WHAT IF Check report

This file was created 2012-01-19 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 pdb2c6f.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.798
CA-only RMS fit for the two chains : 0.520

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 B

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.

1239 ACT   ( 800-)  A  -
1240 ACT   ( 801-)  A  -
1245 ACT   ( 801-)  B  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1224 NAG   ( 691-)  A  -   O4  bound to 1229 NAG   ( 696-)  A  -   C1
1226 NAG   ( 693-)  A  -   O4  bound to 1227 NAG   ( 694-)  A  -   C1
1231 NAG   ( 691-)  B  -   O4  bound to 1236 NAG   ( 696-)  B  -   C1
1233 NAG   ( 693-)  B  -   O4  bound to 1234 NAG   ( 694-)  B  -   C1

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  92 ILE   (  92-)  A  -   CD1
 126 LYS   ( 126-)  A  -   CD
 126 LYS   ( 126-)  A  -   CE
 126 LYS   ( 126-)  A  -   NZ
 274 LYS   ( 274-)  A  -   CE
 274 LYS   ( 274-)  A  -   NZ
 688 GLU   (  77-)  B  -   CD
 688 GLU   (  77-)  B  -   OE1
 688 GLU   (  77-)  B  -   OE2
 737 LYS   ( 126-)  B  -   CD
 737 LYS   ( 126-)  B  -   CE
 885 LYS   ( 274-)  B  -   CD
 885 LYS   ( 274-)  B  -   CE
 885 LYS   ( 274-)  B  -   NZ
 896 GLN   ( 285-)  B  -   CD
 896 GLN   ( 285-)  B  -   OE1
 896 GLN   ( 285-)  B  -   NE2
1019 ILE   ( 408-)  B  -   CD1
1153 LYS   ( 542-)  B  -   CE
1153 LYS   ( 542-)  B  -   NZ

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 LEU   (   1-)  A      CG
   1 LEU   (   1-)  A      CD1
   1 LEU   (   1-)  A      CD2
  22 GLN   (  22-)  A      CG
  22 GLN   (  22-)  A      CD
  22 GLN   (  22-)  A      OE1
  22 GLN   (  22-)  A      NE2
  26 SER   (  26-)  A      OG
  56 GLU   (  56-)  A      CG
  56 GLU   (  56-)  A      CD
  56 GLU   (  56-)  A      OE1
  56 GLU   (  56-)  A      OE2
  70 GLN   (  70-)  A      CG
  70 GLN   (  70-)  A      CD
  70 GLN   (  70-)  A      OE1
  70 GLN   (  70-)  A      NE2
  74 GLU   (  74-)  A      CG
  74 GLU   (  74-)  A      CD
  74 GLU   (  74-)  A      OE1
  74 GLU   (  74-)  A      OE2
 131 ASN   ( 131-)  A      CG
 131 ASN   ( 131-)  A      OD1
 131 ASN   ( 131-)  A      ND2
 132 LYS   ( 132-)  A      CG
 132 LYS   ( 132-)  A      CD
And so on for a total of 230 lines.

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.

1230 NAG   ( 697-)  A    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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

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.

  96 ARG   (  96-)  A
 151 ARG   ( 151-)  A
 199 ARG   ( 199-)  A
 231 ARG   ( 231-)  A
 467 ARG   ( 467-)  A
 762 ARG   ( 151-)  B
 810 ARG   ( 199-)  B
 842 ARG   ( 231-)  B
1078 ARG   ( 467-)  B

Warning: Tyrosine convention problem

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

  76 TYR   (  76-)  A
 186 TYR   ( 186-)  A
 237 TYR   ( 237-)  A
 241 TYR   ( 241-)  A
 368 TYR   ( 368-)  A
 369 TYR   ( 369-)  A
 459 TYR   ( 459-)  A
 501 TYR   ( 501-)  A
 573 TYR   ( 573-)  A
 635 TYR   (  24-)  B
 764 TYR   ( 153-)  B
 797 TYR   ( 186-)  B
 813 TYR   ( 202-)  B
 848 TYR   ( 237-)  B
 852 TYR   ( 241-)  B
 979 TYR   ( 368-)  B
 980 TYR   ( 369-)  B
1070 TYR   ( 459-)  B
1112 TYR   ( 501-)  B
1184 TYR   ( 573-)  B
1218 TYR   ( 607-)  B

Warning: Phenylalanine convention problem

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

  10 PHE   (  10-)  A
  20 PHE   (  20-)  A
  64 PHE   (  64-)  A
 271 PHE   ( 271-)  A
 300 PHE   ( 300-)  A
 343 PHE   ( 343-)  A
 450 PHE   ( 450-)  A
 461 PHE   ( 461-)  A
 490 PHE   ( 490-)  A
 574 PHE   ( 574-)  A
 621 PHE   (  10-)  B
 882 PHE   ( 271-)  B
 911 PHE   ( 300-)  B
 912 PHE   ( 301-)  B
1061 PHE   ( 450-)  B
1095 PHE   ( 484-)  B
1101 PHE   ( 490-)  B
1185 PHE   ( 574-)  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.

  43 ASP   (  43-)  A
  85 ASP   (  85-)  A
 654 ASP   (  43-)  B
 696 ASP   (  85-)  B
 820 ASP   ( 209-)  B
1032 ASP   ( 421-)  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.

  14 GLU   (  14-)  A
  29 GLU   (  29-)  A
  77 GLU   (  77-)  A
 161 GLU   ( 161-)  A
 212 GLU   ( 212-)  A
 219 GLU   ( 219-)  A
 299 GLU   ( 299-)  A
 481 GLU   ( 481-)  A
 518 GLU   ( 518-)  A
 660 GLU   (  49-)  B
 772 GLU   ( 161-)  B
 795 GLU   ( 184-)  B
 819 GLU   ( 208-)  B
 938 GLU   ( 327-)  B
1129 GLU   ( 518-)  B
1201 GLU   ( 590-)  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.

  45 ASN   (  45-)  A      CG   ND2   1.24   -4.1
 117 ASN   ( 117-)  A      CA   CB    1.43   -5.1
 117 ASN   ( 117-)  A      CB   CG    1.38   -5.4
 117 ASN   ( 117-)  A      CG   ND2   1.23   -4.4
 251 HIS   ( 251-)  A      CB   CG    1.56    4.4
 751 ASP   ( 140-)  B      CG   OD2   1.35    5.2
1225 NAG   ( 692-)  A      C8   C7    1.22   -6.2
1232 NAG   ( 692-)  B      C8   C7    1.22   -6.2
1233 NAG   ( 693-)  B      C8   C7    1.32   -4.2
1234 NAG   ( 694-)  B      C8   C7    1.32   -4.2
1237  ZN   ( 701-)  A      SG  -SG*   1.56  -12.0
1237  ZN   ( 701-)  A      SG  -SG*   1.56  -12.0

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.

  25 ASN   (  25-)  A      CB   CG   ND2 110.10   -4.2
  52 ARG   (  52-)  A      CB   CG   CD  105.52   -4.3
  66 GLU   (  66-)  A      CA   CB   CG  104.25   -4.9
 102 ASN   ( 102-)  A      C    CA   CB   99.43   -5.6
 117 ASN   ( 117-)  A      CB   CG   ND2 107.96   -5.6
 135 THR   ( 135-)  A     -C    N    CA  131.81    5.6
 136 CYS   ( 136-)  A     -C    N    CA  129.92    4.6
 245 ARG   ( 245-)  A      CB   CG   CD  105.88   -4.1
 350 ARG   ( 350-)  A     -C    N    CA  110.58   -6.2
 410 LEU   ( 410-)  A     -CA  -C    N   125.62    4.4
 410 LEU   ( 410-)  A     -C    N    CA  108.89   -7.1
 527 GLN   ( 527-)  A      CG   CD   NE2 126.02    6.4
 527 GLN   ( 527-)  A      NE2  CD   OE1 112.33  -10.3
 598 GLN   ( 598-)  A      CG   CD   NE2 126.77    6.9
 598 GLN   ( 598-)  A      NE2  CD   OE1 112.17  -10.4
 614 PRO   (   3-)  B      C    CA   CB  120.48    5.5
 614 PRO   (   3-)  B      CA   CB   CG   93.45   -5.8
 614 PRO   (   3-)  B      CD   N    CA   79.80  -23.0
 615 GLY   (   4-)  B     -CA  -C    N   125.69    4.7
 617 GLN   (   6-)  B      CG   CD   NE2 126.25    6.6
 617 GLN   (   6-)  B      NE2  CD   OE1 112.94   -9.7
 629 GLN   (  18-)  B      CG   CD   NE2 126.89    7.0
 629 GLN   (  18-)  B      NE2  CD   OE1 112.84   -9.8
 641 GLN   (  30-)  B      CG   CD   NE2 127.12    7.1
 641 GLN   (  30-)  B      NE2  CD   OE1 113.18   -9.4
 665 GLN   (  54-)  B      CG   CD   NE2 126.21    6.5
 665 GLN   (  54-)  B      NE2  CD   OE1 113.28   -9.3
 673 GLN   (  62-)  B      CG   CD   NE2 125.88    6.3
 673 GLN   (  62-)  B      NE2  CD   OE1 113.06   -9.5
 698 GLN   (  87-)  B      CG   CD   NE2 126.45    6.7
 698 GLN   (  87-)  B      NE2  CD   OE1 113.24   -9.4
 720 GLN   ( 109-)  B      CG   CD   NE2 126.28    6.6
 720 GLN   ( 109-)  B      NE2  CD   OE1 112.76   -9.8
 721 GLN   ( 110-)  B      CG   CD   NE2 126.17    6.5
 721 GLN   ( 110-)  B      NE2  CD   OE1 113.11   -9.5
 728 ASN   ( 117-)  B      CA   CB   CG  104.37   -8.2
 752 PRO   ( 141-)  B      N    CA   CB   97.97   -4.6
 889 ASP   ( 278-)  B      N    CA   C    99.42   -4.2
 917 LEU   ( 306-)  B      N    CA   C    99.73   -4.1
 960 THR   ( 349-)  B      C    CA   CB  101.99   -4.3
1020 GLY   ( 409-)  B      N    CA   C   127.91    5.3
1055 GLN   ( 444-)  B      CG   CD   NE2 125.91    6.3
1055 GLN   ( 444-)  B      NE2  CD   OE1 112.70   -9.9
1152 ARG   ( 541-)  B      CB   CG   CD  104.86   -4.6
1186 GLN   ( 575-)  B      N    CA   C   122.65    4.1
1218 TYR   ( 607-)  B     -C    N    CA  112.66   -5.0
1219 PRO   ( 608-)  B      CD   N    CA   85.05  -19.2

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.

  14 GLU   (  14-)  A
  29 GLU   (  29-)  A
  43 ASP   (  43-)  A
  77 GLU   (  77-)  A
  85 ASP   (  85-)  A
  96 ARG   (  96-)  A
 151 ARG   ( 151-)  A
 161 GLU   ( 161-)  A
 199 ARG   ( 199-)  A
 212 GLU   ( 212-)  A
 219 GLU   ( 219-)  A
 231 ARG   ( 231-)  A
 299 GLU   ( 299-)  A
 467 ARG   ( 467-)  A
 481 GLU   ( 481-)  A
 518 GLU   ( 518-)  A
 654 ASP   (  43-)  B
 660 GLU   (  49-)  B
 696 ASP   (  85-)  B
 762 ARG   ( 151-)  B
 772 GLU   ( 161-)  B
 795 GLU   ( 184-)  B
 810 ARG   ( 199-)  B
 819 GLU   ( 208-)  B
 820 ASP   ( 209-)  B
 842 ARG   ( 231-)  B
 938 GLU   ( 327-)  B
1032 ASP   ( 421-)  B
1078 ARG   ( 467-)  B
1129 GLU   ( 518-)  B
1201 GLU   ( 590-)  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.

  78 PRO   (  78-)  A      N     -6.2   -22.98    -2.48
 205 PRO   ( 205-)  A      N      6.2    17.85    -2.48
 608 PRO   ( 608-)  A      N     -8.5   -30.41    -2.48
 614 PRO   (   3-)  B      N     14.1    43.65    -2.48
 690 ILE   (  79-)  B      CA   -44.7   -34.21    33.24 Wrong hand
 751 ASP   ( 140-)  B      C      6.4     9.86    -0.01
1021 LEU   ( 410-)  B      CA   -47.3   -38.18    34.19 Wrong hand
1141 ILE   ( 530-)  B      CB   -49.3   -31.79    32.31 Wrong hand
1219 PRO   ( 608-)  B      N     13.5    41.74    -2.48
The average deviation= 0.815

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.

1186 GLN   ( 575-)  B    7.45
 575 GLN   ( 575-)  A    7.06
1047 LEU   ( 436-)  B    6.37
 627 GLY   (  16-)  B    6.28
 444 GLN   ( 444-)  A    5.91
 391 ILE   ( 391-)  A    5.76
1056 TRP   ( 445-)  B    5.39
 441 LEU   ( 441-)  A    5.30
 465 TYR   ( 465-)  A    5.28
 149 SER   ( 149-)  A    5.26
1076 TYR   ( 465-)  B    5.20
1020 GLY   ( 409-)  B    5.14
 172 LYS   ( 172-)  A    5.12
 778 ALA   ( 167-)  B    5.05
 519 ALA   ( 519-)  A    4.85
 290 ALA   ( 290-)  A    4.70
 917 LEU   ( 306-)  B    4.68
  75 LEU   (  75-)  A    4.55
1021 LEU   ( 410-)  B    4.54
 783 LYS   ( 172-)  B    4.53
 523 GLY   ( 523-)  A    4.53
1121 GLN   ( 510-)  B    4.52
 510 GLN   ( 510-)  A    4.45
 927 GLY   ( 316-)  B    4.37
 110 GLN   ( 110-)  A    4.30
 316 GLY   ( 316-)  A    4.26
1048 PRO   ( 437-)  B    4.21
 296 VAL   ( 296-)  A    4.20
 721 GLN   ( 110-)  B    4.19
1074 TRP   ( 463-)  B    4.11
1143 ARG   ( 532-)  B    4.07
 502 PHE   ( 502-)  A    4.02
 889 ASP   ( 278-)  B    4.01

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.748

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.376

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.

 614 PRO   (   3-)  B    -3.1
 608 PRO   ( 608-)  A    -3.1
1219 PRO   ( 608-)  B    -3.0
  78 PRO   (  78-)  A    -2.9
1026 THR   ( 415-)  B    -2.9
 207 PHE   ( 207-)  A    -2.8
 280 THR   ( 280-)  A    -2.7
 875 ILE   ( 264-)  B    -2.7
 245 ARG   ( 245-)  A    -2.7
1022 LEU   ( 411-)  B    -2.6
   7 PRO   (   7-)  A    -2.6
 910 GLU   ( 299-)  B    -2.5
 550 ARG   ( 550-)  A    -2.5
 408 ILE   ( 408-)  A    -2.5
 499 ILE   ( 499-)  A    -2.5
 741 PRO   ( 130-)  B    -2.4
 752 PRO   ( 141-)  B    -2.4
 856 ARG   ( 245-)  B    -2.4
 983 TYR   ( 372-)  B    -2.4
 410 LEU   ( 410-)  A    -2.4
 708 THR   (  97-)  B    -2.4
1095 PHE   ( 484-)  B    -2.4
1019 ILE   ( 408-)  B    -2.4
 350 ARG   ( 350-)  A    -2.4
 453 ARG   ( 453-)  A    -2.4
And so on for a total of 65 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.

   7 PRO   (   7-)  A  Poor phi/psi
  79 ILE   (  79-)  A  Poor phi/psi
  81 GLN   (  81-)  A  Poor phi/psi
 140 ASP   ( 140-)  A  PRO omega poor
 141 PRO   ( 141-)  A  omega poor
 250 ALA   ( 250-)  A  Poor phi/psi
 258 ALA   ( 258-)  A  Poor phi/psi
 273 ASP   ( 273-)  A  Poor phi/psi
 305 GLU   ( 305-)  A  Poor phi/psi
 340 ARG   ( 340-)  A  Poor phi/psi
 348 CYS   ( 348-)  A  Poor phi/psi
 349 THR   ( 349-)  A  omega poor
 413 ARG   ( 413-)  A  Poor phi/psi
 481 GLU   ( 481-)  A  omega poor
 490 PHE   ( 490-)  A  omega poor
 495 VAL   ( 495-)  A  Poor phi/psi
 598 GLN   ( 598-)  A  Poor phi/psi
 607 TYR   ( 607-)  A  PRO omega poor
 614 PRO   (   3-)  B  Poor phi/psi
 624 ASP   (  13-)  B  Poor phi/psi
 658 THR   (  47-)  B  Poor phi/psi
 680 GLY   (  69-)  B  Poor phi/psi
 690 ILE   (  79-)  B  Poor phi/psi, omega poor
 691 TRP   (  80-)  B  Poor phi/psi, omega poor
 741 PRO   ( 130-)  B  Poor phi/psi
 745 ALA   ( 134-)  B  Poor phi/psi
 751 ASP   ( 140-)  B  PRO omega poor
 869 ALA   ( 258-)  B  Poor phi/psi
 886 PRO   ( 275-)  B  Poor phi/psi, omega poor
 916 GLU   ( 305-)  B  Poor phi/psi
 951 ARG   ( 340-)  B  Poor phi/psi
 952 LYS   ( 341-)  B  Poor phi/psi
 959 CYS   ( 348-)  B  Poor phi/psi
 961 ARG   ( 350-)  B  Poor phi/psi
 991 ARG   ( 380-)  B  Poor phi/psi
1018 LYS   ( 407-)  B  omega poor
1019 ILE   ( 408-)  B  Poor phi/psi
1020 GLY   ( 409-)  B  omega poor
1027 ASN   ( 416-)  B  Poor phi/psi
1143 ARG   ( 532-)  B  Poor phi/psi
1148 GLY   ( 537-)  B  Poor phi/psi
1214 LEU   ( 603-)  B  PRO omega poor
1219 PRO   ( 608-)  B  Poor phi/psi
1220 GLU   ( 609-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.986

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 : -3.986

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.

 892 SER   ( 281-)  B    0.33
  35 SER   (  35-)  A    0.35
 281 SER   ( 281-)  A    0.36
 646 SER   (  35-)  B    0.36
 504 SER   ( 504-)  A    0.37
 182 SER   ( 182-)  A    0.37
 793 SER   ( 182-)  B    0.37
 634 SER   (  23-)  B    0.38

Warning: Unusual backbone conformations

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

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

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

   7 PRO   (   7-)  A      0
   9 ASN   (   9-)  A      0
  12 ALA   (  12-)  A      0
  13 ASP   (  13-)  A      0
  44 THR   (  44-)  A      0
  45 ASN   (  45-)  A      0
  74 GLU   (  74-)  A      0
  75 LEU   (  75-)  A      0
  79 ILE   (  79-)  A      0
  80 TRP   (  80-)  A      0
  81 GLN   (  81-)  A      0
  82 ASN   (  82-)  A      0
  83 PHE   (  83-)  A      0
  97 THR   (  97-)  A      0
  98 LEU   (  98-)  A      0
 100 SER   ( 100-)  A      0
 130 PRO   ( 130-)  A      0
 131 ASN   ( 131-)  A      0
 132 LYS   ( 132-)  A      0
 133 THR   ( 133-)  A      0
 136 CYS   ( 136-)  A      0
 139 LEU   ( 139-)  A      0
 140 ASP   ( 140-)  A      0
 149 SER   ( 149-)  A      0
 150 SER   ( 150-)  A      0
And so on for a total of 390 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 : 3.368

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!

   8 GLY   (   8-)  A   2.55   13

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...

 135 THR   ( 135-)  A   1.97

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]

 614 PRO   (   3-)  B    0.74 HIGH
 752 PRO   ( 141-)  B    0.52 HIGH
1213 PRO   ( 602-)  B    0.46 HIGH
1219 PRO   ( 608-)  B    0.63 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].

 104 PRO   ( 104-)  A  -114.0 envelop C-gamma (-108 degrees)
 205 PRO   ( 205-)  A   -44.5 envelop C-alpha (-36 degrees)
 524 PRO   ( 524-)  A    44.7 envelop C-delta (36 degrees)
 604 PRO   ( 604-)  A   109.3 envelop C-beta (108 degrees)
 608 PRO   ( 608-)  A   -39.4 envelop C-alpha (-36 degrees)
 614 PRO   (   3-)  B   171.4 envelop N (180 degrees)
 689 PRO   (  78-)  B   105.7 envelop C-beta (108 degrees)
1048 PRO   ( 437-)  B  -138.1 envelop C-delta (-144 degrees)
1219 PRO   ( 608-)  B  -177.8 envelop N (180 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.

 893 THR   ( 282-)  B      CG2 <-> 1021 LEU   ( 410-)  B      CB     1.02    2.18  INTRA BF
 614 PRO   (   3-)  B      CD  <->  617 GLN   (   6-)  B      NE2    0.97    2.13  INTRA BF
 279 VAL   ( 279-)  A      CG2 <->  410 LEU   ( 410-)  A      CD1    0.83    2.37  INTRA BF
 279 VAL   ( 279-)  A      CG1 <->  410 LEU   ( 410-)  A      CD1    0.66    2.54  INTRA BF
 340 ARG   ( 340-)  A      NH2 <-> 1227 NAG   ( 694-)  A      N2     0.63    2.37  INTRA BF
 740 LEU   ( 129-)  B      CD2 <-> 1223 ASP   ( 612-)  B      CB     0.59    2.61  INTRA BF
 847 ARG   ( 236-)  B      NE  <->  878 MET   ( 267-)  B      CE     0.57    2.53  INTRA BL
 885 LYS   ( 274-)  B      NZ  <-> 1031 SER   ( 420-)  B      CB     0.56    2.54  INTRA
 279 VAL   ( 279-)  A      CG1 <->  410 LEU   ( 410-)  A      CB     0.52    2.68  INTRA BF
 691 TRP   (  80-)  B      CA  <->  694 PHE   (  83-)  B      CE2    0.50    2.70  INTRA BF
 740 LEU   ( 129-)  B      O   <->  742 ASN   ( 131-)  B      N      0.48    2.22  INTRA BF
 614 PRO   (   3-)  B      CA  <->  617 GLN   (   6-)  B      NE2    0.46    2.64  INTRA BF
 691 TRP   (  80-)  B      CA  <->  694 PHE   (  83-)  B      CD2    0.45    2.75  INTRA BF
 206 THR   ( 206-)  A      CG2 <->  210 ASP   ( 210-)  A      OD2    0.44    2.36  INTRA
   6 GLN   (   6-)  A      CG  <->    7 PRO   (   7-)  A      CD     0.43    2.77  INTRA BF
 139 LEU   ( 139-)  A      CD2 <->  163 TRP   ( 163-)  A      CZ2    0.41    2.79  INTRA
 885 LYS   ( 274-)  B      NZ  <-> 1026 THR   ( 415-)  B      CG2    0.40    2.70  INTRA
 347 GLN   ( 347-)  A      NE2 <->  349 THR   ( 349-)  A      OG1    0.39    2.31  INTRA BF
 691 TRP   (  80-)  B      O   <->  700 ARG   (  89-)  B      CG     0.37    2.43  INTRA BF
 740 LEU   ( 129-)  B      C   <->  742 ASN   ( 131-)  B      N      0.37    2.53  INTRA BF
1071 ASN   ( 460-)  B      N   <-> 1092 GLU   ( 481-)  B      OE2    0.36    2.34  INTRA BL
1052 LEU   ( 441-)  B      CD2 <-> 1053 VAL   ( 442-)  B      N      0.36    2.64  INTRA BL
 446 ARG   ( 446-)  A      NH2 <->  496 THR   ( 496-)  A      O      0.35    2.35  INTRA BL
 614 PRO   (   3-)  B      N   <->  617 GLN   (   6-)  B      NE2    0.35    2.65  INTRA BF
 675 PHE   (  64-)  B      CE1 <->  679 TRP   (  68-)  B      NE1    0.35    2.75  INTRA BF
And so on for a total of 367 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.

 597 TYR   ( 597-)  A      -7.36
1064 ARG   ( 453-)  B      -7.10
 453 ARG   ( 453-)  A      -6.75
1208 TYR   ( 597-)  B      -6.57
   6 GLN   (   6-)  A      -6.52
 129 LEU   ( 129-)  A      -6.48
 617 GLN   (   6-)  B      -6.22
1218 TYR   ( 607-)  B      -6.19
1132 TYR   ( 521-)  B      -6.08
 522 GLU   ( 522-)  A      -6.04
 479 ARG   ( 479-)  A      -5.80
 600 HIS   ( 600-)  A      -5.68
 285 GLN   ( 285-)  A      -5.67
 587 GLN   ( 587-)  A      -5.66
1198 GLN   ( 587-)  B      -5.64
 616 LEU   (   5-)  B      -5.60
 851 ARG   ( 240-)  B      -5.59
 286 GLN   ( 286-)  A      -5.57
 937 ARG   ( 326-)  B      -5.56
 885 LYS   ( 274-)  B      -5.52
 742 ASN   ( 131-)  B      -5.52
1138 GLN   ( 527-)  B      -5.51
 607 TYR   ( 607-)  A      -5.49
 527 GLN   ( 527-)  A      -5.47
 314 TRP   ( 314-)  A      -5.46
1211 HIS   ( 600-)  B      -5.44
 925 TRP   ( 314-)  B      -5.44
 606 ASN   ( 606-)  A      -5.43
 621 PHE   (  10-)  B      -5.40
   9 ASN   (   9-)  A      -5.36
 102 ASN   ( 102-)  A      -5.36
 350 ARG   ( 350-)  A      -5.35
 244 LEU   ( 244-)  A      -5.32
 951 ARG   ( 340-)  B      -5.32
1217 ASN   ( 606-)  B      -5.32
1199 ASN   ( 588-)  B      -5.30
 713 ASN   ( 102-)  B      -5.29
 932 LYS   ( 321-)  B      -5.29
 241 TYR   ( 241-)  A      -5.29
 236 ARG   ( 236-)  A      -5.26
 847 ARG   ( 236-)  B      -5.26
1090 ARG   ( 479-)  B      -5.17
 471 GLN   ( 471-)  A      -5.16
 855 LEU   ( 244-)  B      -5.15
1022 LEU   ( 411-)  B      -5.15
 321 LYS   ( 321-)  A      -5.14
 521 TYR   ( 521-)  A      -5.14
 693 ASN   (  82-)  B      -5.05
 591 VAL   ( 591-)  A      -5.05
 276 ASN   ( 276-)  A      -5.01

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.

 235 ARG   ( 235-)  A       237 - TYR    237- ( A)         -4.80
 846 ARG   ( 235-)  B       848 - TYR    237- ( B)         -4.76
 884 ASP   ( 273-)  B       886 - PRO    275- ( B)         -4.66
1017 HIS   ( 406-)  B      1019 - ILE    408- ( B)         -4.45

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

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

 413 ARG   ( 413-)  A   -3.65
 952 LYS   ( 341-)  B   -3.56
1021 LEU   ( 410-)  B   -3.38
 888 LEU   ( 277-)  B   -3.28
 961 ARG   ( 350-)  B   -3.18
1024 ARG   ( 413-)  B   -2.94
 408 ILE   ( 408-)  A   -2.87
 740 LEU   ( 129-)  B   -2.79
 240 ARG   ( 240-)  A   -2.70
 278 ASP   ( 278-)  A   -2.64
 546 ALA   ( 546-)  A   -2.55
1136 LEU   ( 525-)  B   -2.55
1099 ALA   ( 488-)  B   -2.54
 690 ILE   (  79-)  B   -2.50

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.

  72 ALA   (  72-)  A     -   75 LEU   (  75-)  A        -1.73
 886 PRO   ( 275-)  B     -  889 ASP   ( 278-)  B        -2.23

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.

  54 GLN   (  54-)  A
 406 HIS   ( 406-)  A
 491 HIS   ( 491-)  A
 545 GLN   ( 545-)  A
1027 ASN   ( 416-)  B
1102 HIS   ( 491-)  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.

  13 ASP   (  13-)  A      N
  47 THR   (  47-)  A      N
  61 SER   (  61-)  A      OG
  77 GLU   (  77-)  A      N
  79 ILE   (  79-)  A      N
  81 GLN   (  81-)  A      N
  83 PHE   (  83-)  A      N
  97 THR   (  97-)  A      N
 129 LEU   ( 129-)  A      N
 142 ASP   ( 142-)  A      N
 175 TYR   ( 175-)  A      OH
 189 ASP   ( 189-)  A      N
 193 ASP   ( 193-)  A      N
 230 ARG   ( 230-)  A      NE
 230 ARG   ( 230-)  A      NH2
 241 TYR   ( 241-)  A      N
 243 ASN   ( 243-)  A      N
 251 HIS   ( 251-)  A      NE2
 253 LEU   ( 253-)  A      N
 255 ASP   ( 255-)  A      N
 260 SER   ( 260-)  A      N
 262 GLU   ( 262-)  A      N
 263 ASN   ( 263-)  A      N
 265 TYR   ( 265-)  A      N
 277 LEU   ( 277-)  A      N
And so on for a total of 135 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.

 184 GLU   ( 184-)  A      OE1
 286 GLN   ( 286-)  A      OE1
 336 ASP   ( 336-)  A      OD2
 347 GLN   ( 347-)  A      OE1
 471 GLN   ( 471-)  A      OE1
 491 HIS   ( 491-)  A      ND1
 512 HIS   ( 512-)  A      ND1
 529 ASP   ( 529-)  A      OD1
 583 GLU   ( 583-)  A      OE2
 794 ASN   ( 183-)  B      OD1
 837 HIS   ( 226-)  B      ND1
 958 GLN   ( 347-)  B      OE1
1054 ASP   ( 443-)  B      OD2
1194 GLU   ( 583-)  B      OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1237  ZN   ( 701-)  A   -.-  -.-  Too few ligands (3)
1242  ZN   ( 701-)  B   -.-  -.-  Too few ligands (3)

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.

 210 ASP   ( 210-)  A   H-bonding suggests Asn; but Alt-Rotamer
 417 ASP   ( 417-)  A   H-bonding suggests Asn
 787 GLU   ( 176-)  B   H-bonding suggests Gln; but Alt-Rotamer
 910 GLU   ( 299-)  B   H-bonding suggests Gln
 923 GLU   ( 312-)  B   H-bonding suggests Gln; but Alt-Rotamer
 973 GLU   ( 362-)  B   H-bonding suggests Gln
 985 ASP   ( 374-)  B   H-bonding suggests Asn; but Alt-Rotamer
1169 ASP   ( 558-)  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 :  -1.798
  2nd generation packing quality :  -2.438
  Ramachandran plot appearance   :  -4.376 (bad)
  chi-1/chi-2 rotamer normality  :  -3.986 (poor)
  Backbone conformation          :  -0.512

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.470 (tight)
  Bond angles                    :   0.835
  Omega angle restraints         :   0.612 (tight)
  Side chain planarity           :   0.309 (tight)
  Improper dihedral distribution :   0.790
  B-factor distribution          :   0.541
  Inside/Outside distribution    :   1.026

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 : 3.01


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.470 (tight)
  Bond angles                    :   0.835
  Omega angle restraints         :   0.612 (tight)
  Side chain planarity           :   0.309 (tight)
  Improper dihedral distribution :   0.790
  B-factor distribution          :   0.541
  Inside/Outside distribution    :   1.026
==============

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.