WHAT IF Check report

This file was created 2012-01-31 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2uva.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: G and H

All-atom RMS fit for the two chains : 0.708
CA-only RMS fit for the two chains : 0.705

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 I

All-atom RMS fit for the two chains : 0.656
CA-only RMS fit for the two chains : 0.653

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 J

All-atom RMS fit for the two chains : 0.575
CA-only RMS fit for the two chains : 0.572

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 K

All-atom RMS fit for the two chains : 0.652
CA-only RMS fit for the two chains : 0.649

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 K

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 L

All-atom RMS fit for the two chains : 0.846
CA-only RMS fit for the two chains : 0.844

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 6
Highest polymer chain multiplicity according to SEQRES: 5
Warning: one pair of SEQRES sequences is sneakingly different
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 12
Polymer chain multiplicity and SEQRES multiplicity disagree 6 5
Z and NCS seem to support the 3D multiplicity

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 1380468.9
Volume of the Unit Cell V= 18460550.0
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.572
Vm by authors and this calculated Vm do not agree very well
SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

1236  FMN  (3079-) G  -
1236  FMN  (3079-) H  -
1236  FMN  (3079-) I  -
1236  FMN  (3079-) J  -
1236  FMN  (3079-) K  -
1236  FMN  (3079-) L  -

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: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 381 TYR   ( 399-)  G  -
 758 LEU   ( 776-)  G  -
2441 TYR   ( 399-)  H  -
6593 ARG   ( 431-)  J  -

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.

   1 GLN   (  19-)  G  -   High
   2 SER   (  20-)  G  -   High
   3 LEU   (  21-)  G  -   High
   4 ARG   (  22-)  G  -   High
   5 PRO   (  23-)  G  -   High
   6 LEU   (  24-)  G  -   High
   7 VAL   (  25-)  G  -   High
   8 LEU   (  26-)  G  -   High
   9 THR   (  27-)  G  -   High
  10 HIS   (  28-)  G  -   High
  11 GLY   (  29-)  G  -   High
  12 SER   (  30-)  G  -   High
  13 LEU   (  31-)  G  -   High
  14 GLU   (  32-)  G  -   High
  15 PHE   (  33-)  G  -   High
  16 SER   (  34-)  G  -   High
  17 PHE   (  35-)  G  -   High
  18 LEU   (  36-)  G  -   High
  19 VAL   (  37-)  G  -   High
  20 PRO   (  38-)  G  -   High
  21 THR   (  39-)  G  -   High
  22 SER   (  40-)  G  -   High
  23 LEU   (  41-)  G  -   High
  24 HIS   (  42-)  G  -   High
  25 PHE   (  43-)  G  -   High
And so on for a total of 8808 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: 0

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 4.313 over 45143 bonds
Average difference in B over a bond : 15.85
RMS difference in B over a bond : 20.16

Note: B-factor plot

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

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

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

  61 TYR   (  79-)  G  -
 122 TYR   ( 140-)  G  -
 123 TYR   ( 141-)  G  -
 243 TYR   ( 261-)  G  -
 478 TYR   ( 496-)  G  -
 608 TYR   ( 626-)  G  -
 617 TYR   ( 635-)  G  -
 687 TYR   ( 705-)  G  -
 747 TYR   ( 765-)  G  -
 773 TYR   ( 791-)  G  -
 829 TYR   ( 847-)  G  -
 965 TYR   ( 983-)  G  -
 982 TYR   (1000-)  G  -
1057 TYR   (1075-)  G  -
1247 TYR   (1265-)  G  -
1271 TYR   (1289-)  G  -
1362 TYR   (1380-)  G  -
1417 TYR   (1435-)  G  -
1424 TYR   (1442-)  G  -
1581 TYR   (1599-)  G  -
1674 TYR   (1692-)  G  -
1691 TYR   (1709-)  G  -
1712 TYR   (1730-)  G  -
2021 TYR   (2039-)  G  -
2059 TYR   (2077-)  G  -
And so on for a total of 159 lines.

Warning: Phenylalanine convention problem

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

 141 PHE   ( 159-)  G  -
 298 PHE   ( 316-)  G  -
 414 PHE   ( 432-)  G  -
 421 PHE   ( 439-)  G  -
 541 PHE   ( 559-)  G  -
 571 PHE   ( 589-)  G  -
 599 PHE   ( 617-)  G  -
 698 PHE   ( 716-)  G  -
 794 PHE   ( 812-)  G  -
 866 PHE   ( 884-)  G  -
 944 PHE   ( 962-)  G  -
 952 PHE   ( 970-)  G  -
1079 PHE   (1097-)  G  -
1163 PHE   (1181-)  G  -
1178 PHE   (1196-)  G  -
1229 PHE   (1247-)  G  -
1270 PHE   (1288-)  G  -
1283 PHE   (1301-)  G  -
1306 PHE   (1324-)  G  -
1324 PHE   (1342-)  G  -
1428 PHE   (1446-)  G  -
1539 PHE   (1557-)  G  -
1578 PHE   (1596-)  G  -
1708 PHE   (1726-)  G  -
1731 PHE   (1749-)  G  -
And so on for a total of 202 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.

 320 ASP   ( 338-)  G  -
 438 ASP   ( 456-)  G  -
 497 ASP   ( 515-)  G  -
 738 ASP   ( 756-)  G  -
 882 ASP   ( 900-)  G  -
 967 ASP   ( 985-)  G  -
 976 ASP   ( 994-)  G  -
1034 ASP   (1052-)  G  -
1192 ASP   (1210-)  G  -
1390 ASP   (1408-)  G  -
1511 ASP   (1529-)  G  -
1689 ASP   (1707-)  G  -
1802 ASP   (1820-)  G  -
2380 ASP   ( 338-)  H  -
2498 ASP   ( 456-)  H  -
2557 ASP   ( 515-)  H  -
2798 ASP   ( 756-)  H  -
2942 ASP   ( 900-)  H  -
3027 ASP   ( 985-)  H  -
3036 ASP   ( 994-)  H  -
3094 ASP   (1052-)  H  -
3252 ASP   (1210-)  H  -
3450 ASP   (1408-)  H  -
3571 ASP   (1529-)  H  -
3749 ASP   (1707-)  H  -
And so on for a total of 78 lines.

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.

 180 GLU   ( 198-)  G  -
 259 GLU   ( 277-)  G  -
 922 GLU   ( 940-)  G  -
1161 GLU   (1179-)  G  -
1396 GLU   (1414-)  G  -
1498 GLU   (1516-)  G  -
1516 GLU   (1534-)  G  -
1608 GLU   (1626-)  G  -
1710 GLU   (1728-)  G  -
1836 GLU   (1854-)  G  -
1879 GLU   (1897-)  G  -
2240 GLU   ( 198-)  H  -
2319 GLU   ( 277-)  H  -
2982 GLU   ( 940-)  H  -
3221 GLU   (1179-)  H  -
3456 GLU   (1414-)  H  -
3558 GLU   (1516-)  H  -
3576 GLU   (1534-)  H  -
3668 GLU   (1626-)  H  -
3770 GLU   (1728-)  H  -
3896 GLU   (1854-)  H  -
3939 GLU   (1897-)  H  -
4300 GLU   ( 198-)  I  -
4379 GLU   ( 277-)  I  -
5042 GLU   ( 940-)  I  -
And so on for a total of 66 lines.

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

1236  FMN  (3079-) G  -    OP1    O1P
1236  FMN  (3079-) G  -    OP2    O2P
1236  FMN  (3079-) G  -    OP3    O3P
1236  FMN  (3079-) H  -    OP1    O1P
1236  FMN  (3079-) H  -    OP2    O2P
1236  FMN  (3079-) H  -    OP3    O3P
1236  FMN  (3079-) I  -    OP1    O1P
1236  FMN  (3079-) I  -    OP2    O2P
1236  FMN  (3079-) I  -    OP3    O3P
1236  FMN  (3079-) J  -    OP1    O1P
1236  FMN  (3079-) J  -    OP2    O2P
1236  FMN  (3079-) J  -    OP3    O3P
1236  FMN  (3079-) K  -    OP1    O1P
1236  FMN  (3079-) K  -    OP2    O2P
1236  FMN  (3079-) K  -    OP3    O3P
1236  FMN  (3079-) L  -    OP1    O1P
1236  FMN  (3079-) L  -    OP2    O2P
1236  FMN  (3079-) L  -    OP3    O3P

Geometric checks

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

 |  0.998984  0.000011  0.000166|
 |  0.000011  0.999305  0.000090|
 |  0.000166  0.000090  0.998968|
Proposed new scale matrix

 |  0.004626  0.000000  0.001836|
 |  0.000000  0.002415  0.000000|
 |  0.000000  0.000000  0.004862|
With corresponding cell

    A    = 216.153  B   = 414.134  C    = 221.284
    Alpha=  90.002  Beta= 111.648  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 216.370  B   = 414.430  C    = 221.510
    Alpha=  90.000  Beta= 111.650  Gamma=  90.000

Variance: 350.550
(Under-)estimated Z-score: 13.799

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.

1173  HIS  (1457-) L  -    CG   ND1  CE1 109.69    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.

 180 GLU   ( 198-)  G  -
 259 GLU   ( 277-)  G  -
 320 ASP   ( 338-)  G  -
 438 ASP   ( 456-)  G  -
 497 ASP   ( 515-)  G  -
 738 ASP   ( 756-)  G  -
 882 ASP   ( 900-)  G  -
 922 GLU   ( 940-)  G  -
 967 ASP   ( 985-)  G  -
 976 ASP   ( 994-)  G  -
1034 ASP   (1052-)  G  -
1161 GLU   (1179-)  G  -
1192 ASP   (1210-)  G  -
1390 ASP   (1408-)  G  -
1396 GLU   (1414-)  G  -
1498 GLU   (1516-)  G  -
1511 ASP   (1529-)  G  -
1516 GLU   (1534-)  G  -
1608 GLU   (1626-)  G  -
1689 ASP   (1707-)  G  -
1710 GLU   (1728-)  G  -
1802 ASP   (1820-)  G  -
1836 GLU   (1854-)  G  -
1879 GLU   (1897-)  G  -
2240 GLU   ( 198-)  H  -
And so on for a total of 144 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.

6134 PRO   (2032-)  I  -   4.70
4074 PRO   (2032-)  H  -   4.28
1231  PRO  (2032-) L  -   4.28
5464 PHE   (1362-)  I  -   4.28
2014 PRO   (2032-)  G  -   4.27
5905 THR   (1803-)  I  -   4.19
1025  PRO  (2032-) K  -   4.19
8194 PRO   (2032-)  J  -   4.17
1208  THR  (1803-) L  -   4.12

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.512

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.

1587 THR   (1605-)  G  -   -3.6
7767 THR   (1605-)  J  -   -3.6
3647 THR   (1605-)  H  -   -3.6
5707 THR   (1605-)  I  -   -3.6
1188  THR  (1605-) L  -   -3.6
9827 THR   (1605-)  K  -   -3.6
6771 THR   ( 609-)  J  -   -3.4
 591 THR   ( 609-)  G  -   -3.4
4711 THR   ( 609-)  I  -   -3.4
2651 THR   ( 609-)  H  -   -3.4
8831 THR   ( 609-)  K  -   -3.4
1089  THR  ( 609-) L  -   -3.4
8352 THR   ( 130-)  K  -   -3.2
1041  THR  ( 130-) L  -   -3.2
2172 THR   ( 130-)  H  -   -3.2
6292 THR   ( 130-)  J  -   -3.2
 112 THR   ( 130-)  G  -   -3.2
4232 THR   ( 130-)  I  -   -3.2
8148 PRO   (1986-)  J  -   -2.9
1020  PRO  (1986-) K  -   -2.9
1226  PRO  (1986-) L  -   -2.9
4028 PRO   (1986-)  H  -   -2.9
3794 PRO   (1752-)  H  -   -2.9
7914 PRO   (1752-)  J  -   -2.8
5854 PRO   (1752-)  I  -   -2.8
And so on for a total of 584 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.

  11 GLY   (  29-)  G  - Poor phi/psi
  45 LEU   (  63-)  G  - Poor phi/psi
  49 ASP   (  67-)  G  - Poor phi/psi
  52 SER   (  70-)  G  - Poor phi/psi
  72 GLY   (  90-)  G  - Poor phi/psi
  75 ASP   (  93-)  G  - Poor phi/psi
  93 ARG   ( 111-)  G  - Poor phi/psi
  98 GLY   ( 116-)  G  - Poor phi/psi
 112 THR   ( 130-)  G  - Poor phi/psi
 135 PRO   ( 153-)  G  - Poor phi/psi
 136 TYR   ( 154-)  G  - omega poor
 178 PHE   ( 196-)  G  - omega poor
 262 SER   ( 280-)  G  - Poor phi/psi
 268 SER   ( 286-)  G  - Poor phi/psi
 281 ARG   ( 299-)  G  - Poor phi/psi
 326 GLU   ( 344-)  G  - Poor phi/psi
 337 ASP   ( 355-)  G  - Poor phi/psi
 416 PRO   ( 434-)  G  - Poor phi/psi
 422 HIS   ( 440-)  G  - Poor phi/psi
 436 ASP   ( 454-)  G  - omega poor
 465 ASP   ( 483-)  G  - Poor phi/psi
 478 TYR   ( 496-)  G  - Poor phi/psi
 488 VAL   ( 506-)  G  - Poor phi/psi
 502 GLY   ( 520-)  G  - Poor phi/psi
 533 GLU   ( 551-)  G  - Poor phi/psi
And so on for a total of 551 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -5.078

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.

 321 SER   ( 339-)  G  -   0.33
4441 SER   ( 339-)  I  -   0.33
6501 SER   ( 339-)  J  -   0.33
1062  SER  ( 339-) L  -   0.33
2381 SER   ( 339-)  H  -   0.35
8561 SER   ( 339-)  K  -   0.35
3201 SER   (1159-)  H  -   0.35
2684 SER   ( 642-)  H  -   0.36
4868 SER   ( 766-)  I  -   0.36
6928 SER   ( 766-)  J  -   0.36
4061 SER   (2019-)  H  -   0.37
8181 SER   (2019-)  J  -   0.37
1230  SER  (2019-) L  -   0.37
5261 SER   (1159-)  I  -   0.37
1144  SER  (1159-) L  -   0.37
1104  SER  ( 766-) L  -   0.37
1141 SER   (1159-)  G  -   0.38
4297 SER   ( 195-)  I  -   0.38
4461 SER   ( 359-)  I  -   0.38
7321 SER   (1159-)  J  -   0.38
8417 SER   ( 195-)  K  -   0.38
9381 SER   (1159-)  K  -   0.38
2401 SER   ( 359-)  H  -   0.38
1064  SER  ( 359-) L  -   0.38
6521 SER   ( 359-)  J  -   0.38
8581 SER   ( 359-)  K  -   0.38
 748 SER   ( 766-)  G  -   0.39
2237 SER   ( 195-)  H  -   0.39
 341 SER   ( 359-)  G  -   0.39
7969 GLN   (1807-)  J  -   0.39
2808 SER   ( 766-)  H  -   0.39
8988 SER   ( 766-)  K  -   0.39
1047  SER  ( 195-) L  -   0.39
ERROR. Too many residues to use DSSP

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!

   3 LEU   (  21-)  G  -     0
  10 HIS   (  28-)  G  -     0
  12 SER   (  30-)  G  -     0
  24 HIS   (  42-)  G  -     0
  40 GLN   (  58-)  G  -     0
  43 GLU   (  61-)  G  -     0
  44 GLU   (  62-)  G  -     0
  45 LEU   (  63-)  G  -     0
  47 GLN   (  65-)  G  -     0
  48 ASP   (  66-)  G  -     0
  49 ASP   (  67-)  G  -     0
  50 GLU   (  68-)  G  -     0
  71 GLU   (  89-)  G  -     0
  74 GLU   (  92-)  G  -     0
  75 ASP   (  93-)  G  -     0
  76 ALA   (  94-)  G  -     0
  93 ARG   ( 111-)  G  -     0
  96 MET   ( 114-)  G  -     0
  97 ARG   ( 115-)  G  -     0
 111 ILE   ( 129-)  G  -     0
 112 THR   ( 130-)  G  -     0
 135 PRO   ( 153-)  G  -     0
 136 TYR   ( 154-)  G  -     0
 137 ASP   ( 155-)  G  -     0
 148 ASN   ( 166-)  G  -     0
And so on for a total of 4430 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!

2675 GLY   ( 633-)  H  -  1.84   10
8855 GLY   ( 633-)  K  -  1.77   11
1091  GLY  ( 633-) L  -  1.77   11
3066 GLY   (1024-)  H  -  1.76   45
7186 GLY   (1024-)  J  -  1.74   48
4735 GLY   ( 633-)  I  -  1.74   10
6795 GLY   ( 633-)  J  -  1.73   10
5126 GLY   (1024-)  I  -  1.73   44
9246 GLY   (1024-)  K  -  1.72   48
1130  GLY  (1024-) L  -  1.69   44
5587 GLY   (1485-)  I  -  1.68   27
9707 GLY   (1485-)  K  -  1.67   24
 156 GLY   ( 174-)  G  -  1.67   48
1006 GLY   (1024-)  G  -  1.67   46
3527 GLY   (1485-)  H  -  1.67   27
1176  GLY  (1485-) L  -  1.66   24
7647 GLY   (1485-)  J  -  1.64   24
1467 GLY   (1485-)  G  -  1.64   26
2216 GLY   ( 174-)  H  -  1.63   49
6336 GLY   ( 174-)  J  -  1.62   49
8396 GLY   ( 174-)  K  -  1.62   50
1009  GLY  (1877-) K  -  1.59   80
3815 GLY   (1773-)  H  -  1.59   80
4276 GLY   ( 174-)  I  -  1.58   47
5875 GLY   (1773-)  I  -  1.57   80
9995 GLY   (1773-)  K  -  1.57   80
5979 GLY   (1877-)  I  -  1.57   80
1045  GLY  ( 174-) L  -  1.56   48
7935 GLY   (1773-)  J  -  1.56   80
1215  GLY  (1877-) L  -  1.55   80
1205  GLY  (1773-) L  -  1.55   80
8039 GLY   (1877-)  J  -  1.55   80
1755 GLY   (1773-)  G  -  1.55   80
3919 GLY   (1877-)  H  -  1.54   80
1859 GLY   (1877-)  G  -  1.53   80

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]

1137 PRO   (1155-)  G  -   0.10 LOW
3197 PRO   (1155-)  H  -   0.10 LOW
5257 PRO   (1155-)  I  -   0.10 LOW
7317 PRO   (1155-)  J  -   0.11 LOW
9377 PRO   (1155-)  K  -   0.09 LOW
1143  PRO  (1155-) L  -   0.11 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].

  39 PRO   (  57-)  G  -  -65.4 envelop C-beta (-72 degrees)
 133 PRO   ( 151-)  G  -  113.7 envelop C-beta (108 degrees)
 229 PRO   ( 247-)  G  -  101.7 envelop C-beta (108 degrees)
 443 PRO   ( 461-)  G  -   44.6 envelop C-delta (36 degrees)
 450 PRO   ( 468-)  G  -  115.5 envelop C-beta (108 degrees)
 480 PRO   ( 498-)  G  -  108.3 envelop C-beta (108 degrees)
 583 PRO   ( 601-)  G  -  117.3 half-chair C-beta/C-alpha (126 degrees)
 668 PRO   ( 686-)  G  -   50.8 half-chair C-delta/C-gamma (54 degrees)
 772 PRO   ( 790-)  G  -   99.4 envelop C-beta (108 degrees)
 971 PRO   ( 989-)  G  -   29.1 envelop C-delta (36 degrees)
 983 PRO   (1001-)  G  - -117.7 half-chair C-delta/C-gamma (-126 degrees)
1011 PRO   (1029-)  G  -   50.0 half-chair C-delta/C-gamma (54 degrees)
1014 PRO   (1032-)  G  -   49.2 half-chair C-delta/C-gamma (54 degrees)
1180 PRO   (1198-)  G  -  100.2 envelop C-beta (108 degrees)
1194 PRO   (1212-)  G  - -120.1 half-chair C-delta/C-gamma (-126 degrees)
1240 PRO   (1258-)  G  -   30.4 envelop C-delta (36 degrees)
1345 PRO   (1363-)  G  -  129.3 half-chair C-beta/C-alpha (126 degrees)
1550 PRO   (1568-)  G  -   49.9 half-chair C-delta/C-gamma (54 degrees)
1670 PRO   (1688-)  G  -  106.7 envelop C-beta (108 degrees)
1724 PRO   (1742-)  G  -   46.9 half-chair C-delta/C-gamma (54 degrees)
1734 PRO   (1752-)  G  -  110.4 envelop C-beta (108 degrees)
1966 PRO   (1984-)  G  - -133.0 half-chair C-delta/C-gamma (-126 degrees)
1968 PRO   (1986-)  G  -   39.6 envelop C-delta (36 degrees)
1986 PRO   (2004-)  G  -   39.4 envelop C-delta (36 degrees)
2029 PRO   (2047-)  G  -  112.5 envelop C-beta (108 degrees)
And so on for a total of 154 lines.

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.

9079 VAL   ( 857-)  K  -   CG1 <-> 9098 TRP   ( 876-)  K  -   NE1    0.68    2.42  INTRA BL
7500 ARG   (1338-)  J  -   NH2 <-> 1060  PRO  ( 327-) L  -    CD     0.66    2.44  INTRA BL
2085 PHE   (  43-)  H  -   CG  <-> 4124 ARG   (  22-)  I  -   NE     0.61    2.49  INTRA BF
6489 PRO   ( 327-)  J  -   O   <-> 9560 ARG   (1338-)  K  -   NH2    0.61    2.09  INTRA BL
2085 PHE   (  43-)  H  -   CB  <-> 4124 ARG   (  22-)  I  -   NH2    0.61    2.49  INTRA BF
1113  VAL  ( 857-) L  -    CG1 <-> 1115  TRP  ( 876-) L  -    NE1    0.60    2.50  INTRA BL
2899 VAL   ( 857-)  H  -   CG1 <-> 2918 TRP   ( 876-)  H  -   NE1    0.57    2.53  INTRA BL
2085 PHE   (  43-)  H  -   CB  <-> 4124 ARG   (  22-)  I  -   NE     0.53    2.57  INTRA BF
8690 PRO   ( 468-)  K  -   CG  <-> 8701 ARG   ( 479-)  K  -   NH2    0.53    2.57  INTRA BF
2369 PRO   ( 327-)  H  -   CD  <-> 5440 ARG   (1338-)  I  -   NH2    0.52    2.58  INTRA BL
1079  THR  ( 511-) L  -    CG2 <-> 1079  HIS  ( 512-) L  -    CD2    0.52    2.68  INTRA BL
4613 THR   ( 511-)  I  -   CG2 <-> 4614 HIS   ( 512-)  I  -   CD2    0.51    2.69  INTRA BL
7500 ARG   (1338-)  J  -   NH2 <-> 1060  PRO  ( 327-) L  -    N      0.50    2.50  INTRA BF
 450 PRO   ( 468-)  G  -   CG  <->  461 ARG   ( 479-)  G  -   NH2    0.50    2.60  INTRA BF
2085 PHE   (  43-)  H  -   CB  <-> 4124 ARG   (  22-)  I  -   CZ     0.49    2.71  INTRA BF
2553 THR   ( 511-)  H  -   CG2 <-> 2554 HIS   ( 512-)  H  -   CD2    0.49    2.71  INTRA BL
8974 HIS   ( 752-)  K  -   NE2 <-> 9078 THR   ( 856-)  K  -   CG2    0.49    2.61  INTRA BL
7929 GLU   (1767-)  J  -   CB  <-> 8178 PRO   (2016-)  J  -   CG     0.48    2.72  INTRA BF
1075  PRO  ( 468-) L  -    CG  <-> 1076  ARG  ( 479-) L  -    NH2    0.48    2.62  INTRA BF
8723 TRP   ( 501-)  K  -   NE1 <-> 8750 THR   ( 528-)  K  -   CG2    0.48    2.62  INTRA BL
 493 THR   ( 511-)  G  -   CG2 <->  494 HIS   ( 512-)  G  -   CD2    0.48    2.72  INTRA BL
4570 PRO   ( 468-)  I  -   CG  <-> 4581 ARG   ( 479-)  I  -   NH2    0.47    2.63  INTRA BF
4603 TRP   ( 501-)  I  -   NE1 <-> 4630 THR   ( 528-)  I  -   CG2    0.46    2.64  INTRA BL
 734 HIS   ( 752-)  G  -   NE2 <->  838 THR   ( 856-)  G  -   CG2    0.46    2.64  INTRA BL
1357 HIS   (1375-)  G  -   CE1 <-> 1592 MET   (1610-)  G  -   SD     0.46    2.94  INTRA BL
And so on for a total of 2661 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: 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

6101 ARG   (1999-)  I  -     -8.30
4041 ARG   (1999-)  H  -     -8.30
1981 ARG   (1999-)  G  -     -8.29
8161 ARG   (1999-)  J  -     -8.29
1228  ARG  (1999-) L  -     -8.27
1022  ARG  (1999-) K  -     -8.27
1005 ARG   (1023-)  G  -     -7.87
1130  ARG  (1023-) L  -     -7.86
9245 ARG   (1023-)  K  -     -7.84
7185 ARG   (1023-)  J  -     -7.82
3065 ARG   (1023-)  H  -     -7.82
5125 ARG   (1023-)  I  -     -7.81
1253 TYR   (1271-)  G  -     -7.09
7433 TYR   (1271-)  J  -     -7.07
9493 TYR   (1271-)  K  -     -7.00
1155  TYR  (1271-) L  -     -6.95
8858 TYR   ( 636-)  K  -     -6.95
5373 TYR   (1271-)  I  -     -6.91
3313 TYR   (1271-)  H  -     -6.88
1091  TYR  ( 636-) L  -     -6.87
2678 TYR   ( 636-)  H  -     -6.87
4738 TYR   ( 636-)  I  -     -6.85
 618 TYR   ( 636-)  G  -     -6.80
2469 ARG   ( 427-)  H  -     -6.78
7728 LYS   (1566-)  J  -     -6.78
And so on for a total of 336 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.

 899 ARG   ( 917-)  G  -    901 - SER    919- ( G)  -      -4.32
1527 GLN   (1545-)  G  -   1530 - GLY   1548- ( G)  -      -5.17
3587 GLN   (1545-)  H  -   3589 - HIS   1547- ( H)  -      -5.56
5123 GLN   (1021-)  I  -   5125 - ARG   1023- ( I)  -      -6.10
5647 GLN   (1545-)  I  -   5650 - GLY   1548- ( I)  -      -5.18
7183 GLN   (1021-)  J  -   7185 - ARG   1023- ( J)  -      -6.06
7707 GLN   (1545-)  J  -   7710 - GLY   1548- ( J)  -      -5.18
9139 ARG   ( 917-)  K  -   9141 - SER    919- ( K)  -      -4.28
9767 GLN   (1545-)  K  -   9770 - GLY   1548- ( K)  -      -5.17
9773 ILE   (1551-)  K  -   9775 - GLN   1553- ( K)  -      -4.75
1119  ARG  ( 917-) L  -    1120 -  SER   919- (L ) -       -4.26
1130  GLN  (1021-) L  -    1130 -  ARG  1023- (L ) -       -6.08
1182  GLN  (1545-) L  -    1183 -  GLY  1548- (L ) -       -5.18

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

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: K

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: L

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.

5380 MET   (1278-)  I  -  -2.84
1156  MET  (1278-) L  -  -2.83
1260 MET   (1278-)  G  -  -2.82
3320 MET   (1278-)  H  -  -2.81
7440 MET   (1278-)  J  -  -2.81
9500 MET   (1278-)  K  -  -2.79
1236  GLU  (2078-) L  -  -2.69
4675 VAL   ( 573-)  I  -  -2.63
8795 VAL   ( 573-)  K  -  -2.63
2615 VAL   ( 573-)  H  -  -2.62
6735 VAL   ( 573-)  J  -  -2.61
1085  VAL  ( 573-) L  -  -2.60
 555 VAL   ( 573-)  G  -  -2.60
5396 PHE   (1294-)  I  -  -2.59
1157  PHE  (1294-) L  -  -2.58
9516 PHE   (1294-)  K  -  -2.57
3336 PHE   (1294-)  H  -  -2.57
1276 PHE   (1294-)  G  -  -2.57
9814 VAL   (1592-)  K  -  -2.56
7456 PHE   (1294-)  J  -  -2.56
3634 VAL   (1592-)  H  -  -2.52
1574 VAL   (1592-)  G  -  -2.51
5694 VAL   (1592-)  I  -  -2.51
2546 ALA   ( 504-)  H  -  -2.51
7754 VAL   (1592-)  J  -  -2.50
4606 ALA   ( 504-)  I  -  -2.50

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: 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

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

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.

  67 HIS   (  85-)  G  -
  77 HIS   (  95-)  G  -
 147 ASN   ( 165-)  G  -
 211 GLN   ( 229-)  G  -
 242 HIS   ( 260-)  G  -
 319 GLN   ( 337-)  G  -
 398 GLN   ( 416-)  G  -
 740 HIS   ( 758-)  G  -
 805 HIS   ( 823-)  G  -
 889 ASN   ( 907-)  G  -
 918 HIS   ( 936-)  G  -
 964 ASN   ( 982-)  G  -
 991 ASN   (1009-)  G  -
 993 GLN   (1011-)  G  -
1669 GLN   (1687-)  G  -
1684 GLN   (1702-)  G  -
1722 ASN   (1740-)  G  -
1769 ASN   (1787-)  G  -
2024 ASN   (2042-)  G  -
2127 HIS   (  85-)  H  -
2137 HIS   (  95-)  H  -
2271 GLN   ( 229-)  H  -
2302 HIS   ( 260-)  H  -
2379 GLN   ( 337-)  H  -
2458 GLN   ( 416-)  H  -
And so on for a total of 129 lines.

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.

   7 VAL   (  25-)  G  -   N
  27 ALA   (  45-)  G  -   N
  36 ALA   (  54-)  G  -   N
  44 GLU   (  62-)  G  -   N
  52 SER   (  70-)  G  -   N
  53 SER   (  71-)  G  -   N
  56 GLU   (  74-)  G  -   N
  76 ALA   (  94-)  G  -   N
  77 HIS   (  95-)  G  -   N
 101 VAL   ( 119-)  G  -   N
 103 ALA   ( 121-)  G  -   N
 107 ASN   ( 125-)  G  -   N
 112 THR   ( 130-)  G  -   N
 113 ALA   ( 131-)  G  -   N
 114 LYS   ( 132-)  G  -   N
 115 LYS   ( 133-)  G  -   N
 116 ILE   ( 134-)  G  -   N
 127 ALA   ( 145-)  G  -   N
 153 SER   ( 171-)  G  -   OG
 156 GLY   ( 174-)  G  -   N
 158 GLN   ( 176-)  G  -   NE2
 163 GLU   ( 181-)  G  -   N
 164 TYR   ( 182-)  G  -   N
 181 ASP   ( 199-)  G  -   N
 198 ASP   ( 216-)  G  -   N
And so on for a total of 1737 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.

  24 HIS   (  42-)  G  -   ND1
  80 ASN   (  98-)  G  -   OD1
 239 GLN   ( 257-)  G  -   OE1
 384 ASN   ( 402-)  G  -   OD1
 422 HIS   ( 440-)  G  -   ND1
 436 ASP   ( 454-)  G  -   OD2
 471 GLU   ( 489-)  G  -   OE1
 494 HIS   ( 512-)  G  -   ND1
 631 GLU   ( 649-)  G  -   OE1
 643 ASN   ( 661-)  G  -   OD1
 655 GLN   ( 673-)  G  -   OE1
 724 GLN   ( 742-)  G  -   OE1
 733 HIS   ( 751-)  G  -   ND1
 734 HIS   ( 752-)  G  -   NE2
 893 GLN   ( 911-)  G  -   OE1
1033 GLU   (1051-)  G  -   OE2
1203 GLU   (1221-)  G  -   OE2
1258 GLU   (1276-)  G  -   OE1
1360 ASN   (1378-)  G  -   OD1
1439 HIS   (1457-)  G  -   ND1
1560 GLU   (1578-)  G  -   OE2
1650 ASP   (1668-)  G  -   OD1
1707 HIS   (1725-)  G  -   ND1
2035 GLU   (2053-)  G  -   OE1
2041 HIS   (2059-)  G  -   ND1
And so on for a total of 141 lines.

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  32 ASP   (  50-)  G  -  H-bonding suggests Asn
  50 GLU   (  68-)  G  -  H-bonding suggests Gln
  68 GLU   (  86-)  G  -  H-bonding suggests Gln; but Alt-Rotamer
  82 GLU   ( 100-)  G  -  H-bonding suggests Gln; but Alt-Rotamer
 253 GLU   ( 271-)  G  -  H-bonding suggests Gln; but Alt-Rotamer
 285 GLU   ( 303-)  G  -  H-bonding suggests Gln; but Alt-Rotamer
 348 ASP   ( 366-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
 439 ASP   ( 457-)  G  -  H-bonding suggests Asn
 453 ASP   ( 471-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
 528 ASP   ( 546-)  G  -  H-bonding suggests Asn
 553 ASP   ( 571-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
 625 ASP   ( 643-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
 769 ASP   ( 787-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
 816 ASP   ( 834-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
 943 ASP   ( 961-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
 967 ASP   ( 985-)  G  -  H-bonding suggests Asn
 976 ASP   ( 994-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
1033 GLU   (1051-)  G  -  H-bonding suggests Gln; but Alt-Rotamer
1070 ASP   (1088-)  G  -  H-bonding suggests Asn
1108 GLU   (1126-)  G  -  H-bonding suggests Gln
1111 ASP   (1129-)  G  -  H-bonding suggests Asn
1221 ASP   (1239-)  G  -  H-bonding suggests Asn
1296 GLU   (1314-)  G  -  H-bonding suggests Gln
1305 ASP   (1323-)  G  -  H-bonding suggests Asn
1323 ASP   (1341-)  G  -  H-bonding suggests Asn
And so on for a total of 193 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 :  -1.496
  2nd generation packing quality :  -2.055
  Ramachandran plot appearance   :  -4.512 (bad)
  chi-1/chi-2 rotamer normality  :  -5.078 (bad)
  Backbone conformation          :  -0.915

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.317 (tight)
  Bond angles                    :   0.529 (tight)
  Omega angle restraints         :   0.933
  Side chain planarity           :   0.231 (tight)
  Improper dihedral distribution :   0.512
  B-factor distribution          :   4.313 (loose)
  Inside/Outside distribution    :   0.996

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.0
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -2.5
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.317 (tight)
  Bond angles                    :   0.529 (tight)
  Omega angle restraints         :   0.933
  Side chain planarity           :   0.231 (tight)
  Improper dihedral distribution :   0.512
  B-factor distribution          :   4.313 (loose)
  Inside/Outside distribution    :   0.996
==============

WHAT IF
    G.Vriend,
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    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.