WHAT IF Check report

This file was created 2012-01-31 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 pdb2w68.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 : 0.880
CA-only RMS fit for the two chains : 0.558

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

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 C

All-atom RMS fit for the two chains : 1.002
CA-only RMS fit for the two chains : 0.646

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 C

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: B and C

All-atom RMS fit for the two chains : 0.947
CA-only RMS fit for the two chains : 0.613

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: B and C

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 64904.355
Volume of the Unit Cell V= 2272950.8
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.378
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.320

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.

 584 SIA   (1217-)  A  -
 585 GAL   (1219-)  A  -
 586 BGC   (1220-)  A  -
 587 SIA   (1217-)  B  -
 588 GAL   (1219-)  B  -
 589 BGC   (1220-)  B  -
 590 BGC   (1220-)  C  -
 591 GAL   (1219-)  C  -
 592 SIA   (1216-)  C  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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

Warning: Missing atoms

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

   1 ALA   (  22-)  A      CB

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 157 ARG   ( 178-)  A
 350 ARG   ( 178-)  B
 545 ARG   ( 178-)  C

Warning: Tyrosine convention problem

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

 378 TYR   ( 206-)  B

Warning: Phenylalanine convention problem

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

 114 PHE   ( 135-)  A
 190 PHE   ( 211-)  A
 307 PHE   ( 135-)  B
 394 PHE   (  27-)  C
 459 PHE   (  92-)  C
 502 PHE   ( 135-)  C
 523 PHE   ( 156-)  C

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.

  17 ASP   (  38-)  A
  40 ASP   (  61-)  A
 158 ASP   ( 179-)  A
 187 ASP   ( 208-)  A
 210 ASP   (  38-)  B
 351 ASP   ( 179-)  B
 380 ASP   ( 208-)  B
 405 ASP   (  38-)  C

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.

  78 GLU   (  99-)  A
 113 GLU   ( 134-)  A
 131 GLU   ( 152-)  A
 271 GLU   (  99-)  B
 306 GLU   ( 134-)  B
 329 GLU   ( 157-)  B
 466 GLU   (  99-)  C
 501 GLU   ( 134-)  C
 503 GLU   ( 136-)  C
 524 GLU   ( 157-)  C

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

 |  0.998097  0.000066 -0.000129|
 |  0.000066  0.996903  0.000439|
 | -0.000129  0.000439  1.000093|
Proposed new scale matrix

 |  0.007229  0.000000  0.000000|
 |  0.000000  0.005076 -0.000002|
 |  0.000002 -0.000005  0.012050|
With corresponding cell

    A    = 138.336  B   = 197.016  C    =  82.988
    Alpha=  89.950  Beta=  90.008  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 138.600  B   = 197.620  C    =  82.980
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 64.714
(Under-)estimated Z-score: 5.929

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.

  13 ASP   (  34-)  A      C    CA   CB  102.07   -4.2
 462 ARG   (  95-)  C      CB   CG   CD  105.68   -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.

  17 ASP   (  38-)  A
  40 ASP   (  61-)  A
  78 GLU   (  99-)  A
 113 GLU   ( 134-)  A
 131 GLU   ( 152-)  A
 157 ARG   ( 178-)  A
 158 ASP   ( 179-)  A
 187 ASP   ( 208-)  A
 210 ASP   (  38-)  B
 271 GLU   (  99-)  B
 306 GLU   ( 134-)  B
 329 GLU   ( 157-)  B
 350 ARG   ( 178-)  B
 351 ASP   ( 179-)  B
 380 ASP   ( 208-)  B
 405 ASP   (  38-)  C
 466 GLU   (  99-)  C
 501 GLU   ( 134-)  C
 503 GLU   ( 136-)  C
 524 GLU   ( 157-)  C
 545 ARG   ( 178-)  C

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 142 GLY   ( 163-)  A    4.49

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.

 255 THR   (  83-)  B    -2.8
 141 PRO   ( 162-)  A    -2.8
 288 THR   ( 116-)  B    -2.7
  62 THR   (  83-)  A    -2.7
 518 THR   ( 151-)  C    -2.4
 120 ARG   ( 141-)  A    -2.3
 423 VAL   (  56-)  C    -2.3
 428 ASP   (  61-)  C    -2.3
 226 SER   (  54-)  B    -2.3
 577 LYS   ( 210-)  C    -2.2
 399 THR   (  32-)  C    -2.2
 425 THR   (  58-)  C    -2.2
 323 THR   ( 151-)  B    -2.2
 347 LYS   ( 175-)  B    -2.2
 228 VAL   (  56-)  B    -2.2
 241 GLN   (  69-)  B    -2.1
  35 VAL   (  56-)  A    -2.1
 333 LEU   ( 161-)  B    -2.1
 446 TYR   (  79-)  C    -2.1
  95 THR   ( 116-)  A    -2.1
 293 PRO   ( 121-)  B    -2.1
 140 LEU   ( 161-)  A    -2.1
 542 LYS   ( 175-)  C    -2.1
 204 THR   (  32-)  B    -2.1
 359 LYS   ( 187-)  B    -2.1
 558 ILE   ( 191-)  C    -2.1
 230 THR   (  58-)  B    -2.1
  13 ASP   (  34-)  A    -2.0
 436 GLN   (  69-)  C    -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.

   7 ASP   (  28-)  A  omega poor
  17 ASP   (  38-)  A  omega poor
  28 ASN   (  49-)  A  omega poor
  30 ASN   (  51-)  A  Poor phi/psi
  39 ALA   (  60-)  A  Poor phi/psi
  77 THR   (  98-)  A  omega poor
  84 GLY   ( 105-)  A  omega poor
  95 THR   ( 116-)  A  Poor phi/psi
  97 ARG   ( 118-)  A  omega poor
 137 LEU   ( 158-)  A  omega poor
 159 ASN   ( 180-)  A  Poor phi/psi
 165 SER   ( 186-)  A  Poor phi/psi
 169 MET   ( 190-)  A  omega poor
 171 VAL   ( 192-)  A  omega poor
 193 GLN   ( 214-)  A  omega poor
 200 ASP   (  28-)  B  omega poor
 207 THR   (  35-)  B  omega poor
 223 ASN   (  51-)  B  Poor phi/psi
 234 GLY   (  62-)  B  Poor phi/psi
 288 THR   ( 116-)  B  Poor phi/psi
 290 ARG   ( 118-)  B  omega poor
 345 ASP   ( 173-)  B  Poor phi/psi
 352 ASN   ( 180-)  B  Poor phi/psi
 362 MET   ( 190-)  B  Poor phi/psi, omega poor
 364 VAL   ( 192-)  B  omega poor
 377 ALA   ( 205-)  B  omega poor
 379 ARG   ( 207-)  B  omega poor
 387 GLY   ( 215-)  B  omega poor
 400 GLY   (  33-)  C  omega poor
 401 ASP   (  34-)  C  Poor phi/psi
 418 ASN   (  51-)  C  Poor phi/psi
 421 SER   (  54-)  C  Poor phi/psi
 424 LEU   (  57-)  C  omega poor
 425 THR   (  58-)  C  omega poor
 427 ALA   (  60-)  C  Poor phi/psi, omega poor
 428 ASP   (  61-)  C  Poor phi/psi
 429 GLY   (  62-)  C  omega poor
 430 MET   (  63-)  C  PRO omega poor
 437 GLY   (  70-)  C  omega poor
 458 SER   (  91-)  C  Poor phi/psi
 471 SER   ( 104-)  C  Poor phi/psi
 475 ILE   ( 108-)  C  omega poor
 483 THR   ( 116-)  C  Poor phi/psi
 536 SER   ( 169-)  C  omega poor
 546 ASP   ( 179-)  C  omega poor
 557 MET   ( 190-)  C  Poor phi/psi, omega poor
 559 VAL   ( 192-)  C  omega poor
 chi-1/chi-2 correlation Z-score : -3.720

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.720

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.

 262 SER   (  90-)  B    0.33
  69 SER   (  90-)  A    0.36

Warning: Unusual backbone conformations

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

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

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

   3 MET   (  24-)  A      0
  10 ALA   (  31-)  A      0
  11 THR   (  32-)  A      0
  16 PHE   (  37-)  A      0
  17 ASP   (  38-)  A      0
  22 GLN   (  43-)  A      0
  24 TRP   (  45-)  A      0
  28 ASN   (  49-)  A      0
  29 THR   (  50-)  A      0
  30 ASN   (  51-)  A      0
  33 SER   (  54-)  A      0
  39 ALA   (  60-)  A      0
  40 ASP   (  61-)  A      0
  48 GLN   (  69-)  A      0
  50 ILE   (  71-)  A      0
  53 ARG   (  74-)  A      0
  54 ALA   (  75-)  A      0
  55 GLN   (  76-)  A      0
  73 TRP   (  94-)  A      0
  79 MET   ( 100-)  A      0
  83 SER   ( 104-)  A      0
  86 MET   ( 107-)  A      0
  88 THR   ( 109-)  A      0
  90 TYR   ( 111-)  A      0
  93 ASN   ( 114-)  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 : 7.891

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]

 334 PRO   ( 162-)  B    0.11 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].

 100 PRO   ( 121-)  A    19.3 half-chair N/C-delta (18 degrees)
 141 PRO   ( 162-)  A   -41.0 envelop C-alpha (-36 degrees)
 293 PRO   ( 121-)  B   -16.3 half-chair C-alpha/N (-18 degrees)
 488 PRO   ( 121-)  C    36.6 envelop C-delta (36 degrees)
 529 PRO   ( 162-)  C   -40.4 envelop C-alpha (-36 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.

 196 MET   (  24-)  B      CG  <->  594 HOH   (2042 )  B      O      1.01    1.79  INTRA BF
 590 BGC   (1220-)  C      O4  <->  591 GAL   (1219-)  C      C1     0.97    1.43  INTRA BL
 591 GAL   (1219-)  C      O3  <->  592 SIA   (1216-)  C      C2     0.95    1.45  INTRA BL
 246 ARG   (  74-)  B      NH1 <->  587 SIA   (1217-)  B      O1A    0.72    1.98  INTRA BF
 590 BGC   (1220-)  C      C4  <->  591 GAL   (1219-)  C      C1     0.69    2.41  INTRA BL
 591 GAL   (1219-)  C      C3  <->  592 SIA   (1216-)  C      C2     0.62    2.48  INTRA BL
 427 ALA   (  60-)  C      O   <->  429 GLY   (  62-)  C      N      0.54    2.16  INTRA BF
 196 MET   (  24-)  B      CB  <->  594 HOH   (2042 )  B      O      0.43    2.37  INTRA BF
 196 MET   (  24-)  B      N   <->  594 HOH   (2001 )  B      O      0.40    2.30  INTRA BL
 462 ARG   (  95-)  C      NH1 <->  579 GLU   ( 212-)  C      OE1    0.40    2.30  INTRA BF
 465 THR   (  98-)  C      CG2 <->  576 ILE   ( 209-)  C      CD1    0.37    2.83  INTRA BF
 390 ALA   (  23-)  C      O   <->  582 GLY   ( 215-)  C      C      0.36    2.44  INTRA BF
 234 GLY   (  62-)  B      C   <->  235 MET   (  63-)  B      SD     0.34    2.96  INTRA BF
 196 MET   (  24-)  B      SD  <->  594 HOH   (2042 )  B      O      0.32    2.68  INTRA BF
 527 PHE   ( 160-)  C      CG  <->  595 HOH   (2037 )  C      O      0.28    2.52  INTRA BF
 337 ASN   ( 165-)  B      ND2 <->  594 HOH   (2032 )  B      O      0.26    2.44  INTRA BF
 361 ASN   ( 189-)  B      N   <->  594 HOH   (2039 )  B      O      0.23    2.47  INTRA BL
 427 ALA   (  60-)  C      C   <->  429 GLY   (  62-)  C      N      0.23    2.67  INTRA BF
  53 ARG   (  74-)  A      NH1 <->  584 SIA   (1217-)  A      O1B    0.23    2.47  INTRA BF
 254 SER   (  82-)  B      N   <->  257 GLN   (  85-)  B      OE1    0.22    2.48  INTRA BL
 115 GLU   ( 136-)  A      OE2 <->  506 THR   ( 139-)  C      CG2    0.22    2.58  INTRA BL
 451 ASN   (  84-)  C      ND2 <->  595 HOH   (2016 )  C      O      0.21    2.49  INTRA BF
 461 TRP   (  94-)  C      NE1 <->  527 PHE   ( 160-)  C      CD2    0.20    2.90  INTRA BF
 362 MET   ( 190-)  B      CG  <->  364 VAL   ( 192-)  B      CG2    0.19    3.01  INTRA BL
  95 THR   ( 116-)  A      CG2 <->  593 HOH   (2023 )  A      O      0.19    2.61  INTRA BL
And so on for a total of 106 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Warning: Abnormal packing environment for some residues

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

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

 430 MET   (  63-)  C      -6.33
 117 GLN   ( 138-)  A      -5.82
 310 GLN   ( 138-)  B      -5.69
 505 GLN   ( 138-)  C      -5.33
 410 GLN   (  43-)  C      -5.29
  22 GLN   (  43-)  A      -5.26
 215 GLN   (  43-)  B      -5.23
 193 GLN   ( 214-)  A      -5.17
 235 MET   (  63-)  B      -5.14
 459 PHE   (  92-)  C      -5.13
 223 ASN   (  51-)  B      -5.09
  30 ASN   (  51-)  A      -5.03
 359 LYS   ( 187-)  B      -5.02

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Warning: Low packing Z-score for some residues

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

  26 GLN   (  47-)  A   -2.62

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 595 HOH   (2002 )  C      O    -15.95  -35.35    6.71

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.

 594 HOH   (2040 )  B      O
 595 HOH   (2001 )  C      O
 595 HOH   (2004 )  C      O
 595 HOH   (2014 )  C      O
 595 HOH   (2021 )  C      O
 595 HOH   (2048 )  C      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  48 GLN   (  69-)  A
 352 ASN   ( 180-)  B
 397 ASN   (  30-)  C
 451 ASN   (  84-)  C

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.

   1 ALA   (  22-)  A      N
   8 TYR   (  29-)  A      OH
  11 THR   (  32-)  A      N
  18 SER   (  39-)  A      N
  20 ALA   (  41-)  A      N
  40 ASP   (  61-)  A      N
  42 MET   (  63-)  A      N
  61 SER   (  82-)  A      OG
 116 GLY   ( 137-)  A      N
 144 ASN   ( 165-)  A      N
 153 GLY   ( 174-)  A      N
 169 MET   ( 190-)  A      N
 172 TRP   ( 193-)  A      NE1
 177 SER   ( 198-)  A      N
 186 ARG   ( 207-)  A      NE
 186 ARG   ( 207-)  A      NH2
 210 ASP   (  38-)  B      N
 211 SER   (  39-)  B      N
 233 ASP   (  61-)  B      N
 235 MET   (  63-)  B      N
 243 ILE   (  71-)  B      N
 284 TYR   ( 112-)  B      N
 300 SER   ( 128-)  B      N
 309 GLY   ( 137-)  B      N
 365 TRP   ( 193-)  B      NE1
 370 SER   ( 198-)  B      N
 379 ARG   ( 207-)  B      NE
 389 ALA   (  22-)  C      N
 396 TYR   (  29-)  C      OH
 399 THR   (  32-)  C      N
 406 SER   (  39-)  C      N
 428 ASP   (  61-)  C      N
 430 MET   (  63-)  C      N
 436 GLN   (  69-)  C      NE2
 448 LEU   (  81-)  C      N
 451 ASN   (  84-)  C      N
 464 THR   (  97-)  C      OG1
 469 VAL   ( 102-)  C      N
 479 TYR   ( 112-)  C      N
 542 LYS   ( 175-)  C      N
 560 TRP   ( 193-)  C      NE1
 565 SER   ( 198-)  C      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.

  48 GLN   (  69-)  A      OE1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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+.

 583  CA   (1211-)  A   -.-  -.-  Too few ligands (0)

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.

 593 HOH   (2008 )  A      O  0.93  K  6 Ion-B

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.

 105 ASP   ( 126-)  A   H-bonding suggests Asn; but Alt-Rotamer
 180 ASP   ( 201-)  A   H-bonding suggests Asn
 298 ASP   ( 126-)  B   H-bonding suggests Asn; but Alt-Rotamer
 568 ASP   ( 201-)  C   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 :  -0.168
  2nd generation packing quality :  -1.129
  Ramachandran plot appearance   :  -2.151
  chi-1/chi-2 rotamer normality  :  -3.720 (poor)
  Backbone conformation          :  -0.831

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.736
  Bond angles                    :   0.824
  Omega angle restraints         :   1.435 (loose)
  Side chain planarity           :   0.628 (tight)
  Improper dihedral distribution :   0.860
  B-factor distribution          :   0.393
  Inside/Outside distribution    :   0.984

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.736
  Bond angles                    :   0.824
  Omega angle restraints         :   1.435 (loose)
  Side chain planarity           :   0.628 (tight)
  Improper dihedral distribution :   0.860
  B-factor distribution          :   0.393
  Inside/Outside distribution    :   0.984
==============

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.