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 pdb2qc8.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 : 0.361
CA-only RMS fit for the two chains : 0.225

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 : 0.273
CA-only RMS fit for the two chains : 0.160

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 : 0.320
CA-only RMS fit for the two chains : 0.178

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 : 0.306
CA-only RMS fit for the two chains : 0.169

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 : 0.311
CA-only RMS fit for the two chains : 0.151

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: 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.

3564 ADP   ( 501-)  A  -         OK
3565 P3S   ( 601-)  A  -
3571 ADP   ( 501-)  B  -         OK
3572 P3S   ( 601-)  B  -
3577 ADP   ( 501-)  C  -         OK
3578 P3S   ( 601-)  C  -
3583 ADP   ( 501-)  D  -         OK
3584 P3S   ( 601-)  D  -
3588 ADP   ( 501-)  E  -         OK
3589 P3S   ( 601-)  E  -
3594 ADP   ( 501-)  F  -         OK
3595 P3S   ( 601-)  F  -
3601 ADP   ( 501-)  G  -         OK
3602 P3S   ( 601-)  G  -
3606 ADP   ( 501-)  H  -         OK
3607 P3S   ( 601-)  H  -
3612 ADP   ( 501-)  I  -         OK
3617 P3S   ( 601-)  J  -
3618 ADP   ( 501-)  J  -         OK
3619 ADP   ( 601-)  I  -         OK

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

3619 ADP   ( 601-)  I  -

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

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

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'.

  15 GLU   (  24-)  A      CD
  15 GLU   (  24-)  A      OE1
  15 GLU   (  24-)  A      OE2
 371 GLU   (  24-)  B      CD
 371 GLU   (  24-)  B      OE1
 371 GLU   (  24-)  B      OE2
 727 GLU   (  24-)  C      CD
 727 GLU   (  24-)  C      OE1
 727 GLU   (  24-)  C      OE2
1083 GLU   (  24-)  D      CD
1083 GLU   (  24-)  D      OE1
1083 GLU   (  24-)  D      OE2
1439 GLU   (  24-)  E      CD
1439 GLU   (  24-)  E      OE1
1439 GLU   (  24-)  E      OE2
1794 GLU   (  24-)  F      CD
1794 GLU   (  24-)  F      OE1
1794 GLU   (  24-)  F      OE2
2150 GLU   (  24-)  G      CD
2150 GLU   (  24-)  G      OE1
2150 GLU   (  24-)  G      OE2
2506 GLU   (  24-)  H      CD
2506 GLU   (  24-)  H      OE1
2506 GLU   (  24-)  H      OE2
2862 GLU   (  24-)  I      CD
2862 GLU   (  24-)  I      OE1
2862 GLU   (  24-)  I      OE2
3217 GLU   (  24-)  J      CD
3217 GLU   (  24-)  J      OE1
3217 GLU   (  24-)  J      OE2

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: 10

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

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

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.

  98 ARG   ( 107-)  A
 310 ARG   ( 319-)  A
 666 ARG   ( 319-)  B
1022 ARG   ( 319-)  C
1378 ARG   ( 319-)  D
1734 ARG   ( 319-)  E
2089 ARG   ( 319-)  F
2445 ARG   ( 319-)  G
2801 ARG   ( 319-)  H
3156 ARG   ( 319-)  I
3512 ARG   ( 319-)  J

Warning: Tyrosine convention problem

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

  69 TYR   (  78-)  A
  95 TYR   ( 104-)  A
 128 TYR   ( 137-)  A
 171 TYR   ( 180-)  A
 327 TYR   ( 336-)  A
 425 TYR   (  78-)  B
 451 TYR   ( 104-)  B
 484 TYR   ( 137-)  B
 527 TYR   ( 180-)  B
 683 TYR   ( 336-)  B
 720 TYR   (  17-)  C
 781 TYR   (  78-)  C
 807 TYR   ( 104-)  C
 840 TYR   ( 137-)  C
 883 TYR   ( 180-)  C
 888 TYR   ( 185-)  C
1039 TYR   ( 336-)  C
1163 TYR   ( 104-)  D
1239 TYR   ( 180-)  D
1244 TYR   ( 185-)  D
1395 TYR   ( 336-)  D
1519 TYR   ( 104-)  E
1552 TYR   ( 137-)  E
1595 TYR   ( 180-)  E
1600 TYR   ( 185-)  E
And so on for a total of 52 lines.

Warning: Phenylalanine convention problem

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

  53 PHE   (  62-)  A
  76 PHE   (  85-)  A
  93 PHE   ( 102-)  A
 294 PHE   ( 303-)  A
 328 PHE   ( 337-)  A
 409 PHE   (  62-)  B
 432 PHE   (  85-)  B
 449 PHE   ( 102-)  B
 650 PHE   ( 303-)  B
 684 PHE   ( 337-)  B
 765 PHE   (  62-)  C
 788 PHE   (  85-)  C
 805 PHE   ( 102-)  C
 834 PHE   ( 131-)  C
1006 PHE   ( 303-)  C
1040 PHE   ( 337-)  C
1121 PHE   (  62-)  D
1161 PHE   ( 102-)  D
1362 PHE   ( 303-)  D
1371 PHE   ( 312-)  D
1396 PHE   ( 337-)  D
1477 PHE   (  62-)  E
1517 PHE   ( 102-)  E
1647 PHE   ( 232-)  E
1718 PHE   ( 303-)  E
And so on for a total of 58 lines.

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.

  67 ASP   (  76-)  A
 423 ASP   (  76-)  B
 779 ASP   (  76-)  C
1135 ASP   (  76-)  D
1491 ASP   (  76-)  E
1654 ASP   ( 239-)  E
1846 ASP   (  76-)  F
2202 ASP   (  76-)  G
2558 ASP   (  76-)  H
2914 ASP   (  76-)  I
3269 ASP   (  76-)  J
3432 ASP   ( 239-)  J

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.

 187 GLU   ( 196-)  A
 296 GLU   ( 305-)  A
 543 GLU   ( 196-)  B
 652 GLU   ( 305-)  B
 899 GLU   ( 196-)  C
1255 GLU   ( 196-)  D
1364 GLU   ( 305-)  D
1611 GLU   ( 196-)  E
1720 GLU   ( 305-)  E
1966 GLU   ( 196-)  F
2322 GLU   ( 196-)  G
2678 GLU   ( 196-)  H
2787 GLU   ( 305-)  H
3034 GLU   ( 196-)  I
3389 GLU   ( 196-)  J

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 757 VAL   (  54-)  C      CA   CB    1.62    4.4

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999148 -0.000169  0.000012|
 | -0.000169  0.998901 -0.000003|
 |  0.000012 -0.000003  0.998620|
Proposed new scale matrix

 |  0.005523  0.000000  0.000206|
 |  0.000001  0.007940  0.000000|
 |  0.000000  0.000000  0.005325|
With corresponding cell

    A    = 181.071  B   = 125.949  C    = 187.912
    Alpha=  90.001  Beta=  92.140  Gamma=  90.011

The CRYST1 cell dimensions

    A    = 181.210  B   = 126.080  C    = 188.170
    Alpha=  90.000  Beta=  92.140  Gamma=  90.000

Variance: 153.171
(Under-)estimated Z-score: 9.121

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.

 136 HIS   ( 145-)  A      CG   ND1  CE1 109.67    4.1
 564 HIS   ( 217-)  B      CG   ND1  CE1 109.63    4.0
 631 HIS   ( 284-)  B      CG   ND1  CE1 109.70    4.1
 756 CYS   (  53-)  C      N    CA   C    99.35   -4.2
1276 HIS   ( 217-)  D      CG   ND1  CE1 109.62    4.0
1339 ARG   ( 280-)  D      CG   CD   NE  117.50    4.1
1632 HIS   ( 217-)  E      CG   ND1  CE1 109.98    4.4
1677 ARG   ( 262-)  E      CG   CD   NE  117.87    4.3
1695 ARG   ( 280-)  E      CG   CD   NE  118.15    4.5
1987 HIS   ( 217-)  F      CG   ND1  CE1 109.71    4.1
2343 HIS   ( 217-)  G      CG   ND1  CE1 109.61    4.0
2735 HIS   ( 253-)  H      CG   ND1  CE1 109.62    4.0
3055 HIS   ( 217-)  I      CG   ND1  CE1 109.66    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.

  67 ASP   (  76-)  A
  98 ARG   ( 107-)  A
 187 GLU   ( 196-)  A
 296 GLU   ( 305-)  A
 310 ARG   ( 319-)  A
 423 ASP   (  76-)  B
 543 GLU   ( 196-)  B
 652 GLU   ( 305-)  B
 666 ARG   ( 319-)  B
 779 ASP   (  76-)  C
 899 GLU   ( 196-)  C
1022 ARG   ( 319-)  C
1135 ASP   (  76-)  D
1255 GLU   ( 196-)  D
1364 GLU   ( 305-)  D
1378 ARG   ( 319-)  D
1491 ASP   (  76-)  E
1611 GLU   ( 196-)  E
1654 ASP   ( 239-)  E
1720 GLU   ( 305-)  E
1734 ARG   ( 319-)  E
1846 ASP   (  76-)  F
1966 GLU   ( 196-)  F
2089 ARG   ( 319-)  F
2202 ASP   (  76-)  G
2322 GLU   ( 196-)  G
2445 ARG   ( 319-)  G
2558 ASP   (  76-)  H
2678 GLU   ( 196-)  H
2787 GLU   ( 305-)  H
2801 ARG   ( 319-)  H
2914 ASP   (  76-)  I
3034 GLU   ( 196-)  I
3156 ARG   ( 319-)  I
3269 ASP   (  76-)  J
3389 GLU   ( 196-)  J
3432 ASP   ( 239-)  J
3512 ARG   ( 319-)  J

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

2690 PRO   ( 208-)  H      N     -6.2   -22.78    -2.48
The average deviation= 0.929

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.

 756 CYS   (  53-)  C    4.66
1229 ALA   ( 170-)  D    4.17

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.

2931 PRO   (  93-)  I    -3.1
1863 PRO   (  93-)  F    -3.1
1152 PRO   (  93-)  D    -3.1
  84 PRO   (  93-)  A    -3.1
1508 PRO   (  93-)  E    -3.1
2575 PRO   (  93-)  H    -3.1
3286 PRO   (  93-)  J    -3.0
 796 PRO   (  93-)  C    -3.0
2219 PRO   (  93-)  G    -3.0
 440 PRO   (  93-)  B    -2.9
2906 LEU   (  68-)  I    -2.8
  59 LEU   (  68-)  A    -2.8
1483 LEU   (  68-)  E    -2.7
 415 LEU   (  68-)  B    -2.7
2194 LEU   (  68-)  G    -2.7
 771 LEU   (  68-)  C    -2.7
2810 THR   ( 328-)  H    -2.6
1127 LEU   (  68-)  D    -2.6
3335 THR   ( 142-)  J    -2.6
2406 ARG   ( 280-)  G    -2.5
 627 ARG   ( 280-)  B    -2.5
2550 LEU   (  68-)  H    -2.5
2050 ARG   ( 280-)  F    -2.5
 983 ARG   ( 280-)  C    -2.4
2762 ARG   ( 280-)  H    -2.4
And so on for a total of 95 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.

  51 TRP   (  60-)  A  Poor phi/psi
  59 LEU   (  68-)  A  Poor phi/psi
  65 ASN   (  74-)  A  omega poor
  82 LYS   (  91-)  A  Poor phi/psi
  83 ASP   (  92-)  A  PRO omega poor
  85 ASN   (  94-)  A  omega poor
  90 CYS   (  99-)  A  omega poor
  97 ARG   ( 106-)  A  Poor phi/psi
 143 ASN   ( 152-)  A  Poor phi/psi
 160 ARG   ( 169-)  A  Poor phi/psi
 185 ASN   ( 194-)  A  omega poor
 191 ALA   ( 200-)  A  Poor phi/psi
 198 GLY   ( 207-)  A  PRO omega poor
 237 ASN   ( 246-)  A  Poor phi/psi
 256 ASN   ( 265-)  A  Poor phi/psi
 278 ALA   ( 287-)  A  omega poor
 279 TYR   ( 288-)  A  omega poor
 296 GLU   ( 305-)  A  Poor phi/psi
 308 ALA   ( 317-)  A  Poor phi/psi
 407 TRP   (  60-)  B  Poor phi/psi
 415 LEU   (  68-)  B  Poor phi/psi
 421 ASN   (  74-)  B  omega poor
 438 LYS   (  91-)  B  Poor phi/psi
 439 ASP   (  92-)  B  PRO omega poor
 446 CYS   (  99-)  B  omega poor
And so on for a total of 224 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.

1409 SER   ( 350-)  D    0.33
1765 SER   ( 350-)  E    0.33
3543 SER   ( 350-)  J    0.33
2597 HIS   ( 115-)  H    0.36
2120 SER   ( 350-)  F    0.36
2476 SER   ( 350-)  G    0.38
3187 SER   ( 350-)  I    0.38

Warning: Unusual backbone conformations

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

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

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

  15 GLU   (  24-)  A      0
  33 CYS   (  42-)  A      0
  43 LYS   (  52-)  A      0
  44 CYS   (  53-)  A      0
  51 TRP   (  60-)  A      0
  52 ASN   (  61-)  A      0
  58 THR   (  67-)  A      0
  59 LEU   (  68-)  A      0
  60 GLN   (  69-)  A      0
  66 SER   (  75-)  A      0
  67 ASP   (  76-)  A      0
  72 PRO   (  81-)  A      0
  73 ALA   (  82-)  A      0
  81 ARG   (  90-)  A      0
  82 LYS   (  91-)  A      0
  83 ASP   (  92-)  A      0
  84 PRO   (  93-)  A      0
  85 ASN   (  94-)  A      0
  97 ARG   ( 106-)  A      0
 104 LEU   ( 113-)  A      0
 119 HIS   ( 128-)  A      0
 120 PRO   ( 129-)  A      0
 138 PHE   ( 147-)  A      0
 140 TRP   ( 149-)  A      0
 142 SER   ( 151-)  A      0
And so on for a total of 1351 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!

2337 GLY   ( 211-)  G   1.89   12
3528 GLY   ( 335-)  J   1.85   17
2693 GLY   ( 211-)  H   1.73   13
1270 GLY   ( 211-)  D   1.71   15
1981 GLY   ( 211-)  F   1.67   14
 558 GLY   ( 211-)  B   1.66   16
3404 GLY   ( 211-)  J   1.64   12
2461 GLY   ( 335-)  G   1.58   16
2817 GLY   ( 335-)  H   1.56   12
 682 GLY   ( 335-)  B   1.56   20

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]

  49 PRO   (  58-)  A    0.13 LOW
 235 PRO   ( 244-)  A    0.17 LOW
 368 PRO   (  21-)  B    0.11 LOW
 405 PRO   (  58-)  B    0.13 LOW
 546 PRO   ( 199-)  B    0.19 LOW
 591 PRO   ( 244-)  B    0.11 LOW
 860 PRO   ( 157-)  C    0.12 LOW
 947 PRO   ( 244-)  C    0.16 LOW
1080 PRO   (  21-)  D    0.11 LOW
1216 PRO   ( 157-)  D    0.15 LOW
1436 PRO   (  21-)  E    0.16 LOW
1466 PRO   (  51-)  E    0.17 LOW
1969 PRO   ( 199-)  F    0.19 LOW
2325 PRO   ( 199-)  G    0.11 LOW
2808 PRO   ( 326-)  H    0.20 LOW
3082 PRO   ( 244-)  I    0.19 LOW
3163 PRO   ( 326-)  I    0.18 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].

 151 PRO   ( 160-)  A   -61.0 half-chair C-beta/C-alpha (-54 degrees)
 339 PRO   ( 348-)  A  -118.0 half-chair C-delta/C-gamma (-126 degrees)
 455 PRO   ( 108-)  B    99.1 envelop C-beta (108 degrees)
 695 PRO   ( 348-)  B  -113.5 envelop C-gamma (-108 degrees)
 724 PRO   (  21-)  C  -123.5 half-chair C-delta/C-gamma (-126 degrees)
 993 PRO   ( 290-)  C    48.2 half-chair C-delta/C-gamma (54 degrees)
1267 PRO   ( 208-)  D    27.3 envelop C-delta (36 degrees)
1503 PRO   (  88-)  E   -64.7 envelop C-beta (-72 degrees)
1705 PRO   ( 290-)  E    43.5 envelop C-delta (36 degrees)
1858 PRO   (  88-)  F   -61.5 half-chair C-beta/C-alpha (-54 degrees)
1930 PRO   ( 160-)  F   -32.8 envelop C-alpha (-36 degrees)
2060 PRO   ( 290-)  F    42.9 envelop C-delta (36 degrees)
2366 PRO   ( 240-)  G   -66.0 envelop C-beta (-72 degrees)
2416 PRO   ( 290-)  G    33.8 envelop C-delta (36 degrees)
2563 PRO   (  81-)  H   103.7 envelop C-beta (108 degrees)
2570 PRO   (  88-)  H   -65.3 envelop C-beta (-72 degrees)
2575 PRO   (  93-)  H   -64.7 envelop C-beta (-72 degrees)
2642 PRO   ( 160-)  H   -60.2 half-chair C-beta/C-alpha (-54 degrees)
2772 PRO   ( 290-)  H    20.8 half-chair N/C-delta (18 degrees)
3128 PRO   ( 290-)  I    27.0 envelop C-delta (36 degrees)
3433 PRO   ( 240-)  J   -53.4 half-chair C-beta/C-alpha (-54 degrees)
3437 PRO   ( 244-)  J    40.8 envelop C-delta (36 degrees)
3483 PRO   ( 290-)  J    39.9 envelop C-delta (36 degrees)
3541 PRO   ( 348-)  J  -118.8 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 756 CYS   (  53-)  C      SG  <->  759 GLU   (  56-)  C      OE2    1.08    1.92  INTRA BL
 438 LYS   (  91-)  B      NZ  <-> 3619 HOH   ( 739 )  B      O      1.01    1.69  INTRA BF
  44 CYS   (  53-)  A      SG  <->   47 GLU   (  56-)  A      OE2    0.74    2.26  INTRA BL
2574 ASP   (  92-)  H      OD1 <-> 3625 HOH   ( 604 )  H      O      0.59    1.81  INTRA BF
 756 CYS   (  53-)  C      SG  <->  759 GLU   (  56-)  C      CD     0.44    2.96  INTRA BF
2402 LYS   ( 276-)  G      NZ  <-> 2488 ASN   ( 362-)  G      OD1    0.44    2.26  INTRA BF
1837 THR   (  67-)  F      OG1 <-> 1839 GLN   (  69-)  F      NE2    0.38    2.32  INTRA BF
2568 ARG   (  86-)  H      NH2 <-> 2574 ASP   (  92-)  H      OD2    0.34    2.36  INTRA BL
 967 GLU   ( 264-)  C      OE2 <-> 1037 LYS   ( 334-)  C      NZ     0.33    2.37  INTRA BF
 414 THR   (  67-)  B      OG1 <->  416 GLN   (  69-)  B      NE2    0.33    2.37  INTRA BF
1007 HIS   ( 304-)  C      ND1 <-> 3620 HOH   ( 733 )  C      O      0.32    2.38  INTRA
3434 LYS   ( 241-)  J      NZ  <-> 3440 TRP   ( 247-)  J      O      0.32    2.38  INTRA BL
2034 GLU   ( 264-)  F      OE2 <-> 2104 LYS   ( 334-)  F      NZ     0.31    2.39  INTRA BF
1679 GLU   ( 264-)  E      OE2 <-> 1749 LYS   ( 334-)  E      NZ     0.30    2.40  INTRA BF
  94 LYS   ( 103-)  A      NZ  <->  101 GLU   ( 110-)  A      OE2    0.30    2.40  INTRA BF
2535 CYS   (  53-)  H      SG  <-> 2538 GLU   (  56-)  H      OE2    0.29    2.71  INTRA BF
 789 ARG   (  86-)  C      NH2 <->  795 ASP   (  92-)  C      OD2    0.29    2.41  INTRA BL
 485 THR   ( 138-)  B      CG2 <->  545 MET   ( 198-)  B      CE     0.29    2.91  INTRA BF
1323 GLU   ( 264-)  D      OE2 <-> 1393 LYS   ( 334-)  D      NZ     0.29    2.41  INTRA BF
  58 THR   (  67-)  A      OG1 <->   60 GLN   (  69-)  A      NE2    0.29    2.41  INTRA BF
3279 ARG   (  86-)  J      NH2 <-> 3285 ASP   (  92-)  J      OD2    0.28    2.42  INTRA BL
2763 HIS   ( 281-)  H      NE2 <-> 2791 ILE   ( 309-)  H      O      0.28    2.42  INTRA BF
 770 THR   (  67-)  C      OG1 <->  772 GLN   (  69-)  C      NE2    0.27    2.43  INTRA BF
3457 GLU   ( 264-)  J      OE2 <-> 3527 LYS   ( 334-)  J      NZ     0.27    2.43  INTRA BF
3469 LYS   ( 276-)  J      NZ  <-> 3555 ASN   ( 362-)  J      OD1    0.26    2.44  INTRA BF
And so on for a total of 288 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

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.

1519 TYR   ( 104-)  E      -6.25
3141 PHE   ( 303-)  I      -6.10
 807 TYR   ( 104-)  C      -5.96
2890 LYS   (  52-)  I      -5.92
2230 TYR   ( 104-)  G      -5.90
 399 LYS   (  52-)  B      -5.87
 451 TYR   ( 104-)  B      -5.87
1111 LYS   (  52-)  D      -5.83
1467 LYS   (  52-)  E      -5.82
3297 TYR   ( 104-)  J      -5.82
2178 LYS   (  52-)  G      -5.78
3245 LYS   (  52-)  J      -5.77
2586 TYR   ( 104-)  H      -5.67
  95 TYR   ( 104-)  A      -5.63
1874 TYR   ( 104-)  F      -5.61
2942 TYR   ( 104-)  I      -5.58
1163 TYR   ( 104-)  D      -5.57
2232 ARG   ( 106-)  G      -5.55
  43 LYS   (  52-)  A      -5.48
1165 ARG   ( 106-)  D      -5.45
1876 ARG   ( 106-)  F      -5.45
2504 GLN   (  22-)  H      -5.43
2944 ARG   ( 106-)  I      -5.42
2588 ARG   ( 106-)  H      -5.42
2429 PHE   ( 303-)  G      -5.42
And so on for a total of 79 lines.

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

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: I

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: J

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.

1779 THR   ( 364-)  E   -3.95
1520 ASN   ( 105-)  E   -2.57
  96 ASN   ( 105-)  A   -2.56
1164 ASN   ( 105-)  D   -2.56
1875 ASN   ( 105-)  F   -2.56
2231 ASN   ( 105-)  G   -2.56
2587 ASN   ( 105-)  H   -2.55
 808 ASN   ( 105-)  C   -2.55
 452 ASN   ( 105-)  B   -2.55
3298 ASN   ( 105-)  J   -2.53
2943 ASN   ( 105-)  I   -2.53

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

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

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.

  60 GLN   (  69-)  A
 416 GLN   (  69-)  B
 473 ASN   ( 126-)  B
 951 ASN   ( 248-)  C
1307 ASN   ( 248-)  D
1839 GLN   (  69-)  F
2907 GLN   (  69-)  I

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.

   2 LYS   (  11-)  A      N
  23 TRP   (  32-)  A      NE1
  36 ARG   (  45-)  A      NH1
  46 GLU   (  55-)  A      N
  52 ASN   (  61-)  A      N
  96 ASN   ( 105-)  A      N
 134 ASP   ( 143-)  A      N
 152 TYR   ( 161-)  A      N
 153 TYR   ( 162-)  A      N
 156 VAL   ( 165-)  A      N
 165 ASP   ( 174-)  A      N
 192 GLN   ( 201-)  A      NE2
 234 ILE   ( 243-)  A      N
 244 HIS   ( 253-)  A      N
 244 HIS   ( 253-)  A      NE2
 248 SER   ( 257-)  A      OG
 256 ASN   ( 265-)  A      N
 280 ASP   ( 289-)  A      N
 287 ASN   ( 296-)  A      ND2
 310 ARG   ( 319-)  A      NE
 327 TYR   ( 336-)  A      N
 331 ARG   ( 340-)  A      NE
 331 ARG   ( 340-)  A      NH1
 331 ARG   ( 340-)  A      NH2
 332 ARG   ( 341-)  A      NH1
And so on for a total of 236 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.

  18 GLN   (  27-)  A      OE1
 652 GLU   ( 305-)  B      OE2
 759 GLU   (  56-)  C      OE2
 772 GLN   (  69-)  C      OE1
1008 GLU   ( 305-)  C      OE1
1086 GLN   (  27-)  D      OE1
1364 GLU   ( 305-)  D      OE2
1720 GLU   ( 305-)  E      OE2
1797 GLN   (  27-)  F      OE1
2075 GLU   ( 305-)  F      OE1
2153 GLN   (  27-)  G      OE1
2195 GLN   (  69-)  G      OE1
2431 GLU   ( 305-)  G      OE1
2551 GLN   (  69-)  H      OE1
2787 GLU   ( 305-)  H      OE2
2865 GLN   (  27-)  I      OE1
3498 GLU   ( 305-)  J      OE1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

3621 HOH   ( 715 )  D      O  0.90  K  4 Ion-B H2O-B

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.

 381 ASP   (  34-)  B   H-bonding suggests Asn; but Alt-Rotamer
1370 ASP   ( 311-)  D   H-bonding suggests Asn; but Alt-Rotamer
2081 ASP   ( 311-)  F   H-bonding suggests Asn
2248 ASP   ( 122-)  G   H-bonding suggests Asn
2437 ASP   ( 311-)  G   H-bonding suggests Asn
2604 ASP   ( 122-)  H   H-bonding suggests Asn
2793 ASP   ( 311-)  H   H-bonding suggests Asn
2960 ASP   ( 122-)  I   H-bonding suggests Asn; but Alt-Rotamer
3148 ASP   ( 311-)  I   H-bonding suggests Asn
3504 ASP   ( 311-)  J   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.500
  2nd generation packing quality :  -0.717
  Ramachandran plot appearance   :  -1.450
  chi-1/chi-2 rotamer normality  :  -0.889
  Backbone conformation          :  -0.111

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.693
  Bond angles                    :   0.759
  Omega angle restraints         :   1.125
  Side chain planarity           :   0.644 (tight)
  Improper dihedral distribution :   0.761
  B-factor distribution          :   0.373
  Inside/Outside distribution    :   1.040

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :   1.1
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.693
  Bond angles                    :   0.759
  Omega angle restraints         :   1.125
  Side chain planarity           :   0.644 (tight)
  Improper dihedral distribution :   0.761
  B-factor distribution          :   0.373
  Inside/Outside distribution    :   1.040
==============

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.