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 pdb2uvc.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 : 0.658
CA-only RMS fit for the two chains : 0.656

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 : 0.533
CA-only RMS fit for the two chains : 0.529

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 : 0.561
CA-only RMS fit for the two chains : 0.558

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 : 0.680
CA-only RMS fit for the two chains : 0.677

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 : 0.786
CA-only RMS fit for the two chains : 0.784

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: 1382262.9
Volume of the Unit Cell V= 18295320.0
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.515
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  NAP  (3080-) H  -
1236  NAP  (3080-) I  -
1236  NAP  (3080-) J  -
1236  NAP  (3080-) K  -
1237  NAP  (3080-) L  -
1237  NAP  (3080-) G  -

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.

9121 ARG   ( 899-)  K  -
1195  THR  (1674-) L  -
1212  VAL  (1845-) L  -

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 8379 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 : 4.171 over 46969 bonds
Average difference in B over a bond : 15.24
RMS difference in B over a bond : 19.41

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

 122 TYR   ( 140-)  G  -
 136 TYR   ( 154-)  G  -
 172 TYR   ( 190-)  G  -
 175 TYR   ( 193-)  G  -
 243 TYR   ( 261-)  G  -
 425 TYR   ( 443-)  G  -
 478 TYR   ( 496-)  G  -
 536 TYR   ( 554-)  G  -
 608 TYR   ( 626-)  G  -
 617 TYR   ( 635-)  G  -
 618 TYR   ( 636-)  G  -
 687 TYR   ( 705-)  G  -
 747 TYR   ( 765-)  G  -
 773 TYR   ( 791-)  G  -
 784 TYR   ( 802-)  G  -
 829 TYR   ( 847-)  G  -
 883 TYR   ( 901-)  G  -
 913 TYR   ( 931-)  G  -
 965 TYR   ( 983-)  G  -
 982 TYR   (1000-)  G  -
1022 TYR   (1040-)  G  -
1151 TYR   (1169-)  G  -
1185 TYR   (1203-)  G  -
1362 TYR   (1380-)  G  -
1417 TYR   (1435-)  G  -
And so on for a total of 216 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  -
 155 PHE   ( 173-)  G  -
 178 PHE   ( 196-)  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  -
 764 PHE   ( 782-)  G  -
 866 PHE   ( 884-)  G  -
 944 PHE   ( 962-)  G  -
 952 PHE   ( 970-)  G  -
1079 PHE   (1097-)  G  -
1142 PHE   (1160-)  G  -
1163 PHE   (1181-)  G  -
1229 PHE   (1247-)  G  -
1243 PHE   (1261-)  G  -
1270 PHE   (1288-)  G  -
1283 PHE   (1301-)  G  -
1306 PHE   (1324-)  G  -
1317 PHE   (1335-)  G  -
1324 PHE   (1342-)  G  -
1344 PHE   (1362-)  G  -
And so on for a total of 225 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.

 198 ASP   ( 216-)  G  -
 320 ASP   ( 338-)  G  -
 438 ASP   ( 456-)  G  -
 704 ASP   ( 722-)  G  -
 738 ASP   ( 756-)  G  -
 882 ASP   ( 900-)  G  -
 976 ASP   ( 994-)  G  -
1034 ASP   (1052-)  G  -
1284 ASP   (1302-)  G  -
1349 ASP   (1367-)  G  -
1390 ASP   (1408-)  G  -
1511 ASP   (1529-)  G  -
1689 ASP   (1707-)  G  -
1802 ASP   (1820-)  G  -
2258 ASP   ( 216-)  H  -
2380 ASP   ( 338-)  H  -
2498 ASP   ( 456-)  H  -
2764 ASP   ( 722-)  H  -
2798 ASP   ( 756-)  H  -
2942 ASP   ( 900-)  H  -
3036 ASP   ( 994-)  H  -
3094 ASP   (1052-)  H  -
3344 ASP   (1302-)  H  -
3409 ASP   (1367-)  H  -
3450 ASP   (1408-)  H  -
And so on for a total of 84 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  -
 922 GLU   ( 940-)  G  -
1396 GLU   (1414-)  G  -
1498 GLU   (1516-)  G  -
1516 GLU   (1534-)  G  -
1710 GLU   (1728-)  G  -
1879 GLU   (1897-)  G  -
2240 GLU   ( 198-)  H  -
2982 GLU   ( 940-)  H  -
3456 GLU   (1414-)  H  -
3558 GLU   (1516-)  H  -
3576 GLU   (1534-)  H  -
3770 GLU   (1728-)  H  -
3939 GLU   (1897-)  H  -
4300 GLU   ( 198-)  I  -
5042 GLU   ( 940-)  I  -
5516 GLU   (1414-)  I  -
5618 GLU   (1516-)  I  -
5636 GLU   (1534-)  I  -
5830 GLU   (1728-)  I  -
5999 GLU   (1897-)  I  -
6360 GLU   ( 198-)  J  -
7102 GLU   ( 940-)  J  -
7576 GLU   (1414-)  J  -
7678 GLU   (1516-)  J  -
7696 GLU   (1534-)  J  -
7890 GLU   (1728-)  J  -
8059 GLU   (1897-)  J  -
8420 GLU   ( 198-)  K  -
9162 GLU   ( 940-)  K  -
9636 GLU   (1414-)  K  -
9738 GLU   (1516-)  K  -
9756 GLU   (1534-)  K  -
9950 GLU   (1728-)  K  -
1011  GLU  (1897-) K  -
1048  GLU  ( 198-) L  -
1122  GLU  ( 940-) L  -
1169  GLU  (1414-) L  -
1179  GLU  (1516-) L  -
1181  GLU  (1534-) L  -
1201  GLU  (1728-) L  -
1217  GLU  (1897-) L  -

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
1237  FMN  (3079-) L  -    OP1    O1P
1237  FMN  (3079-) L  -    OP2    O2P
1237  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

 |  0.999261 -0.000004  0.000086|
 | -0.000004  0.999756  0.000048|
 |  0.000086  0.000048  0.999293|
Proposed new scale matrix

 |  0.004637  0.000000  0.001833|
 |  0.000000  0.002424  0.000000|
 |  0.000000  0.000000  0.004871|
With corresponding cell

    A    = 215.646  B   = 412.611  C    = 220.733
    Alpha=  90.002  Beta= 111.568  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 215.780  B   = 412.670  C    = 220.900
    Alpha=  90.000  Beta= 111.570  Gamma=  90.000

Variance: 139.630
(Under-)estimated Z-score: 8.709

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  -
 198 ASP   ( 216-)  G  -
 320 ASP   ( 338-)  G  -
 438 ASP   ( 456-)  G  -
 704 ASP   ( 722-)  G  -
 738 ASP   ( 756-)  G  -
 882 ASP   ( 900-)  G  -
 922 GLU   ( 940-)  G  -
 976 ASP   ( 994-)  G  -
1034 ASP   (1052-)  G  -
1284 ASP   (1302-)  G  -
1349 ASP   (1367-)  G  -
1390 ASP   (1408-)  G  -
1396 GLU   (1414-)  G  -
1498 GLU   (1516-)  G  -
1511 ASP   (1529-)  G  -
1516 GLU   (1534-)  G  -
1689 ASP   (1707-)  G  -
1710 GLU   (1728-)  G  -
1802 ASP   (1820-)  G  -
1879 GLU   (1897-)  G  -
2240 GLU   ( 198-)  H  -
2258 ASP   ( 216-)  H  -
2380 ASP   ( 338-)  H  -
2498 ASP   ( 456-)  H  -
And so on for a total of 126 lines.

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.

1968 PRO   (1986-)  G  -   N      7.3    21.34    -2.48
4028 PRO   (1986-)  H  -   N      7.4    21.74    -2.48
6088 PRO   (1986-)  I  -   N      7.3    21.62    -2.48
8148 PRO   (1986-)  J  -   N      7.1    20.74    -2.48
1020  PRO  (1986-) K  -    N      7.2    21.20    -2.48
1226  PRO  (1986-) L  -    N      7.2    21.17    -2.48
The average deviation= 0.630

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.

5905 THR   (1803-)  I  -   4.68
3052 ALA   (1010-)  H  -   4.66
1208  THR  (1803-) L  -   4.65
1002  THR  (1803-) K  -   4.51
5112 ALA   (1010-)  I  -   4.50
1129  ALA  (1010-) L  -   4.49
6134 PRO   (2032-)  I  -   4.46
1785 THR   (1803-)  G  -   4.43
3845 THR   (1803-)  H  -   4.42
9232 ALA   (1010-)  K  -   4.40
1029 LEU   (1047-)  G  -   4.39
5149 LEU   (1047-)  I  -   4.38
9393 TRP   (1171-)  K  -   4.37
1231  PRO  (2032-) L  -   4.34
7172 ALA   (1010-)  J  -   4.30
4074 PRO   (2032-)  H  -   4.29
2014 PRO   (2032-)  G  -   4.27
1153 TRP   (1171-)  G  -   4.27
8194 PRO   (2032-)  J  -   4.19
7965 THR   (1803-)  J  -   4.19
1025  PRO  (2032-) K  -   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 : -4.543

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.

4711 THR   ( 609-)  I  -   -3.6
6771 THR   ( 609-)  J  -   -3.6
 591 THR   ( 609-)  G  -   -3.6
8831 THR   ( 609-)  K  -   -3.6
2651 THR   ( 609-)  H  -   -3.6
1089  THR  ( 609-) L  -   -3.6
3647 THR   (1605-)  H  -   -3.2
9827 THR   (1605-)  K  -   -3.2
5707 THR   (1605-)  I  -   -3.2
1188  THR  (1605-) L  -   -3.2
1587 THR   (1605-)  G  -   -3.2
7767 THR   (1605-)  J  -   -3.2
3794 PRO   (1752-)  H  -   -3.0
9974 PRO   (1752-)  K  -   -2.9
7914 PRO   (1752-)  J  -   -2.9
1734 PRO   (1752-)  G  -   -2.9
5854 PRO   (1752-)  I  -   -2.9
1203  PRO  (1752-) L  -   -2.9
8198 ILE   (2036-)  J  -   -2.9
2018 ILE   (2036-)  G  -   -2.9
4078 ILE   (2036-)  H  -   -2.9
6138 ILE   (2036-)  I  -   -2.9
1231  ILE  (2036-) L  -   -2.9
1025  ILE  (2036-) K  -   -2.9
1020  PRO  (1986-) K  -   -2.8
And so on for a total of 646 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.

  39 PRO   (  57-)  G  - Poor phi/psi
  44 GLU   (  62-)  G  - Poor phi/psi
  46 ALA   (  64-)  G  - Poor phi/psi
  49 ASP   (  67-)  G  - Poor phi/psi
  72 GLY   (  90-)  G  - omega poor
  93 ARG   ( 111-)  G  - Poor phi/psi
  97 ARG   ( 115-)  G  - Poor phi/psi
 135 PRO   ( 153-)  G  - Poor phi/psi
 136 TYR   ( 154-)  G  - omega poor
 147 ASN   ( 165-)  G  - Poor phi/psi
 160 ASN   ( 178-)  G  - Poor phi/psi
 178 PHE   ( 196-)  G  - omega poor
 262 SER   ( 280-)  G  - Poor phi/psi
 268 SER   ( 286-)  G  - Poor phi/psi
 337 ASP   ( 355-)  G  - Poor phi/psi
 413 ARG   ( 431-)  G  - Poor phi/psi
 416 PRO   ( 434-)  G  - Poor phi/psi
 417 ILE   ( 435-)  G  - omega poor
 422 HIS   ( 440-)  G  - Poor phi/psi
 424 PRO   ( 442-)  G  - Poor phi/psi
 446 SER   ( 464-)  G  - Poor phi/psi
 462 GLU   ( 480-)  G  - Poor phi/psi
 464 GLY   ( 482-)  G  - Poor phi/psi
 465 ASP   ( 483-)  G  - Poor phi/psi
 482 ASN   ( 500-)  G  - Poor phi/psi
And so on for a total of 607 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 : -5.124

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.

1003  SER  (1817-) K  -   0.34
3865 SER   (1823-)  H  -   0.35
5925 SER   (1823-)  I  -   0.35
7985 SER   (1823-)  J  -   0.35
1004  SER  (1823-) K  -   0.35
1799 SER   (1817-)  G  -   0.35
3859 SER   (1817-)  H  -   0.35
1209  SER  (1817-) L  -   0.35
1805 SER   (1823-)  G  -   0.35
5919 SER   (1817-)  I  -   0.35
7979 SER   (1817-)  J  -   0.36
1210  SER  (1823-) L  -   0.37
2001 SER   (2019-)  G  -   0.37
6121 SER   (2019-)  I  -   0.37
4142 SER   (  40-)  I  -   0.37
6202 SER   (  40-)  J  -   0.37
1006  SER  (1842-) K  -   0.38
8181 SER   (2019-)  J  -   0.38
1024  SER  (2019-) K  -   0.38
2082 SER   (  40-)  H  -   0.38
1032  SER  (  40-) L  -   0.38
1230  SER  (2019-) L  -   0.38
8262 SER   (  40-)  K  -   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
  12 SER   (  30-)  G  -     0
  14 GLU   (  32-)  G  -     0
  24 HIS   (  42-)  G  -     0
  39 PRO   (  57-)  G  -     0
  40 GLN   (  58-)  G  -     0
  43 GLU   (  61-)  G  -     0
  44 GLU   (  62-)  G  -     0
  45 LEU   (  63-)  G  -     0
  46 ALA   (  64-)  G  -     0
  47 GLN   (  65-)  G  -     0
  48 ASP   (  66-)  G  -     0
  49 ASP   (  67-)  G  -     0
  71 GLU   (  89-)  G  -     0
  73 ASP   (  91-)  G  -     0
  76 ALA   (  94-)  G  -     0
  77 HIS   (  95-)  G  -     0
  93 ARG   ( 111-)  G  -     0
  96 MET   ( 114-)  G  -     0
  97 ARG   ( 115-)  G  -     0
 108 VAL   ( 126-)  G  -     0
 109 ALA   ( 127-)  G  -     0
 135 PRO   ( 153-)  G  -     0
 148 ASN   ( 166-)  G  -     0
 158 GLN   ( 176-)  G  -     0
And so on for a total of 4371 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!

8396 GLY   ( 174-)  K  -  1.91   53
 156 GLY   ( 174-)  G  -  1.89   51
4276 GLY   ( 174-)  I  -  1.88   52
2216 GLY   ( 174-)  H  -  1.86   51
6336 GLY   ( 174-)  J  -  1.86   52
1045  GLY  ( 174-) L  -  1.86   49

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  -   17.1 half-chair N/C-delta (18 degrees)
 229 PRO   ( 247-)  G  - -117.7 half-chair C-delta/C-gamma (-126 degrees)
 331 PRO   ( 349-)  G  -   52.8 half-chair C-delta/C-gamma (54 degrees)
 402 PRO   ( 420-)  G  -  102.7 envelop C-beta (108 degrees)
 772 PRO   ( 790-)  G  -  102.4 envelop C-beta (108 degrees)
 905 PRO   ( 923-)  G  -   31.1 envelop C-delta (36 degrees)
 935 PRO   ( 953-)  G  -  104.6 envelop C-beta (108 degrees)
 959 PRO   ( 977-)  G  -   49.3 half-chair C-delta/C-gamma (54 degrees)
 971 PRO   ( 989-)  G  -   29.1 envelop C-delta (36 degrees)
 983 PRO   (1001-)  G  - -118.2 half-chair C-delta/C-gamma (-126 degrees)
1011 PRO   (1029-)  G  -   37.5 envelop C-delta (36 degrees)
1180 PRO   (1198-)  G  -  103.6 envelop C-beta (108 degrees)
1194 PRO   (1212-)  G  - -121.4 half-chair C-delta/C-gamma (-126 degrees)
1204 PRO   (1222-)  G  -   48.8 half-chair C-delta/C-gamma (54 degrees)
1240 PRO   (1258-)  G  -   29.7 envelop C-delta (36 degrees)
1345 PRO   (1363-)  G  -  137.6 envelop C-alpha (144 degrees)
1556 PRO   (1574-)  G  -   52.4 half-chair C-delta/C-gamma (54 degrees)
1724 PRO   (1742-)  G  -   51.6 half-chair C-delta/C-gamma (54 degrees)
1734 PRO   (1752-)  G  -  112.5 envelop C-beta (108 degrees)
1966 PRO   (1984-)  G  -   33.4 envelop C-delta (36 degrees)
1968 PRO   (1986-)  G  -  144.7 envelop C-alpha (144 degrees)
1986 PRO   (2004-)  G  -   51.8 half-chair C-delta/C-gamma (54 degrees)
2029 PRO   (2047-)  G  -  123.4 half-chair C-beta/C-alpha (126 degrees)
2099 PRO   (  57-)  H  -   18.9 half-chair N/C-delta (18 degrees)
2289 PRO   ( 247-)  H  - -117.9 half-chair C-delta/C-gamma (-126 degrees)
And so on for a total of 139 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.

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    0.59    2.11  INTRA BF
9079 VAL   ( 857-)  K  -   CG1 <-> 9098 TRP   ( 876-)  K  -   NE1    0.57    2.53  INTRA BL
7502 LYS   (1340-)  J  -   CG  <-> 1065  ARG  ( 376-) L  -    NH2    0.57    2.53  INTRA BF
1113  VAL  ( 857-) L  -    CG1 <-> 1115  TRP  ( 876-) L  -    NE1    0.56    2.54  INTRA BL
8147 GLN   (1985-)  J  -   O   <-> 8149 VAL   (1987-)  J  -   N      0.51    2.19  INTRA BF
1967 GLN   (1985-)  G  -   O   <-> 1969 VAL   (1987-)  G  -   N      0.51    2.19  INTRA BF
4027 GLN   (1985-)  H  -   O   <-> 4029 VAL   (1987-)  H  -   N      0.51    2.19  INTRA BF
8974 HIS   ( 752-)  K  -   NE2 <-> 9078 THR   ( 856-)  K  -   CG2    0.50    2.60  INTRA BL
1020  GLN  (1985-) K  -    O   <-> 1020  VAL  (1987-) K  -    N      0.50    2.20  INTRA BF
2794 HIS   ( 752-)  H  -   NE2 <-> 2898 THR   ( 856-)  H  -   CG2    0.49    2.61  INTRA BL
1226  GLN  (1985-) L  -    O   <-> 1226  VAL  (1987-) L  -    N      0.48    2.22  INTRA BF
2899 VAL   ( 857-)  H  -   CG1 <-> 2918 TRP   ( 876-)  H  -   NE1    0.48    2.62  INTRA BL
3236 ARG   (1194-)  H  -   NH2 <-> 3643 ASN   (1601-)  H  -   CG     0.48    2.62  INTRA BF
2369 PRO   ( 327-)  H  -   CD  <-> 5440 ARG   (1338-)  I  -   NH2    0.48    2.62  INTRA BF
6087 GLN   (1985-)  I  -   O   <-> 6089 VAL   (1987-)  I  -   N      0.48    2.22  INTRA BF
 734 HIS   ( 752-)  G  -   NE2 <->  838 THR   ( 856-)  G  -   CG2    0.46    2.64  INTRA BL
1103  HIS  ( 752-) L  -    NE2 <-> 1113  THR  ( 856-) L  -    CG2    0.45    2.65  INTRA BF
6489 PRO   ( 327-)  J  -   N   <-> 9560 ARG   (1338-)  K  -   NH2    0.45    2.55  INTRA BF
4854 HIS   ( 752-)  I  -   NE2 <-> 4958 THR   ( 856-)  I  -   CG2    0.45    2.65  INTRA BF
6914 HIS   ( 752-)  J  -   NE2 <-> 7018 THR   ( 856-)  J  -   CG2    0.44    2.66  INTRA BL
4094 LYS   (2052-)  H  -   CD  <-> 4116 TRP   (2074-)  H  -   NE1    0.44    2.66  INTRA BF
8974 HIS   ( 752-)  K  -   CE1 <-> 9069 TYR   ( 847-)  K  -   CE1    0.44    2.76  INTRA BL
1171  ARG  (1436-) L  -    NH2 <-> 1188  LEU  (1602-) L  -    CD1    0.44    2.66  INTRA BF
7598 ARG   (1436-)  J  -   NH2 <-> 7764 LEU   (1602-)  J  -   CD1    0.43    2.67  INTRA BF
And so on for a total of 3121 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.

1981 ARG   (1999-)  G  -     -8.28
6101 ARG   (1999-)  I  -     -8.26
1022  ARG  (1999-) K  -     -8.26
8161 ARG   (1999-)  J  -     -8.25
1228  ARG  (1999-) L  -     -8.25
4041 ARG   (1999-)  H  -     -8.23
9245 ARG   (1023-)  K  -     -7.35
3065 ARG   (1023-)  H  -     -7.34
7185 ARG   (1023-)  J  -     -7.33
1130  ARG  (1023-) L  -     -7.33
5125 ARG   (1023-)  I  -     -7.32
1005 ARG   (1023-)  G  -     -7.30
9279 TYR   (1057-)  K  -     -6.74
1039 TYR   (1057-)  G  -     -6.67
3608 LYS   (1566-)  H  -     -6.67
1548 LYS   (1566-)  G  -     -6.66
7728 LYS   (1566-)  J  -     -6.66
5668 LYS   (1566-)  I  -     -6.66
1133  TYR  (1057-) L  -     -6.65
9788 LYS   (1566-)  K  -     -6.65
1184  LYS  (1566-) L  -     -6.64
3099 TYR   (1057-)  H  -     -6.63
1253 TYR   (1271-)  G  -     -6.63
7219 TYR   (1057-)  J  -     -6.63
4529 ARG   ( 427-)  I  -     -6.62
And so on for a total of 371 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.

1003 GLN   (1021-)  G  -   1005 - ARG   1023- ( G)  -      -5.99
1527 GLN   (1545-)  G  -   1530 - GLY   1548- ( G)  -      -5.19
1533 ILE   (1551-)  G  -   1535 - GLN   1553- ( G)  -      -4.96
1970 GLN   (1988-)  G  -   1973 - ARG   1991- ( G)  -      -5.29
3063 GLN   (1021-)  H  -   3065 - ARG   1023- ( H)  -      -5.98
3587 GLN   (1545-)  H  -   3590 - GLY   1548- ( H)  -      -5.20
3593 ILE   (1551-)  H  -   3595 - GLN   1553- ( H)  -      -5.08
4030 GLN   (1988-)  H  -   4033 - ARG   1991- ( H)  -      -5.22
5123 GLN   (1021-)  I  -   5125 - ARG   1023- ( I)  -      -5.98
5647 GLN   (1545-)  I  -   5650 - GLY   1548- ( I)  -      -5.20
5653 ILE   (1551-)  I  -   5655 - GLN   1553- ( I)  -      -5.13
6090 GLN   (1988-)  I  -   6093 - ARG   1991- ( I)  -      -5.23
7183 GLN   (1021-)  J  -   7185 - ARG   1023- ( J)  -      -5.97
7707 GLN   (1545-)  J  -   7710 - GLY   1548- ( J)  -      -5.21
7713 ILE   (1551-)  J  -   7715 - GLN   1553- ( J)  -      -5.06
8150 GLN   (1988-)  J  -   8153 - ARG   1991- ( J)  -      -5.23
9243 GLN   (1021-)  K  -   9245 - ARG   1023- ( K)  -      -6.00
9767 GLN   (1545-)  K  -   9770 - GLY   1548- ( K)  -      -5.20
9773 ILE   (1551-)  K  -   9775 - GLN   1553- ( K)  -      -5.28
1021  GLN  (1988-) K  -    1021 -  ARG  1991- (K ) -       -5.26
1130  GLN  (1021-) L  -    1130 -  ARG  1023- (L ) -       -6.01
1182  GLN  (1545-) L  -    1183 -  GLY  1548- (L ) -       -5.22
1183  ILE  (1551-) L  -    1183 -  GLN  1553- (L ) -       -5.00
1227  GLN  (1988-) L  -    1227 -  ARG  1991- (L ) -       -5.23

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.

8885 ILE   ( 663-)  K  -  -2.82
2705 ILE   ( 663-)  H  -  -2.81
1094  ILE  ( 663-) L  -  -2.80
 645 ILE   ( 663-)  G  -  -2.79
4765 ILE   ( 663-)  I  -  -2.78
6825 ILE   ( 663-)  J  -  -2.77
1236  GLU  (2078-) L  -  -2.76
2219 GLY   ( 177-)  H  -  -2.53

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

1871 SER   (1889-)  G  -  - 1874 SER   (1892-)  G  -     -1.65
3931 SER   (1889-)  H  -  - 3934 SER   (1892-)  H  -     -1.66
4769 PRO   ( 667-)  I  -  - 4772 MET   ( 670-)  I  -     -1.77
5991 SER   (1889-)  I  -  - 5994 SER   (1892-)  I  -     -1.64
8051 SER   (1889-)  J  -  - 8054 SER   (1892-)  J  -     -1.64
1011  SER  (1889-) K  -   - 1011  SER  (1892-) K  -      -1.63
1217  SER  (1889-) L  -   - 1217  SER  (1892-) L  -      -1.64
ERROR. Too many residues to use DSSP

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.

 147 ASN   ( 165-)  G  -
 242 HIS   ( 260-)  G  -
 398 GLN   ( 416-)  G  -
 422 HIS   ( 440-)  G  -
 531 ASN   ( 549-)  G  -
 643 ASN   ( 661-)  G  -
 740 HIS   ( 758-)  G  -
 889 ASN   ( 907-)  G  -
 918 HIS   ( 936-)  G  -
 964 ASN   ( 982-)  G  -
1007 GLN   (1025-)  G  -
1031 GLN   (1049-)  G  -
1155 HIS   (1173-)  G  -
1248 HIS   (1266-)  G  -
1529 HIS   (1547-)  G  -
1684 GLN   (1702-)  G  -
1722 ASN   (1740-)  G  -
1769 ASN   (1787-)  G  -
1956 GLN   (1974-)  G  -
2024 ASN   (2042-)  G  -
2302 HIS   ( 260-)  H  -
2458 GLN   ( 416-)  H  -
2482 HIS   ( 440-)  H  -
2492 HIS   ( 450-)  H  -
2591 ASN   ( 549-)  H  -
And so on for a total of 122 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.

   9 THR   (  27-)  G  -   N
  18 LEU   (  36-)  G  -   N
  24 HIS   (  42-)  G  -   NE2
  25 PHE   (  43-)  G  -   N
  44 GLU   (  62-)  G  -   N
  52 SER   (  70-)  G  -   N
  53 SER   (  71-)  G  -   N
  56 GLU   (  74-)  G  -   N
  75 ASP   (  93-)  G  -   N
  76 ALA   (  94-)  G  -   N
  77 HIS   (  95-)  G  -   N
  79 THR   (  97-)  G  -   OG1
 100 ASP   ( 118-)  G  -   N
 101 VAL   ( 119-)  G  -   N
 103 ALA   ( 121-)  G  -   N
 124 ALA   ( 142-)  G  -   N
 150 LYS   ( 168-)  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
 165 PHE   ( 183-)  G  -   N
 166 ASP   ( 184-)  G  -   N
 181 ASP   ( 199-)  G  -   N
And so on for a total of 1667 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.

  68 GLU   (  86-)  G  -   OE1
 239 GLN   ( 257-)  G  -   OE1
 269 GLN   ( 287-)  G  -   OE1
 305 GLN   ( 323-)  G  -   OE1
 384 ASN   ( 402-)  G  -   OD1
 436 ASP   ( 454-)  G  -   OD2
 471 GLU   ( 489-)  G  -   OE1
 471 GLU   ( 489-)  G  -   OE2
 655 GLN   ( 673-)  G  -   OE1
 724 GLN   ( 742-)  G  -   OE1
 734 HIS   ( 752-)  G  -   NE2
 826 GLU   ( 844-)  G  -   OE2
 845 GLU   ( 863-)  G  -   OE2
1027 ASP   (1045-)  G  -   OD2
1033 GLU   (1051-)  G  -   OE2
1050 GLN   (1068-)  G  -   OE1
1076 HIS   (1094-)  G  -   ND1
1203 GLU   (1221-)  G  -   OE2
1423 ASP   (1441-)  G  -   OD2
1439 HIS   (1457-)  G  -   ND1
1468 GLN   (1486-)  G  -   OE1
1707 HIS   (1725-)  G  -   ND1
2084 HIS   (  42-)  H  -   ND1
2128 GLU   (  86-)  H  -   OE1
2299 GLN   ( 257-)  H  -   OE1
And so on for a total of 132 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; but Alt-Rotamer
  68 GLU   (  86-)  G  -  H-bonding suggests Gln; but Alt-Rotamer
  92 GLU   ( 110-)  G  -  H-bonding suggests Gln
 253 GLU   ( 271-)  G  -  H-bonding suggests Gln
 348 ASP   ( 366-)  G  -  H-bonding suggests Asn
 453 ASP   ( 471-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
 465 ASP   ( 483-)  G  -  H-bonding suggests Asn
 467 ASP   ( 485-)  G  -  H-bonding suggests Asn
 471 GLU   ( 489-)  G  -  H-bonding suggests Gln
 553 ASP   ( 571-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
 665 ASP   ( 683-)  G  -  H-bonding suggests Asn
 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; but Alt-Rotamer
 969 ASP   ( 987-)  G  -  H-bonding suggests Asn
1033 GLU   (1051-)  G  -  H-bonding suggests Gln
1070 ASP   (1088-)  G  -  H-bonding suggests Asn
1075 ASP   (1093-)  G  -  H-bonding suggests Asn
1083 ASP   (1101-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
1086 ASP   (1104-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
1096 GLU   (1114-)  G  -  H-bonding suggests Gln
1111 ASP   (1129-)  G  -  H-bonding suggests Asn; but Alt-Rotamer
1296 GLU   (1314-)  G  -  H-bonding suggests Gln
And so on for a total of 187 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 :  -1.419
  2nd generation packing quality :  -1.943
  Ramachandran plot appearance   :  -4.543 (bad)
  chi-1/chi-2 rotamer normality  :  -5.124 (bad)
  Backbone conformation          :  -0.970

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.317 (tight)
  Bond angles                    :   0.542 (tight)
  Omega angle restraints         :   0.961
  Side chain planarity           :   0.247 (tight)
  Improper dihedral distribution :   0.545
  B-factor distribution          :   4.171 (loose)
  Inside/Outside distribution    :   1.003

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 :  -0.2
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.317 (tight)
  Bond angles                    :   0.542 (tight)
  Omega angle restraints         :   0.961
  Side chain planarity           :   0.247 (tight)
  Improper dihedral distribution :   0.545
  B-factor distribution          :   4.171 (loose)
  Inside/Outside distribution    :   1.003
==============

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.