WHAT IF Check report

This file was created 2011-12-18 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 pdb1ylk.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 : 0.723
CA-only RMS fit for the two chains : 0.199

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 : 0.720
CA-only RMS fit for the two chains : 0.262

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: A and D

All-atom RMS fit for the two chains : 0.602
CA-only RMS fit for the two chains : 0.183

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 D

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 : 0.627
CA-only RMS fit for the two chains : 0.225

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

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 D

All-atom RMS fit for the two chains : 0.677
CA-only RMS fit for the two chains : 0.188

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 D

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.

 654 SCN   ( 502-)  B  -
 655 SCN   ( 505-)  A  -
 657 SCN   ( 501-)  A  -
 659 SCN   ( 503-)  C  -
 661 SCN   ( 504-)  D  -

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

Note: Ramachandran plot

Chain identifier: D

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

Warning: Occupancies atoms do not add up to 1.0.

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

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

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

  44 ARG   (  44-)  A    0.50

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :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

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Phenylalanine convention problem

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

 139 PHE   ( 139-)  A
 302 PHE   ( 139-)  B
 465 PHE   ( 139-)  C
 628 PHE   ( 139-)  D

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.

 285 ASP   ( 122-)  B
 611 ASP   ( 122-)  D

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.

  82 GLU   (  82-)  A
 125 GLU   ( 125-)  A
 213 GLU   (  50-)  B
 245 GLU   (  82-)  B
 271 GLU   ( 108-)  B
 288 GLU   ( 125-)  B
 376 GLU   (  50-)  C
 408 GLU   (  82-)  C
 451 GLU   ( 125-)  C
 539 GLU   (  50-)  D
 571 GLU   (  82-)  D
 649 GLU   ( 160-)  D

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

 |  0.997864  0.000140  0.000180|
 |  0.000140  0.995875  0.000024|
 |  0.000180  0.000024  0.996358|
Proposed new scale matrix

 |  0.010005 -0.000001 -0.000002|
 |  0.000000  0.006517  0.000000|
 | -0.000001  0.000000  0.006395|
With corresponding cell

    A    =  99.946  B   = 153.448  C    = 156.365
    Alpha=  90.002  Beta=  89.979  Gamma=  89.993

The CRYST1 cell dimensions

    A    = 100.164  B   = 154.074  C    = 156.943
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 235.909
(Under-)estimated Z-score: 11.320

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.

  87 HIS   (  87-)  A      CG   ND1  CE1 109.63    4.0

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.

  82 GLU   (  82-)  A
 125 GLU   ( 125-)  A
 213 GLU   (  50-)  B
 245 GLU   (  82-)  B
 271 GLU   ( 108-)  B
 285 ASP   ( 122-)  B
 288 GLU   ( 125-)  B
 376 GLU   (  50-)  C
 408 GLU   (  82-)  C
 451 GLU   ( 125-)  C
 539 GLU   (  50-)  D
 571 GLU   (  82-)  D
 611 ASP   ( 122-)  D
 649 GLU   ( 160-)  D

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.

 610 PRO   ( 121-)  D    -2.6
 192 HIS   (  29-)  B    -2.6
 249 LEU   (  86-)  B    -2.5
 412 LEU   (  86-)  C    -2.5
 284 PRO   ( 121-)  B    -2.4
 575 LEU   (  86-)  D    -2.3
 345 LYS   (  19-)  C    -2.1
 462 VAL   ( 136-)  C    -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.

  20 GLY   (  20-)  A  PRO omega poor
  52 GLU   (  52-)  A  omega poor
  78 LEU   (  78-)  A  omega poor
  86 LEU   (  86-)  A  omega poor
  90 ASP   (  90-)  A  Poor phi/psi
 118 GLU   ( 118-)  A  Poor phi/psi
 183 GLY   (  20-)  B  PRO omega poor
 215 GLU   (  52-)  B  omega poor
 216 ALA   (  53-)  B  omega poor
 249 LEU   (  86-)  B  omega poor
 253 ASP   (  90-)  B  Poor phi/psi
 281 GLU   ( 118-)  B  Poor phi/psi
 346 GLY   (  20-)  C  PRO omega poor
 378 GLU   (  52-)  C  omega poor
 387 CYS   (  61-)  C  Poor phi/psi
 404 LEU   (  78-)  C  omega poor
 416 ASP   (  90-)  C  Poor phi/psi
 444 GLU   ( 118-)  C  Poor phi/psi
 475 PHE   ( 149-)  C  omega poor
 488 THR   ( 162-)  C  Poor phi/psi
 509 GLY   (  20-)  D  PRO omega poor
 541 GLU   (  52-)  D  omega poor
 575 LEU   (  86-)  D  omega poor
 579 ASP   (  90-)  D  Poor phi/psi
 607 GLU   ( 118-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.407

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.

 179 SER   (  16-)  B    0.36
 233 SER   (  70-)  B    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!

  19 LYS   (  19-)  A      0
  24 MET   (  24-)  A      0
  25 PRO   (  25-)  A      0
  29 HIS   (  29-)  A      0
  36 MET   (  36-)  A      0
  46 LEU   (  46-)  A      0
  50 GLU   (  50-)  A      0
  52 GLU   (  52-)  A      0
  53 ALA   (  53-)  A      0
  57 ARG   (  57-)  A      0
  58 ASN   (  58-)  A      0
  59 ALA   (  59-)  A      0
  61 CYS   (  61-)  A      0
  62 VAL   (  62-)  A      0
  78 LEU   (  78-)  A      0
  80 THR   (  80-)  A      0
  89 THR   (  89-)  A      0
  91 CYS   (  91-)  A      0
  95 THR   (  95-)  A      0
 113 PRO   ( 113-)  A      0
 115 TRP   ( 115-)  A      0
 118 GLU   ( 118-)  A      0
 119 SER   ( 119-)  A      0
 140 VAL   ( 140-)  A      0
 141 THR   ( 141-)  A      0
And so on for a total of 250 lines.

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].

 184 PRO   (  21-)  B   -54.1 half-chair C-beta/C-alpha (-54 degrees)
 284 PRO   ( 121-)  B   -60.5 half-chair C-beta/C-alpha (-54 degrees)
 347 PRO   (  21-)  C   -35.2 envelop C-alpha (-36 degrees)
 447 PRO   ( 121-)  C   -55.6 half-chair C-beta/C-alpha (-54 degrees)
 610 PRO   ( 121-)  D   -57.6 half-chair C-beta/C-alpha (-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.

 591 LYS   ( 102-)  D      NZ  <->  665 HOH   ( 475 )  D      O      0.44    2.26  INTRA
 238 GLN   (  75-)  B      NE2 <->  663 HOH   ( 564 )  B      O      0.43    2.27  INTRA
 265 LYS   ( 102-)  B      NZ  <->  663 HOH   ( 567 )  B      O      0.42    2.28  INTRA
 454 ARG   ( 128-)  C      NE  <->  489 PRO   ( 163-)  C      CD     0.28    2.82  INTRA
  44 ARG   (  44-)  A      NH2 <->  662 HOH   ( 551 )  A      O      0.22    2.48  INTRA
 428 LYS   ( 102-)  C      NZ  <->  664 HOH   ( 556 )  C      O      0.21    2.49  INTRA
 361 CYS   (  35-)  C      SG  <->  362 MET   (  36-)  C      N      0.16    3.04  INTRA
 198 CYS   (  35-)  B      SG  <->  199 MET   (  36-)  B      N      0.16    3.04  INTRA
 570 ARG   (  81-)  D      O   <->  633 THR   ( 144-)  D      N      0.15    2.55  INTRA
 402 ARG   (  76-)  C      NH2 <->  597 GLU   ( 108-)  D      OE2    0.14    2.56  INTRA
 524 CYS   (  35-)  D      SG  <->  525 MET   (  36-)  D      N      0.13    3.07  INTRA
 198 CYS   (  35-)  B      SG  <->  223 GLY   (  60-)  B      N      0.12    3.18  INTRA
 543 HIS   (  54-)  D      ND1 <->  563 SER   (  74-)  D      OG     0.10    2.60  INTRA BL
  35 CYS   (  35-)  A      SG  <->   36 MET   (  36-)  A      N      0.09    3.11  INTRA
 187 MET   (  24-)  B      N   <->  188 PRO   (  25-)  B      CD     0.09    2.91  INTRA
  51 GLY   (  51-)  A      N   <->  201 ALA   (  38-)  B      O      0.08    2.62  INTRA BL
 295 ARG   ( 132-)  B      NH2 <->  663 HOH   ( 554 )  B      O      0.07    2.63  INTRA BF
 521 ILE   (  32-)  D      O   <->  545 ILE   (  56-)  D      N      0.07    2.63  INTRA BL
  38 ALA   (  38-)  A      O   <->  214 GLY   (  51-)  B      N      0.07    2.63  INTRA BL
  60 GLY   (  60-)  A      CA  <->   93 MET   (  93-)  A      CG     0.07    3.13  INTRA
  44 ARG   (  44-)  A      NE  <->  662 HOH   ( 549 )  A      O      0.07    2.63  INTRA
 291 ARG   ( 128-)  B      NE  <->  325 THR   ( 162-)  B      O      0.06    2.64  INTRA
 108 GLU   ( 108-)  A      OE2 <->  239 ARG   (  76-)  B      NH2    0.06    2.64  INTRA
 354 LYS   (  28-)  C      NZ  <->  378 GLU   (  52-)  C      OE2    0.06    2.64  INTRA
 532 TYR   (  43-)  D      O   <->  537 ILE   (  48-)  D      N      0.06    2.64  INTRA BL
And so on for a total of 51 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

  19 LYS   (  19-)  A      -6.56
 182 LYS   (  19-)  B      -6.33
 508 LYS   (  19-)  D      -6.33
  24 MET   (  24-)  A      -5.83
 513 MET   (  24-)  D      -5.76
 350 MET   (  24-)  C      -5.71
 187 MET   (  24-)  B      -5.70
 345 LYS   (  19-)  C      -5.50
 597 GLU   ( 108-)  D      -5.00

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

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: D

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

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

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.

 664 HOH   ( 566 )  C      O
Metal-coordinating Histidine residue  88 fixed to   1
Metal-coordinating Histidine residue 251 fixed to   1
Metal-coordinating Histidine residue 414 fixed to   1
Metal-coordinating Histidine residue 577 fixed to   1

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.

 306 HIS   ( 143-)  B
 355 HIS   (  29-)  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.

  30 ILE   (  30-)  A      N
  98 ASP   (  98-)  A      N
  99 ASP   (  99-)  A      N
 115 TRP   ( 115-)  A      N
 122 ASP   ( 122-)  A      N
 143 HIS   ( 143-)  A      N
 193 ILE   (  30-)  B      N
 259 PHE   (  96-)  B      N
 285 ASP   ( 122-)  B      N
 306 HIS   ( 143-)  B      N
 345 LYS   (  19-)  C      N
 356 ILE   (  30-)  C      N
 418 GLY   (  92-)  C      N
 441 TRP   ( 115-)  C      N
 448 ASP   ( 122-)  C      N
 519 ILE   (  30-)  D      N
 585 PHE   (  96-)  D      N
 611 ASP   ( 122-)  D      N
 632 HIS   ( 143-)  D      N
Only metal coordination for   88 HIS  (  88-) A      NE2
Only metal coordination for  251 HIS  (  88-) B      NE2
Only metal coordination for  414 HIS  (  88-) C      NE2
Only metal coordination for  577 HIS  (  88-) D      NE2

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.

  52 GLU   (  52-)  A      OE2
  87 HIS   (  87-)  A      ND1
 250 HIS   (  87-)  B      ND1
 322 ASN   ( 159-)  B      OD1
 413 HIS   (  87-)  C      ND1
 576 HIS   (  87-)  D      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.

 663 HOH   ( 551 )  B      O  1.18 NA  5 *2 Ion-B
 664 HOH   ( 537 )  C      O  0.95  K  4 Ion-B
 665 HOH   ( 462 )  D      O  1.05  K  5 Ion-B
 665 HOH   ( 477 )  D      O  0.88  K  5 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.

 107 ASP   ( 107-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.811
  2nd generation packing quality :  -0.266
  Ramachandran plot appearance   :   0.683
  chi-1/chi-2 rotamer normality  :  -1.407
  Backbone conformation          :   0.409

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.496 (tight)
  Bond angles                    :   0.664 (tight)
  Omega angle restraints         :   1.078
  Side chain planarity           :   0.495 (tight)
  Improper dihedral distribution :   0.623
  B-factor distribution          :   0.370
  Inside/Outside distribution    :   0.963

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.3
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   1.2
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.496 (tight)
  Bond angles                    :   0.664 (tight)
  Omega angle restraints         :   1.078
  Side chain planarity           :   0.495 (tight)
  Improper dihedral distribution :   0.623
  B-factor distribution          :   0.370
  Inside/Outside distribution    :   0.963
==============

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