WHAT IF Check report

This file was created 2012-01-30 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 pdb3ly6.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.

2050 ATP   ( 701-)  B  -
2051 ATP   ( 702-)  C  -
2052 ATP   ( 700-)  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

Note: Ramachandran plot

Chain identifier: C

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

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.

   1 GLU   (   4-)  A    High
   4 LEU   (   7-)  A    High
   5 GLU   (   8-)  A    High
   6 ARG   (   9-)  A    High
   7 CYS   (  10-)  A    High
  16 ARG   (  19-)  A    High
  26 GLU   (  29-)  A    High
  38 LEU   (  41-)  A    High
  41 HIS   (  44-)  A    High
  43 GLU   (  46-)  A    High
  44 GLY   (  47-)  A    High
  45 ARG   (  48-)  A    High
  48 GLU   (  51-)  A    High
  51 VAL   (  54-)  A    High
  52 ASP   (  55-)  A    High
  53 SER   (  56-)  A    High
  57 SER   (  60-)  A    High
  73 ARG   (  76-)  A    High
  78 ASP   (  81-)  A    High
  80 VAL   (  83-)  A    High
  82 ASP   (  87-)  A    High
  90 GLN   (  95-)  A    High
  91 GLN   (  96-)  A    High
  92 ASP   (  97-)  A    High
  93 CYS   (  98-)  A    High
And so on for a total of 515 lines.

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) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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

  47 TYR   (  50-)  A
 296 TYR   ( 301-)  A
 310 TYR   ( 315-)  A
 523 TYR   ( 528-)  A
 730 TYR   (  50-)  B
 979 TYR   ( 301-)  B
 993 TYR   ( 315-)  B
1206 TYR   ( 528-)  B
1413 TYR   (  50-)  C
1662 TYR   ( 301-)  C
1676 TYR   ( 315-)  C
1889 TYR   ( 528-)  C

Warning: Phenylalanine convention problem

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

  56 PHE   (  59-)  A
 125 PHE   ( 130-)  A
 161 PHE   ( 166-)  A
 198 PHE   ( 203-)  A
 451 PHE   ( 456-)  A
 532 PHE   ( 537-)  A
 739 PHE   (  59-)  B
 808 PHE   ( 130-)  B
 844 PHE   ( 166-)  B
 881 PHE   ( 203-)  B
1134 PHE   ( 456-)  B
1215 PHE   ( 537-)  B
1422 PHE   (  59-)  C
1491 PHE   ( 130-)  C
1527 PHE   ( 166-)  C
1564 PHE   ( 203-)  C
1817 PHE   ( 456-)  C
1898 PHE   ( 537-)  C

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.

  22 ASP   (  25-)  A
  52 ASP   (  55-)  A
  78 ASP   (  81-)  A
  89 ASP   (  94-)  A
 182 ASP   ( 187-)  A
 237 ASP   ( 242-)  A
 254 ASP   ( 259-)  A
 395 ASP   ( 400-)  A
 403 ASP   ( 408-)  A
 666 ASP   ( 671-)  A
 705 ASP   (  25-)  B
 735 ASP   (  55-)  B
 761 ASP   (  81-)  B
 772 ASP   (  94-)  B
 865 ASP   ( 187-)  B
 920 ASP   ( 242-)  B
 937 ASP   ( 259-)  B
1078 ASP   ( 400-)  B
1086 ASP   ( 408-)  B
1349 ASP   ( 671-)  B
1388 ASP   (  25-)  C
1418 ASP   (  55-)  C
1444 ASP   (  81-)  C
1455 ASP   (  94-)  C
1548 ASP   ( 187-)  C
1603 ASP   ( 242-)  C
1620 ASP   ( 259-)  C
1761 ASP   ( 400-)  C
1769 ASP   ( 408-)  C
2032 ASP   ( 671-)  C

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.

   1 GLU   (   4-)  A
  12 GLU   (  15-)  A
  43 GLU   (  46-)  A
 148 GLU   ( 153-)  A
 150 GLU   ( 155-)  A
 314 GLU   ( 319-)  A
 317 GLU   ( 322-)  A
 361 GLU   ( 366-)  A
 376 GLU   ( 381-)  A
 430 GLU   ( 435-)  A
 447 GLU   ( 452-)  A
 465 GLU   ( 470-)  A
 518 GLU   ( 523-)  A
 552 GLU   ( 557-)  A
 580 GLU   ( 585-)  A
 583 GLU   ( 588-)  A
 627 GLU   ( 632-)  A
 638 GLU   ( 643-)  A
 641 GLU   ( 646-)  A
 642 GLU   ( 647-)  A
 664 GLU   ( 669-)  A
 684 GLU   (   4-)  B
 695 GLU   (  15-)  B
 726 GLU   (  46-)  B
 831 GLU   ( 153-)  B
And so on for a total of 63 lines.

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.

  82 ASP   (  87-)  A      N    CA   C   127.66    5.9
 268 LYS   ( 273-)  A      N    CA   C   122.50    4.0
 765 ASP   (  87-)  B      N    CA   C   127.24    5.7
1448 ASP   (  87-)  C      N    CA   C   128.47    6.2

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.

   1 GLU   (   4-)  A
  12 GLU   (  15-)  A
  22 ASP   (  25-)  A
  43 GLU   (  46-)  A
  52 ASP   (  55-)  A
  78 ASP   (  81-)  A
  89 ASP   (  94-)  A
 148 GLU   ( 153-)  A
 150 GLU   ( 155-)  A
 182 ASP   ( 187-)  A
 237 ASP   ( 242-)  A
 254 ASP   ( 259-)  A
 314 GLU   ( 319-)  A
 317 GLU   ( 322-)  A
 361 GLU   ( 366-)  A
 376 GLU   ( 381-)  A
 395 ASP   ( 400-)  A
 403 ASP   ( 408-)  A
 430 GLU   ( 435-)  A
 447 GLU   ( 452-)  A
 465 GLU   ( 470-)  A
 518 GLU   ( 523-)  A
 552 GLU   ( 557-)  A
 580 GLU   ( 585-)  A
 583 GLU   ( 588-)  A
And so on for a total of 93 lines.

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.

 268 LYS   ( 273-)  A    6.04
1448 ASP   (  87-)  C    5.82
1634 LYS   ( 273-)  C    5.81
 951 LYS   ( 273-)  B    5.71
  82 ASP   (  87-)  A    5.55
 952 TYR   ( 274-)  B    5.44
 765 ASP   (  87-)  B    5.40
1635 TYR   ( 274-)  C    5.38
 269 TYR   ( 274-)  A    5.20
1228 LYS   ( 550-)  B    5.11
1911 LYS   ( 550-)  C    4.96
 545 LYS   ( 550-)  A    4.93
 837 TYR   ( 159-)  B    4.63
1520 TYR   ( 159-)  C    4.61
 154 TYR   ( 159-)  A    4.56
 272 CYS   ( 277-)  A    4.40
 422 SER   ( 427-)  A    4.39
1638 CYS   ( 277-)  C    4.33
1136 ARG   ( 458-)  B    4.28
 453 ARG   ( 458-)  A    4.18
1105 SER   ( 427-)  B    4.11
1788 SER   ( 427-)  C    4.03
2038 LYS   ( 677-)  C    4.00

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.611

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.

 125 PHE   ( 130-)  A    -3.1
1491 PHE   ( 130-)  C    -3.1
 808 PHE   ( 130-)  B    -3.1
 196 PRO   ( 201-)  A    -2.7
 879 PRO   ( 201-)  B    -2.6
1562 PRO   ( 201-)  C    -2.6
1143 LEU   ( 465-)  B    -2.5
 460 LEU   ( 465-)  A    -2.5
1826 LEU   ( 465-)  C    -2.5
1887 THR   ( 526-)  C    -2.4
 668 LEU   ( 673-)  A    -2.4
1204 THR   ( 526-)  B    -2.4
  26 GLU   (  29-)  A    -2.4
 709 GLU   (  29-)  B    -2.4
1392 GLU   (  29-)  C    -2.4
1351 LEU   ( 673-)  B    -2.4
2034 LEU   ( 673-)  C    -2.4
   7 CYS   (  10-)  A    -2.4
 225 CYS   ( 230-)  A    -2.4
1373 CYS   (  10-)  C    -2.4
 423 THR   ( 428-)  A    -2.4
1991 THR   ( 630-)  C    -2.4
 521 THR   ( 526-)  A    -2.3
 690 CYS   (  10-)  B    -2.3
1106 THR   ( 428-)  B    -2.3
And so on for a total of 108 lines.

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.

   4 LEU   (   7-)  A  Poor phi/psi
   5 GLU   (   8-)  A  Poor phi/psi
   7 CYS   (  10-)  A  Poor phi/psi
   8 ASP   (  11-)  A  Poor phi/psi
  11 LEU   (  14-)  A  Poor phi/psi
  19 HIS   (  22-)  A  Poor phi/psi
  27 LYS   (  30-)  A  Poor phi/psi
  44 GLY   (  47-)  A  Poor phi/psi
  46 ASN   (  49-)  A  Poor phi/psi
  50 SER   (  53-)  A  Poor phi/psi
  61 GLY   (  64-)  A  Poor phi/psi
  65 SER   (  68-)  A  Poor phi/psi
  77 ARG   (  80-)  A  Poor phi/psi
  79 ALA   (  82-)  A  Poor phi/psi
  82 ASP   (  87-)  A  Poor phi/psi
  89 ASP   (  94-)  A  Poor phi/psi
  90 GLN   (  95-)  A  Poor phi/psi
  92 ASP   (  97-)  A  Poor phi/psi
  93 CYS   (  98-)  A  Poor phi/psi
 118 THR   ( 123-)  A  Poor phi/psi
 120 TYR   ( 125-)  A  Poor phi/psi
 121 GLN   ( 126-)  A  Poor phi/psi
 164 GLN   ( 169-)  A  Poor phi/psi
 178 GLY   ( 183-)  A  Poor phi/psi
 183 GLY   ( 188-)  A  Poor phi/psi
And so on for a total of 156 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.276

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.

 220 SER   ( 225-)  A    0.35

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 GLU   (   8-)  A      0
   6 ARG   (   9-)  A      0
   7 CYS   (  10-)  A      0
   8 ASP   (  11-)  A      0
  10 GLU   (  13-)  A      0
  11 LEU   (  14-)  A      0
  19 HIS   (  22-)  A      0
  20 THR   (  23-)  A      0
  24 CYS   (  27-)  A      0
  25 ARG   (  28-)  A      0
  26 GLU   (  29-)  A      0
  27 LYS   (  30-)  A      0
  32 ARG   (  35-)  A      0
  37 TRP   (  40-)  A      0
  43 GLU   (  46-)  A      0
  45 ARG   (  48-)  A      0
  46 ASN   (  49-)  A      0
  50 SER   (  53-)  A      0
  51 VAL   (  54-)  A      0
  60 THR   (  63-)  A      0
  63 ALA   (  66-)  A      0
  64 PRO   (  67-)  A      0
  70 THR   (  73-)  A      0
  71 LYS   (  74-)  A      0
  77 ARG   (  80-)  A      0
And so on for a total of 898 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 : 1.175

Warning: Backbone oxygen evaluation

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

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

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

 640 GLY   ( 645-)  A   2.06   33
2006 GLY   ( 645-)  C   2.04   34
1323 GLY   ( 645-)  B   2.03   34
1304 GLY   ( 626-)  B   1.89   21
 621 GLY   ( 626-)  A   1.87   21
1987 GLY   ( 626-)  C   1.84   22
1387 ALA   (  24-)  C   1.62   11
  21 ALA   (  24-)  A   1.62   11
 418 GLY   ( 423-)  A   1.60   11
1101 GLY   ( 423-)  B   1.57   11
1531 GLY   ( 170-)  C   1.56   12
1784 GLY   ( 423-)  C   1.55   11
 704 ALA   (  24-)  B   1.55   12
 165 GLY   ( 170-)  A   1.53   10
 848 GLY   ( 170-)  B   1.52   10

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...

 268 LYS   ( 273-)  A   2.24
 382 LYS   ( 387-)  A   2.09
 951 LYS   ( 273-)  B   1.97
1065 LYS   ( 387-)  B   2.07
1634 LYS   ( 273-)  C   1.86
1748 LYS   ( 387-)  C   2.11

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]

 289 PRO   ( 294-)  A    0.45 HIGH
 634 PRO   ( 639-)  A    0.46 HIGH

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].

 344 PRO   ( 349-)  A   100.0 envelop C-beta (108 degrees)
1027 PRO   ( 349-)  B    99.8 envelop C-beta (108 degrees)
1710 PRO   ( 349-)  C   100.7 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 236 TRP   ( 241-)  A      CD1 <->  512 ASN   ( 517-)  A      ND2    0.47    2.63  INTRA BL
1602 TRP   ( 241-)  C      CD1 <-> 1878 ASN   ( 517-)  C      ND2    0.46    2.64  INTRA BF
 919 TRP   ( 241-)  B      CD1 <-> 1195 ASN   ( 517-)  B      ND2    0.44    2.66  INTRA BF
1524 GLN   ( 163-)  C      CG  <-> 1545 GLN   ( 184-)  C      NE2    0.40    2.70  INTRA BL
 841 GLN   ( 163-)  B      CG  <->  862 GLN   ( 184-)  B      NE2    0.38    2.72  INTRA BL
1638 CYS   ( 277-)  C      SG  <-> 1877 TYR   ( 516-)  C      OH     0.37    2.63  INTRA BL
 158 GLN   ( 163-)  A      CG  <->  179 GLN   ( 184-)  A      NE2    0.35    2.75  INTRA BL
 955 CYS   ( 277-)  B      SG  <-> 1194 TYR   ( 516-)  B      OH     0.35    2.65  INTRA BF
 272 CYS   ( 277-)  A      SG  <->  511 TYR   ( 516-)  A      OH     0.33    2.67  INTRA BL
1004 ASP   ( 326-)  B      C   <-> 1006 SER   ( 328-)  B      N      0.32    2.58  INTRA BF
1779 ARG   ( 418-)  C      NH2 <-> 1831 GLU   ( 470-)  C      CB     0.31    2.79  INTRA BF
1687 ASP   ( 326-)  C      C   <-> 1689 SER   ( 328-)  C      N      0.31    2.59  INTRA BF
 471 ARG   ( 476-)  A      NH1 <-> 2052 ATP   ( 700-)  A      O1G    0.31    2.39  INTRA BL
 413 ARG   ( 418-)  A      NH2 <->  465 GLU   ( 470-)  A      CB     0.31    2.79  INTRA BF
 321 ASP   ( 326-)  A      C   <->  323 SER   ( 328-)  A      N      0.31    2.59  INTRA BF
1096 ARG   ( 418-)  B      NH2 <-> 1148 GLU   ( 470-)  B      CB     0.30    2.80  INTRA BF
1217 GLU   ( 539-)  B      N   <-> 1900 GLU   ( 539-)  C      O      0.30    2.40  INTRA BL
 473 ARG   ( 478-)  A      NE  <-> 2052 ATP   ( 700-)  A      O3G    0.28    2.42  INTRA BL
1944 TYR   ( 583-)  C      N   <-> 2051 ATP   ( 702-)  C      N6     0.28    2.72  INTRA BL
 831 GLU   ( 153-)  B      OE1 <->  834 ARG   ( 156-)  B      NH1    0.28    2.42  INTRA BL
1000 GLU   ( 322-)  B      O   <-> 1002 GLN   ( 324-)  B      N      0.28    2.42  INTRA BF
 317 GLU   ( 322-)  A      O   <->  319 GLN   ( 324-)  A      N      0.28    2.42  INTRA BL
1514 GLU   ( 153-)  C      OE1 <-> 1517 ARG   ( 156-)  C      NH1    0.27    2.43  INTRA BF
1683 GLU   ( 322-)  C      O   <-> 1685 GLN   ( 324-)  C      N      0.27    2.43  INTRA BF
 148 GLU   ( 153-)  A      OE1 <->  151 ARG   ( 156-)  A      NH1    0.26    2.44  INTRA BL
And so on for a total of 615 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

1486 TYR   ( 125-)  C      -8.54
 120 TYR   ( 125-)  A      -8.53
 803 TYR   ( 125-)  B      -8.52
1026 GLN   ( 348-)  B      -6.91
1709 GLN   ( 348-)  C      -6.88
 343 GLN   ( 348-)  A      -6.88
2020 MET   ( 659-)  C      -6.05
1337 MET   ( 659-)  B      -6.01
1372 ARG   (   9-)  C      -5.98
 689 ARG   (   9-)  B      -5.97
   6 ARG   (   9-)  A      -5.94
 654 MET   ( 659-)  A      -5.94
1143 LEU   ( 465-)  B      -5.90
1826 LEU   ( 465-)  C      -5.90
 460 LEU   ( 465-)  A      -5.89
 383 TYR   ( 388-)  A      -5.84
1066 TYR   ( 388-)  B      -5.81
1749 TYR   ( 388-)  C      -5.74
 701 HIS   (  21-)  B      -5.71
  18 HIS   (  21-)  A      -5.70
1384 HIS   (  21-)  C      -5.70
  26 GLU   (  29-)  A      -5.62
1727 GLU   ( 366-)  C      -5.62
 709 GLU   (  29-)  B      -5.62
1392 GLU   (  29-)  C      -5.62
1044 GLU   ( 366-)  B      -5.60
 361 GLU   ( 366-)  A      -5.57
 595 LYS   ( 600-)  A      -5.45
1961 LYS   ( 600-)  C      -5.41
1047 TYR   ( 369-)  B      -5.27
1730 TYR   ( 369-)  C      -5.25
1288 GLN   ( 610-)  B      -5.23
  25 ARG   (  28-)  A      -5.21
1971 GLN   ( 610-)  C      -5.21
 774 GLN   (  96-)  B      -5.19
1457 GLN   (  96-)  C      -5.19
 708 ARG   (  28-)  B      -5.18
  91 GLN   (  96-)  A      -5.18
 605 GLN   ( 610-)  A      -5.17
1336 HIS   ( 658-)  B      -5.17
 364 TYR   ( 369-)  A      -5.14
2019 HIS   ( 658-)  C      -5.13
1391 ARG   (  28-)  C      -5.12
 168 LYS   ( 173-)  A      -5.11
 653 HIS   ( 658-)  A      -5.11

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 463 LYS   ( 468-)  A       465 - GLU    470- ( A)         -4.51
1146 LYS   ( 468-)  B      1148 - GLU    470- ( B)         -4.53
1829 LYS   ( 468-)  C      1831 - GLU    470- ( C)         -4.52

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

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.

1195 ASN   ( 517-)  B   -2.90
1878 ASN   ( 517-)  C   -2.90
 512 ASN   ( 517-)  A   -2.87
 307 LEU   ( 312-)  A   -2.62

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

  41 HIS   (  44-)  A
  66 GLN   (  69-)  A
 224 ASN   ( 229-)  A
 229 GLN   ( 234-)  A
 238 ASN   ( 243-)  A
 265 GLN   ( 270-)  A
 302 GLN   ( 307-)  A
 357 GLN   ( 362-)  A
 724 HIS   (  44-)  B
 749 GLN   (  69-)  B
 907 ASN   ( 229-)  B
 912 GLN   ( 234-)  B
 921 ASN   ( 243-)  B
 948 GLN   ( 270-)  B
 985 GLN   ( 307-)  B
1013 HIS   ( 335-)  B
1040 GLN   ( 362-)  B
1407 HIS   (  44-)  C
1432 GLN   (  69-)  C
1590 ASN   ( 229-)  C
1595 GLN   ( 234-)  C
1604 ASN   ( 243-)  C
1631 GLN   ( 270-)  C
1668 GLN   ( 307-)  C
1723 GLN   ( 362-)  C

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   3 VAL   (   6-)  A      N
   4 LEU   (   7-)  A      N
   5 GLU   (   8-)  A      N
   6 ARG   (   9-)  A      NE
  14 ASN   (  17-)  A      ND2
  31 ARG   (  34-)  A      NH1
  31 ARG   (  34-)  A      NH2
  34 GLN   (  37-)  A      N
  41 HIS   (  44-)  A      N
  43 GLU   (  46-)  A      N
  45 ARG   (  48-)  A      NE
  45 ARG   (  48-)  A      NH1
  45 ARG   (  48-)  A      NH2
  46 ASN   (  49-)  A      N
  46 ASN   (  49-)  A      ND2
  51 VAL   (  54-)  A      N
  61 GLY   (  64-)  A      N
  63 ALA   (  66-)  A      N
  65 SER   (  68-)  A      N
  79 ALA   (  82-)  A      N
  80 VAL   (  83-)  A      N
  92 ASP   (  97-)  A      N
 101 THR   ( 106-)  A      OG1
 105 ALA   ( 110-)  A      N
 118 THR   ( 123-)  A      N
And so on for a total of 231 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

   8 ASP   (  11-)  A      OD1
   8 ASP   (  11-)  A      OD2
  10 GLU   (  13-)  A      OE2
 159 GLN   ( 164-)  A      OE1
 179 GLN   ( 184-)  A      OE1
 295 ASN   ( 300-)  A      OD1
 330 HIS   ( 335-)  A      ND1
 350 GLN   ( 355-)  A      OE1
 456 HIS   ( 461-)  A      ND1
 485 ASP   ( 490-)  A      OD1
 492 ASN   ( 497-)  A      OD1
 580 GLU   ( 585-)  A      OE1
 691 ASP   (  11-)  B      OD1
 691 ASP   (  11-)  B      OD2
 693 GLU   (  13-)  B      OE2
 862 GLN   ( 184-)  B      OE1
 978 ASN   ( 300-)  B      OD1
1033 GLN   ( 355-)  B      OE1
1074 GLU   ( 396-)  B      OE1
1139 HIS   ( 461-)  B      ND1
1168 ASP   ( 490-)  B      OD1
1175 ASN   ( 497-)  B      OD1
1263 GLU   ( 585-)  B      OE1
1374 ASP   (  11-)  C      OD1
1374 ASP   (  11-)  C      OD2
1376 GLU   (  13-)  C      OE2
1545 GLN   ( 184-)  C      OE1
1661 ASN   ( 300-)  C      OD1
1696 HIS   ( 335-)  C      ND1
1716 GLN   ( 355-)  C      OE1
1822 HIS   ( 461-)  C      ND1
1851 ASP   ( 490-)  C      OD1
1858 ASN   ( 497-)  C      OD1
1946 GLU   ( 585-)  C      OE1

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.

   8 ASP   (  11-)  A   H-bonding suggests Asn
  10 GLU   (  13-)  A   H-bonding suggests Gln
  17 ASP   (  20-)  A   H-bonding suggests Asn
  48 GLU   (  51-)  A   H-bonding suggests Gln; but Alt-Rotamer
 193 ASP   ( 198-)  A   H-bonding suggests Asn
 353 ASP   ( 358-)  A   H-bonding suggests Asn; but Alt-Rotamer
 358 GLU   ( 363-)  A   H-bonding suggests Gln
 395 ASP   ( 400-)  A   H-bonding suggests Asn; but Alt-Rotamer
 464 GLU   ( 469-)  A   H-bonding suggests Gln
 465 GLU   ( 470-)  A   H-bonding suggests Gln
 485 ASP   ( 490-)  A   H-bonding suggests Asn; but Alt-Rotamer
 691 ASP   (  11-)  B   H-bonding suggests Asn
 693 GLU   (  13-)  B   H-bonding suggests Gln
 700 ASP   (  20-)  B   H-bonding suggests Asn
 731 GLU   (  51-)  B   H-bonding suggests Gln; but Alt-Rotamer
1036 ASP   ( 358-)  B   H-bonding suggests Asn; but Alt-Rotamer
1041 GLU   ( 363-)  B   H-bonding suggests Gln
1074 GLU   ( 396-)  B   H-bonding suggests Gln; but Alt-Rotamer
1078 ASP   ( 400-)  B   H-bonding suggests Asn; but Alt-Rotamer
1147 GLU   ( 469-)  B   H-bonding suggests Gln
1148 GLU   ( 470-)  B   H-bonding suggests Gln
1168 ASP   ( 490-)  B   H-bonding suggests Asn; but Alt-Rotamer
1374 ASP   (  11-)  C   H-bonding suggests Asn
1376 GLU   (  13-)  C   H-bonding suggests Gln
1383 ASP   (  20-)  C   H-bonding suggests Asn
1414 GLU   (  51-)  C   H-bonding suggests Gln; but Alt-Rotamer
1719 ASP   ( 358-)  C   H-bonding suggests Asn; but Alt-Rotamer
1724 GLU   ( 363-)  C   H-bonding suggests Gln
1761 ASP   ( 400-)  C   H-bonding suggests Asn; but Alt-Rotamer
1830 GLU   ( 469-)  C   H-bonding suggests Gln
1831 GLU   ( 470-)  C   H-bonding suggests Gln
1851 ASP   ( 490-)  C   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.992
  2nd generation packing quality :  -2.507
  Ramachandran plot appearance   :  -3.611 (poor)
  chi-1/chi-2 rotamer normality  :  -4.276 (bad)
  Backbone conformation          :  -0.296

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.342 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   0.214 (tight)
  Side chain planarity           :   0.226 (tight)
  Improper dihedral distribution :   0.622
  B-factor distribution          :   1.287
  Inside/Outside distribution    :   1.039

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 : 3.14


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.342 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   0.214 (tight)
  Side chain planarity           :   0.226 (tight)
  Improper dihedral distribution :   0.622
  B-factor distribution          :   1.287
  Inside/Outside distribution    :   1.039
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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
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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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    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,
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      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,
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    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.