP   ( 163-)  B      OD1
 644 ASN   ( 318-)  B      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 722  MG   (1396-)  A   -.-  -.-  Part of ionic cluster
 727  MG   (1396-)  B   -.-  -.-  Part of ionic cluster

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.

  30 ASP   (  63-)  A   H-bonding suggests Asn
 104 ASP   ( 137-)  A   H-bonding suggests Asn; but Alt-Rotamer
 130 ASP   ( 163-)  A   H-bonding suggests Asn; but Alt-Rotamer
 389 ASP   (  63-)  B   H-bonding suggests Asn; Ligand-contact
 489 ASP   ( 163-)  B   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 :   0.185
  2nd generation packing quality :  -1.579
  Ramachandran plot appearance   :   0.017
  chi-1/chi-2 rotamer normality  :  -0.863
  Backbone conformation          :  -0.975

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.810
  Bond angles                    :   0.920
  Omega angle restraints         :   1.073
  Side chain planarity           :   1.410
  Improper dihedral distribution :   1.137
  B-factor distribution          :   0.486
  Inside/Outside distribution    :   0.933

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 : 1.69


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.810
  Bond angles                    :   0.920
  Omega angle restraints         :   1.073
  Side chain planarity           :   1.410
  Improper dihedral distribution :   1.137
  B-factor distribution          :   0.486
  Inside/Outside distribution    :   0.933
==============

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

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Bond lengths and angles, DNA/RNA
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      New parameters for the refinement of nucleic acid-containing structures
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DSSP
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      Dictionary of protein secondary structure: pattern
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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,
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    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.