WHAT IF Check report

This file was created 2013-12-09 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 pdb3tei.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 357 ANP   ( 401-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: 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'.

  51 GLU   (  60-)  A      CG
  51 GLU   (  60-)  A      CD
  51 GLU   (  60-)  A      OE1
  51 GLU   (  60-)  A      OE2
 170 GLU   ( 186-)  A      CG
 170 GLU   ( 186-)  A      CD
 170 GLU   ( 186-)  A      OE1
 170 GLU   ( 186-)  A      OE2
 185 ASN   ( 201-)  A      CG
 185 ASN   ( 201-)  A      OD1
 185 ASN   ( 201-)  A      ND2
 186 TYR   ( 205-)  A      CG
 186 TYR   ( 205-)  A      CD1
 186 TYR   ( 205-)  A      CD2
 186 TYR   ( 205-)  A      CE1
 186 TYR   ( 205-)  A      CE2
 186 TYR   ( 205-)  A      CZ
 186 TYR   ( 205-)  A      OH
 214 TYR   ( 233-)  A      CG
 214 TYR   ( 233-)  A      CD1
 214 TYR   ( 233-)  A      CD2
 214 TYR   ( 233-)  A      CE1
 214 TYR   ( 233-)  A      CE2
 214 TYR   ( 233-)  A      CZ
 214 TYR   ( 233-)  A      OH
 234 ASN   ( 253-)  A      CG
 234 ASN   ( 253-)  A      OD1
 234 ASN   ( 253-)  A      ND2
 239 LEU   ( 258-)  A      CG
 239 LEU   ( 258-)  A      CD1
 239 LEU   ( 258-)  A      CD2
 240 LYS   ( 259-)  A      CG
 240 LYS   ( 259-)  A      CD
 240 LYS   ( 259-)  A      CE
 240 LYS   ( 259-)  A      NZ
 243 ASN   ( 262-)  A      CG
 243 ASN   ( 262-)  A      OD1
 243 ASN   ( 262-)  A      ND2
 317 ASP   ( 336-)  A      CG
 317 ASP   ( 336-)  A      OD1
 317 ASP   ( 336-)  A      OD2
 356 ARG   ( 728-)  B      CG
 356 ARG   ( 728-)  B      CD
 356 ARG   ( 728-)  B      NE
 356 ARG   ( 728-)  B      CZ
 356 ARG   ( 728-)  B      NH1
 356 ARG   ( 728-)  B      NH2

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.

 167 PRO   ( 176-)  A    High
 168 ASP   ( 177-)  A    High
 169 HIS   ( 178-)  A    High
 170 GLU   ( 186-)  A    High
 171 TYR   ( 187-)  A    High
 230 GLN   ( 249-)  A    High
 231 GLU   ( 250-)  A    High
 234 ASN   ( 253-)  A    High
 235 CYS   ( 254-)  A    High
 236 ILE   ( 255-)  A    High
 237 ILE   ( 256-)  A    High
 238 ASN   ( 257-)  A    High
 239 LEU   ( 258-)  A    High
 240 LYS   ( 259-)  A    High
 242 ARG   ( 261-)  A    High
 258 ARG   ( 277-)  A    High
 313 ASP   ( 332-)  A    High
 314 MET   ( 333-)  A    High
 315 GLU   ( 334-)  A    High
 316 LEU   ( 335-)  A    High
 318 ASP   ( 337-)  A    High
 341 GLN   ( 713-)  B    High
 355 VAL   ( 727-)  B    High
 356 ARG   ( 728-)  B    High

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 7

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Arginine nomenclature problem

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

  61 ARG   (  70-)  A
 139 ARG   ( 148-)  A
 334 ARG   ( 353-)  A

Warning: Tyrosine convention problem

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

  27 TYR   (  36-)  A
  55 TYR   (  64-)  A
  93 TYR   ( 102-)  A
 130 TYR   ( 139-)  A
 171 TYR   ( 187-)  A
 339 TYR   ( 358-)  A

Warning: Phenylalanine convention problem

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

 312 PHE   ( 331-)  A

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.

 115 ASP   ( 124-)  A
 153 ASP   ( 162-)  A
 168 ASP   ( 177-)  A
 264 ASP   ( 283-)  A
 313 ASP   ( 332-)  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.

   3 GLU   (  12-)  A
  24 GLU   (  33-)  A
  62 GLU   (  71-)  A
  87 GLU   (  96-)  A
 100 GLU   ( 109-)  A
 286 GLU   ( 305-)  A
 307 GLU   ( 326-)  A
 326 GLU   ( 345-)  A

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.

  71 HIS   (  80-)  A      CG   ND1  CE1 109.72    4.1
 111 HIS   ( 120-)  A      CG   ND1  CE1 109.63    4.0
 138 HIS   ( 147-)  A      CG   ND1  CE1 109.72    4.1
 169 HIS   ( 178-)  A      CG   ND1  CE1 109.79    4.2
 232 ASP   ( 251-)  A      N    CA   C    99.98   -4.0
 242 ARG   ( 261-)  A      N    CA   C    97.49   -4.9
 280 HIS   ( 299-)  A      CG   ND1  CE1 109.60    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.

   3 GLU   (  12-)  A
  24 GLU   (  33-)  A
  61 ARG   (  70-)  A
  62 GLU   (  71-)  A
  87 GLU   (  96-)  A
 100 GLU   ( 109-)  A
 115 ASP   ( 124-)  A
 139 ARG   ( 148-)  A
 153 ASP   ( 162-)  A
 168 ASP   ( 177-)  A
 264 ASP   ( 283-)  A
 286 GLU   ( 305-)  A
 307 GLU   ( 326-)  A
 313 ASP   ( 332-)  A
 326 GLU   ( 345-)  A
 334 ARG   ( 353-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 172 VAL   ( 188-)  A      CA    -6.1    24.37    33.23
The average deviation= 0.705

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.

 242 ARG   ( 261-)  A    9.00

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.

 260 PHE   ( 279-)  A    -3.3
 101 THR   ( 110-)  A    -3.0
 167 PRO   ( 176-)  A    -2.8
  27 TYR   (  36-)  A    -2.5
 242 ARG   ( 261-)  A    -2.4
 316 LEU   ( 335-)  A    -2.3
 305 ILE   ( 324-)  A    -2.3
 312 PHE   ( 331-)  A    -2.2
 151 THR   ( 160-)  A    -2.2
 210 PRO   ( 229-)  A    -2.2
 213 HIS   ( 232-)  A    -2.1
  90 LYS   (  99-)  A    -2.0
  40 VAL   (  49-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  13 GLY   (  22-)  A  PRO omega poor
  18 ASN   (  27-)  A  Poor phi/psi
  27 TYR   (  36-)  A  Poor phi/psi
  31 CYS   (  40-)  A  omega poor
  39 LYS   (  48-)  A  Poor phi/psi
  49 PRO   (  58-)  A  omega poor
 109 THR   ( 118-)  A  omega poor
 135 ASN   ( 144-)  A  Poor phi/psi
 139 ARG   ( 148-)  A  Poor phi/psi
 152 CYS   ( 161-)  A  Poor phi/psi
 158 ASP   ( 167-)  A  Poor phi/psi
 167 PRO   ( 176-)  A  omega poor
 171 TYR   ( 187-)  A  omega poor
 172 VAL   ( 188-)  A  Poor phi/psi
 205 ASN   ( 224-)  A  Poor phi/psi
 210 PRO   ( 229-)  A  Poor phi/psi
 229 SER   ( 248-)  A  omega poor
 230 GLN   ( 249-)  A  Poor phi/psi, omega poor
 231 GLU   ( 250-)  A  Poor phi/psi
 232 ASP   ( 251-)  A  omega poor
 234 ASN   ( 253-)  A  Poor phi/psi, omega poor
 241 ALA   ( 260-)  A  omega poor
 258 ARG   ( 277-)  A  omega poor
 311 LYS   ( 330-)  A  omega poor
 312 PHE   ( 331-)  A  omega poor
 316 LEU   ( 335-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.871

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.

 194 SER   ( 213-)  A    0.38

Warning: Unusual backbone conformations

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

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

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

   5 VAL   (  14-)  A      0
   6 ARG   (  15-)  A      0
  12 VAL   (  21-)  A      0
  13 GLY   (  22-)  A      0
  17 THR   (  26-)  A      0
  18 ASN   (  27-)  A      0
  21 TYR   (  30-)  A      0
  22 ILE   (  31-)  A      0
  26 ALA   (  35-)  A      0
  27 TYR   (  36-)  A      0
  39 LYS   (  48-)  A      0
  48 SER   (  57-)  A      0
  49 PRO   (  58-)  A      0
  51 GLU   (  60-)  A      0
  52 HIS   (  61-)  A      0
  68 ALA   (  77-)  A      0
  69 PHE   (  78-)  A      0
  70 ARG   (  79-)  A      0
  71 HIS   (  80-)  A      0
  78 ASN   (  87-)  A      0
  79 ASP   (  88-)  A      0
  82 ARG   (  91-)  A      0
  85 THR   (  94-)  A      0
  89 MET   (  98-)  A      0
  91 ASP   ( 100-)  A      0
And so on for a total of 139 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].

  49 PRO   (  58-)  A   -64.3 envelop C-beta (-72 degrees)
 180 PRO   ( 196-)  A  -113.8 envelop C-gamma (-108 degrees)
 340 PRO   ( 712-)  B    20.5 half-chair N/C-delta (18 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.

  48 SER   (  57-)  A      N   <->  358 HOH   ( 556 )  A      O      0.57    2.13  INTRA BF
 158 ASP   ( 167-)  A      OD2 <->  357 ANP   ( 401-)  A      N3B    0.48    2.22  INTRA BF
 321 LYS   ( 340-)  A      NZ  <->  322 GLU   ( 341-)  A      OE2    0.42    2.28  INTRA BF
  41 ARG   (  50-)  A      NH1 <->  358 HOH   ( 572 )  A      O      0.37    2.33  INTRA BL
  27 TYR   (  36-)  A      OH  <->   58 ARG   (  67-)  A      NE     0.35    2.35  INTRA BF
 230 GLN   ( 249-)  A      C   <->  232 ASP   ( 251-)  A      N      0.33    2.57  INTRA BF
 302 ASP   ( 321-)  A      OD2 <->  354 ARG   ( 726-)  B      NH2    0.33    2.37  INTRA BF
 230 GLN   ( 249-)  A      O   <->  232 ASP   ( 251-)  A      N      0.28    2.42  INTRA BF
  27 TYR   (  36-)  A      O   <->  358 HOH   ( 556 )  A      O      0.27    2.13  INTRA BF
   8 GLN   (  17-)  A      OE1 <->   46 LYS   (  55-)  A      NZ     0.25    2.45  INTRA BF
  26 ALA   (  35-)  A      N   <->  357 ANP   ( 401-)  A      O2B    0.23    2.47  INTRA BF
 186 TYR   ( 205-)  A      N   <->  358 HOH   ( 565 )  A      O      0.23    2.47  INTRA BF
 168 ASP   ( 177-)  A      OD1 <->  169 HIS   ( 178-)  A      N      0.21    2.39  INTRA BF
 181 GLU   ( 197-)  A      O   <->  185 ASN   ( 201-)  A      N      0.19    2.51  INTRA BF
  41 ARG   (  50-)  A      O   <->  358 HOH   ( 545 )  A      O      0.19    2.21  INTRA BL
 231 GLU   ( 250-)  A      OE1 <->  281 LYS   ( 300-)  A      NZ     0.18    2.52  INTRA BF
  48 SER   (  57-)  A      OG  <->   91 ASP   ( 100-)  A      OD1    0.18    2.22  INTRA BL
 122 TYR   ( 131-)  A      OH  <->  354 ARG   ( 726-)  B      NH1    0.18    2.52  INTRA BF
 113 SER   ( 122-)  A      OG  <->  116 HIS   ( 125-)  A      ND1    0.17    2.53  INTRA BF
  72 GLU   (  81-)  A      OE1 <->  353 ARG   ( 725-)  B      NH2    0.17    2.53  INTRA BF
  25 GLY   (  34-)  A      O   <->  358 HOH   ( 557 )  A      O      0.15    2.25  INTRA BF
 105 LYS   ( 114-)  A      NZ  <->  358 HOH   ( 515 )  A      O      0.15    2.55  INTRA BL
 132 HIS   ( 141-)  A      O   <->  188 LYS   ( 207-)  A      NZ     0.15    2.55  INTRA BL
 344 PRO   ( 716-)  B      O   <->  347 SER   ( 719-)  B      OG     0.15    2.25  INTRA BF
 108 LYS   ( 117-)  A      O   <->  358 HOH   ( 558 )  A      O      0.15    2.25  INTRA BF
And so on for a total of 60 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

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

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

 171 TYR   ( 187-)  A      -7.74
  70 ARG   (  79-)  A      -7.15
   6 ARG   (  15-)  A      -6.40
 237 ILE   ( 256-)  A      -6.08
 212 LYS   ( 231-)  A      -6.07
  24 GLU   (  33-)  A      -6.02
 230 GLN   ( 249-)  A      -5.97
 307 GLU   ( 326-)  A      -5.91
 258 ARG   ( 277-)  A      -5.35
  27 TYR   (  36-)  A      -5.34
 178 ARG   ( 194-)  A      -5.33
 314 MET   ( 333-)  A      -5.21
 354 ARG   ( 726-)  B      -5.17
 250 HIS   ( 269-)  A      -5.16
  82 ARG   (  91-)  A      -5.05

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

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.

 186 TYR   ( 205-)  A   -2.80
  26 ALA   (  35-)  A   -2.73

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.

  48 SER   (  57-)  A     -   51 GLU   (  60-)  A        -1.66

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

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.

 358 HOH   ( 612 )  A      O    -19.29  -18.52   39.58

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.

 358 HOH   ( 584 )  A      O
 358 HOH   ( 589 )  A      O
 358 HOH   ( 597 )  A      O
 358 HOH   ( 603 )  A      O
 358 HOH   ( 604 )  A      O
 358 HOH   ( 607 )  A      O
 358 HOH   ( 609 )  A      O
 358 HOH   ( 612 )  A      O
 359 HOH   ( 803 )  B      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.

 110 GLN   ( 119-)  A
 220 HIS   ( 239-)  A
 336 GLN   ( 355-)  A

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   3 GLU   (  12-)  A      N
   9 VAL   (  18-)  A      N
  38 ASN   (  47-)  A      N
  48 SER   (  57-)  A      N
  53 GLN   (  62-)  A      NE2
  85 THR   (  94-)  A      N
  99 MET   ( 108-)  A      N
 102 ASP   ( 111-)  A      N
 123 GLN   ( 132-)  A      NE2
 135 ASN   ( 144-)  A      N
 142 LYS   ( 151-)  A      N
 151 THR   ( 160-)  A      N
 176 TRP   ( 192-)  A      N
 178 ARG   ( 194-)  A      NE
 187 THR   ( 206-)  A      N
 206 ARG   ( 225-)  A      N
 217 GLN   ( 236-)  A      NE2
 232 ASP   ( 251-)  A      N
 233 LEU   ( 252-)  A      N
 234 ASN   ( 253-)  A      N
 236 ILE   ( 255-)  A      N
 242 ARG   ( 261-)  A      N
 251 LYS   ( 270-)  A      N
 260 PHE   ( 279-)  A      N
 267 ALA   ( 286-)  A      N
 276 THR   ( 295-)  A      N
 287 GLN   ( 306-)  A      N
 303 GLU   ( 322-)  A      N
 312 PHE   ( 331-)  A      N
 314 MET   ( 333-)  A      N
 316 LEU   ( 335-)  A      N
 317 ASP   ( 336-)  A      N
 322 GLU   ( 341-)  A      N
 338 GLY   ( 357-)  A      N
 346 GLU   ( 718-)  B      N
 349 ILE   ( 721-)  B      N
 356 ARG   ( 728-)  B      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.

   3 GLU   (  12-)  A      OE2
 145 ASN   ( 154-)  A      OD1
 158 ASP   ( 167-)  A      OD2
 315 GLU   ( 334-)  A      OE2

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.

   3 GLU   (  12-)  A   H-bonding suggests Gln; but Alt-Rotamer
  91 ASP   ( 100-)  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 :  -1.029
  2nd generation packing quality :  -1.857
  Ramachandran plot appearance   :  -0.774
  chi-1/chi-2 rotamer normality  :  -2.871
  Backbone conformation          :  -0.583

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.265 (tight)
  Bond angles                    :   0.599 (tight)
  Omega angle restraints         :   1.113
  Side chain planarity           :   0.302 (tight)
  Improper dihedral distribution :   0.636
  B-factor distribution          :   0.566
  Inside/Outside distribution    :   1.024

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.265 (tight)
  Bond angles                    :   0.599 (tight)
  Omega angle restraints         :   1.113
  Side chain planarity           :   0.302 (tight)
  Improper dihedral distribution :   0.636
  B-factor distribution          :   0.566
  Inside/Outside distribution    :   1.024
==============

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.