WHAT IF Check report

This file was created 2012-01-13 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 pdb1s9v.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 : 0.637
CA-only RMS fit for the two chains : 0.267

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: C and F

All-atom RMS fit for the two chains : 0.830
CA-only RMS fit for the two chains : 0.216

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: C and F

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.

 742 EDO   ( 501-)  A  -
 743 EDO   ( 504-)  A  -
 744 EDO   ( 502-)  D  -
 745 EDO   ( 503-)  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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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'.

 305 ASP   ( 135-)  B      CB
 305 ASP   ( 135-)  B      CG
 305 ASP   ( 135-)  B      OD1
 305 ASP   ( 135-)  B      OD2
 361 LEU   (   1-)  C      CB
 361 LEU   (   1-)  C      CG
 361 LEU   (   1-)  C      CD1
 361 LEU   (   1-)  C      CD2
 362 GLN   (   2-)  C      CB
 362 GLN   (   2-)  C      CG
 362 GLN   (   2-)  C      CD
 362 GLN   (   2-)  C      OE1
 362 GLN   (   2-)  C      NE2
 371 TYR   (  11-)  C      CB
 371 TYR   (  11-)  C      CG
 371 TYR   (  11-)  C      CD1
 371 TYR   (  11-)  C      CD2
 371 TYR   (  11-)  C      CE1
 371 TYR   (  11-)  C      CE2
 371 TYR   (  11-)  C      CZ
 371 TYR   (  11-)  C      OH
 673 ASP   ( 135-)  E      CB
 673 ASP   ( 135-)  E      CG
 673 ASP   ( 135-)  E      OD1
 673 ASP   ( 135-)  E      OD2
 674 GLN   ( 136-)  E      CB
 674 GLN   ( 136-)  E      CG
 674 GLN   ( 136-)  E      CD
 674 GLN   ( 136-)  E      OE1
 674 GLN   ( 136-)  E      NE2
 729 LEU   (   1-)  F      CB
 729 LEU   (   1-)  F      CG
 729 LEU   (   1-)  F      CD1
 729 LEU   (   1-)  F      CD2
 730 GLN   (   2-)  F      CB
 730 GLN   (   2-)  F      CG
 730 GLN   (   2-)  F      CD
 730 GLN   (   2-)  F      OE1
 730 GLN   (   2-)  F      NE2

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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

Crystal temperature (K) :200.000

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

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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.

 319 ARG   ( 149-)  B
 687 ARG   ( 149-)  E

Warning: Tyrosine convention problem

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

  22 TYR   (  22-)  A
 186 TYR   (   9-)  B
 555 TYR   (   9-)  E

Warning: Phenylalanine convention problem

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

  91 PHE   (  92-)  A
 292 PHE   ( 122-)  B
 325 PHE   ( 155-)  B
 462 PHE   (  92-)  D
 516 PHE   ( 146-)  D
 593 PHE   (  47-)  E
 660 PHE   ( 122-)  E
 693 PHE   ( 155-)  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.

 183 ASP   (   6-)  B
 322 ASP   ( 152-)  B
 374 ASP   (   4-)  D
 552 ASP   (   6-)  E
 659 ASP   ( 121-)  E

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.

 133 GLU   ( 134-)  A
 157 GLU   ( 158-)  A
 165 GLU   ( 166-)  A
 199 GLU   (  22-)  B
 246 GLU   (  69-)  B
 273 GLU   (  96-)  B
 357 GLU   ( 187-)  B
 411 GLU   (  40-)  D
 504 GLU   ( 134-)  D
 528 GLU   ( 158-)  D
 592 GLU   (  46-)  E
 632 GLU   (  86-)  E
 642 GLU   (  96-)  E
 675 GLU   ( 137-)  E
 676 GLU   ( 138-)  E
 714 GLU   ( 176-)  E

Geometric checks

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.

  10 VAL   (  10-)  A      N    CA   C    96.95   -5.1
 381 VAL   (  10-)  D      N    CA   C    95.51   -5.6

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.

 133 GLU   ( 134-)  A
 157 GLU   ( 158-)  A
 165 GLU   ( 166-)  A
 183 ASP   (   6-)  B
 199 GLU   (  22-)  B
 246 GLU   (  69-)  B
 273 GLU   (  96-)  B
 319 ARG   ( 149-)  B
 322 ASP   ( 152-)  B
 357 GLU   ( 187-)  B
 374 ASP   (   4-)  D
 411 GLU   (  40-)  D
 504 GLU   ( 134-)  D
 528 GLU   ( 158-)  D
 552 ASP   (   6-)  E
 592 GLU   (  46-)  E
 632 GLU   (  86-)  E
 642 GLU   (  96-)  E
 659 ASP   ( 121-)  E
 675 GLU   ( 137-)  E
 676 GLU   ( 138-)  E
 687 ARG   ( 149-)  E
 714 GLU   ( 176-)  E

Error: Tau angle problems

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

 381 VAL   (  10-)  D    6.02
  10 VAL   (  10-)  A    5.37
 290 THR   ( 120-)  B    4.24

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.

 523 LEU   ( 153-)  D    -2.7
 152 LEU   ( 153-)  A    -2.7
 417 PRO   (  46-)  D    -2.5
 365 PRO   (   5-)  C    -2.4
 487 VAL   ( 117-)  D    -2.3
  46 PRO   (  46-)  A    -2.3
 116 VAL   ( 117-)  A    -2.2
 733 PRO   (   5-)  F    -2.2
 545 LEU   ( 175-)  D    -2.2
   9 GLY   (   9-)  A    -2.2
 380 GLY   (   9-)  D    -2.2
 139 LYS   ( 140-)  A    -2.2
 416 LEU   (  45-)  D    -2.1
 227 VAL   (  50-)  B    -2.1
 596 VAL   (  50-)  E    -2.1
  45 LEU   (  45-)  A    -2.1
 388 GLY   (  17-)  D    -2.0
 701 MET   ( 163-)  E    -2.0
  17 GLY   (  17-)  A    -2.0
 359 ARG   ( 189-)  B    -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.

  17 GLY   (  17-)  A  PRO omega poor
  77 ASN   (  78-)  A  Poor phi/psi
 112 PHE   ( 113-)  A  PRO omega poor
 142 HIS   ( 143-)  A  Poor phi/psi
 210 ASN   (  33-)  B  Poor phi/psi
 266 THR   (  89-)  B  Poor phi/psi
 293 TYR   ( 123-)  B  PRO omega poor
 305 ASP   ( 135-)  B  Poor phi/psi
 323 TRP   ( 153-)  B  Poor phi/psi
 388 GLY   (  17-)  D  PRO omega poor
 448 ASN   (  78-)  D  Poor phi/psi
 483 PHE   ( 113-)  D  PRO omega poor
 485 PRO   ( 115-)  D  Poor phi/psi
 513 HIS   ( 143-)  D  Poor phi/psi
 565 ASN   (  19-)  E  Poor phi/psi
 579 ASN   (  33-)  E  Poor phi/psi
 635 THR   (  89-)  E  Poor phi/psi
 661 TYR   ( 123-)  E  PRO omega poor
 673 ASP   ( 135-)  E  Poor phi/psi
 691 TRP   ( 153-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.670

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.

  71 SER   (  72-)  A    0.36
 442 SER   (  72-)  D    0.36

Warning: Unusual backbone conformations

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

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

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

   3 ASP   (   4-)  A      0
   8 TYR   (   9-)  A      0
  11 ASN   (  11-)  A      0
  16 TYR   (  16-)  A      0
  18 PRO   (  18-)  A      0
  19 SER   (  19-)  A      0
  26 PHE   (  26-)  A      0
  31 GLN   (  31-)  A      0
  32 PHE   (  32-)  A      0
  38 ARG   (  38-)  A      0
  44 CYS   (  44-)  A      0
  50 GLN   (  50-)  A      0
  51 PHE   (  51-)  A      0
  78 SER   (  79-)  A      0
  79 THR   (  80-)  A      0
  98 LEU   (  99-)  A      0
 109 ASP   ( 110-)  A      0
 112 PHE   ( 113-)  A      0
 113 PRO   ( 114-)  A      0
 114 PRO   ( 115-)  A      0
 115 VAL   ( 116-)  A      0
 122 SER   ( 123-)  A      0
 129 GLU   ( 130-)  A      0
 131 VAL   ( 132-)  A      0
 132 SER   ( 133-)  A      0
And so on for a total of 257 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.471

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 290 THR   ( 120-)  B   1.65

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.

 100 GLN   ( 101-)  A      NE2 <->  746 HOH   ( 515 )  A      O      0.30    2.40  INTRA
 294 PRO   ( 124-)  B      CG  <->  296 GLN   ( 126-)  B      NE2    0.25    2.85  INTRA
  11 ASN   (  11-)  A      ND2 <->   61 ASN   (  62-)  A      ND2    0.18    2.67  INTRA BL
 559 GLY   (  13-)  E      C   <->  734 GLN   (   6-)  F      NE2    0.18    2.92  INTRA BL
 187 GLN   (  10-)  B      O   <->  208 ILE   (  31-)  B      N      0.17    2.53  INTRA BL
 582 GLU   (  36-)  E      OE2 <->  585 ARG   (  39-)  E      NE     0.15    2.55  INTRA BL
 537 HIS   ( 167-)  D      CD2 <->  539 GLY   ( 169-)  D      N      0.15    2.95  INTRA
 617 LYS   (  71-)  E      NZ  <->  750 HOH   ( 209 )  E      O      0.13    2.57  INTRA
 185 VAL   (   8-)  B      O   <->  210 ASN   (  33-)  B      N      0.13    2.57  INTRA BL
  11 ASN   (  11-)  A      ND2 <->   22 TYR   (  22-)  A      CE2    0.13    2.97  INTRA BL
 556 GLN   (  10-)  E      O   <->  577 ILE   (  31-)  E      N      0.13    2.57  INTRA BL
   3 ASP   (   4-)  A      OD2 <->  196 ASN   (  19-)  B      N      0.11    2.59  INTRA
 681 VAL   ( 143-)  E      O   <->  698 MET   ( 160-)  E      N      0.10    2.60  INTRA BL
 251 ALA   (  74-)  B      O   <->  255 VAL   (  78-)  B      N      0.10    2.60  INTRA
 385 GLN   (  14-)  D      NE2 <->  552 ASP   (   6-)  E      OD2    0.10    2.60  INTRA
 482 ILE   ( 112-)  D      N   <->  515 PHE   ( 145-)  D      O      0.09    2.61  INTRA BL
 554 VAL   (   8-)  E      O   <->  579 ASN   (  33-)  E      N      0.09    2.61  INTRA BL
 117 ASN   ( 118-)  A      ND2 <->  746 HOH   ( 517 )  A      O      0.09    2.61  INTRA
 232 LEU   (  55-)  B      N   <->  233 PRO   (  56-)  B      CD     0.09    2.91  INTRA
 294 PRO   ( 124-)  B      CB  <->  296 GLN   ( 126-)  B      NE2    0.09    3.01  INTRA
 224 PHE   (  47-)  B      O   <->  239 ASN   (  62-)  B      ND2    0.08    2.62  INTRA
  91 PHE   (  92-)  A      O   <->  105 ILE   ( 106-)  A      N      0.08    2.62  INTRA BL
 166 HIS   ( 167-)  A      CD2 <->  168 GLY   ( 169-)  A      N      0.08    3.02  INTRA
 382 ASN   (  11-)  D      OD1 <->  432 ASN   (  62-)  D      ND2    0.07    2.63  INTRA BL
  35 ASP   (  35-)  A      N   <->   40 GLU   (  40-)  A      O      0.07    2.63  INTRA BL
And so on for a total of 81 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

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.

 351 GLN   ( 181-)  B      -7.19
 719 GLN   ( 181-)  E      -7.13
 727 ARG   ( 189-)  E      -6.70
 705 ARG   ( 167-)  E      -6.63
  52 ARG   (  52-)  A      -6.14
 337 ARG   ( 167-)  B      -6.14
 423 ARG   (  52-)  D      -5.93
 664 GLN   ( 126-)  E      -5.84
 296 GLN   ( 126-)  B      -5.80
 634 ARG   (  88-)  E      -5.63
  98 LEU   (  99-)  A      -5.53
 687 ARG   ( 149-)  E      -5.48
  50 GLN   (  50-)  A      -5.48
 421 GLN   (  50-)  D      -5.37
 319 ARG   ( 149-)  B      -5.37
 638 GLN   (  92-)  E      -5.29
 269 GLN   (  92-)  B      -5.27
  16 TYR   (  16-)  A      -5.11
 336 GLN   ( 166-)  B      -5.06
 469 LEU   (  99-)  D      -5.06

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

Warning: Low packing Z-score for some residues

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

 362 GLN   (   2-)  C   -3.78
 371 TYR   (  11-)  C   -2.99
 730 GLN   (   2-)  F   -2.93
  47 VAL   (  47-)  A   -2.92
 418 VAL   (  47-)  D   -2.89
 674 GLN   ( 136-)  E   -2.82
 729 LEU   (   1-)  F   -2.68

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

  46 PRO   (  46-)  A     -   50 GLN   (  50-)  A        -1.96
 417 PRO   (  46-)  D     -  421 GLN   (  50-)  D        -1.95

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

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

 750 HOH   ( 270 )  E      O

Warning: Water molecules need moving

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

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

 746 HOH   ( 547 )  A      O    118.20   49.14   23.63
 746 HOH   ( 564 )  A      O    115.31   51.56   23.42
 747 HOH   ( 219 )  B      O     56.95   12.97   31.49
 747 HOH   ( 243 )  B      O    114.44   39.87    6.79
 749 HOH   ( 542 )  D      O     75.90   30.02    0.15
 750 HOH   ( 206 )  E      O     92.71   58.85   26.40

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.

 746 HOH   ( 537 )  A      O
 747 HOH   ( 219 )  B      O
 747 HOH   ( 248 )  B      O
 747 HOH   ( 252 )  B      O
 747 HOH   ( 258 )  B      O
 747 HOH   ( 259 )  B      O
 747 HOH   ( 268 )  B      O
 749 HOH   ( 542 )  D      O
 749 HOH   ( 543 )  D      O
 749 HOH   ( 550 )  D      O
 749 HOH   ( 552 )  D      O
 749 HOH   ( 572 )  D      O
 749 HOH   ( 576 )  D      O
 749 HOH   ( 601 )  D      O
 750 HOH   ( 206 )  E      O
 750 HOH   ( 261 )  E      O
 750 HOH   ( 269 )  E      O
 750 HOH   ( 270 )  E      O

Error: HIS, ASN, GLN side chain flips

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

   4 HIS   (   5-)  A
  11 ASN   (  11-)  A
  14 GLN   (  14-)  A
  67 HIS   (  68-)  A
 166 HIS   ( 167-)  A
 241 GLN   (  64-)  B
 283 ASN   ( 113-)  B
 304 ASN   ( 134-)  B
 306 GLN   ( 136-)  B
 336 GLN   ( 166-)  B
 481 ASN   ( 111-)  D
 537 HIS   ( 167-)  D
 610 GLN   (  64-)  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.

   9 GLY   (   9-)  A      N
  31 GLN   (  31-)  A      NE2
  45 LEU   (  45-)  A      N
 157 GLU   ( 158-)  A      N
 210 ASN   (  33-)  B      ND2
 211 ARG   (  34-)  B      NH1
 223 GLU   (  46-)  B      N
 225 ARG   (  48-)  B      NE
 252 VAL   (  75-)  B      N
 259 ASN   (  82-)  B      ND2
 282 ARG   ( 105-)  B      N
 296 GLN   ( 126-)  B      NE2
 304 ASN   ( 134-)  B      N
 319 ARG   ( 149-)  B      NH1
 336 GLN   ( 166-)  B      N
 359 ARG   ( 189-)  B      N
 366 GLN   (   6-)  C      NE2
 380 GLY   (   9-)  D      N
 385 GLN   (  14-)  D      NE2
 432 ASN   (  62-)  D      ND2
 528 GLU   ( 158-)  D      N
 531 TYR   ( 161-)  D      N
 531 TYR   ( 161-)  D      OH
 538 TRP   ( 168-)  D      N
 580 ARG   (  34-)  E      NH1
 592 GLU   (  46-)  E      N
 597 THR   (  51-)  E      OG1
 628 ASN   (  82-)  E      ND2
 687 ARG   ( 149-)  E      NH1
 704 GLN   ( 166-)  E      N
 720 SER   ( 182-)  E      N
 727 ARG   ( 189-)  E      N
 734 GLN   (   6-)  F      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.

  14 GLN   (  14-)  A      OE1
  24 HIS   (  24-)  A      ND1
  31 GLN   (  31-)  A      OE1
 100 GLN   ( 101-)  A      OE1
 183 ASP   (   6-)  B      OD2

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.

 746 HOH   ( 505 )  A      O  0.98  K  5
 747 HOH   ( 235 )  B      O  1.00  K  4
 749 HOH   ( 512 )  D      O  1.04  K  4
 750 HOH   ( 222 )  E      O  0.92  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.

  25 GLU   (  25-)  A   H-bonding suggests Gln
 332 GLU   ( 162-)  B   H-bonding suggests Gln; but Alt-Rotamer
 532 ASP   ( 162-)  D   H-bonding suggests Asn; but Alt-Rotamer
 700 GLU   ( 162-)  E   H-bonding suggests Gln

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 :   0.335
  2nd generation packing quality :  -0.823
  Ramachandran plot appearance   :  -1.214
  chi-1/chi-2 rotamer normality  :  -1.670
  Backbone conformation          :  -0.013

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.306 (tight)
  Bond angles                    :   0.650 (tight)
  Omega angle restraints         :   0.267 (tight)
  Side chain planarity           :   0.209 (tight)
  Improper dihedral distribution :   0.616
  B-factor distribution          :   0.521
  Inside/Outside distribution    :   1.070

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 : 2.22


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :  -0.3
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :   0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.306 (tight)
  Bond angles                    :   0.650 (tight)
  Omega angle restraints         :   0.267 (tight)
  Side chain planarity           :   0.209 (tight)
  Improper dihedral distribution :   0.616
  B-factor distribution          :   0.521
  Inside/Outside distribution    :   1.070
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.