WHAT IF Check report

This file was created 2012-01-29 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 pdb3bwe.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 : 0.607
CA-only RMS fit for the two chains : 0.242

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

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 C

All-atom RMS fit for the two chains : 0.569
CA-only RMS fit for the two chains : 0.309

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 C

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 D

All-atom RMS fit for the two chains : 0.604
CA-only RMS fit for the two chains : 0.311

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 D

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 : 0.708
CA-only RMS fit for the two chains : 0.323

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: A and F

All-atom RMS fit for the two chains : 0.557
CA-only RMS fit for the two chains : 0.258

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 F

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.

1312 PO4   ( 191-)  B  A
1317 PO4   (   5-)  G  F

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.

1311 PO4   ( 190-)  A  -
1312 PO4   ( 191-)  B  A
1313 PO4   (   3-)  C  -
1314 PO4   (   1-)  D  -
1315 PO4   (   6-)  E  -
1316 PO4   (   4-)  F  -
1317 PO4   (   5-)  G  F

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

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 MSE   (   1-)  A      CG
   1 MSE   (   1-)  A     SE
   1 MSE   (   1-)  A      CE
  41 LYS   (  41-)  A      CG
  41 LYS   (  41-)  A      CD
  41 LYS   (  41-)  A      CE
  41 LYS   (  41-)  A      NZ
  63 LYS   (  63-)  A      CG
  63 LYS   (  63-)  A      CD
  63 LYS   (  63-)  A      CE
  63 LYS   (  63-)  A      NZ
  99 LYS   (  99-)  A      CG
  99 LYS   (  99-)  A      CD
  99 LYS   (  99-)  A      CE
  99 LYS   (  99-)  A      NZ
 228 LYS   ( 241-)  B      CG
 228 LYS   ( 241-)  B      CD
 228 LYS   ( 241-)  B      CE
 228 LYS   ( 241-)  B      NZ
 246 GLU   ( 259-)  B      CG
 246 GLU   ( 259-)  B      CD
 246 GLU   ( 259-)  B      OE1
 246 GLU   ( 259-)  B      OE2
 250 LYS   ( 263-)  B      CG
 250 LYS   ( 263-)  B      CD
And so on for a total of 145 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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

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.

 145 ARG   ( 145-)  A
 332 ARG   ( 345-)  B
 520 ARG   ( 545-)  C
 706 ARG   ( 745-)  D
 893 ARG   ( 945-)  E
1080 ARG   (1145-)  F

Warning: Tyrosine convention problem

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

 326 TYR   ( 339-)  B
 442 TYR   ( 467-)  C
 514 TYR   ( 539-)  C
 700 TYR   ( 739-)  D
 887 TYR   ( 939-)  E

Warning: Phenylalanine convention problem

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

 349 PHE   ( 362-)  B
 537 PHE   ( 562-)  C
 867 PHE   ( 919-)  E
 910 PHE   ( 962-)  E

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.

  42 ASP   (  42-)  A
  55 ASP   (  55-)  A
  60 ASP   (  60-)  A
 242 ASP   ( 255-)  B
 247 ASP   ( 260-)  B
 255 ASP   ( 268-)  B
 318 ASP   ( 331-)  B
 417 ASP   ( 442-)  C
 430 ASP   ( 455-)  C
 506 ASP   ( 531-)  C
 616 ASP   ( 655-)  D
 692 ASP   ( 731-)  D
 790 ASP   ( 842-)  E
 803 ASP   ( 855-)  E
 879 ASP   ( 931-)  E
 990 ASP   (1055-)  F
1066 ASP   (1131-)  F
1176 ASP   (1255-)  G
1181 ASP   (1260-)  G
1189 ASP   (1268-)  G
1252 ASP   (1331-)  G
1270 ASP   (1349-)  G

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.

  15 GLU   (  15-)  A
  18 GLU   (  18-)  A
 143 GLU   ( 143-)  A
 170 GLU   ( 170-)  A
 202 GLU   ( 215-)  B
 203 GLU   ( 216-)  B
 205 GLU   ( 218-)  B
 330 GLU   ( 343-)  B
 357 GLU   ( 370-)  B
 390 GLU   ( 415-)  C
 393 GLU   ( 418-)  C
 465 GLU   ( 490-)  C
 518 GLU   ( 543-)  C
 538 GLU   ( 563-)  C
 545 GLU   ( 570-)  C
 576 GLU   ( 615-)  D
 577 GLU   ( 616-)  D
 579 GLU   ( 618-)  D
 704 GLU   ( 743-)  D
 763 GLU   ( 815-)  E
 764 GLU   ( 816-)  E
 766 GLU   ( 818-)  E
 812 GLU   ( 864-)  E
 891 GLU   ( 943-)  E
 918 GLU   ( 970-)  E
 950 GLU   (1015-)  F
 951 GLU   (1016-)  F
 953 GLU   (1018-)  F
1078 GLU   (1143-)  F
1105 GLU   (1170-)  F
1137 GLU   (1216-)  G
1139 GLU   (1218-)  G
1264 GLU   (1343-)  G

Geometric checks

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

 156 ARG   ( 156-)  A      N    CA   C   123.10    4.2
 343 ARG   ( 356-)  B      N    CA   C   122.62    4.1
 531 ARG   ( 556-)  C      N    CA   C   124.66    4.8
 615 PRO   ( 654-)  D      N    CA   C   122.59    4.3
 984 ASP   (1049-)  F      N    CA   C   122.67    4.1

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.

  15 GLU   (  15-)  A
  18 GLU   (  18-)  A
  42 ASP   (  42-)  A
  55 ASP   (  55-)  A
  60 ASP   (  60-)  A
 143 GLU   ( 143-)  A
 145 ARG   ( 145-)  A
 170 GLU   ( 170-)  A
 202 GLU   ( 215-)  B
 203 GLU   ( 216-)  B
 205 GLU   ( 218-)  B
 242 ASP   ( 255-)  B
 247 ASP   ( 260-)  B
 255 ASP   ( 268-)  B
 318 ASP   ( 331-)  B
 330 GLU   ( 343-)  B
 332 ARG   ( 345-)  B
 357 GLU   ( 370-)  B
 390 GLU   ( 415-)  C
 393 GLU   ( 418-)  C
 417 ASP   ( 442-)  C
 430 ASP   ( 455-)  C
 465 GLU   ( 490-)  C
 506 ASP   ( 531-)  C
 518 GLU   ( 543-)  C
And so on for a total of 61 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.

 843 GLN   ( 895-)  E    6.74
 842 GLU   ( 894-)  E    6.55
 806 LEU   ( 858-)  E    5.31
 531 ARG   ( 556-)  C    5.00
 486 ALA   ( 511-)  C    4.99
 391 GLU   ( 416-)  C    4.59
1232 ALA   (1311-)  G    4.50
 359 LEU   ( 372-)  B    4.43
 156 ARG   ( 156-)  A    4.41
 844 GLU   ( 896-)  E    4.35
 298 ALA   ( 311-)  B    4.24
 343 ARG   ( 356-)  B    4.24
 933 LEU   ( 985-)  E    4.17
 859 ALA   ( 911-)  E    4.16
 315 LEU   ( 328-)  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 : 1.537

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.

1248 PRO   (1327-)  G    -2.8
 125 THR   ( 125-)  A    -2.6
1237 GLU   (1316-)  G    -2.5
 779 ILE   ( 831-)  E    -2.5
 119 PHE   ( 119-)  A    -2.5
 812 GLU   ( 864-)  E    -2.4
1258 GLY   (1337-)  G    -2.4
 423 ARG   ( 448-)  C    -2.3
 345 PRO   ( 358-)  B    -2.3
 314 PRO   ( 327-)  B    -2.3
 137 GLY   ( 137-)  A    -2.3
1273 ILE   (1352-)  G    -2.3
1257 GLY   (1336-)  G    -2.2
 983 ARG   (1048-)  F    -2.2
 906 PRO   ( 958-)  E    -2.2
 259 LEU   ( 272-)  B    -2.2
1121 VAL   (1186-)  F    -2.2
1245 THR   (1324-)  G    -2.2
 609 ARG   ( 648-)  D    -2.2
 444 VAL   ( 469-)  C    -2.2
 846 ARG   ( 898-)  E    -2.2
 885 GLY   ( 937-)  E    -2.2
1007 LEU   (1072-)  F    -2.2
 306 PHE   ( 319-)  B    -2.1
 758 LEU   ( 810-)  E    -2.1
 630 VAL   ( 669-)  D    -2.1
  48 ARG   (  48-)  A    -2.1
 817 VAL   ( 869-)  E    -2.1
1256 ASN   (1335-)  G    -2.1
 688 PRO   ( 727-)  D    -2.1
 324 GLY   ( 337-)  B    -2.1
 667 CYS   ( 706-)  D    -2.1
 782 THR   ( 834-)  E    -2.1
 373 VAL   ( 386-)  B    -2.1
1307 VAL   (1386-)  G    -2.1
 116 GLU   ( 116-)  A    -2.1
1053 GLY   (1118-)  F    -2.1
1062 PRO   (1127-)  F    -2.1
 999 GLU   (1064-)  F    -2.0
 592 ILE   ( 631-)  D    -2.0
 820 LEU   ( 872-)  E    -2.0
 256 VAL   ( 269-)  B    -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.

   2 ALA   (   2-)  A  Poor phi/psi
  49 ASP   (  49-)  A  Poor phi/psi
  65 GLY   (  65-)  A  Poor phi/psi
  99 LYS   (  99-)  A  Poor phi/psi
 106 CYS   ( 106-)  A  Poor phi/psi
 137 GLY   ( 137-)  A  Poor phi/psi
 236 ASP   ( 249-)  B  Poor phi/psi
 252 GLY   ( 265-)  B  Poor phi/psi
 263 ASN   ( 276-)  B  Poor phi/psi
 286 LYS   ( 299-)  B  Poor phi/psi
 293 CYS   ( 306-)  B  Poor phi/psi
 324 GLY   ( 337-)  B  Poor phi/psi
 373 VAL   ( 386-)  B  Poor phi/psi
 377 ALA   ( 402-)  C  Poor phi/psi
 424 ASP   ( 449-)  C  Poor phi/psi
 431 ALA   ( 456-)  C  Poor phi/psi
 439 GLU   ( 464-)  C  Poor phi/psi
 474 LYS   ( 499-)  C  Poor phi/psi
 481 CYS   ( 506-)  C  Poor phi/psi
 506 ASP   ( 531-)  C  Poor phi/psi
 513 HIS   ( 538-)  C  Poor phi/psi
 610 ASP   ( 649-)  D  Poor phi/psi
 626 GLY   ( 665-)  D  Poor phi/psi
 660 LYS   ( 699-)  D  Poor phi/psi
 667 CYS   ( 706-)  D  Poor phi/psi
And so on for a total of 58 lines.

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.

  83 SER   (  83-)  A    0.35
1204 SER   (1283-)  G    0.36
 644 SER   ( 683-)  D    0.37

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!

  12 LYS   (  12-)  A      0
  17 MSE   (  17-)  A      0
  26 MSE   (  26-)  A      0
  39 ALA   (  39-)  A      0
  41 LYS   (  41-)  A      0
  48 ARG   (  48-)  A      0
  49 ASP   (  49-)  A      0
  64 GLU   (  64-)  A      0
  66 PRO   (  66-)  A      0
  98 ARG   (  98-)  A      0
 105 ILE   ( 105-)  A      0
 106 CYS   ( 106-)  A      0
 107 ALA   ( 107-)  A      0
 119 PHE   ( 119-)  A      0
 126 HIS   ( 126-)  A      0
 133 MSE   ( 133-)  A      0
 134 MSE   ( 134-)  A      0
 138 HIS   ( 138-)  A      0
 144 ASN   ( 144-)  A      0
 145 ARG   ( 145-)  A      0
 149 ASP   ( 149-)  A      0
 151 LEU   ( 151-)  A      0
 156 ARG   ( 156-)  A      0
 173 ASN   ( 173-)  A      0
 186 VAL   ( 186-)  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 : 1.225

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]

 418 PRO   ( 443-)  C    0.46 HIGH

Warning: Unusual PRO puckering phases

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

 109 PRO   ( 109-)  A  -131.5 half-chair C-delta/C-gamma (-126 degrees)
1044 PRO   (1109-)  F  -115.0 envelop C-gamma (-108 degrees)
1230 PRO   (1309-)  G  -122.3 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 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 811 LYS   ( 863-)  E      O    <->   813 GLY   ( 865-)  E      N    0.47    2.23  INTRA BF
 801 CYS   ( 853-)  E      SG   <->   988 CYS   (1053-)  F      SG   0.45    3.00  INTRA BF
  53 CYS   (  53-)  A      SG   <->   240 CYS   ( 253-)  B      SG   0.45    3.00  INTRA
 332 ARG   ( 345-)  B      NH1  <->   350 GLU   ( 363-)  B      OE2  0.39    2.31  INTRA
 795 SER   ( 847-)  E      OG   <->   796 ARG   ( 848-)  E      NH1  0.39    2.31  INTRA
 203 GLU   ( 216-)  B      OE2  <->   235 ARG   ( 248-)  B      N    0.35    2.35  INTRA
 562 LEU   ( 587-)  C      C    <->   706 ARG   ( 745-)  D      NH2  0.34    2.76  INTRA
 145 ARG   ( 145-)  A      NH1  <->   163 GLU   ( 163-)  A      OE2  0.31    2.39  INTRA
 930 LYS   ( 982-)  E      NZ   <->  1322 HOH   ( 235 )  E      O    0.30    2.40  INTRA
 481 CYS   ( 506-)  C      SG   <->   482 ALA   ( 507-)  C      N    0.29    2.91  INTRA
 936 LYS   ( 988-)  E      CB   <->  1080 ARG   (1145-)  F      NH1  0.28    2.82  INTRA
 188 LYS   ( 188-)  A      N    <->   332 ARG   ( 345-)  B      NH2  0.27    2.58  INTRA
1137 GLU   (1216-)  G      OE2  <->  1169 ARG   (1248-)  G      N    0.27    2.43  INTRA
 520 ARG   ( 545-)  C      NH2  <->   747 VAL   ( 786-)  D      O    0.27    2.43  INTRA
  92 LEU   (  92-)  A      CB   <->   117 ILE   ( 117-)  A      CD1  0.27    2.93  INTRA
 148 LYS   ( 148-)  A      NZ   <->   150 GLY   ( 150-)  A      O    0.26    2.44  INTRA
 331 ASN   ( 344-)  B      ND2  <->   334 GLU   ( 347-)  B      OE1  0.26    2.44  INTRA
 113 LEU   ( 113-)  A      CB   <->   133 MSE   ( 133-)  A      CE   0.26    2.94  INTRA
 730 VAL   ( 769-)  D      O    <->   734 ASN   ( 773-)  D      N    0.25    2.45  INTRA BL
  67 TYR   (  67-)  A      N    <->  1318 HOH   ( 200 )  A      O    0.25    2.45  INTRA
1290 VAL   (1369-)  G      O    <->  1294 ASN   (1373-)  G      N    0.24    2.46  INTRA
 380 ARG   ( 405-)  C      NH2  <->   439 GLU   ( 464-)  C      O    0.24    2.46  INTRA BF
 332 ARG   ( 345-)  B      NH1  <->   350 GLU   ( 363-)  B      CD   0.24    2.86  INTRA
 573 LYS   ( 612-)  D      NZ   <->  1321 HOH   ( 246 )  D      O    0.24    2.46  INTRA
 820 LEU   ( 872-)  E      N    <->   851 ALA   ( 903-)  E      O    0.23    2.47  INTRA
And so on for a total of 336 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

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.

 846 ARG   ( 898-)  E      -6.78
 789 LYS   ( 841-)  E      -6.18
 659 ARG   ( 698-)  D      -6.05
 602 LYS   ( 641-)  D      -6.04
 510 ASN   ( 535-)  C      -5.82
  98 ARG   (  98-)  A      -5.72
 135 ASN   ( 135-)  A      -5.49
 883 ASN   ( 935-)  E      -5.43
1218 ASN   (1297-)  G      -5.42
  97 ASN   (  97-)  A      -5.40
 845 ASN   ( 897-)  E      -5.40
1149 ARG   (1228-)  G      -5.36
 696 ASN   ( 735-)  D      -5.36
 589 ARG   ( 628-)  D      -5.35
 215 ARG   ( 228-)  B      -5.34
 963 ARG   (1028-)  F      -5.31
  28 ARG   (  28-)  A      -5.29
 403 ARG   ( 428-)  C      -5.26
 473 ARG   ( 498-)  C      -5.25
1070 ASN   (1135-)  F      -5.25
1256 ASN   (1335-)  G      -5.24
 709 LYS   ( 748-)  D      -5.23
 776 ARG   ( 828-)  E      -5.23
 285 ARG   ( 298-)  B      -5.20
 921 ASN   ( 973-)  E      -5.17
 322 ASN   ( 335-)  B      -5.15
1294 ASN   (1373-)  G      -5.14
 173 ASN   ( 173-)  A      -5.13
1108 ASN   (1173-)  F      -5.11
 548 ASN   ( 573-)  C      -5.10
 360 ASN   ( 373-)  B      -5.08
 734 ASN   ( 773-)  D      -5.07
1217 GLU   (1296-)  G      -5.04

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

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.

  99 LYS   (  99-)  A   -3.24
 936 LYS   ( 988-)  E   -2.62
 404 ALA   ( 429-)  C   -2.62
 777 ALA   ( 829-)  E   -2.60
 216 ALA   ( 229-)  B   -2.58
 590 ALA   ( 629-)  D   -2.58
 964 ALA   (1029-)  F   -2.58
  29 ALA   (  29-)  A   -2.55

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

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1319 HOH   ( 390 )  B      O     -9.15   -7.90   45.45
1320 HOH   ( 230 )  C      O     72.60   21.34    0.94

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.

1318 HOH   ( 195 )  A      O
1318 HOH   ( 199 )  A      O
1318 HOH   ( 213 )  A      O
1318 HOH   ( 218 )  A      O
1318 HOH   ( 219 )  A      O
1318 HOH   ( 227 )  A      O
1319 HOH   ( 428 )  B      O
1319 HOH   ( 448 )  B      O
1320 HOH   (  68 )  C      O
1320 HOH   (  73 )  C      O
1320 HOH   (  74 )  C      O
1320 HOH   ( 222 )  C      O
1320 HOH   ( 230 )  C      O
1320 HOH   ( 231 )  C      O
1320 HOH   ( 232 )  C      O
1321 HOH   ( 122 )  D      O
1321 HOH   ( 124 )  D      O
1321 HOH   ( 125 )  D      O
1321 HOH   ( 252 )  D      O
1321 HOH   ( 253 )  D      O
1321 HOH   ( 263 )  D      O
1321 HOH   ( 267 )  D      O
1322 HOH   ( 130 )  E      O
1322 HOH   ( 143 )  E      O
1322 HOH   ( 144 )  E      O
1322 HOH   ( 234 )  E      O
1322 HOH   ( 250 )  E      O
1322 HOH   ( 273 )  E      O
1322 HOH   ( 274 )  E      O
1322 HOH   ( 275 )  E      O
1323 HOH   ( 163 )  F      O
1324 HOH   ( 169 )  G      O
1324 HOH   ( 175 )  G      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.

  80 GLN   (  80-)  A
 126 HIS   ( 126-)  A
 232 GLN   ( 245-)  B
 313 HIS   ( 326-)  B
 360 ASN   ( 373-)  B
 501 HIS   ( 526-)  C
 687 HIS   ( 726-)  D
 793 GLN   ( 845-)  E
 843 GLN   ( 895-)  E
 874 HIS   ( 926-)  E
1061 HIS   (1126-)  F
1108 ASN   (1173-)  F
1166 GLN   (1245-)  G
1247 HIS   (1326-)  G

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.

  27 ARG   (  27-)  A      NH2
  42 ASP   (  42-)  A      N
  48 ARG   (  48-)  A      NH1
  50 VAL   (  50-)  A      N
  75 GLY   (  75-)  A      N
 138 HIS   ( 138-)  A      N
 139 TYR   ( 139-)  A      N
 145 ARG   ( 145-)  A      NH1
 180 GLN   ( 180-)  A      NE2
 235 ARG   ( 248-)  B      NH1
 250 LYS   ( 263-)  B      N
 263 ASN   ( 276-)  B      N
 325 HIS   ( 338-)  B      N
 325 HIS   ( 338-)  B      NE2
 326 TYR   ( 339-)  B      N
 367 GLN   ( 380-)  B      NE2
 417 ASP   ( 442-)  C      N
 423 ARG   ( 448-)  C      N
 423 ARG   ( 448-)  C      NH1
 451 ASN   ( 476-)  C      N
 487 LEU   ( 512-)  C      N
 513 HIS   ( 538-)  C      N
 514 TYR   ( 539-)  C      N
 537 PHE   ( 562-)  C      N
 538 GLU   ( 563-)  C      N
And so on for a total of 76 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.

  16 GLU   (  16-)  A      OE2
  18 GLU   (  18-)  A      OE2
  24 ASP   (  24-)  A      OD2
 176 GLU   ( 176-)  A      OE2
 205 GLU   ( 218-)  B      OE2
 211 ASP   ( 224-)  B      OD2
 363 GLU   ( 376-)  B      OE2
 393 GLU   ( 418-)  C      OE2
 399 ASP   ( 424-)  C      OD2
 579 GLU   ( 618-)  D      OE2
 585 ASP   ( 624-)  D      OD2
 737 GLU   ( 776-)  D      OE2
 766 GLU   ( 818-)  E      OE2
 953 GLU   (1018-)  F      OE2
 959 ASP   (1024-)  F      OD2
1139 GLU   (1218-)  G      OE2
1145 ASP   (1224-)  G      OD2

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.

 391 GLU   ( 416-)  C   H-bonding suggests Gln
 577 GLU   ( 616-)  D   H-bonding suggests Gln
 625 GLU   ( 664-)  D   H-bonding suggests Gln
1003 ASP   (1068-)  F   H-bonding suggests Asn
1268 GLU   (1347-)  G   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 :  -0.436
  2nd generation packing quality :  -0.661
  Ramachandran plot appearance   :  -2.552
  chi-1/chi-2 rotamer normality  :  -2.728
  Backbone conformation          :   0.674

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.363 (tight)
  Bond angles                    :   0.654 (tight)
  Omega angle restraints         :   0.223 (tight)
  Side chain planarity           :   0.259 (tight)
  Improper dihedral distribution :   0.591
  B-factor distribution          :   0.467
  Inside/Outside distribution    :   0.930

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.363 (tight)
  Bond angles                    :   0.654 (tight)
  Omega angle restraints         :   0.223 (tight)
  Side chain planarity           :   0.259 (tight)
  Improper dihedral distribution :   0.591
  B-factor distribution          :   0.467
  Inside/Outside distribution    :   0.930
==============

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.