WHAT IF Check report

This file was created 2011-12-16 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 pdb2i87.ent

Checks that need to be done early-on in validation

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.

 690 SO4   ( 401-)  A  -
 691 SO4   ( 402-)  B  -

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: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 6

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

  34 TYR   (  36-)  A
  86 TYR   (  88-)  A
 114 TYR   ( 116-)  A
 156 TYR   ( 158-)  A
 170 TYR   ( 172-)  A
 228 TYR   ( 230-)  A
 290 TYR   ( 303-)  A
 306 TYR   ( 319-)  A
 317 TYR   ( 330-)  A
 379 TYR   (  36-)  B
 430 TYR   (  88-)  B
 456 TYR   ( 116-)  B
 498 TYR   ( 158-)  B
 570 TYR   ( 230-)  B
 632 TYR   ( 303-)  B
 648 TYR   ( 319-)  B
 659 TYR   ( 330-)  B

Warning: Phenylalanine convention problem

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

 135 PHE   ( 137-)  A
 202 PHE   ( 204-)  A
 204 PHE   ( 206-)  A
 268 PHE   ( 281-)  A
 282 PHE   ( 295-)  A
 303 PHE   ( 316-)  A
 477 PHE   ( 137-)  B
 544 PHE   ( 204-)  B
 546 PHE   ( 206-)  B
 610 PHE   ( 281-)  B
 624 PHE   ( 295-)  B
 645 PHE   ( 316-)  B

Warning: Aspartic acid convention problem

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

  30 ASP   (  32-)  A
  61 ASP   (  63-)  A
 100 ASP   ( 102-)  A
 272 ASP   ( 285-)  A
 286 ASP   ( 299-)  A
 375 ASP   (  32-)  B
 391 ASP   (  48-)  B
 595 ASP   ( 266-)  B
 597 ASP   ( 268-)  B
 614 ASP   ( 285-)  B
 628 ASP   ( 299-)  B

Warning: Glutamic acid convention problem

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

  99 GLU   ( 101-)  A
 136 GLU   ( 138-)  A
 154 GLU   ( 156-)  A
 191 GLU   ( 193-)  A
 196 GLU   ( 198-)  A
 200 GLU   ( 202-)  A
 236 GLU   ( 238-)  A
 311 GLU   ( 324-)  A
 319 GLU   ( 332-)  A
 361 GLU   (  18-)  B
 414 GLU   (  71-)  B
 478 GLU   ( 138-)  B
 496 GLU   ( 156-)  B
 533 GLU   ( 193-)  B
 535 GLU   ( 195-)  B
 553 GLU   ( 213-)  B
 560 GLU   ( 220-)  B
 572 GLU   ( 232-)  B
 578 GLU   ( 238-)  B

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

  99 GLU   ( 101-)  A      CB   CG    1.65    4.4
  99 GLU   ( 101-)  A      CD   OE2   1.33    4.2
 220 GLU   ( 222-)  A      CG   CD    1.33   -7.4
 532 ASN   ( 192-)  B      CG   OD1   1.35    5.7
 532 ASN   ( 192-)  B      CG   ND2   1.49    7.8
 549 LYS   ( 209-)  B      CG   CD    1.64    4.0
 639 MET   ( 310-)  B      C    O     1.15   -4.0
 667 ILE   ( 338-)  B      CA   CB    1.63    4.8
 677 LYS   ( 348-)  B      CG   CD    1.66    4.5

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.

  69 GLU   (  71-)  A      N    CA   CB  117.46    4.1
  99 GLU   ( 101-)  A      CB   CG   CD  120.22    4.5
 100 ASP   ( 102-)  A      C    CA   CB  118.01    4.2
 124 SER   ( 126-)  A      C    CA   CB  117.88    4.1
 133 GLN   ( 135-)  A      CB   CG   CD  105.40   -4.2
 146 ILE   ( 148-)  A      CA   CB   CG2 119.27    5.2
 150 ARG   ( 152-)  A      CD   NE   CZ  129.02    4.1
 223 VAL   ( 225-)  A      CG1  CB   CG2 120.41    4.4
 310 TRP   ( 323-)  A      CA   CB   CG  105.80   -4.1
 463 SER   ( 123-)  B      CA   CB   OG  100.86   -5.1
 520 ASN   ( 180-)  B      C    CA   CB  101.37   -4.6
 556 VAL   ( 216-)  B      N    CA   CB  118.84    4.9
 556 VAL   ( 216-)  B      C    CA   CB  102.34   -4.1
 559 ARG   ( 219-)  B      CB   CG   CD  104.75   -4.7
 689 HIS   ( 360-)  B      CG   ND1  CE1 109.87    4.3

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.

  30 ASP   (  32-)  A
  61 ASP   (  63-)  A
  99 GLU   ( 101-)  A
 100 ASP   ( 102-)  A
 136 GLU   ( 138-)  A
 154 GLU   ( 156-)  A
 191 GLU   ( 193-)  A
 196 GLU   ( 198-)  A
 200 GLU   ( 202-)  A
 236 GLU   ( 238-)  A
 272 ASP   ( 285-)  A
 286 ASP   ( 299-)  A
 311 GLU   ( 324-)  A
 319 GLU   ( 332-)  A
 361 GLU   (  18-)  B
 375 ASP   (  32-)  B
 391 ASP   (  48-)  B
 414 GLU   (  71-)  B
 478 GLU   ( 138-)  B
 496 GLU   ( 156-)  B
 533 GLU   ( 193-)  B
 535 GLU   ( 195-)  B
 553 GLU   ( 213-)  B
 560 GLU   ( 220-)  B
 572 GLU   ( 232-)  B
 578 GLU   ( 238-)  B
 595 ASP   ( 266-)  B
 597 ASP   ( 268-)  B
 614 ASP   ( 285-)  B
 628 ASP   ( 299-)  B

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.

 223 VAL   ( 225-)  A      CB    13.3   -15.57   -32.96
The average deviation= 1.401

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.

 362 VAL   (  19-)  B    4.23
  77 LEU   (  79-)  A    4.04

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 475 GLN   ( 135-)  B    5.48
 133 GLN   ( 135-)  A    4.58
 117 ASN   ( 119-)  A    4.25

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.

 360 HIS   (  17-)  B    -3.1
 405 THR   (  62-)  B    -2.6
  94 HIS   (  96-)  A    -2.6
  96 PRO   (  98-)  A    -2.5
 277 VAL   ( 290-)  A    -2.3
  90 PHE   (  92-)  A    -2.3
 536 LEU   ( 196-)  B    -2.3
 434 PHE   (  92-)  B    -2.3
 619 VAL   ( 290-)  B    -2.3
  15 HIS   (  17-)  A    -2.3
 402 ILE   (  59-)  B    -2.3
 297 MET   ( 310-)  A    -2.3
 239 LYS   ( 241-)  A    -2.3
 146 ILE   ( 148-)  A    -2.3
 556 VAL   ( 216-)  B    -2.2
  91 PRO   (  93-)  A    -2.1
   8 PHE   (  10-)  A    -2.1
  93 LEU   (  95-)  A    -2.1
 588 LEU   ( 259-)  B    -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.

  11 LYS   (  13-)  A  Poor phi/psi
  13 ALA   (  15-)  A  omega poor
  51 ASN   (  53-)  A  omega poor
  52 ASN   (  54-)  A  Poor phi/psi
  65 LEU   (  67-)  A  Poor phi/psi
  71 LEU   (  73-)  A  omega poor
  94 HIS   (  96-)  A  Poor phi/psi, omega poor
  99 GLU   ( 101-)  A  omega poor
 111 ASP   ( 113-)  A  Poor phi/psi
 170 TYR   ( 172-)  A  PRO omega poor
 177 ALA   ( 179-)  A  omega poor
 180 GLY   ( 182-)  A  omega poor
 182 SER   ( 184-)  A  Poor phi/psi
 187 LYS   ( 189-)  A  omega poor
 226 ASN   ( 228-)  A  Poor phi/psi
 232 THR   ( 234-)  A  omega poor
 248 ILE   ( 261-)  A  PRO omega poor
 276 LEU   ( 289-)  A  omega poor
 281 PHE   ( 294-)  A  omega poor
 287 ASN   ( 300-)  A  Poor phi/psi
 293 GLU   ( 306-)  A  omega poor
 358 ALA   (  15-)  B  omega poor
 375 ASP   (  32-)  B  omega poor
 437 LEU   (  95-)  B  omega poor
 439 GLY   (  97-)  B  PRO omega poor
 453 ASP   ( 113-)  B  Poor phi/psi
 512 TYR   ( 172-)  B  PRO omega poor
 519 ALA   ( 179-)  B  omega poor
 521 LEU   ( 181-)  B  omega poor
 522 GLY   ( 182-)  B  omega poor
 524 SER   ( 184-)  B  Poor phi/psi
 568 ASN   ( 228-)  B  Poor phi/psi
 574 THR   ( 234-)  B  omega poor
 590 ILE   ( 261-)  B  PRO omega poor
 618 LEU   ( 289-)  B  omega poor
 619 VAL   ( 290-)  B  omega poor
 629 ASN   ( 300-)  B  Poor phi/psi
 635 GLU   ( 306-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -2.014

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.

  18 SER   (  20-)  A    0.35
 493 SER   ( 153-)  B    0.37
 466 SER   ( 126-)  B    0.38
 151 SER   ( 153-)  A    0.38
 463 SER   ( 123-)  B    0.40

Warning: Unusual backbone conformations

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

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

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

   3 ASN   (   5-)  A      0
   8 PHE   (  10-)  A      0
  11 LYS   (  13-)  A      0
  13 ALA   (  15-)  A      0
  14 GLU   (  16-)  A      0
  31 LYS   (  33-)  A      0
  33 LYS   (  35-)  A      0
  51 ASN   (  53-)  A      0
  52 ASN   (  54-)  A      0
  58 LYS   (  60-)  A      0
  63 LEU   (  65-)  A      0
  64 HIS   (  66-)  A      0
  65 LEU   (  67-)  A      0
  66 GLU   (  68-)  A      0
  73 ILE   (  75-)  A      0
  82 SER   (  84-)  A      0
  91 PRO   (  93-)  A      0
  92 LEU   (  94-)  A      0
  93 LEU   (  95-)  A      0
  94 HIS   (  96-)  A      0
  95 GLY   (  97-)  A      0
  97 ASN   (  99-)  A      0
  99 GLU   ( 101-)  A      0
 100 ASP   ( 102-)  A      0
 102 THR   ( 104-)  A      0
And so on for a total of 252 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.162

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  96 PRO   (  98-)  A    0.19 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 435 PRO   (  93-)  B   -54.3 half-chair C-beta/C-alpha (-54 degrees)
 440 PRO   (  98-)  B  -115.5 envelop C-gamma (-108 degrees)
 518 PRO   ( 178-)  B   102.2 envelop C-beta (108 degrees)
 591 PRO   ( 262-)  B   -55.0 half-chair C-beta/C-alpha (-54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 128 LYS   ( 130-)  A      NZ  <->  179 LEU   ( 181-)  A      O      0.50    2.20  INTRA BF
 286 ASP   ( 299-)  A      OD1 <->  288 GLN   ( 301-)  A      NE2    0.46    2.24  INTRA BF
 611 LYS   ( 282-)  B      NZ  <->  693 HOH   ( 438 )  B      O      0.45    2.25  INTRA BL
 157 GLU   ( 159-)  A      OE2 <->  195 LYS   ( 197-)  A      NZ     0.38    2.32  INTRA BF
 163 LEU   ( 165-)  A      CD2 <->  167 LYS   ( 169-)  A      CG     0.37    2.83  INTRA BF
 286 ASP   ( 299-)  A      CG  <->  288 GLN   ( 301-)  A      NE2    0.35    2.75  INTRA BF
 681 LYS   ( 352-)  B      NZ  <->  685 ASP   ( 356-)  B      OD2    0.33    2.37  INTRA BF
 346 LYS   (   3-)  B      NZ  <->  377 ASP   (  34-)  B      O      0.31    2.39  INTRA BF
 469 ASP   ( 129-)  B      OD2 <->  549 LYS   ( 209-)  B      NZ     0.29    2.41  INTRA BL
 299 GLY   ( 312-)  A      N   <->  690 SO4   ( 401-)  A      O2     0.25    2.45  INTRA BF
 333 GLN   ( 346-)  A      O   <->  337 LYS   ( 350-)  A      CD     0.25    2.55  INTRA BF
 360 HIS   (  17-)  B      NE2 <->  385 TYR   (  42-)  B      OH     0.24    2.46  INTRA BF
 380 HIS   (  37-)  B      NE2 <->  425 SER   (  83-)  B      OG     0.24    2.46  INTRA BF
 641 GLY   ( 312-)  B      N   <->  691 SO4   ( 402-)  B      O4     0.24    2.46  INTRA BF
 578 GLU   ( 238-)  B      OE1 <->  589 GLN   ( 260-)  B      NE2    0.23    2.47  INTRA BL
 474 LYS   ( 134-)  B      NZ  <->  693 HOH   ( 431 )  B      O      0.23    2.47  INTRA BF
 628 ASP   ( 299-)  B      OD1 <->  630 GLN   ( 301-)  B      NE2    0.22    2.48  INTRA BF
 538 GLU   ( 198-)  B      OE1 <->  542 GLU   ( 202-)  B      CG     0.21    2.59  INTRA BF
 204 PHE   ( 206-)  A      C   <->  680 ASN   ( 351-)  B      OD1    0.20    2.60  INTRA BF
 375 ASP   (  32-)  B      CG  <->  378 LYS   (  35-)  B      CD     0.19    3.01  INTRA BF
 542 GLU   ( 202-)  B      O   <->  545 GLN   ( 205-)  B      NE2    0.19    2.51  INTRA BF
 217 ARG   ( 219-)  A      CD  <->  236 GLU   ( 238-)  A      OE2    0.19    2.61  INTRA BF
 438 HIS   (  96-)  B      ND1 <->  442 ASP   ( 102-)  B      OD1    0.18    2.52  INTRA BF
 629 ASN   ( 300-)  B      ND2 <->  693 HOH   ( 432 )  B      O      0.18    2.52  INTRA BF
  94 HIS   (  96-)  A      CE1 <->  100 ASP   ( 102-)  A      OD2    0.18    2.62  INTRA BF
And so on for a total of 107 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.

 228 TYR   ( 230-)  A      -6.56
 570 TYR   ( 230-)  B      -6.52
 688 HIS   ( 359-)  B      -6.09
 639 MET   ( 310-)  B      -6.06
 479 HIS   ( 139-)  B      -5.95
 297 MET   ( 310-)  A      -5.92
 137 HIS   ( 139-)  A      -5.84
 344 ARG   ( 357-)  A      -5.72
  94 HIS   (  96-)  A      -5.33
  11 LYS   (  13-)  A      -5.30
 480 ARG   ( 140-)  B      -5.27
 138 ARG   ( 140-)  A      -5.24
 654 ASN   ( 325-)  B      -5.14
  67 ASN   (  69-)  A      -5.12
 356 LYS   (  13-)  B      -5.10
 312 ASN   ( 325-)  A      -5.09
 411 GLU   (  68-)  B      -5.03

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

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.

  75 GLN   (  77-)  A     -   78 LYS   (  80-)  A        -1.93

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

 159 ASN   ( 161-)  A
 369 ASN   (  26-)  B
 396 ASN   (  53-)  B
 409 HIS   (  66-)  B
 428 GLN   (  86-)  B
 689 HIS   ( 360-)  B

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.

  12 SER   (  14-)  A      N
  15 HIS   (  17-)  A      N
  16 GLU   (  18-)  A      N
  66 GLU   (  68-)  A      N
  74 SER   (  76-)  A      N
  99 GLU   ( 101-)  A      N
 104 GLN   ( 106-)  A      NE2
 153 TYR   ( 155-)  A      OH
 179 LEU   ( 181-)  A      N
 190 ASN   ( 192-)  A      N
 241 VAL   ( 243-)  A      N
 243 PHE   ( 245-)  A      N
 256 VAL   ( 269-)  A      N
 294 THR   ( 307-)  A      OG1
 357 SER   (  14-)  B      N
 375 ASP   (  32-)  B      N
 391 ASP   (  48-)  B      N
 394 LYS   (  51-)  B      N
 396 ASN   (  53-)  B      ND2
 412 ASN   (  69-)  B      N
 423 GLU   (  81-)  B      N
 426 SER   (  84-)  B      OG
 437 LEU   (  95-)  B      N
 442 ASP   ( 102-)  B      N
 467 SER   ( 127-)  B      OG
 487 TYR   ( 147-)  B      OH
 495 TYR   ( 155-)  B      OH
 501 ASN   ( 161-)  B      N
 521 LEU   ( 181-)  B      N
 523 SER   ( 183-)  B      OG
 532 ASN   ( 192-)  B      N
 583 VAL   ( 243-)  B      N
 628 ASP   ( 299-)  B      N
 645 PHE   ( 316-)  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.

   2 GLU   (   4-)  A      OE1
  51 ASN   (  53-)  A      OD1
 218 GLU   ( 220-)  A      OE1
 220 GLU   ( 222-)  A      OE1
 254 GLU   ( 267-)  A      OE2
 347 GLU   (   4-)  B      OE1
 396 ASN   (  53-)  B      OD1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  62 GLU   (  64-)  A   H-bonding suggests Gln; but Alt-Rotamer
  99 GLU   ( 101-)  A   H-bonding suggests Gln; but Alt-Rotamer
 218 GLU   ( 220-)  A   H-bonding suggests Gln; but Alt-Rotamer
 441 GLU   ( 101-)  B   H-bonding suggests Gln
 442 ASP   ( 102-)  B   H-bonding suggests Asn
 582 ASP   ( 242-)  B   H-bonding suggests Asn; but Alt-Rotamer
 676 ASP   ( 347-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.864
  2nd generation packing quality :   0.006
  Ramachandran plot appearance   :  -0.195
  chi-1/chi-2 rotamer normality  :  -2.014
  Backbone conformation          :   0.312

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.024
  Bond angles                    :   0.978
  Omega angle restraints         :   1.302 (loose)
  Side chain planarity           :   1.328
  Improper dihedral distribution :   1.185
  B-factor distribution          :   0.513
  Inside/Outside distribution    :   1.032

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.4
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.024
  Bond angles                    :   0.978
  Omega angle restraints         :   1.302 (loose)
  Side chain planarity           :   1.328
  Improper dihedral distribution :   1.185
  B-factor distribution          :   0.513
  Inside/Outside distribution    :   1.032
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
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Puckering parameters
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      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
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      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.