WHAT IF Check report

This file was created 2013-12-10 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 pdb4esj.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: C 1 2 1
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
There is also strong SEQRES evidence for a multiplicity of: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 16
Polymer chain multiplicity and SEQRES multiplicity disagree 2 4
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)
There is some evidence, though, for multiplicity and Z: 2 8

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.

 532 AZI   ( 303-)  A  -

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

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

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

  76 ASP   (  78-)  A  -   CG
  76 ASP   (  78-)  A  -   OD1
  76 ASP   (  78-)  A  -   OD2
 320 ASP   (  78-)  B  -   CG
 320 ASP   (  78-)  B  -   OD1
 320 ASP   (  78-)  B  -   OD2
 345 LYS   ( 103-)  B  -   CG
 345 LYS   ( 103-)  B  -   CD
 345 LYS   ( 103-)  B  -   CE
 345 LYS   ( 103-)  B  -   NZ

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: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

 369 LYS   ( 127-)  B    High
 370 PRO   ( 128-)  B    High
 371 TRP   ( 138-)  B    High
 433 GLU   ( 200-)  B    High
 444 ARG   ( 211-)  B    High
 450 LYS   ( 217-)  B    High
 451 ASN   ( 218-)  B    High
 454 VAL   ( 221-)  B    High
 455 LYS   ( 222-)  B    High
 481 ARG   ( 248-)  B    High
 485 ARG   ( 252-)  B    High
 523 DCYT  (   8-)  F    High

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: Arginine nomenclature problem

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

 368 ARG   ( 126-)  B

Warning: Tyrosine convention problem

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

  31 TYR   (  29-)  A
  35 TYR   (  33-)  A
  79 TYR   (  81-)  A
 297 TYR   (  55-)  B
 323 TYR   (  81-)  B
 343 TYR   ( 101-)  B

Warning: Phenylalanine convention problem

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

  52 PHE   (  54-)  A
 164 PHE   ( 172-)  A
 169 PHE   ( 177-)  A
 291 PHE   (  45-)  B
 388 PHE   ( 155-)  B
 405 PHE   ( 172-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  28 ASP   (  26-)  A
  76 ASP   (  78-)  A
 320 ASP   (  78-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

   4 GLU   (   2-)  A
  13 GLU   (  11-)  A
 158 GLU   ( 166-)  A
 348 GLU   ( 106-)  B
 424 GLU   ( 191-)  B
 433 GLU   ( 200-)  B

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

 |  0.998545 -0.000392 -0.000547|
 | -0.000392  0.998240 -0.000305|
 | -0.000547 -0.000305  0.998582|
Proposed new scale matrix

 |  0.007675  0.000004  0.003138|
 |  0.000004  0.010179  0.000003|
 |  0.000007  0.000004  0.012895|
With corresponding cell

    A    = 130.324  B   =  98.242  C    =  83.797
    Alpha=  90.015  Beta= 112.267  Gamma=  90.045

The CRYST1 cell dimensions

    A    = 130.518  B   =  98.411  C    =  83.884
    Alpha=  90.000  Beta= 112.210  Gamma=  90.000

Variance: 80.306
(Under-)estimated Z-score: 6.605

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.

 497 DGUA  (  10-)  C      N9   C8   N7  113.14    4.1
 501 DGUA  (   4-)  D      N9   C8   N7  113.18    4.2
 507 DGUA  (  10-)  D      N9   C8   N7  113.14    4.1
 508 DGUA  (   3-)  E      N9   C8   N7  113.22    4.2
 509 DGUA  (   4-)  E      N9   C8   N7  113.16    4.1
 515 DGUA  (  10-)  E      N9   C8   N7  113.18    4.2
 518 DGUA  (   3-)  F      N9   C8   N7  113.12    4.0
 519 DGUA  (   4-)  F      N9   C8   N7  113.18    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   (   2-)  A
  13 GLU   (  11-)  A
  28 ASP   (  26-)  A
  76 ASP   (  78-)  A
 158 GLU   ( 166-)  A
 320 ASP   (  78-)  B
 348 GLU   ( 106-)  B
 368 ARG   ( 126-)  B
 424 GLU   ( 191-)  B
 433 GLU   ( 200-)  B

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.

 287 PRO   (  41-)  B    -2.7
 353 LEU   ( 111-)  B    -2.2
 478 PHE   ( 245-)  B    -2.2
 109 LEU   ( 111-)  A    -2.1
 347 PHE   ( 105-)  B    -2.1
 127 LEU   ( 129-)  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.

   6 HIS   (   4-)  A  omega poor
  17 SER   (  15-)  A  Poor phi/psi
  32 ARG   (  30-)  A  omega poor
  42 ASN   (  40-)  A  PRO omega poor
  45 ASN   (  43-)  A  omega poor
  58 SER   (  60-)  A  Poor phi/psi
  76 ASP   (  78-)  A  Poor phi/psi
  89 ASP   (  91-)  A  Poor phi/psi, omega poor
  92 PRO   (  94-)  A  omega poor
  94 PHE   (  96-)  A  omega poor
 103 PHE   ( 105-)  A  Poor phi/psi
 112 PRO   ( 114-)  A  omega poor
 125 LYS   ( 127-)  A  Poor phi/psi
 134 ASN   ( 142-)  A  omega poor
 233 GLU   ( 241-)  A  Poor phi/psi
 240 ARG   ( 248-)  A  Poor phi/psi
 286 ASN   (  40-)  B  PRO omega poor
 289 ASN   (  43-)  B  omega poor
 291 PHE   (  45-)  B  omega poor
 302 SER   (  60-)  B  Poor phi/psi
 320 ASP   (  78-)  B  Poor phi/psi, omega poor
 333 ASP   (  91-)  B  Poor phi/psi, omega poor
 336 PRO   (  94-)  B  omega poor
 346 ASN   ( 104-)  B  omega poor
 347 PHE   ( 105-)  B  Poor phi/psi
 356 PRO   ( 114-)  B  omega poor
 474 GLU   ( 241-)  B  Poor phi/psi
 481 ARG   ( 248-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.887

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.

 177 SER   ( 185-)  A    0.39
 418 SER   ( 185-)  B    0.40
 447 SER   ( 214-)  B    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!

   5 LEU   (   3-)  A      0
   7 PHE   (   5-)  A      0
   8 ASN   (   6-)  A      0
   9 LEU   (   7-)  A      0
  16 LYS   (  14-)  A      0
  17 SER   (  15-)  A      0
  32 ARG   (  30-)  A      0
  33 GLN   (  31-)  A      0
  34 SER   (  32-)  A      0
  36 CYS   (  34-)  A      0
  39 CYS   (  37-)  A      0
  41 ASN   (  39-)  A      0
  42 ASN   (  40-)  A      0
  46 HIS   (  44-)  A      0
  47 PHE   (  45-)  A      0
  48 PRO   (  50-)  A      0
  49 VAL   (  51-)  A      0
  50 ALA   (  52-)  A      0
  57 CYS   (  59-)  A      0
  58 SER   (  60-)  A      0
  67 LYS   (  69-)  A      0
  69 ASN   (  71-)  A      0
  76 ASP   (  78-)  A      0
  78 ALA   (  80-)  A      0
  90 ASN   (  92-)  A      0
And so on for a total of 206 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]

 281 PRO   (  35-)  B    0.13 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].

   1 PRO   (  -1-)  A   -47.8 half-chair C-beta/C-alpha (-54 degrees)
  48 PRO   (  50-)  A   100.6 envelop C-beta (108 degrees)
 370 PRO   ( 128-)  B    48.8 half-chair C-delta/C-gamma (54 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.

 320 ASP   (  78-)  B      CG  <->  321 GLY   (  79-)  B      N      0.38    2.62  INTRA BF
  76 ASP   (  78-)  A      CG  <->   77 GLY   (  79-)  A      N      0.28    2.72  INTRA
 511 DTHY  (   6-)  E      N3  <->  520 6MA   (   5-)  F      N1     0.27    2.73  INTRA BF
 510 6MA   (   5-)  E      N1  <->  521 DTHY  (   6-)  F      N3     0.22    2.78  INTRA BF
 492 6MA   (   5-)  C      N1  <->  503 DTHY  (   6-)  D      N3     0.22    2.78  INTRA BL
 508 DGUA  (   3-)  E      N1  <->  523 DCYT  (   8-)  F      N3     0.21    2.79  INTRA BF
 493 DTHY  (   6-)  C      N3  <->  502 6MA   (   5-)  D      N1     0.19    2.81  INTRA BL
 492 6MA   (   5-)  C      N3  <->  529 UNX   ( 101-)  C     UNK     0.17    2.93  INTRA BL
 143 LYS   ( 151-)  A      NZ  <->  166 GLN   ( 174-)  A      OE1    0.17    2.53  INTRA BF
 503 DTHY  (   6-)  D      O2  <->  530 UNX   ( 102-)  D     UNK     0.17    2.63  INTRA BL
   8 ASN   (   6-)  A      ND2 <->  532 AZI   ( 303-)  A      N1     0.16    2.84  INTRA BL
 283 CYS   (  37-)  B      SG  <->  285 ASN   (  39-)  B      ND2    0.16    3.14  INTRA BF
 312 GLY   (  70-)  B      N   <->  343 TYR   ( 101-)  B      O      0.16    2.54  INTRA BF
 508 DGUA  (   3-)  E      O6  <->  523 DCYT  (   8-)  F      N4     0.15    2.55  INTRA BF
  85 ARG   (  87-)  A      NH1 <->   90 ASN   (  92-)  A      O      0.15    2.55  INTRA BF
   2 HIS   (   0-)  A      ND1 <->  533 HOH   ( 491 )  A      O      0.14    2.56  INTRA BL
 504 DCYT  (   7-)  D      O2  <->  529 UNX   ( 101-)  C     UNK     0.14    2.66  INTRA BL
 515 DGUA  (  10-)  E      N1  <->  516 DCYT  (   1-)  F      N3     0.13    2.87  INTRA BF
  41 ASN   (  39-)  A      ND2 <->   54 CYS   (  56-)  A      SG     0.13    3.17  INTRA BL
 496 DADE  (   9-)  C      N1  <->  499 DTHY  (   2-)  D      N3     0.13    2.87  INTRA BL
 529 UNX   ( 101-)  C     UNK  <->  535 HOH   ( 205 )  C      O      0.12    2.68  INTRA BL
 227 GLN   ( 235-)  A      NE2 <->  492 6MA   (   5-)  C      N7     0.12    2.88  INTRA BL
 512 DCYT  (   7-)  E      N3  <->  519 DGUA  (   4-)  F      N1     0.12    2.88  INTRA BF
 488 DCYT  (   1-)  C      N3  <->  507 DGUA  (  10-)  D      N1     0.09    2.91  INTRA BL
  49 VAL   (  51-)  A      CG1 <->   51 ASP   (  53-)  A      OD2    0.09    2.71  INTRA BF
And so on for a total of 73 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

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

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

 481 ARG   ( 248-)  B      -7.51
 240 ARG   ( 248-)  A      -7.34
 124 ARG   ( 126-)  A      -7.06
 369 LYS   ( 127-)  B      -7.01
 368 ARG   ( 126-)  B      -6.82
 433 GLU   ( 200-)  B      -5.94
 192 GLU   ( 200-)  A      -5.61
 125 LYS   ( 127-)  A      -5.54
 277 GLN   (  31-)  B      -5.48
 380 GLN   ( 147-)  B      -5.47
 139 GLN   ( 147-)  A      -5.44
  33 GLN   (  31-)  A      -5.32
 155 ARG   ( 163-)  A      -5.29
   2 HIS   (   0-)  A      -5.14
 396 ARG   ( 163-)  B      -5.09
 276 ARG   (  30-)  B      -5.03

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: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

  75 ASN   (  77-)  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.

  32 ARG   (  30-)  A      NE
  35 TYR   (  33-)  A      N
  73 THR   (  75-)  A      N
  81 THR   (  83-)  A      N
 197 THR   ( 205-)  A      OG1
 216 ASN   ( 224-)  A      N
 227 GLN   ( 235-)  A      NE2
 230 ARG   ( 238-)  A      NH1
 250 HIS   (   4-)  B    A N
 279 TYR   (  33-)  B      N
 289 ASN   (  43-)  B      ND2
 290 HIS   (  44-)  B      N
 315 SER   (  73-)  B      N
 335 ASN   (  93-)  B      N
 342 THR   ( 100-)  B      OG1
 346 ASN   ( 104-)  B      N
 456 ASN   ( 223-)  B      ND2
 457 ASN   ( 224-)  B      N
 468 GLN   ( 235-)  B      NE2
 483 LYS   ( 250-)  B      N
 493 DTHY  (   6-)  C      N3
 503 DTHY  (   6-)  D      N3
 511 DTHY  (   6-)  E      N3
 521 DTHY  (   6-)  F      N3
Only metal coordination for    6 HIS  (   4-) A      ND1

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.

 217 HIS   ( 225-)  A      ND1
 300 HIS   (  58-)  B      ND1
 306 GLU   (  64-)  B      OE1
 320 ASP   (  78-)  B      OD2
 458 HIS   ( 225-)  B      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.

 533 HOH   ( 415 )  A      O  0.91  K  4 *2
 534 HOH   ( 444 )  B      O  1.09  K  4 *2 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.

 231 ASP   ( 239-)  A   H-bonding suggests Asn
 430 ASP   ( 197-)  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 :   0.215
  2nd generation packing quality :  -0.510
  Ramachandran plot appearance   :  -0.385
  chi-1/chi-2 rotamer normality  :  -0.887
  Backbone conformation          :  -0.288

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.499 (tight)
  Bond angles                    :   0.654 (tight)
  Omega angle restraints         :   1.065
  Side chain planarity           :   0.602 (tight)
  Improper dihedral distribution :   0.659
  B-factor distribution          :   0.568
  Inside/Outside distribution    :   0.994

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 : 2.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.499 (tight)
  Bond angles                    :   0.654 (tight)
  Omega angle restraints         :   1.065
  Side chain planarity           :   0.602 (tight)
  Improper dihedral distribution :   0.659
  B-factor distribution          :   0.568
  Inside/Outside distribution    :   0.994
==============

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Checking checks
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