WHAT IF Check report

This file was created 2012-01-31 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 pdb2oje.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 137.735  B   = 179.555  C    = 179.952
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 137.735  B   = 144.563  C    = 144.563
    Alpha=  76.983  Beta= 118.450  Gamma= 118.450

Dimensions of the conventional cell

    A    = 179.952  B   = 179.555  C    = 137.735
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  0.000000 -1.000000|
 |  0.000000 -1.000000  0.000000|
 |  1.000000  0.000000  0.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: I 2 2 2

Bravais type of conventional cell is: I

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.699
CA-only RMS fit for the two chains : 0.216

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and F

All-atom RMS fit for the two chains : 0.697
CA-only RMS fit for the two chains : 0.230

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and G

All-atom RMS fit for the two chains : 0.897
CA-only RMS fit for the two chains : 0.304

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and G

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: D and H

All-atom RMS fit for the two chains : 0.942
CA-only RMS fit for the two chains : 0.042

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

1203 PO4   ( 202-)  D  C

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.

1203 PO4   ( 202-)  D  C
1204 PO4   ( 214-)  D  -
1205 PO4   ( 204-)  E  -
1206 PO4   ( 214-)  H  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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'.

 969 LYS   ( 307-)  G      CG
 969 LYS   ( 307-)  G      CD
 969 LYS   ( 307-)  G      CE
 969 LYS   ( 307-)  G      NZ

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

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

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.

  43 ARG   (  44-)  A
  75 ARG   (  76-)  A
 122 ARG   ( 123-)  A
 184 ARG   (   4-)  B
 235 ARG   (  55-)  B
 251 ARG   (  71-)  B
 252 ARG   (  72-)  B
 310 ARG   ( 130-)  B
 346 ARG   ( 166-)  B
 475 ARG   (  91-)  D
 486 ARG   ( 102-)  D
 548 ARG   ( 164-)  D
 564 ARG   ( 180-)  D
 646 ARG   (  50-)  E
 719 ARG   ( 123-)  E
 742 ARG   ( 146-)  E
 781 ARG   (   4-)  F
 783 ARG   (   6-)  F
 802 ARG   (  25-)  F
 832 ARG   (  55-)  F
 848 ARG   (  71-)  F
 849 ARG   (  72-)  F
 870 ARG   (  93-)  F
 907 ARG   ( 130-)  F
 943 ARG   ( 166-)  F
 966 ARG   ( 189-)  F
1038 ARG   (  57-)  H

Warning: Tyrosine convention problem

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

 149 TYR   ( 150-)  A
 282 TYR   ( 102-)  B
 351 TYR   ( 171-)  B
 417 TYR   (  33-)  D
 440 TYR   (  56-)  D
 578 TYR   ( 194-)  D
 879 TYR   ( 102-)  F
 948 TYR   ( 171-)  F
 970 TYR   ( 308-)  G
1014 TYR   (  33-)  H
1175 TYR   ( 194-)  H

Warning: Phenylalanine convention problem

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

  47 PHE   (  48-)  A
 111 PHE   ( 112-)  A
 144 PHE   ( 145-)  A
 179 PHE   ( 180-)  A
 193 PHE   (  13-)  B
 408 PHE   (  24-)  D
 444 PHE   (  60-)  D
 471 PHE   (  87-)  D
 505 PHE   ( 121-)  D
 595 PHE   ( 211-)  D
 644 PHE   (  48-)  E
 704 PHE   ( 108-)  E
 794 PHE   (  17-)  F
1041 PHE   (  60-)  H
1102 PHE   ( 121-)  H

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.

  24 ASP   (  25-)  A
  26 ASP   (  27-)  A
  28 ASP   (  29-)  A
  65 ASP   (  66-)  A
 158 ASP   ( 159-)  A
 161 ASP   ( 162-)  A
 221 ASP   (  41-)  B
 223 ASP   (  43-)  B
 332 ASP   ( 152-)  B
 499 ASP   ( 115-)  D
 501 ASP   ( 117-)  D
 597 ASP   ( 213-)  D
 662 ASP   (  66-)  E
 706 ASP   ( 110-)  E
 779 ASP   (   2-)  F
 929 ASP   ( 152-)  F
1114 ASP   ( 133-)  H
1136 ASP   ( 155-)  H
1194 ASP   ( 213-)  H

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.

  45 GLU   (  46-)  A
  87 GLU   (  88-)  A
  97 GLU   (  98-)  A
 133 GLU   ( 134-)  A
 171 GLU   ( 172-)  A
 208 GLU   (  28-)  B
 239 GLU   (  59-)  B
 317 GLU   ( 137-)  B
 318 GLU   ( 138-)  B
 342 GLU   ( 162-)  B
 349 GLU   ( 169-)  B
 356 GLU   ( 176-)  B
 414 GLU   (  30-)  D
 423 GLU   (  39-)  D
 458 GLU   (  74-)  D
 514 GLU   ( 130-)  D
 525 GLU   ( 141-)  D
 541 GLU   ( 157-)  D
 559 GLU   ( 175-)  D
 583 GLU   ( 199-)  D
 599 GLU   (   3-)  E
 626 GLU   (  30-)  E
 651 GLU   (  55-)  E
 667 GLU   (  71-)  E
 697 GLU   ( 101-)  E
 762 GLU   ( 166-)  E
 768 GLU   ( 172-)  E
 846 GLU   (  69-)  F
 864 GLU   (  87-)  F
 914 GLU   ( 137-)  F
 939 GLU   ( 162-)  F
 953 GLU   ( 176-)  F
1011 GLU   (  30-)  H
1020 GLU   (  39-)  H
1021 GLU   (  40-)  H
1024 GLU   (  43-)  H
1055 GLU   (  74-)  H
1079 GLU   (  98-)  H
1138 GLU   ( 157-)  H

Geometric checks

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  24 ASP   (  25-)  A
  26 ASP   (  27-)  A
  28 ASP   (  29-)  A
  43 ARG   (  44-)  A
  45 GLU   (  46-)  A
  65 ASP   (  66-)  A
  75 ARG   (  76-)  A
  87 GLU   (  88-)  A
  97 GLU   (  98-)  A
 122 ARG   ( 123-)  A
 133 GLU   ( 134-)  A
 158 ASP   ( 159-)  A
 161 ASP   ( 162-)  A
 171 GLU   ( 172-)  A
 184 ARG   (   4-)  B
 208 GLU   (  28-)  B
 221 ASP   (  41-)  B
 223 ASP   (  43-)  B
 235 ARG   (  55-)  B
 239 GLU   (  59-)  B
 251 ARG   (  71-)  B
 252 ARG   (  72-)  B
 310 ARG   ( 130-)  B
 317 GLU   ( 137-)  B
 318 GLU   ( 138-)  B
And so on for a total of 85 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.

1156 GLU   ( 175-)  H    6.12
 559 GLU   ( 175-)  D    6.04
1181 LEU   ( 200-)  H    5.51
 584 LEU   ( 200-)  D    5.41
 300 SER   ( 120-)  B    4.47
 450 TYR   (  66-)  D    4.47
1047 TYR   (  66-)  H    4.37
 897 SER   ( 120-)  F    4.15
 864 GLU   (  87-)  F    4.11

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.

 709 THR   ( 113-)  E    -2.5
1181 LEU   ( 200-)  H    -2.5
 804 LEU   (  27-)  F    -2.5
 207 LEU   (  27-)  B    -2.5
  89 THR   (  90-)  A    -2.4
 112 THR   ( 113-)  A    -2.4
 337 THR   ( 157-)  B    -2.4
 174 LEU   ( 175-)  A    -2.4
  99 ARG   ( 100-)  A    -2.3
 695 LEU   (  99-)  E    -2.3
 612 PRO   (  16-)  E    -2.3
 934 THR   ( 157-)  F    -2.3
 684 GLU   (  88-)  E    -2.3
 686 THR   (  90-)  E    -2.3
 780 THR   (   3-)  F    -2.3
 178 GLU   ( 179-)  A    -2.2
 313 ARG   ( 133-)  B    -2.2
 852 VAL   (  75-)  F    -2.2
  15 PRO   (  16-)  A    -2.2
 776 PHE   ( 180-)  E    -2.2
 255 VAL   (  75-)  B    -2.2
 179 PHE   ( 180-)  A    -2.2
 186 ARG   (   6-)  B    -2.1
  98 LEU   (  99-)  A    -2.1
 133 GLU   ( 134-)  A    -2.1
  82 THR   (  83-)  A    -2.1
  39 GLU   (  40-)  A    -2.1
 280 THR   ( 100-)  B    -2.1
 183 THR   (   3-)  B    -2.1
 771 LEU   ( 175-)  E    -2.1
 152 PHE   ( 153-)  A    -2.1
 584 LEU   ( 200-)  D    -2.1
 226 GLU   (  46-)  B    -2.1
 694 GLU   (  98-)  E    -2.0
 635 LYS   (  39-)  E    -2.0
 596 GLU   ( 212-)  D    -2.0
  11 PHE   (  12-)  A    -2.0
 219 ARG   (  39-)  B    -2.0
 244 GLN   (  64-)  B    -2.0
 783 ARG   (   6-)  F    -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.

  14 ASN   (  15-)  A  PRO omega poor
  17 GLN   (  18-)  A  Poor phi/psi
  50 PHE   (  51-)  A  Poor phi/psi
  77 ASN   (  78-)  A  Poor phi/psi
  99 ARG   ( 100-)  A  Poor phi/psi
 112 THR   ( 113-)  A  Poor phi/psi, PRO omega poor
 114 PRO   ( 115-)  A  Poor phi/psi
 142 HIS   ( 143-)  A  Poor phi/psi
 179 PHE   ( 180-)  A  Poor phi/psi
 213 ASN   (  33-)  B  Poor phi/psi
 270 THR   (  90-)  B  Poor phi/psi
 291 HIS   ( 111-)  B  Poor phi/psi
 303 TYR   ( 123-)  B  PRO omega poor
 314 ASN   ( 134-)  B  Poor phi/psi
 315 GLY   ( 135-)  B  Poor phi/psi
 333 TRP   ( 153-)  B  Poor phi/psi
 420 SER   (  36-)  D  Poor phi/psi
 588 SER   ( 204-)  D  Poor phi/psi
 611 ASN   (  15-)  E  PRO omega poor
 614 GLN   (  18-)  E  Poor phi/psi
 647 PHE   (  51-)  E  Poor phi/psi
 674 ASN   (  78-)  E  Poor phi/psi
 696 ARG   ( 100-)  E  Poor phi/psi
 709 THR   ( 113-)  E  Poor phi/psi, PRO omega poor
 711 PRO   ( 115-)  E  Poor phi/psi
 720 ASN   ( 124-)  E  Poor phi/psi
 739 HIS   ( 143-)  E  Poor phi/psi
 776 PHE   ( 180-)  E  Poor phi/psi
 810 ASN   (  33-)  F  Poor phi/psi
 867 THR   (  90-)  F  Poor phi/psi
 888 HIS   ( 111-)  F  Poor phi/psi
 889 HIS   ( 112-)  F  Poor phi/psi
 900 TYR   ( 123-)  F  PRO omega poor
 911 ASN   ( 134-)  F  Poor phi/psi
 912 GLY   ( 135-)  F  Poor phi/psi
 930 TRP   ( 153-)  F  Poor phi/psi
 996 PHE   (  15-)  H  Poor phi/psi
1149 GLY   ( 168-)  H  Poor phi/psi
1181 LEU   ( 200-)  H  Poor phi/psi
1185 SER   ( 204-)  H  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.448

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.448

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.

1104 SER   ( 123-)  H    0.38
 507 SER   ( 123-)  D    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!

  10 GLU   (  11-)  A      0
  14 ASN   (  15-)  A      0
  16 ASP   (  17-)  A      0
  17 GLN   (  18-)  A      0
  22 MSE   (  23-)  A      0
  25 PHE   (  26-)  A      0
  30 ILE   (  31-)  A      0
  31 PHE   (  32-)  A      0
  35 MSE   (  36-)  A      0
  38 LYS   (  39-)  A      0
  43 ARG   (  44-)  A      0
  50 PHE   (  51-)  A      0
  72 MSE   (  73-)  A      0
  76 SER   (  77-)  A      0
  77 ASN   (  78-)  A      0
  78 TYR   (  79-)  A      0
  98 LEU   (  99-)  A      0
  99 ARG   ( 100-)  A      0
 101 PRO   ( 102-)  A      0
 109 ASP   ( 110-)  A      0
 110 LYS   ( 111-)  A      0
 111 PHE   ( 112-)  A      0
 112 THR   ( 113-)  A      0
 113 PRO   ( 114-)  A      0
 114 PRO   ( 115-)  A      0
And so on for a total of 409 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 : 1.256

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]

  85 PRO   (  86-)  A    0.46 HIGH
 698 PRO   ( 102-)  E    0.45 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].

 363 PRO   ( 183-)  B  -114.8 envelop C-gamma (-108 degrees)
 692 PRO   (  96-)  E  -118.2 half-chair C-delta/C-gamma (-126 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.

 178 GLU   ( 179-)  A      O   <->  180 ASP   ( 181-)  A      N      0.56    2.14  INTRA BF
 225 GLY   (  45-)  B      O   <->  252 ARG   (  72-)  B      NH1    0.39    2.31  INTRA BL
 308 GLU   ( 128-)  B      OE1 <->  310 ARG   ( 130-)  B      NH2    0.38    2.32  INTRA BF
 779 ASP   (   2-)  F      CG  <->  783 ARG   (   6-)  F      NH2    0.37    2.73  INTRA BF
1094 LYS   ( 113-)  H      NZ  <-> 1098 ASP   ( 117-)  H      OD1    0.37    2.33  INTRA BL
 982 MET   (   1-)  H      CE  <-> 1113 TRP   ( 132-)  H      CB     0.36    2.84  INTRA BF
 775 GLU   ( 179-)  E      O   <->  777 ASP   ( 181-)  E      N      0.35    2.35  INTRA BF
 599 GLU   (   3-)  E      OE2 <->  793 HIS   (  16-)  F      ND1    0.35    2.35  INTRA BF
 884 GLN   ( 107-)  F      NE2 <->  886 LEU   ( 109-)  F      CD2    0.34    2.76  INTRA BF
 829 GLU   (  52-)  F      OE1 <->  832 ARG   (  55-)  F      NH1    0.33    2.37  INTRA BF
1032 LYS   (  51-)  H      NZ  <-> 1035 GLN   (  54-)  H      OE1    0.30    2.40  INTRA BL
 577 TYR   ( 193-)  D      CE1 <-> 1035 GLN   (  54-)  H      NE2    0.30    2.80  INTRA BL
 398 HIS   (  14-)  D      CD2 <->  462 MET   (  78-)  D      SD     0.30    3.10  INTRA BL
 178 GLU   ( 179-)  A      C   <->  180 ASP   ( 181-)  A      N      0.29    2.61  INTRA BF
 954 HIS   ( 177-)  F      ND1 <->  956 SER   ( 179-)  F      N      0.29    2.71  INTRA BL
 802 ARG   (  25-)  F      NH2 <->  818 ASP   (  41-)  F      OD2    0.28    2.42  INTRA BL
1094 LYS   ( 113-)  H      NZ  <-> 1098 ASP   ( 117-)  H      CG     0.27    2.83  INTRA BL
 776 PHE   ( 180-)  E      CD2 <->  777 ASP   ( 181-)  E      N      0.27    2.73  INTRA BF
 798 THR   (  21-)  F      O   <->  857 ARG   (  80-)  F      NH1    0.27    2.43  INTRA
 122 ARG   ( 123-)  A      NH1 <->  160 TYR   ( 161-)  A      CE2    0.25    2.85  INTRA BF
 671 LYS   (  75-)  E      O   <->  674 ASN   (  78-)  E      N      0.25    2.45  INTRA
 911 ASN   ( 134-)  F      ND2 <->  947 VAL   ( 170-)  F      CG1    0.25    2.85  INTRA BF
 273 ARG   (  93-)  B      NH1 <->  333 TRP   ( 153-)  B      O      0.24    2.46  INTRA BL
 870 ARG   (  93-)  F      NH1 <->  930 TRP   ( 153-)  F      O      0.24    2.46  INTRA BL
 813 GLU   (  36-)  F      OE2 <->  816 ARG   (  39-)  F      NE     0.24    2.46  INTRA
And so on for a total of 236 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

1135 ARG   ( 154-)  H      -7.39
 696 ARG   ( 100-)  E      -6.13
  99 ARG   ( 100-)  A      -5.97
 369 ARG   ( 189-)  B      -5.71
 179 PHE   ( 180-)  A      -5.68
  49 ARG   (  50-)  A      -5.44
 646 ARG   (  50-)  E      -5.34
 966 ARG   ( 189-)  F      -5.30
 983 LYS   (   2-)  H      -5.28
 943 ARG   ( 166-)  F      -5.27
 991 LYS   (  10-)  H      -5.25
 695 LEU   (  99-)  E      -5.23
 886 LEU   ( 109-)  F      -5.22
 394 LYS   (  10-)  D      -5.20
 386 LYS   (   2-)  D      -5.17
 346 ARG   ( 166-)  B      -5.13
 776 PHE   ( 180-)  E      -5.05
 289 LEU   ( 109-)  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

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

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: H

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.

1051 LEU   (  70-)  H   -2.59
 454 LEU   (  70-)  D   -2.59

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.

 581 ASP   ( 197-)  D     -  584 LEU   ( 200-)  D        -1.44

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

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Water, ion, and hydrogenbond related checks

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.

1212 HOH   ( 194 )  F      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.

 250 GLN   (  70-)  B
 291 HIS   ( 111-)  B
 314 ASN   ( 134-)  B
 336 GLN   ( 156-)  B
 376 GLN   ( 311-)  C
 421 ASN   (  37-)  D
 533 GLN   ( 149-)  D
 720 ASN   ( 124-)  E
 739 HIS   ( 143-)  E
 841 GLN   (  64-)  F
 887 GLN   ( 110-)  F
 911 ASN   ( 134-)  F
 933 GLN   ( 156-)  F
1076 ASN   (  95-)  H
1153 ASN   ( 172-)  H

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.

  21 PHE   (  22-)  A      N
  29 GLU   (  30-)  A      N
  44 LEU   (  45-)  A      N
  54 GLU   (  55-)  A      N
  98 LEU   (  99-)  A      N
 120 TRP   ( 121-)  A      NE1
 179 PHE   ( 180-)  A      N
 180 ASP   ( 181-)  A      N
 189 TRP   (   9-)  B      NE1
 209 ARG   (  29-)  B      NE
 217 SER   (  37-)  B      OG
 226 GLU   (  46-)  B      N
 227 TYR   (  47-)  B      OH
 251 ARG   (  71-)  B      NH1
 252 ARG   (  72-)  B      NH1
 255 VAL   (  75-)  B      N
 273 ARG   (  93-)  B      NH1
 286 THR   ( 106-)  B      N
 287 GLN   ( 107-)  B      N
 289 LEU   ( 109-)  B      N
 331 GLY   ( 151-)  B      N
 333 TRP   ( 153-)  B      N
 334 THR   ( 154-)  B      N
 380 LYS   ( 315-)  C      NZ
 395 ALA   (  11-)  D      N
And so on for a total of 78 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.

  28 ASP   (  29-)  A      OD2
  65 ASP   (  66-)  A      OD2
 148 HIS   ( 149-)  A      ND1
 178 GLU   ( 179-)  A      OE1
 318 GLU   ( 138-)  B      OE2
 376 GLN   ( 311-)  C      OE1
 398 HIS   (  14-)  D      NE2
 599 GLU   (   3-)  E      OE2
 607 GLU   (  11-)  E      OE1
 621 ASP   (  25-)  E      OD1
 662 ASP   (  66-)  E      OD2
 745 HIS   ( 149-)  E      ND1
 758 ASP   ( 162-)  E      OD1
 834 ASP   (  57-)  F      OD2
 913 GLN   ( 136-)  F      OE1
 995 HIS   (  14-)  H      NE2
1046 ASP   (  65-)  H      OD1

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.

  20 GLU   (  21-)  A   H-bonding suggests Gln
  24 ASP   (  25-)  A   H-bonding suggests Asn
  65 ASP   (  66-)  A   H-bonding suggests Asn; but Alt-Rotamer
  97 GLU   (  98-)  A   H-bonding suggests Gln
 158 ASP   ( 159-)  A   H-bonding suggests Asn; but Alt-Rotamer
 161 ASP   ( 162-)  A   H-bonding suggests Asn
 202 GLU   (  22-)  B   H-bonding suggests Gln
 349 GLU   ( 169-)  B   H-bonding suggests Gln
 415 ASP   (  31-)  D   H-bonding suggests Asn
 477 GLU   (  93-)  D   H-bonding suggests Gln
 517 ASP   ( 133-)  D   H-bonding suggests Asn
 617 GLU   (  21-)  E   H-bonding suggests Gln
 621 ASP   (  25-)  E   H-bonding suggests Asn
 662 ASP   (  66-)  E   H-bonding suggests Asn; but Alt-Rotamer
 755 ASP   ( 159-)  E   H-bonding suggests Asn; but Alt-Rotamer
 846 GLU   (  69-)  F   H-bonding suggests Gln
 987 GLU   (   6-)  H   H-bonding suggests Gln
1012 ASP   (  31-)  H   H-bonding suggests Asn
1074 GLU   (  93-)  H   H-bonding suggests Gln
1176 GLU   ( 195-)  H   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.252
  2nd generation packing quality :  -0.830
  Ramachandran plot appearance   :  -1.986
  chi-1/chi-2 rotamer normality  :  -3.448 (poor)
  Backbone conformation          :   0.408

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.343 (tight)
  Bond angles                    :   0.645 (tight)
  Omega angle restraints         :   0.228 (tight)
  Side chain planarity           :   0.248 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.446
  Inside/Outside distribution    :   1.043

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.2
  2nd generation packing quality :   0.9
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.343 (tight)
  Bond angles                    :   0.645 (tight)
  Omega angle restraints         :   0.228 (tight)
  Side chain planarity           :   0.248 (tight)
  Improper dihedral distribution :   0.626
  B-factor distribution          :   0.446
  Inside/Outside distribution    :   1.043
==============

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.