WHAT IF Check report

This file was created 2011-12-17 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 pdb3odm.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: B and F

All-atom RMS fit for the two chains : 0.637
CA-only RMS fit for the two chains : 0.378

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: B and F

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: G and H

All-atom RMS fit for the two chains : 6.214
CA-only RMS fit for the two chains : 5.863

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: G and H

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

4226 AUC   ( 607-)  A  -         Atom types
4229 A10   ( 631-)  H  -         Atom types
4230 MLI   ( 901-)  A  -         OK
4233 A11   ( 610-)  B  -         Atom types
4239 A12   ( 602-)  C  -         Atom types
4242 MLI   ( 901-)  C  -         OK
4243 A13   ( 603-)  D  -         Atom types
4247 MLI   ( 901-)  D  -         OK
4249 A14   ( 606-)  E  -         Atom types
4252 MLI   ( 901-)  E  -         OK
4255 A15   ( 614-)  F  -         Atom types
4259 A16   ( 615-)  G  -         Atom types
4262 A17   ( 611-)  H  -         Atom types
4266 MLI   ( 901-)  H  -         OK

Administrative problems that can generate validation failures

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.

2639 CYS   (   5-)  F  -   SG
3834 MET   ( 144-)  H  -   SD
4185 MET   ( 505-)  H  -   SD
4192 MET   ( 512-)  H  -   SD

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

1402 ALA   ( 348-)  C  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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

Warning: Missing atoms

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

 865 LYS   ( 340-)  B      CG
 865 LYS   ( 340-)  B      CD
 865 LYS   ( 340-)  B      CE
 865 LYS   ( 340-)  B      NZ
 872 ASN   ( 355-)  B      CG
 872 ASN   ( 355-)  B      OD1
 872 ASN   ( 355-)  B      ND2
 875 VAL   ( 358-)  B      CG1
 875 VAL   ( 358-)  B      CG2
 886 LYS   ( 369-)  B      CD
 886 LYS   ( 369-)  B      CE
 886 LYS   ( 369-)  B      NZ
1402 ALA   ( 348-)  C      C
1402 ALA   ( 348-)  C      O
1402 ALA   ( 348-)  C      CB
1403 ARG   ( 356-)  C      CG
1403 ARG   ( 356-)  C      CD
1403 ARG   ( 356-)  C      NE
1403 ARG   ( 356-)  C      CZ
1403 ARG   ( 356-)  C      NH1
1403 ARG   ( 356-)  C      NH2
1405 VAL   ( 358-)  C      CG1
1405 VAL   ( 358-)  C      CG2
1437 ARG   ( 390-)  C      CD
1437 ARG   ( 390-)  C      NE
And so on for a total of 66 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.

 369 ASP   ( 381-)  A    High
 371 SER   ( 383-)  A    High
 372 LYS   ( 384-)  A    High
 373 GLU   ( 385-)  A    High
 378 ARG   ( 390-)  A    High
 692 VAL   ( 167-)  B    High
 693 PRO   ( 168-)  B    High
 696 ALA   ( 171-)  B    High
 700 ARG   ( 175-)  B    High
 754 LYS   ( 229-)  B    High
 829 GLU   ( 304-)  B    High
 872 ASN   ( 355-)  B    High
 873 ARG   ( 356-)  B    High
 874 GLU   ( 357-)  B    High
 875 VAL   ( 358-)  B    High
 879 ASP   ( 362-)  B    High
 880 ASN   ( 363-)  B    High
 883 ASP   ( 366-)  B    High
 884 LEU   ( 367-)  B    High
 885 VAL   ( 368-)  B    High
 886 LYS   ( 369-)  B    High
 887 ASP   ( 370-)  B    High
 888 GLU   ( 371-)  B    High
 889 VAL   ( 372-)  B    High
 892 GLN   ( 375-)  B    High
And so on for a total of 236 lines.

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

   1 MET   (   1-)  A    0.45
   7 MET   (   7-)  A    0.73
   8 MET   (   8-)  A    0.54
  46 MET   (  46-)  A    0.68
 197 MET   ( 197-)  A    0.55
 218 MET   ( 218-)  A    0.12
 309 MET   ( 309-)  A    0.70
 316 CYS   ( 316-)  A    0.57
 456 MET   ( 468-)  A    0.32
 493 MET   ( 505-)  A    0.63
 532 MET   (   7-)  B    0.94
 533 MET   (   8-)  B    0.70
 765 CYS   ( 240-)  B    0.68
 841 CYS   ( 316-)  B    0.57
 915 MET   ( 398-)  B    0.85
 920 MET   ( 403-)  B    0.69
 925 MET   ( 408-)  B    0.57
 927 MET   ( 410-)  B    0.49
 985 MET   ( 468-)  B    0.49
1022 MET   ( 505-)  B    0.20
1046 MET   ( 529-)  B    0.86
1150 MET   (  96-)  C    0.57
1153 MET   (  99-)  C    0.11
1198 MET   ( 144-)  C    0.97
1251 MET   ( 197-)  C    0.89
And so on for a total of 93 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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 58

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Nomenclature related problems

Warning: Tyrosine convention problem

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

  56 TYR   (  56-)  A
 374 TYR   ( 386-)  A
 387 TYR   ( 399-)  A
 409 TYR   ( 421-)  A
 478 TYR   ( 490-)  A
 916 TYR   ( 399-)  B
1110 TYR   (  56-)  C
1446 TYR   ( 399-)  C
1468 TYR   ( 421-)  C
1537 TYR   ( 490-)  C
1765 TYR   ( 181-)  D
1791 TYR   ( 207-)  D
1972 TYR   ( 399-)  D
2037 TYR   ( 464-)  D
2063 TYR   ( 490-)  D
2128 TYR   (  18-)  E
2166 TYR   (  56-)  E
2259 TYR   ( 149-)  E
2496 TYR   ( 399-)  E
2587 TYR   ( 490-)  E
3025 TYR   ( 399-)  F
3047 TYR   ( 421-)  F
3219 TYR   (  56-)  G
3552 TYR   ( 399-)  G
3643 TYR   ( 490-)  G
3746 TYR   (  56-)  H
4066 TYR   ( 386-)  H
4170 TYR   ( 490-)  H

Warning: Phenylalanine convention problem

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

  92 PHE   (  92-)  A
 269 PHE   ( 269-)  A
 301 PHE   ( 301-)  A
 324 PHE   ( 324-)  A
 333 PHE   ( 333-)  A
 430 PHE   ( 442-)  A
 471 PHE   ( 483-)  A
 617 PHE   (  92-)  B
 794 PHE   ( 269-)  B
 849 PHE   ( 324-)  B
 959 PHE   ( 442-)  B
1146 PHE   (  92-)  C
1323 PHE   ( 269-)  C
1355 PHE   ( 301-)  C
1378 PHE   ( 324-)  C
1489 PHE   ( 442-)  C
1530 PHE   ( 483-)  C
1676 PHE   (  92-)  D
1851 PHE   ( 267-)  D
1853 PHE   ( 269-)  D
1908 PHE   ( 324-)  D
2015 PHE   ( 442-)  D
2056 PHE   ( 483-)  D
2202 PHE   (  92-)  E
2379 PHE   ( 269-)  E
2434 PHE   ( 324-)  E
2539 PHE   ( 442-)  E
2580 PHE   ( 483-)  E
2726 PHE   (  92-)  F
2901 PHE   ( 267-)  F
2903 PHE   ( 269-)  F
2958 PHE   ( 324-)  F
2971 PHE   ( 337-)  F
3068 PHE   ( 442-)  F
3255 PHE   (  92-)  G
3430 PHE   ( 267-)  G
3432 PHE   ( 269-)  G
3464 PHE   ( 301-)  G
3487 PHE   ( 324-)  G
3595 PHE   ( 442-)  G
3782 PHE   (  92-)  H
3957 PHE   ( 267-)  H
3959 PHE   ( 269-)  H
4014 PHE   ( 324-)  H
4122 PHE   ( 442-)  H

Warning: Aspartic acid convention problem

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

 174 ASP   ( 174-)  A
 350 ASP   ( 362-)  A
 718 ASP   ( 193-)  B
 974 ASP   ( 457-)  B
1228 ASP   ( 174-)  C
1397 ASP   ( 343-)  C
1428 ASP   ( 381-)  C
1620 ASP   (  36-)  D
1758 ASP   ( 174-)  D
1786 ASP   ( 202-)  D
1927 ASP   ( 343-)  D
2030 ASP   ( 457-)  D
2284 ASP   ( 174-)  E
2288 ASP   ( 178-)  E
2453 ASP   ( 343-)  E
2459 ASP   ( 362-)  E
2467 ASP   ( 370-)  E
2554 ASP   ( 457-)  E
2800 ASP   ( 166-)  F
2808 ASP   ( 174-)  F
2977 ASP   ( 343-)  F
3317 ASP   ( 154-)  G
3356 ASP   ( 193-)  G
3365 ASP   ( 202-)  G
3726 ASP   (  36-)  H
3856 ASP   ( 166-)  H
3868 ASP   ( 178-)  H
4137 ASP   ( 457-)  H

Warning: Glutamic acid convention problem

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

 130 GLU   ( 130-)  A
 165 GLU   ( 165-)  A
 279 GLU   ( 279-)  A
 280 GLU   ( 280-)  A
 447 GLU   ( 459-)  A
 454 GLU   ( 466-)  A
 541 GLU   (  16-)  B
 614 GLU   (  89-)  B
 655 GLU   ( 130-)  B
 704 GLU   ( 179-)  B
 983 GLU   ( 466-)  B
1025 GLU   ( 508-)  B
1184 GLU   ( 130-)  C
1219 GLU   ( 165-)  C
1345 GLU   ( 291-)  C
1365 GLU   ( 311-)  C
1418 GLU   ( 371-)  C
1506 GLU   ( 459-)  C
1513 GLU   ( 466-)  C
1520 GLU   ( 473-)  C
1694 GLU   ( 110-)  D
1714 GLU   ( 130-)  D
1812 GLU   ( 228-)  D
1888 GLU   ( 304-)  D
1944 GLU   ( 371-)  D
And so on for a total of 60 lines.

Geometric checks

Warning: Unusual bond angles

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

 607 ARG   (  82-)  B      CB   CG   CD  102.60   -5.8
1153 MET   (  99-)  C      CG   SD   CE   91.73   -4.2
2285 ARG   ( 175-)  E      CG   CD   NE  118.68    4.8
2358 HIS   ( 248-)  E      CG   ND1  CE1 109.66    4.1
3393 HIS   ( 230-)  G      CG   ND1  CE1 109.64    4.0
3772 ARG   (  82-)  H      CB   CG   CD  105.90   -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.

 130 GLU   ( 130-)  A
 165 GLU   ( 165-)  A
 174 ASP   ( 174-)  A
 279 GLU   ( 279-)  A
 280 GLU   ( 280-)  A
 350 ASP   ( 362-)  A
 447 GLU   ( 459-)  A
 454 GLU   ( 466-)  A
 541 GLU   (  16-)  B
 614 GLU   (  89-)  B
 655 GLU   ( 130-)  B
 704 GLU   ( 179-)  B
 718 ASP   ( 193-)  B
 974 ASP   ( 457-)  B
 983 GLU   ( 466-)  B
1025 GLU   ( 508-)  B
1184 GLU   ( 130-)  C
1219 GLU   ( 165-)  C
1228 ASP   ( 174-)  C
1345 GLU   ( 291-)  C
1365 GLU   ( 311-)  C
1397 ASP   ( 343-)  C
1418 GLU   ( 371-)  C
1428 ASP   ( 381-)  C
1506 GLU   ( 459-)  C
And so on for a total of 88 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.

1795 SER   ( 211-)  D    4.83
2801 VAL   ( 167-)  F    4.70
3422 ALA   ( 259-)  G    4.61
2608 VAL   ( 511-)  E    4.51
2658 GLU   (  24-)  F    4.50
3714 GLU   (  24-)  H    4.30
2962 ILE   ( 328-)  F    4.26
 732 TYR   ( 207-)  B    4.19
 778 ASN   ( 253-)  B    4.09
2317 TYR   ( 207-)  E    4.06
2926 LYS   ( 292-)  F    4.00

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.

2358 HIS   ( 248-)  E    -2.8
2882 HIS   ( 248-)  F    -2.8
1832 HIS   ( 248-)  D    -2.8
3749 THR   (  59-)  H    -2.8
 248 HIS   ( 248-)  A    -2.8
3938 HIS   ( 248-)  H    -2.7
1302 HIS   ( 248-)  C    -2.7
3557 PRO   ( 404-)  G    -2.7
3411 HIS   ( 248-)  G    -2.7
 971 LYS   ( 454-)  B    -2.7
 773 HIS   ( 248-)  B    -2.7
3607 LYS   ( 454-)  G    -2.7
 537 PRO   (  12-)  B    -2.7
 921 PRO   ( 404-)  B    -2.6
1596 PRO   (  12-)  D    -2.6
2551 LYS   ( 454-)  E    -2.6
 442 LYS   ( 454-)  A    -2.6
1957 LYS   ( 384-)  D    -2.6
2477 ILE   ( 380-)  E    -2.5
1621 LYS   (  37-)  D    -2.5
3082 ILE   ( 456-)  F    -2.5
3080 LYS   ( 454-)  F    -2.5
2486 PRO   ( 389-)  E    -2.5
1401 LYS   ( 347-)  C    -2.5
2534 ARG   ( 437-)  E    -2.5
And so on for a total of 132 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.

  12 PRO   (  12-)  A  Poor phi/psi
  15 VAL   (  15-)  A  omega poor
  51 GLY   (  51-)  A  omega poor
  89 GLU   (  89-)  A  Poor phi/psi
 126 GLU   ( 126-)  A  Poor phi/psi
 156 ASN   ( 156-)  A  Poor phi/psi
 160 ILE   ( 160-)  A  omega poor
 222 GLY   ( 222-)  A  Poor phi/psi
 248 HIS   ( 248-)  A  Poor phi/psi
 277 HIS   ( 277-)  A  omega poor
 345 LEU   ( 345-)  A  omega poor
 367 SER   ( 379-)  A  omega poor
 371 SER   ( 383-)  A  Poor phi/psi, omega poor
 372 LYS   ( 384-)  A  omega poor
 397 GLY   ( 409-)  A  Poor phi/psi
 437 GLY   ( 449-)  A  omega poor
 442 LYS   ( 454-)  A  Poor phi/psi
 464 ASN   ( 476-)  A  Poor phi/psi
 466 GLY   ( 478-)  A  Poor phi/psi
 498 ASN   ( 510-)  A  omega poor
 503 SER   ( 515-)  A  omega poor
 576 GLY   (  51-)  B  omega poor
 578 LEU   (  53-)  B  Poor phi/psi
 614 GLU   (  89-)  B  Poor phi/psi
 681 ASN   ( 156-)  B  Poor phi/psi
And so on for a total of 149 lines.

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 : -3.989

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.

 100 SER   ( 100-)  A    0.35
2321 SER   ( 211-)  E    0.35
  68 SER   (  68-)  A    0.35
 736 SER   ( 211-)  B    0.36
2774 SER   ( 140-)  F    0.36
3208 VAL   (  45-)  G    0.36
3221 GLN   (  58-)  G    0.36
3790 SER   ( 100-)  H    0.37
3374 SER   ( 211-)  G    0.37
2170 SER   (  60-)  E    0.38
1684 SER   ( 100-)  D    0.38
  45 VAL   (  45-)  A    0.38
1545 LYS   ( 498-)  C    0.38
 633 SER   ( 108-)  B    0.39
 910 SER   ( 393-)  B    0.39
3124 LYS   ( 498-)  F    0.39

Warning: Unusual backbone conformations

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

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

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

   5 CYS   (   5-)  A      0
   6 SER   (   6-)  A      0
  11 HIS   (  11-)  A      0
  12 PRO   (  12-)  A      0
  15 VAL   (  15-)  A      0
  16 GLU   (  16-)  A      0
  37 LYS   (  37-)  A      0
  40 LEU   (  40-)  A      0
  42 ILE   (  42-)  A      0
  43 GLU   (  43-)  A      0
  49 PHE   (  49-)  A      0
  57 HIS   (  57-)  A      0
  73 PRO   (  73-)  A      0
  85 ASN   (  85-)  A      0
  88 LYS   (  88-)  A      0
  89 GLU   (  89-)  A      0
 112 THR   ( 112-)  A      0
 117 ILE   ( 117-)  A      0
 124 MET   ( 124-)  A      0
 126 GLU   ( 126-)  A      0
 149 TYR   ( 149-)  A      0
 151 THR   ( 151-)  A      0
 155 LEU   ( 155-)  A      0
 157 SER   ( 157-)  A      0
 173 ILE   ( 173-)  A      0
And so on for a total of 1124 lines.

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!

1023 GLY   ( 506-)  B   1.98   21
3562 GLY   ( 409-)  G   1.67   11

Warning: Unusual PRO puckering amplitudes

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

 115 PRO   ( 115-)  A    0.17 LOW
3218 PRO   (  55-)  G    0.19 LOW

Warning: Unusual PRO puckering phases

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

  34 PRO   (  34-)  A   109.8 envelop C-beta (108 degrees)
 168 PRO   ( 168-)  A  -112.3 envelop C-gamma (-108 degrees)
 236 PRO   ( 236-)  A    43.5 envelop C-delta (36 degrees)
 298 PRO   ( 298-)  A   125.6 half-chair C-beta/C-alpha (126 degrees)
 422 PRO   ( 434-)  A  -134.6 half-chair C-delta/C-gamma (-126 degrees)
 537 PRO   (  12-)  B   -62.9 half-chair C-beta/C-alpha (-54 degrees)
 559 PRO   (  34-)  B  -127.7 half-chair C-delta/C-gamma (-126 degrees)
 640 PRO   ( 115-)  B  -117.8 half-chair C-delta/C-gamma (-126 degrees)
 693 PRO   ( 168-)  B   114.7 envelop C-beta (108 degrees)
 761 PRO   ( 236-)  B    14.4 half-chair N/C-delta (18 degrees)
 823 PRO   ( 298-)  B  -137.1 envelop C-delta (-144 degrees)
 906 PRO   ( 389-)  B   -39.4 envelop C-alpha (-36 degrees)
 921 PRO   ( 404-)  B   122.5 half-chair C-beta/C-alpha (126 degrees)
1079 PRO   (  25-)  C   104.4 envelop C-beta (108 degrees)
1088 PRO   (  34-)  C   114.8 envelop C-beta (108 degrees)
1222 PRO   ( 168-)  C   119.0 half-chair C-beta/C-alpha (126 degrees)
1290 PRO   ( 236-)  C    34.0 envelop C-delta (36 degrees)
1436 PRO   ( 389-)  C   -18.8 half-chair C-alpha/N (-18 degrees)
1451 PRO   ( 404-)  C    99.2 envelop C-beta (108 degrees)
1588 PRO   (   4-)  D   -50.5 half-chair C-beta/C-alpha (-54 degrees)
1820 PRO   ( 236-)  D    22.5 half-chair N/C-delta (18 degrees)
1882 PRO   ( 298-)  D  -139.8 envelop C-delta (-144 degrees)
1962 PRO   ( 389-)  D    52.0 half-chair C-delta/C-gamma (54 degrees)
2194 PRO   (  84-)  E  -113.2 envelop C-gamma (-108 degrees)
2225 PRO   ( 115-)  E  -124.6 half-chair C-delta/C-gamma (-126 degrees)
2233 PRO   ( 123-)  E    50.0 half-chair C-delta/C-gamma (54 degrees)
2278 PRO   ( 168-)  E  -179.4 envelop N (180 degrees)
2346 PRO   ( 236-)  E   -29.7 envelop C-alpha (-36 degrees)
2486 PRO   ( 389-)  E     5.9 envelop N (0 degrees)
2501 PRO   ( 404-)  E   105.3 envelop C-beta (108 degrees)
2659 PRO   (  25-)  F    99.1 envelop C-beta (108 degrees)
2668 PRO   (  34-)  F  -127.2 half-chair C-delta/C-gamma (-126 degrees)
2802 PRO   ( 168-)  F   125.1 half-chair C-beta/C-alpha (126 degrees)
2870 PRO   ( 236-)  F    11.4 half-chair N/C-delta (18 degrees)
2932 PRO   ( 298-)  F  -145.9 envelop C-delta (-144 degrees)
3015 PRO   ( 389-)  F   -26.6 half-chair C-alpha/N (-18 degrees)
3197 PRO   (  34-)  G  -146.8 envelop C-delta (-144 degrees)
3236 PRO   (  73-)  G    50.6 half-chair C-delta/C-gamma (54 degrees)
3286 PRO   ( 123-)  G    41.9 envelop C-delta (36 degrees)
3331 PRO   ( 168-)  G   108.2 envelop C-beta (108 degrees)
3407 PRO   ( 244-)  G   101.5 envelop C-beta (108 degrees)
3461 PRO   ( 298-)  G   111.5 envelop C-beta (108 degrees)
3557 PRO   ( 404-)  G   117.5 half-chair C-beta/C-alpha (126 degrees)
3558 PRO   ( 405-)  G  -118.4 half-chair C-delta/C-gamma (-126 degrees)
3813 PRO   ( 123-)  H    29.7 envelop C-delta (36 degrees)
3926 PRO   ( 236-)  H    33.0 envelop C-delta (36 degrees)
4029 PRO   ( 339-)  H  -116.1 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

1495 ASN   ( 448-)  C      ND2 <-> 1538 HIS   ( 491-)  C      ND1    0.47    2.53  INTRA BL
1102 ASP   (  48-)  C      OD1 <-> 1104 GLU   (  50-)  C      N      0.39    2.31  INTRA BL
1953 ILE   ( 380-)  D      CG2 <-> 1954 ASP   ( 381-)  D      N      0.39    2.61  INTRA BF
 854 ASP   ( 329-)  B      OD2 <->  901 LYS   ( 384-)  B      NZ     0.38    2.32  INTRA BF
3686 ARG   ( 533-)  G      NH2 <-> 3689 ILE   ( 536-)  G      O      0.36    2.34  INTRA BL
1072 TYR   (  18-)  C      OH  <-> 1397 ASP   ( 343-)  C      OD1    0.35    2.05  INTRA BL
 869 ARG   ( 344-)  B      NH1 <-> 4233 A11   ( 610-)  B      C2     0.35    2.75  INTRA BF
 778 ASN   ( 253-)  B      OD1 <->  955 LYS   ( 438-)  B      NZ     0.33    2.37  INTRA BF
2098 TRP   ( 525-)  D      CZ2 <-> 2622 TRP   ( 525-)  E      CZ2    0.33    2.87  INTRA BF
2320 ILE   ( 210-)  E      CD1 <-> 2507 MET   ( 410-)  E      SD     0.33    3.07  INTRA BL
 869 ARG   ( 344-)  B      NH1 <-> 4233 A11   ( 610-)  B      N2     0.32    2.68  INTRA BF
1431 LYS   ( 384-)  C      O   <-> 1433 TYR   ( 386-)  C      N      0.29    2.41  INTRA BF
4023 PHE   ( 333-)  H      CE2 <-> 4185 MET   ( 505-)  H      CG     0.29    2.91  INTRA BF
3590 ARG   ( 437-)  G      NH2 <-> 3628 LEU   ( 475-)  G      O      0.28    2.42  INTRA BF
2621 GLU   ( 524-)  E      OE2 <-> 2625 ARG   ( 528-)  E      NH2    0.28    2.42  INTRA BF
 343 ASP   ( 343-)  A      OD2 <-> 2132 GLN   (  22-)  E      NE2    0.27    2.43  INTRA BL
4128 ASN   ( 448-)  H      ND2 <-> 4171 HIS   ( 491-)  H      ND1    0.27    2.73  INTRA BL
3677 GLU   ( 524-)  G      OE2 <-> 3681 ARG   ( 528-)  G      NH2    0.27    2.43  INTRA BF
 323 THR   ( 323-)  A      OG1 <->  400 ARG   ( 412-)  A      NH2    0.27    2.43  INTRA BL
3307 MET   ( 144-)  G      O   <-> 3311 ASN   ( 148-)  G      ND2    0.26    2.44  INTRA BF
1520 GLU   ( 473-)  C      O   <-> 1523 ASN   ( 476-)  C      ND2    0.26    2.44  INTRA BF
2685 GLY   (  51-)  F      O   <-> 2979 LEU   ( 345-)  F      N      0.26    2.44  INTRA BF
 359 GLU   ( 371-)  A      OE2 <->  363 GLN   ( 375-)  A      NE2    0.25    2.45  INTRA BF
3357 LEU   ( 194-)  G      N   <-> 3396 THR   ( 233-)  G      O      0.25    2.45  INTRA BF
2754 VAL   ( 120-)  F      O   <-> 2795 ILE   ( 161-)  F      N      0.25    2.45  INTRA BL
And so on for a total of 513 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

1401 LYS   ( 347-)  C      -6.25
1056 LYS   (   2-)  C      -6.25
1586 LYS   (   2-)  D      -6.24
4065 GLU   ( 385-)  H      -6.20
3165 LYS   (   2-)  G      -6.18
 527 LYS   (   2-)  B      -6.14
2636 LYS   (   2-)  F      -6.13
   2 LYS   (   2-)  A      -6.11
2340 HIS   ( 230-)  E      -6.09
3692 LYS   (   2-)  H      -6.07
1284 HIS   ( 230-)  C      -6.04
 230 HIS   ( 230-)  A      -6.03
3920 HIS   ( 230-)  H      -5.98
2112 LYS   (   2-)  E      -5.97
 755 HIS   ( 230-)  B      -5.95
 873 ARG   ( 356-)  B      -5.92
 870 LEU   ( 345-)  B      -5.70
3508 LEU   ( 345-)  G      -5.67
4035 LEU   ( 345-)  H      -5.53
1929 LEU   ( 345-)  D      -5.52
4039 ARG   ( 356-)  H      -5.49
2979 LEU   ( 345-)  F      -5.47
2455 LEU   ( 345-)  E      -5.43
2482 GLU   ( 385-)  E      -5.39
 345 LEU   ( 345-)  A      -5.38
And so on for a total of 68 lines.

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.

 526 MET   (   1-)  B       528 - ILE      3- ( B)         -4.89
 869 ARG   ( 344-)  B       871 - THR    346- ( B)         -5.07
1055 MET   (   1-)  C      1057 - ILE      3- ( C)         -4.94
1585 MET   (   1-)  D      1587 - ILE      3- ( D)         -5.07
1928 ARG   ( 344-)  D      1930 - THR    346- ( D)         -4.74
2454 ARG   ( 344-)  E      2456 - THR    346- ( E)         -4.85
2635 MET   (   1-)  F      2637 - ILE      3- ( F)         -5.02
3111 ASN   ( 485-)  F      3113 - ASN    487- ( F)         -4.58
3507 ARG   ( 344-)  G      3509 - THR    346- ( G)         -5.25
3691 MET   (   1-)  H      3693 - ILE      3- ( H)         -4.89
4034 ARG   ( 344-)  H      4036 - THR    346- ( H)         -4.83

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Warning: Low packing Z-score for some residues

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

 871 THR   ( 346-)  B   -4.11
2456 THR   ( 346-)  E   -4.05
2993 LEU   ( 367-)  F   -2.99
1957 LYS   ( 384-)  D   -2.87
3101 LEU   ( 475-)  F   -2.74
4155 LEU   ( 475-)  H   -2.67
 992 LEU   ( 475-)  B   -2.60
2024 VAL   ( 451-)  D   -2.58
2048 LEU   ( 475-)  D   -2.56
 865 LYS   ( 340-)  B   -2.55
 968 VAL   ( 451-)  B   -2.54
3520 LEU   ( 367-)  G   -2.54
 439 VAL   ( 451-)  A   -2.54
2532 ILE   ( 435-)  E   -2.51
 952 ILE   ( 435-)  B   -2.51

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.

 611 ALA   (  86-)  B     -  614 GLU   (  89-)  B        -1.71

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Water, ion, and hydrogenbond related checks

Error: 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.

 403 ASN   ( 415-)  A
 475 ASN   ( 487-)  A
1004 ASN   ( 487-)  B
1226 ASN   ( 172-)  C
1756 ASN   ( 172-)  D
1868 HIS   ( 284-)  D
2049 ASN   ( 476-)  D
2197 ASN   (  87-)  E
2432 GLN   ( 322-)  E
2584 ASN   ( 487-)  E
2721 ASN   (  87-)  F
2989 ASN   ( 363-)  F
3113 ASN   ( 487-)  F
3149 ASN   ( 523-)  F
3640 ASN   ( 487-)  G
3713 GLN   (  23-)  H
3862 ASN   ( 172-)  H
4167 ASN   ( 487-)  H

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   6 SER   (   6-)  A      N
   9 THR   (   9-)  A      OG1
  10 GLN   (  10-)  A      N
  17 THR   (  17-)  A      N
  52 LYS   (  52-)  A      N
  82 ARG   (  82-)  A      NH1
  86 ALA   (  86-)  A      N
  91 VAL   (  91-)  A      N
  93 ARG   (  93-)  A      NE
  94 GLN   (  94-)  A      NE2
 151 THR   ( 151-)  A      N
 167 VAL   ( 167-)  A      N
 173 ILE   ( 173-)  A      N
 193 ASP   ( 193-)  A      N
 201 SER   ( 201-)  A      N
 201 SER   ( 201-)  A      OG
 242 SER   ( 242-)  A      N
 243 LEU   ( 243-)  A      N
 253 ASN   ( 253-)  A      ND2
 270 GLN   ( 270-)  A      NE2
 272 ALA   ( 272-)  A      N
 341 ASN   ( 341-)  A      N
 342 ARG   ( 342-)  A      N
 344 ARG   ( 344-)  A      NH2
 372 LYS   ( 384-)  A      N
And so on for a total of 299 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.

  11 HIS   (  11-)  A      NE2
  89 GLU   (  89-)  A      OE1
 505 GLU   ( 517-)  A      OE1
1008 HIS   ( 491-)  B      ND1
1065 HIS   (  11-)  C      NE2
1161 GLN   ( 107-)  C      OE1
1595 HIS   (  11-)  D      NE2
1691 GLN   ( 107-)  D      OE1
1764 HIS   ( 180-)  D      NE2
1989 GLU   ( 416-)  D      OE2
2121 HIS   (  11-)  E      NE2
2153 GLU   (  43-)  E      OE1
2363 ASN   ( 253-)  E      OD1
2677 GLU   (  43-)  F      OE1
2695 GLN   (  61-)  F      OE1
2741 GLN   ( 107-)  F      OE1
3206 GLU   (  43-)  G      OE1
3701 HIS   (  11-)  H      NE2
3725 GLN   (  35-)  H      OE1
3942 GLU   ( 252-)  H      OE1
3974 HIS   ( 284-)  H      ND1
4001 GLU   ( 311-)  H      OE1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  13 ASP   (  13-)  A   H-bonding suggests Asn; but Alt-Rotamer
 182 GLU   ( 182-)  A   H-bonding suggests Gln; but Alt-Rotamer
 256 GLU   ( 256-)  A   H-bonding suggests Gln; but Alt-Rotamer
 474 GLU   ( 486-)  A   H-bonding suggests Gln; but Alt-Rotamer
 506 GLU   ( 518-)  A   H-bonding suggests Gln; but Alt-Rotamer
 614 GLU   (  89-)  B   H-bonding suggests Gln
 781 GLU   ( 256-)  B   H-bonding suggests Gln
 813 GLU   ( 288-)  B   H-bonding suggests Gln; but Alt-Rotamer
 883 ASP   ( 366-)  B   H-bonding suggests Asn
 944 ASP   ( 427-)  B   H-bonding suggests Asn
 956 ASP   ( 439-)  B   H-bonding suggests Asn
1003 GLU   ( 486-)  B   H-bonding suggests Gln
1035 GLU   ( 518-)  B   H-bonding suggests Gln; but Alt-Rotamer
1067 ASP   (  13-)  C   H-bonding suggests Asn
1143 GLU   (  89-)  C   H-bonding suggests Gln
1342 GLU   ( 288-)  C   H-bonding suggests Gln; but Alt-Rotamer
1390 ASP   ( 336-)  C   H-bonding suggests Asn
1520 GLU   ( 473-)  C   H-bonding suggests Gln; but Alt-Rotamer
1565 GLU   ( 518-)  C   H-bonding suggests Gln
1597 ASP   (  13-)  D   H-bonding suggests Asn; but Alt-Rotamer
1786 ASP   ( 202-)  D   H-bonding suggests Asn; Ligand-contact
1840 GLU   ( 256-)  D   H-bonding suggests Gln; but Alt-Rotamer
1891 ASP   ( 307-)  D   H-bonding suggests Asn
1939 ASP   ( 366-)  D   H-bonding suggests Asn
1949 GLU   ( 376-)  D   H-bonding suggests Gln
And so on for a total of 53 lines.

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 :  -0.215
  2nd generation packing quality :  -1.379
  Ramachandran plot appearance   :  -2.604
  chi-1/chi-2 rotamer normality  :  -3.989 (poor)
  Backbone conformation          :   0.450

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.521 (tight)
  Bond angles                    :   0.672
  Omega angle restraints         :   1.054
  Side chain planarity           :   0.416 (tight)
  Improper dihedral distribution :   0.683
  B-factor distribution          :   0.436
  Inside/Outside distribution    :   0.984

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 : 2.95


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :   1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.521 (tight)
  Bond angles                    :   0.672
  Omega angle restraints         :   1.054
  Side chain planarity           :   0.416 (tight)
  Improper dihedral distribution :   0.683
  B-factor distribution          :   0.436
  Inside/Outside distribution    :   0.984
==============

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.