WHAT IF Check report

This file was created 2011-12-17 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3qxd.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 D

All-atom RMS fit for the two chains : 1.181
CA-only RMS fit for the two chains : 0.701

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 E

All-atom RMS fit for the two chains : 1.511
CA-only RMS fit for the two chains : 1.252

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 E

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: F and C

All-atom RMS fit for the two chains : 3.194
CA-only RMS fit for the two chains : 2.321

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: F and C

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.

  95 GLU   (  98-)  A  -   CB
  95 GLU   (  98-)  A  -   CG
  95 GLU   (  98-)  A  -   CD
  95 GLU   (  98-)  A  -   OE1
  95 GLU   (  98-)  A  -   OE2
 313 GLN   ( 136-)  B  -   CG
 313 GLN   ( 136-)  B  -   CD
 313 GLN   ( 136-)  B  -   OE1
 313 GLN   ( 136-)  B  -   NE2
 604 TYR   (  60-)  E  -   CG
 604 TYR   (  60-)  E  -   CD1
 604 TYR   (  60-)  E  -   CD2
 604 TYR   (  60-)  E  -   CE1
 604 TYR   (  60-)  E  -   CE2
 604 TYR   (  60-)  E  -   CZ
 604 TYR   (  60-)  E  -   OH
 651 GLN   ( 107-)  E  -   CB
 651 GLN   ( 107-)  E  -   CG
 651 GLN   ( 107-)  E  -   CD
 651 GLN   ( 107-)  E  -   OE1
 651 GLN   ( 107-)  E  -   NE2
 653 LEU   ( 109-)  E  -   CB
 653 LEU   ( 109-)  E  -   CG
 653 LEU   ( 109-)  E  -   CD1
 653 LEU   ( 109-)  E  -   CD2
 749 PRO   (  87-)  C  -   CB
 749 PRO   (  87-)  C  -   CG
 749 PRO   (  87-)  C  -   CD

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

  95 GLU   (  98-)  A  -   N
  95 GLU   (  98-)  A  -   CA
  95 GLU   (  98-)  A  -   C
  95 GLU   (  98-)  A  -   O
 749 PRO   (  87-)  C  -   N
 749 PRO   (  87-)  C  -   CA
Residue with missing backbone atom(s)  748 GLN  ( 100-) F  -

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 748 GLN   ( 100-)  F  -

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: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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'.

 609 LYS   (  65-)  E      CB
 609 LYS   (  65-)  E      CG
 609 LYS   (  65-)  E      CD
 609 LYS   (  65-)  E      CE
 609 LYS   (  65-)  E      NZ
 748 GLN   ( 100-)  F      O
 748 GLN   ( 100-)  F      CG
 748 GLN   ( 100-)  F      CD
 748 GLN   ( 100-)  F      OE1
 748 GLN   ( 100-)  F      NE2

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.

  79 ILE   (  82-)  A    Zero

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

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 3.28

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: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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.

  47 ARG   (  50-)  A
 248 ARG   (  71-)  B
 257 ARG   (  80-)  B
 307 ARG   ( 130-)  B
 414 ARG   (  50-)  D
 615 ARG   (  71-)  E
 624 ARG   (  80-)  E
 674 ARG   ( 130-)  E

Warning: Tyrosine convention problem

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

  76 TYR   (  79-)  A
 147 TYR   ( 150-)  A
 158 TYR   ( 161-)  A
 224 TYR   (  47-)  B
 348 TYR   ( 171-)  B
 377 TYR   (  13-)  D
 443 TYR   (  79-)  D
 514 TYR   ( 150-)  D
 604 TYR   (  60-)  E
 715 TYR   ( 171-)  E

Warning: Phenylalanine convention problem

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

 105 PHE   ( 108-)  A
 109 PHE   ( 112-)  A
 177 PHE   ( 180-)  A
 190 PHE   (  13-)  B
 194 PHE   (  17-)  B
 217 PHE   (  40-)  B
 266 PHE   (  89-)  B
 415 PHE   (  51-)  D
 476 PHE   ( 112-)  D
 509 PHE   ( 145-)  D
 557 PHE   (  13-)  E
 633 PHE   (  89-)  E

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.

 168 ASP   ( 171-)  A

Warning: Glutamic acid convention problem

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

  27 GLU   (  30-)  A
  68 GLU   (  71-)  A
 138 GLU   ( 141-)  A
 176 GLU   ( 179-)  A
 199 GLU   (  22-)  B
 315 GLU   ( 138-)  B
 368 GLU   (   4-)  D
 394 GLU   (  30-)  D
 543 GLU   ( 179-)  D
 682 GLU   ( 138-)  E

Geometric checks

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.

  27 GLU   (  30-)  A
  47 ARG   (  50-)  A
  68 GLU   (  71-)  A
 138 GLU   ( 141-)  A
 168 ASP   ( 171-)  A
 176 GLU   ( 179-)  A
 199 GLU   (  22-)  B
 248 ARG   (  71-)  B
 257 ARG   (  80-)  B
 307 ARG   ( 130-)  B
 315 GLU   ( 138-)  B
 368 GLU   (   4-)  D
 394 GLU   (  30-)  D
 414 ARG   (  50-)  D
 543 GLU   ( 179-)  D
 615 ARG   (  71-)  E
 624 ARG   (  80-)  E
 674 ARG   ( 130-)  E
 682 GLU   ( 138-)  E

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.

 456 LEU   (  92-)  D    -2.8
 110 THR   ( 113-)  A    -2.6
 150 PHE   ( 153-)  A    -2.6
 380 PRO   (  16-)  D    -2.6
 477 THR   ( 113-)  D    -2.6
  13 PRO   (  16-)  A    -2.5
 340 THR   ( 163-)  B    -2.5
 334 THR   ( 157-)  B    -2.5
 649 LYS   ( 105-)  E    -2.4
 750 VAL   (  88-)  C    -2.3
 701 THR   ( 157-)  E    -2.3
 464 ARG   ( 100-)  D    -2.2
 517 PHE   ( 153-)  D    -2.2
  96 LEU   (  99-)  A    -2.1
 582 VAL   (  38-)  E    -2.1
 215 VAL   (  38-)  B    -2.1
 173 LYS   ( 176-)  A    -2.1
 114 VAL   ( 117-)  A    -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.

  12 ASN   (  15-)  A  PRO omega poor
  15 GLN   (  18-)  A  Poor phi/psi
  75 ASN   (  78-)  A  Poor phi/psi
  76 TYR   (  79-)  A  Poor phi/psi
 106 ILE   ( 109-)  A  omega poor
 108 LYS   ( 111-)  A  Poor phi/psi
 110 THR   ( 113-)  A  PRO omega poor
 140 HIS   ( 143-)  A  Poor phi/psi
 210 ASN   (  33-)  B  Poor phi/psi
 267 THR   (  90-)  B  Poor phi/psi
 287 GLN   ( 110-)  B  Poor phi/psi
 300 TYR   ( 123-)  B  PRO omega poor
 311 ASN   ( 134-)  B  Poor phi/psi
 330 TRP   ( 153-)  B  Poor phi/psi
 379 ASN   (  15-)  D  PRO omega poor
 382 GLN   (  18-)  D  Poor phi/psi
 442 ASN   (  78-)  D  Poor phi/psi
 464 ARG   ( 100-)  D  Poor phi/psi
 475 LYS   ( 111-)  D  Poor phi/psi
 477 THR   ( 113-)  D  PRO omega poor
 479 PRO   ( 115-)  D  Poor phi/psi
 507 HIS   ( 143-)  D  Poor phi/psi
 540 LYS   ( 176-)  D  omega poor
 577 ASN   (  33-)  E  Poor phi/psi
 649 LYS   ( 105-)  E  Poor phi/psi
 654 GLN   ( 110-)  E  Poor phi/psi
 667 TYR   ( 123-)  E  PRO omega poor
 697 TRP   ( 153-)  E  Poor phi/psi
 750 VAL   (  88-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.211

Warning: Unusual backbone conformations

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

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

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

   8 GLU   (  11-)  A      0
  12 ASN   (  15-)  A      0
  23 PHE   (  26-)  A      0
  29 PHE   (  32-)  A      0
  30 HIS   (  33-)  A      0
  48 PHE   (  51-)  A      0
  76 TYR   (  79-)  A      0
  96 LEU   (  99-)  A      0
  97 ARG   ( 100-)  A      0
 100 ASN   ( 103-)  A      0
 107 ASP   ( 110-)  A      0
 108 LYS   ( 111-)  A      0
 109 PHE   ( 112-)  A      0
 110 THR   ( 113-)  A      0
 111 PRO   ( 114-)  A      0
 112 PRO   ( 115-)  A      0
 113 VAL   ( 116-)  A      0
 120 ARG   ( 123-)  A      0
 127 THR   ( 130-)  A      0
 134 PHE   ( 137-)  A      0
 140 HIS   ( 143-)  A      0
 164 HIS   ( 167-)  A      0
 169 GLU   ( 172-)  A      0
 175 TRP   ( 178-)  A      0
 176 GLU   ( 179-)  A      0
And so on for a total of 298 lines.

Warning: Backbone oxygen evaluation

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

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

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

 302 GLY   ( 125-)  B   1.63   59

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].

  99 PRO   ( 102-)  A   102.8 envelop C-beta (108 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.

 599 ARG   (  55-)  E      NH2 <->  768 HOH   ( 461 )  E      O      0.41    2.29  INTRA BF
 767 HOH   ( 392 )  D      O   <->  768 HOH   ( 386 )  E      O      0.39    2.01  INTRA
 176 GLU   ( 179-)  A      OE2 <->  649 LYS   ( 105-)  E      NZ     0.37    2.33  INTRA BF
 172 LEU   ( 175-)  A      O   <->  765 HOH   ( 319 )  A      O      0.36    2.04  INTRA BL
 765 HOH   ( 413 )  A      O   <->  765 HOH   ( 415 )  A      O      0.35    1.85  INTRA
 494 THR   ( 130-)  D      O   <->  767 HOH   ( 432 )  D      O      0.27    2.13  INTRA
 466 PRO   ( 102-)  D      O   <->  767 HOH   ( 202 )  D      O      0.26    2.14  INTRA
 123 LYS   ( 126-)  A      NZ  <->  765 HOH   ( 314 )  A      O      0.25    2.45  INTRA BF
 144 LYS   ( 147-)  A      NZ  <->  146 HIS   ( 149-)  A      NE2    0.25    2.75  INTRA BL
 767 HOH   ( 226 )  D      O   <->  767 HOH   ( 245 )  D      O      0.24    1.96  INTRA
 604 TYR   (  60-)  E      O   <->  607 SER   (  63-)  E      N      0.24    2.46  INTRA
 179 ASP   (   2-)  B      N   <->  766 HOH   ( 290 )  B      O      0.24    2.46  INTRA
 765 HOH   ( 356 )  A      O   <->  770 HOH   ( 402 )  C      O      0.23    2.17  INTRA
 143 ARG   ( 146-)  A      NH1 <->  765 HOH   ( 376 )  A      O      0.23    2.47  INTRA
 749 PRO   (  87-)  C      CD  <->  754 ARG   (  92-)  C      NE     0.22    2.88  INTRA
 765 HOH   ( 302 )  A      O   <->  770 HOH   ( 305 )  C      O      0.22    2.18  INTRA BL
 572 GLU   (  28-)  E      OE1 <->  615 ARG   (  71-)  E      NH1    0.22    2.48  INTRA
 586 SER   (  42-)  E      OG  <->  768 HOH   ( 227 )  E      O      0.20    2.20  INTRA BL
 511 LYS   ( 147-)  D      CE  <->  513 HIS   ( 149-)  D      CE1    0.20    3.00  INTRA
 768 HOH   ( 287 )  E      O   <->  768 HOH   ( 288 )  E      O      0.19    2.01  INTRA
 674 ARG   ( 130-)  E      NH1 <->  720 GLU   ( 176-)  E      OE1    0.18    2.52  INTRA BF
 578 GLN   (  34-)  E      O   <->  768 HOH   ( 416 )  E      O      0.18    2.22  INTRA
 767 HOH   ( 293 )  D      O   <->  767 HOH   ( 321 )  D      O      0.18    2.02  INTRA
 249 ARG   (  72-)  B      O   <->  766 HOH   ( 217 )  B      O      0.18    2.22  INTRA
 765 HOH   ( 296 )  A      O   <->  765 HOH   ( 297 )  A      O      0.18    2.02  INTRA
And so on for a total of 108 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: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

  97 ARG   ( 100-)  A      -6.13
 464 ARG   ( 100-)  D      -5.93
 286 LEU   ( 109-)  B      -5.74
 683 LYS   ( 139-)  E      -5.72
 316 LYS   ( 139-)  B      -5.65
 746 LEU   (  98-)  F      -5.34
 382 GLN   (  18-)  D      -5.31
 177 PHE   ( 180-)  A      -5.26
  15 GLN   (  18-)  A      -5.20
 747 MET   (  99-)  F      -5.15
  76 TYR   (  79-)  A      -5.05
 443 TYR   (  79-)  D      -5.04
 653 LEU   ( 109-)  E      -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: D

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: E

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: F

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: 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: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: C

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.

  91 ASN   (  94-)  A
 187 GLN   (  10-)  B
 554 GLN   (  10-)  E
 608 GLN   (  64-)  E
 614 GLN   (  70-)  E

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.

  42 LEU   (  45-)  A      N
  92 SER   (  95-)  A      N
 118 TRP   ( 121-)  A      NE1
 127 THR   ( 130-)  A      N
 129 VAL   ( 132-)  A      N
 156 ASP   ( 159-)  A      N
 206 ARG   (  29-)  B      NE
 223 GLU   (  46-)  B      N
 232 ARG   (  55-)  B      NE
 234 ASP   (  57-)  B      N
 252 VAL   (  75-)  B      N
 289 HIS   ( 112-)  B      N
 440 ARG   (  76-)  D      NH1
 523 ASP   ( 159-)  D      N
 548 ARG   (   4-)  E      N
 573 ARG   (  29-)  E      NE
 590 GLU   (  46-)  E      N
 752 LYS   (  90-)  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.

   8 GLU   (  11-)  A      OE1
  63 ASP   (  66-)  A      OD2
 375 GLU   (  11-)  D      OE1
 430 ASP   (  66-)  D      OD2
 513 HIS   ( 149-)  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.

 765 HOH   ( 213 )  A      O  0.95  K  4
 765 HOH   ( 221 )  A      O  1.11  K  4
 765 HOH   ( 232 )  A      O  0.78 NA  4 *2
 766 HOH   ( 412 )  B      O  0.91 NA  4 *2 H2O-B
 766 HOH   ( 424 )  B      O  0.84 NA  4 *2 Ion-B H2O-B
 767 HOH   ( 187 )  D      O  0.98  K  4
 767 HOH   ( 195 )  D      O  0.85 NA  4 *2
 768 HOH   ( 192 )  E      O  1.11  K  4

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.

  18 GLU   (  21-)  A   H-bonding suggests Gln
 159 ASP   ( 162-)  A   H-bonding suggests Asn; but Alt-Rotamer
 243 ASP   (  66-)  B   H-bonding suggests Asn; but Alt-Rotamer
 385 GLU   (  21-)  D   H-bonding suggests Gln
 430 ASP   (  66-)  D   H-bonding suggests Asn; but Alt-Rotamer

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 :   0.464
  2nd generation packing quality :  -0.909
  Ramachandran plot appearance   :  -0.112
  chi-1/chi-2 rotamer normality  :  -0.211
  Backbone conformation          :   0.139

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.218 (tight)
  Bond angles                    :   0.482 (tight)
  Omega angle restraints         :   0.921
  Side chain planarity           :   0.217 (tight)
  Improper dihedral distribution :   0.449
  B-factor distribution          :   1.254
  Inside/Outside distribution    :   1.046

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.2
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   1.1
  chi-1/chi-2 rotamer normality  :   1.0
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.218 (tight)
  Bond angles                    :   0.482 (tight)
  Omega angle restraints         :   0.921
  Side chain planarity           :   0.217 (tight)
  Improper dihedral distribution :   0.449
  B-factor distribution          :   1.254
  Inside/Outside distribution    :   1.046
==============

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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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Ramachandran plot
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Symmetry Checks
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Ion Checks
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      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
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    M.Nayal and E.Di Cera,
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      Binding Sites
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
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    Acta Cryst. D 59 32--37 (2003).

Checking checks
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      Who checks the checkers
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