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 pdb2uv8.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.494
CA-only RMS fit for the two chains : 0.491

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.243
CA-only RMS fit for the two chains : 0.239

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.437
CA-only RMS fit for the two chains : 0.435

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: G and H

All-atom RMS fit for the two chains : 0.670
CA-only RMS fit for the two chains : 0.667

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 : 0.529
CA-only RMS fit for the two chains : 0.528

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 41 21 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 3
Highest polymer chain multiplicity according to SEQRES: 6
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 24
Polymer chain multiplicity and SEQRES multiplicity disagree 3 6
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very 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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 1218974.5
Volume of the Unit Cell V= 41697584.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 8.552
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.330 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.

1094  FMN  (3051-) G  -
1094  FMN  (3051-) H  -
1094  FMN  (3051-) I  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

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.

 135 GVL   ( 180-)  A  -
1749 GVL   ( 180-)  B  -
3363 GVL   ( 180-)  C  -
5498 GLN   ( 660-)  G  -

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 MET   (   1-)  A  -   High
   2 LYS   (   2-)  A  -   High
   3 PRO   (   3-)  A  -   High
   4 GLU   (   4-)  A  -   High
   5 VAL   (   5-)  A  -   High
   6 GLU   (   6-)  A  -   High
   7 GLN   (   7-)  A  -   High
   8 GLU   (   8-)  A  -   High
   9 LEU   (   9-)  A  -   High
  10 ALA   (  10-)  A  -   High
  11 HIS   (  11-)  A  -   High
  12 ILE   (  12-)  A  -   High
  15 THR   (  15-)  A  -   High
  16 GLU   (  16-)  A  -   High
  20 TYR   (  20-)  A  -   High
  21 GLN   (  21-)  A  -   High
  22 PHE   (  22-)  A  -   High
  23 ALA   (  23-)  A  -   High
  24 SER   (  24-)  A  -   High
  27 ARG   (  27-)  A  -   High
  28 TRP   (  28-)  A  -   High
  29 ILE   (  29-)  A  -   High
  30 GLU   (  30-)  A  -   High
  33 ASP   (  33-)  A  -   High
  35 PHE   (  35-)  A  -   High
And so on for a total of 4465 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 : 4.233 over 58268 bonds
Average difference in B over a bond : 15.45
RMS difference in B over a bond : 19.42

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

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

  20 TYR   (  20-)  A  -
  65 TYR   (  65-)  A  -
  81 TYR   (  81-)  A  -
 383 TYR   ( 453-)  A  -
 549 TYR   ( 677-)  A  -
 844 TYR   ( 977-)  A  -
1104 TYR   (1237-)  A  -
1305 TYR   (1438-)  A  -
1490 TYR   (1623-)  A  -
1527 TYR   (1660-)  A  -
1634 TYR   (  20-)  B  -
1679 TYR   (  65-)  B  -
1695 TYR   (  81-)  B  -
1997 TYR   ( 453-)  B  -
2069 TYR   ( 525-)  B  -
2163 TYR   ( 677-)  B  -
2458 TYR   ( 977-)  B  -
2718 TYR   (1237-)  B  -
2919 TYR   (1438-)  B  -
3104 TYR   (1623-)  B  -
3141 TYR   (1660-)  B  -
3248 TYR   (  20-)  C  -
3293 TYR   (  65-)  C  -
3309 TYR   (  81-)  C  -
3611 TYR   ( 453-)  C  -
And so on for a total of 83 lines.

Warning: Phenylalanine convention problem

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

 168 PHE   ( 213-)  A  -
 196 PHE   ( 241-)  A  -
 316 PHE   ( 386-)  A  -
 540 PHE   ( 668-)  A  -
 582 PHE   ( 710-)  A  -
 799 PHE   ( 932-)  A  -
 891 PHE   (1024-)  A  -
 909 PHE   (1042-)  A  -
1001 PHE   (1134-)  A  -
1202 PHE   (1335-)  A  -
1379 PHE   (1512-)  A  -
1443 PHE   (1576-)  A  -
1565 PHE   (1698-)  A  -
1782 PHE   ( 213-)  B  -
1810 PHE   ( 241-)  B  -
1930 PHE   ( 386-)  B  -
2154 PHE   ( 668-)  B  -
2196 PHE   ( 710-)  B  -
2319 PHE   ( 833-)  B  -
2413 PHE   ( 932-)  B  -
2505 PHE   (1024-)  B  -
2523 PHE   (1042-)  B  -
2615 PHE   (1134-)  B  -
2816 PHE   (1335-)  B  -
2993 PHE   (1512-)  B  -
And so on for a total of 153 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.

5667 ASP   ( 829-)  G  -
6343 ASP   (1518-)  G  -
7700 ASP   ( 829-)  H  -
8376 ASP   (1518-)  H  -
9733 ASP   ( 829-)  I  -
1040  ASP  (1518-) I  -

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.

   4 GLU   (   4-)  A  -
   8 GLU   (   8-)  A  -
  16 GLU   (  16-)  A  -
 458 GLU   ( 528-)  A  -
 648 GLU   ( 776-)  A  -
 756 GLU   ( 889-)  A  -
 819 GLU   ( 952-)  A  -
1420 GLU   (1553-)  A  -
1618 GLU   (   4-)  B  -
1622 GLU   (   8-)  B  -
1630 GLU   (  16-)  B  -
2072 GLU   ( 528-)  B  -
2262 GLU   ( 776-)  B  -
2370 GLU   ( 889-)  B  -
2433 GLU   ( 952-)  B  -
3034 GLU   (1553-)  B  -
3232 GLU   (   4-)  C  -
3236 GLU   (   8-)  C  -
3244 GLU   (  16-)  C  -
3686 GLU   ( 528-)  C  -
3876 GLU   ( 776-)  C  -
3984 GLU   ( 889-)  C  -
4047 GLU   ( 952-)  C  -
4648 GLU   (1553-)  C  -
4891 GLU   (  53-)  G  -
And so on for a total of 58 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.

1094  FMN  (3051-) G  -    OP1    O1P
1094  FMN  (3051-) G  -    OP2    O2P
1094  FMN  (3051-) G  -    OP3    O3P
1094  FMN  (3051-) H  -    OP1    O1P
1094  FMN  (3051-) H  -    OP2    O2P
1094  FMN  (3051-) H  -    OP3    O3P
1094  FMN  (3051-) I  -    OP1    O1P
1094  FMN  (3051-) I  -    OP2    O2P
1094  FMN  (3051-) I  -    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

 |  0.999558 -0.000097 -0.000201|
 | -0.000097  0.999718  0.000000|
 | -0.000201  0.000000  0.999491|
Proposed new scale matrix

 |  0.004339  0.000000  0.000000|
 |  0.000000  0.004338  0.000000|
 |  0.000000  0.000000  0.001276|
With corresponding cell

    A    = 230.472  B   = 230.509  C    = 783.914
    Alpha=  90.006  Beta=  90.006  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 230.600  B   = 230.600  C    = 784.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 65.853
(Under-)estimated Z-score: 5.981

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.

 470 GLN   ( 540-)  A  -   N    CA   C    95.81   -5.5
 471 MET   ( 599-)  A  -   N    CA   C    92.32   -6.7
 664 HIS   ( 792-)  A  -   CG   ND1  CE1 109.73    4.1
2084 GLN   ( 540-)  B  -   N    CA   C    95.69   -5.5
2085 MET   ( 599-)  B  -   N    CA   C    92.35   -6.7
3698 GLN   ( 540-)  C  -   N    CA   C    95.81   -5.5
3699 MET   ( 599-)  C  -   N    CA   C    92.36   -6.7
3892 HIS   ( 792-)  C  -   CG   ND1  CE1 109.69    4.1
5947 VAL   (1109-)  G  -   N    CA   C    98.52   -4.5
7980 VAL   (1109-)  H  -   N    CA   C    98.13   -4.7
9404 HIS   ( 500-)  I  -   CG   ND1  CE1 109.62    4.0
1001  VAL  (1109-) I  -    N    CA   C    98.29   -4.6

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.

   4 GLU   (   4-)  A  -
   8 GLU   (   8-)  A  -
  16 GLU   (  16-)  A  -
 458 GLU   ( 528-)  A  -
 648 GLU   ( 776-)  A  -
 756 GLU   ( 889-)  A  -
 819 GLU   ( 952-)  A  -
1420 GLU   (1553-)  A  -
1618 GLU   (   4-)  B  -
1622 GLU   (   8-)  B  -
1630 GLU   (  16-)  B  -
2072 GLU   ( 528-)  B  -
2262 GLU   ( 776-)  B  -
2370 GLU   ( 889-)  B  -
2433 GLU   ( 952-)  B  -
3034 GLU   (1553-)  B  -
3232 GLU   (   4-)  C  -
3236 GLU   (   8-)  C  -
3244 GLU   (  16-)  C  -
3686 GLU   ( 528-)  C  -
3876 GLU   ( 776-)  C  -
3984 GLU   ( 889-)  C  -
4047 GLU   ( 952-)  C  -
4648 GLU   (1553-)  C  -
4891 GLU   (  53-)  G  -
And so on for a total of 64 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.

2084 GLN   ( 540-)  B  -   6.16
3698 GLN   ( 540-)  C  -   6.11
 470 GLN   ( 540-)  A  -   6.11
 259 GLU   ( 329-)  A  -   6.03
3487 GLU   ( 329-)  C  -   6.03
1873 GLU   ( 329-)  B  -   6.00
 471 MET   ( 599-)  A  -   5.70
2085 MET   ( 599-)  B  -   5.69
3699 MET   ( 599-)  C  -   5.69
2198 LYS   ( 712-)  B  -   5.07
 584 LYS   ( 712-)  A  -   4.89
7980 VAL   (1109-)  H  -   4.83
1001  VAL  (1109-) I  -   4.75
5947 VAL   (1109-)  G  -   4.65
4787 MET   (1692-)  C  -   4.58
9138 ILE   ( 234-)  I  -   4.51
4713 LEU   (1618-)  C  -   4.49
7105 ILE   ( 234-)  H  -   4.42
5072 ILE   ( 234-)  G  -   4.33
3812 LYS   ( 712-)  C  -   4.29
1559 MET   (1692-)  A  -   4.23
1087  LYS  (1986-) I  -   4.16
8844 LYS   (1986-)  H  -   4.14
1872 LEU   ( 328-)  B  -   4.02

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.533

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.

 807 THR   ( 940-)  A  -   -3.2
 940 THR   (1073-)  A  -   -3.1
2421 THR   ( 940-)  B  -   -3.1
4168 THR   (1073-)  C  -   -3.1
2554 THR   (1073-)  B  -   -3.1
4035 THR   ( 940-)  C  -   -3.0
4883 THR   (  45-)  G  -   -3.0
3320 PRO   (  92-)  C  -   -3.0
1706 PRO   (  92-)  B  -   -3.0
  92 PRO   (  92-)  A  -   -3.0
8949 THR   (  45-)  I  -   -3.0
6916 THR   (  45-)  H  -   -2.9
8815 PRO   (1957-)  H  -   -2.9
1084  PRO  (1957-) I  -   -2.9
6782 PRO   (1957-)  G  -   -2.9
6210 PRO   (1385-)  G  -   -2.8
2779 ILE   (1298-)  B  -   -2.8
1165 ILE   (1298-)  A  -   -2.8
7142 THR   ( 271-)  H  -   -2.8
5109 THR   ( 271-)  G  -   -2.8
8243 PRO   (1385-)  H  -   -2.8
4393 ILE   (1298-)  C  -   -2.8
4953 THR   ( 115-)  G  -   -2.8
9019 THR   ( 115-)  I  -   -2.8
9175 THR   ( 271-)  I  -   -2.8
And so on for a total of 458 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.

  27 ARG   (  27-)  A  - Poor phi/psi
  40 ASN   (  40-)  A  - Poor phi/psi
  64 LYS   (  64-)  A  - Poor phi/psi
  90 TYR   (  90-)  A  - Poor phi/psi
 115 LYS   ( 160-)  A  - Poor phi/psi
 256 ASP   ( 301-)  A  - omega poor
 281 LYS   ( 351-)  A  - Poor phi/psi
 323 SER   ( 393-)  A  - Poor phi/psi
 332 PHE   ( 402-)  A  - omega poor
 333 ASP   ( 403-)  A  - omega poor
 334 SER   ( 404-)  A  - Poor phi/psi
 374 ASN   ( 444-)  A  - omega poor
 415 ASP   ( 485-)  A  - Poor phi/psi
 434 ASP   ( 504-)  A  - Poor phi/psi
 467 LYS   ( 537-)  A  - Poor phi/psi
 468 GLU   ( 538-)  A  - Poor phi/psi
 469 SER   ( 539-)  A  - omega poor
 476 ALA   ( 604-)  A  - omega poor
 477 LEU   ( 605-)  A  - Poor phi/psi
 505 GLU   ( 633-)  A  - Poor phi/psi
 547 ASP   ( 675-)  A  - Poor phi/psi
 574 LYS   ( 702-)  A  - omega poor
 642 PRO   ( 770-)  A  - Poor phi/psi
 657 ASP   ( 785-)  A  - Poor phi/psi
 706 GLY   ( 834-)  A  - Poor phi/psi
And so on for a total of 453 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 : -4.591

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.

3942 SER   ( 842-)  C  -   0.35
 714 SER   ( 842-)  A  -   0.35
1956 SER   ( 412-)  B  -   0.35
1978 SER   ( 434-)  B  -   0.36
6411 SER   (1586-)  G  -   0.36
9543 SER   ( 639-)  I  -   0.36
3592 SER   ( 434-)  C  -   0.36
5477 SER   ( 639-)  G  -   0.36
7510 SER   ( 639-)  H  -   0.36
7067 SER   ( 196-)  H  -   0.36
2328 SER   ( 842-)  B  -   0.36
1550 SER   (1683-)  A  -   0.36
3164 SER   (1683-)  B  -   0.36
4778 SER   (1683-)  C  -   0.36
 364 SER   ( 434-)  A  -   0.37
2297 SER   ( 811-)  B  -   0.37
8444 SER   (1586-)  H  -   0.37
 683 SER   ( 811-)  A  -   0.38
1545 SER   (1678-)  A  -   0.38
3159 SER   (1678-)  B  -   0.38
3911 SER   ( 811-)  C  -   0.38
1959 SER   ( 415-)  B  -   0.38
 342 SER   ( 412-)  A  -   0.38
3570 SER   ( 412-)  C  -   0.39
1047  SER  (1586-) I  -   0.39
5034 SER   ( 196-)  G  -   0.39
9100 SER   ( 196-)  I  -   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!

  24 SER   (  24-)  A  -     0
  27 ARG   (  27-)  A  -     0
  28 TRP   (  28-)  A  -     0
  38 ASP   (  38-)  A  -     0
  41 THR   (  41-)  A  -     0
  43 ARG   (  43-)  A  -     0
  47 ILE   (  47-)  A  -     0
  49 PRO   (  49-)  A  -     0
  51 PRO   (  51-)  A  -     0
  63 ASN   (  63-)  A  -     0
  64 LYS   (  64-)  A  -     0
  65 TYR   (  65-)  A  -     0
  84 ASP   (  84-)  A  -     0
  93 ASP   (  93-)  A  -     0
  94 PRO   (  94-)  A  -     0
  95 ILE   ( 140-)  A  -     0
  96 ALA   ( 141-)  A  -     0
 115 LYS   ( 160-)  A  -     0
 118 LEU   ( 163-)  A  -     0
 122 PRO   ( 167-)  A  -     0
 123 MET   ( 168-)  A  -     0
 125 LYS   ( 170-)  A  -     0
 131 VAL   ( 176-)  A  -     0
 134 LYS   ( 179-)  A  -     0
 135 GVL   ( 180-)  A  -     0
And so on for a total of 3641 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!

 194 GLY   ( 239-)  A  -  3.18   27
3422 GLY   ( 239-)  C  -  3.15   25
1808 GLY   ( 239-)  B  -  3.15   25
2512 GLY   (1031-)  B  -  2.03   17
4126 GLY   (1031-)  C  -  2.00   17
 898 GLY   (1031-)  A  -  1.98   19
6112 GLY   (1287-)  G  -  1.97   21
1017  GLY  (1287-) I  -  1.96   20
8145 GLY   (1287-)  H  -  1.95   22
4804 GLU   (1709-)  C  -  1.74   10
1576 GLU   (1709-)  A  -  1.74   10
3190 GLU   (1709-)  B  -  1.72   10
7697 GLY   ( 826-)  H  -  1.69   25
5664 GLY   ( 826-)  G  -  1.67   26
9730 GLY   ( 826-)  I  -  1.67   25
3378 GLY   ( 195-)  C  -  1.52   12
2336 PHE   ( 850-)  B  -  1.51   13

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].

   3 PRO   (   3-)  A  -  107.5 envelop C-beta (108 degrees)
  51 PRO   (  51-)  A  -   41.0 envelop C-delta (36 degrees)
  92 PRO   (  92-)  A  -   24.2 half-chair N/C-delta (18 degrees)
  94 PRO   (  94-)  A  -  145.1 envelop C-alpha (144 degrees)
 122 PRO   ( 167-)  A  -   38.6 envelop C-delta (36 degrees)
 153 PRO   ( 198-)  A  - -112.5 envelop C-gamma (-108 degrees)
 418 PRO   ( 488-)  A  -   52.8 half-chair C-delta/C-gamma (54 degrees)
 429 PRO   ( 499-)  A  -   31.9 envelop C-delta (36 degrees)
 608 PRO   ( 736-)  A  -   40.9 envelop C-delta (36 degrees)
 642 PRO   ( 770-)  A  -   26.1 half-chair N/C-delta (18 degrees)
 647 PRO   ( 775-)  A  -   49.0 half-chair C-delta/C-gamma (54 degrees)
 697 PRO   ( 825-)  A  -   28.6 envelop C-delta (36 degrees)
 700 PRO   ( 828-)  A  -   39.0 envelop C-delta (36 degrees)
 860 PRO   ( 993-)  A  -   46.5 half-chair C-delta/C-gamma (54 degrees)
 938 PRO   (1071-)  A  -   43.6 envelop C-delta (36 degrees)
 950 PRO   (1083-)  A  -   52.0 half-chair C-delta/C-gamma (54 degrees)
1077 PRO   (1210-)  A  -  115.6 envelop C-beta (108 degrees)
1168 PRO   (1301-)  A  -   46.9 half-chair C-delta/C-gamma (54 degrees)
1229 PRO   (1362-)  A  -  100.3 envelop C-beta (108 degrees)
1288 PRO   (1421-)  A  -   39.3 envelop C-delta (36 degrees)
1384 PRO   (1517-)  A  -   38.3 envelop C-delta (36 degrees)
1438 PRO   (1571-)  A  -   42.1 envelop C-delta (36 degrees)
1451 PRO   (1584-)  A  -   -2.8 envelop N (0 degrees)
1494 PRO   (1627-)  A  -   47.3 half-chair C-delta/C-gamma (54 degrees)
1617 PRO   (   3-)  B  -  107.8 envelop C-beta (108 degrees)
And so on for a total of 159 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.

7648 THR   ( 777-)  H  -   CG2 <-> 7952 HIS   (1081-)  H  -   NE2    0.70    2.40  INTRA BL
5615 THR   ( 777-)  G  -   CG2 <-> 5919 HIS   (1081-)  G  -   NE2    0.68    2.42  INTRA BL
7612 HIS   ( 741-)  H  -   NE2 <-> 7726 HIS   ( 855-)  H  -   CE1    0.68    2.42  INTRA BF
9681 THR   ( 777-)  I  -   CG2 <-> 9985 HIS   (1081-)  I  -   NE2    0.67    2.43  INTRA BL
4080 ARG   ( 985-)  C  -   NH1 <-> 9857 ARG   ( 953-)  I  -   CZ     0.62    2.48  INTRA BF
5694 LYS   ( 856-)  G  -   NZ  <-> 5890 CYS   (1052-)  G  -   SG     0.61    2.69  INTRA BL
7612 HIS   ( 741-)  H  -   CE1 <-> 7716 THR   ( 845-)  H  -   CG2    0.60    2.60  INTRA BF
9760 LYS   ( 856-)  I  -   NZ  <-> 9956 CYS   (1052-)  I  -   SG     0.60    2.70  INTRA BF
7727 LYS   ( 856-)  H  -   NZ  <-> 7923 CYS   (1052-)  H  -   SG     0.60    2.70  INTRA BL
9645 HIS   ( 741-)  I  -   NE2 <-> 9759 HIS   ( 855-)  I  -   CE1    0.58    2.52  INTRA BF
2511 TRP   (1030-)  B  -   NE1 <-> 3061 LEU   (1580-)  B  -   CD2    0.56    2.54  INTRA BL
 265 HIS   ( 335-)  A  -   CE1 <-> 3493 HIS   ( 335-)  C  -   CE1    0.56    2.64  INTRA BF
2466 ARG   ( 985-)  B  -   NH1 <-> 7824 ARG   ( 953-)  H  -   CZ     0.55    2.55  INTRA BF
 897 TRP   (1030-)  A  -   NE1 <-> 1447 LEU   (1580-)  A  -   CD2    0.53    2.57  INTRA BL
4125 TRP   (1030-)  C  -   NE1 <-> 4675 LEU   (1580-)  C  -   CD2    0.52    2.58  INTRA BL
9645 HIS   ( 741-)  I  -   CE1 <-> 9749 THR   ( 845-)  I  -   CG2    0.52    2.68  INTRA BF
7612 HIS   ( 741-)  H  -   CE1 <-> 7726 HIS   ( 855-)  H  -   CE1    0.51    2.69  INTRA BF
5579 HIS   ( 741-)  G  -   CE1 <-> 5683 THR   ( 845-)  G  -   CG2    0.51    2.69  INTRA BF
 852 ARG   ( 985-)  A  -   NH1 <-> 5791 ARG   ( 953-)  G  -   CZ     0.50    2.60  INTRA BF
5579 HIS   ( 741-)  G  -   NE2 <-> 5693 HIS   ( 855-)  G  -   CE1    0.49    2.61  INTRA BF
2634 ASP   (1153-)  B  -   OD2 <-> 3517 ARG   ( 359-)  C  -   NH2    0.48    2.22  INTRA BF
9636 TRP   ( 732-)  I  -   CG  <-> 9654 MET   ( 750-)  I  -   CE     0.47    2.73  INTRA BF
4462 ARG   (1367-)  C  -   NH1 <-> 4467 THR   (1372-)  C  -   CB     0.45    2.65  INTRA BF
1879 HIS   ( 335-)  B  -   CE1 <-> 3493 HIS   ( 335-)  C  -   CE1    0.45    2.75  INTRA BF
9645 HIS   ( 741-)  I  -   CE1 <-> 9759 HIS   ( 855-)  I  -   CE1    0.44    2.76  INTRA BF
And so on for a total of 1861 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

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.

1305 TYR   (1438-)  A  -     -7.29
4533 TYR   (1438-)  C  -     -7.28
5849 MET   (1011-)  G  -     -7.27
2919 TYR   (1438-)  B  -     -7.25
9915 MET   (1011-)  I  -     -7.21
7882 MET   (1011-)  H  -     -7.18
1382 ARG   (1515-)  A  -     -6.90
2996 ARG   (1515-)  B  -     -6.88
4610 ARG   (1515-)  C  -     -6.85
1085  ARG  (1962-) I  -     -6.73
6787 ARG   (1962-)  G  -     -6.65
8820 ARG   (1962-)  H  -     -6.62
1280 LYS   (1413-)  A  -     -6.55
2894 LYS   (1413-)  B  -     -6.52
4508 LYS   (1413-)  C  -     -6.52
3184 HIS   (1703-)  B  -     -6.37
4798 HIS   (1703-)  C  -     -6.36
1570 HIS   (1703-)  A  -     -6.36
1030  ARG  (1413-) I  -     -6.32
6238 ARG   (1413-)  G  -     -6.32
7496 PHE   ( 625-)  H  -     -6.28
3732 ARG   ( 632-)  C  -     -6.25
8271 ARG   (1413-)  H  -     -6.23
5463 PHE   ( 625-)  G  -     -6.23
2118 ARG   ( 632-)  B  -     -6.22
And so on for a total of 255 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.

1013 HIS   (1146-)  A  -   1015 - HIS   1148- ( A)  -      -5.30
1280 LYS   (1413-)  A  -   1283 - ARG   1416- ( A)  -      -5.56
1342 GLU   (1475-)  A  -   1344 - ILE   1477- ( A)  -      -4.62
2627 HIS   (1146-)  B  -   2629 - HIS   1148- ( B)  -      -5.24
4241 HIS   (1146-)  C  -   4243 - HIS   1148- ( C)  -      -5.30
4508 LYS   (1413-)  C  -   4511 - ARG   1416- ( C)  -      -5.58
4570 GLU   (1475-)  C  -   4572 - ILE   1477- ( C)  -      -4.62
4976 ASP   ( 138-)  G  -   4978 - LYS    140- ( G)  -      -4.15
5926 GLN   (1088-)  G  -   5928 - TYR   1090- ( G)  -      -4.61
7959 GLN   (1088-)  H  -   7961 - TYR   1090- ( H)  -      -4.60
9992 GLN   (1088-)  I  -   9994 - TYR   1090- ( I)  -      -4.61

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: 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

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.

4675 LEU   (1580-)  C  -  -2.92
3061 LEU   (1580-)  B  -  -2.92
1447 LEU   (1580-)  A  -  -2.89
7980 VAL   (1109-)  H  -  -2.69
1001  VAL  (1109-) I  -  -2.69
5947 VAL   (1109-)  G  -  -2.69
7704 GLU   ( 833-)  H  -  -2.68
9737 GLU   ( 833-)  I  -  -2.68
5671 GLU   ( 833-)  G  -  -2.66
 667 MET   ( 795-)  A  -  -2.58
3895 MET   ( 795-)  C  -  -2.57
2281 MET   ( 795-)  B  -  -2.56
1637 ALA   (  23-)  B  -  -2.54
5878 LEU   (1040-)  G  -  -2.50

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.

 650 GLY   ( 778-)  A  -  -  653 LEU   ( 781-)  A  -     -1.75
1443 PHE   (1576-)  A  -  - 1447 LEU   (1580-)  A  -     -2.07
2264 GLY   ( 778-)  B  -  - 2267 LEU   ( 781-)  B  -     -1.76
3057 PHE   (1576-)  B  -  - 3061 LEU   (1580-)  B  -     -2.05
3878 GLY   ( 778-)  C  -  - 3881 LEU   ( 781-)  C  -     -1.72
4671 PHE   (1576-)  C  -  - 4675 LEU   (1580-)  C  -     -2.04
5268 HIS   ( 430-)  G  -  - 5271 VAL   ( 433-)  G  -     -1.70
7301 HIS   ( 430-)  H  -  - 7304 VAL   ( 433-)  H  -     -1.68
8718 GLY   (1860-)  H  -  - 8721 ALA   (1863-)  H  -     -1.61
9334 HIS   ( 430-)  I  -  - 9337 VAL   ( 433-)  I  -     -1.88
1075  GLY  (1860-) I  -   - 1075  ALA  (1863-) I  -      -1.59
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: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

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.

  11 HIS   (  11-)  A  -
  21 GLN   (  21-)  A  -
 309 ASN   ( 379-)  A  -
 337 ASN   ( 407-)  A  -
 341 GLN   ( 411-)  A  -
 357 ASN   ( 427-)  A  -
 368 ASN   ( 438-)  A  -
 405 GLN   ( 475-)  A  -
 591 GLN   ( 719-)  A  -
 610 ASN   ( 738-)  A  -
 655 HIS   ( 783-)  A  -
 664 HIS   ( 792-)  A  -
 854 ASN   ( 987-)  A  -
 856 GLN   ( 989-)  A  -
1106 HIS   (1239-)  A  -
1138 GLN   (1271-)  A  -
1299 HIS   (1432-)  A  -
1309 ASN   (1442-)  A  -
1325 GLN   (1458-)  A  -
1349 GLN   (1482-)  A  -
1377 ASN   (1510-)  A  -
1409 HIS   (1542-)  A  -
1477 ASN   (1610-)  A  -
1562 ASN   (1695-)  A  -
1625 HIS   (  11-)  B  -
And so on for a total of 157 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.

  15 THR   (  15-)  A  -   OG1
  28 TRP   (  28-)  A  -   NE1
  30 GLU   (  30-)  A  -   N
  43 ARG   (  43-)  A  -   NE
  48 GLY   (  48-)  A  -   N
  50 SER   (  50-)  A  -   N
  87 GLU   (  87-)  A  -   N
  98 GLU   ( 143-)  A  -   N
 100 VAL   ( 145-)  A  -   N
 126 THR   ( 171-)  A  -   N
 126 THR   ( 171-)  A  -   OG1
 129 ASP   ( 174-)  A  -   N
 134 LYS   ( 179-)  A  -   N
 135 GVL   ( 180-)  A  -   N
 151 THR   ( 196-)  A  -   N
 157 GLU   ( 202-)  A  -   N
 171 THR   ( 216-)  A  -   N
 174 GLY   ( 219-)  A  -   N
 175 ALA   ( 220-)  A  -   N
 180 SER   ( 225-)  A  -   OG
 198 ILE   ( 243-)  A  -   N
 199 THR   ( 244-)  A  -   N
 200 VAL   ( 245-)  A  -   N
 209 TRP   ( 254-)  A  -   N
 237 ASP   ( 282-)  A  -   N
And so on for a total of 1151 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  16 GLU   (  16-)  A  -   OE1
  33 ASP   (  33-)  A  -   OD1
  40 ASN   (  40-)  A  -   OD1
 148 GLU   ( 193-)  A  -   OE2
 216 GLN   ( 261-)  A  -   OE1
 648 GLU   ( 776-)  A  -   OE2
 702 HIS   ( 830-)  A  -   ND1
 794 ASN   ( 927-)  A  -   OD1
 930 HIS   (1063-)  A  -   ND1
1222 GLU   (1355-)  A  -   OE1
1252 GLN   (1385-)  A  -   OE1
1409 HIS   (1542-)  A  -   NE2
1450 HIS   (1583-)  A  -   ND1
1762 GLU   ( 193-)  B  -   OE2
2262 GLU   ( 776-)  B  -   OE2
2278 HIS   ( 792-)  B  -   NE2
2316 HIS   ( 830-)  B  -   ND1
2408 ASN   ( 927-)  B  -   OD1
2441 GLU   ( 960-)  B  -   OE1
2544 HIS   (1063-)  B  -   ND1
2575 GLU   (1094-)  B  -   OE1
2628 GLN   (1147-)  B  -   OE1
2836 GLU   (1355-)  B  -   OE1
2859 GLU   (1378-)  B  -   OE1
2957 GLU   (1476-)  B  -   OE2
And so on for a total of 93 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.

  46 GLU   (  46-)  A  -  H-bonding suggests Gln; but Alt-Rotamer
 148 GLU   ( 193-)  A  -  H-bonding suggests Gln
 170 ASP   ( 215-)  A  -  H-bonding suggests Asn
 243 ASP   ( 288-)  A  -  H-bonding suggests Asn
 306 ASP   ( 376-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 753 GLU   ( 886-)  A  -  H-bonding suggests Gln
 792 ASP   ( 925-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
1076 ASP   (1209-)  A  -  H-bonding suggests Asn
1200 ASP   (1333-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
1328 ASP   (1461-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
1479 ASP   (1612-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
1660 GLU   (  46-)  B  -  H-bonding suggests Gln; but Alt-Rotamer
1762 GLU   ( 193-)  B  -  H-bonding suggests Gln
1784 ASP   ( 215-)  B  -  H-bonding suggests Asn
1857 ASP   ( 288-)  B  -  H-bonding suggests Asn
1920 ASP   ( 376-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
2367 GLU   ( 886-)  B  -  H-bonding suggests Gln
2406 ASP   ( 925-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
2690 ASP   (1209-)  B  -  H-bonding suggests Asn
2814 ASP   (1333-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
2942 ASP   (1461-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
3093 ASP   (1612-)  B  -  H-bonding suggests Asn; but Alt-Rotamer
3274 GLU   (  46-)  C  -  H-bonding suggests Gln; but Alt-Rotamer
3376 GLU   ( 193-)  C  -  H-bonding suggests Gln
3398 ASP   ( 215-)  C  -  H-bonding suggests Asn
And so on for a total of 76 lines.

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.932
  2nd generation packing quality :  -1.584
  Ramachandran plot appearance   :  -3.533 (poor)
  chi-1/chi-2 rotamer normality  :  -4.591 (bad)
  Backbone conformation          :  -0.595

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.343 (tight)
  Bond angles                    :   0.567 (tight)
  Omega angle restraints         :   1.002
  Side chain planarity           :   0.283 (tight)
  Improper dihedral distribution :   0.582
  B-factor distribution          :   4.233 (loose)
  Inside/Outside distribution    :   1.004

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 :   0.4
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -2.1
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.343 (tight)
  Bond angles                    :   0.567 (tight)
  Omega angle restraints         :   1.002
  Side chain planarity           :   0.283 (tight)
  Improper dihedral distribution :   0.582
  B-factor distribution          :   4.233 (loose)
  Inside/Outside distribution    :   1.004
==============

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.