WHAT IF Check report

This file was created 2012-01-13 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 pdb1smy.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 K

All-atom RMS fit for the two chains : 0.810
CA-only RMS fit for the two chains : 0.498

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 K

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and L

All-atom RMS fit for the two chains : 0.791
CA-only RMS fit for the two chains : 0.433

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 L

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: C and M

All-atom RMS fit for the two chains : 1.137
CA-only RMS fit for the two chains : 0.754

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: D and N

All-atom RMS fit for the two chains : 1.046
CA-only RMS fit for the two chains : 0.665

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: D and N

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: E and O

All-atom RMS fit for the two chains : 0.918
CA-only RMS fit for the two chains : 0.030

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: 775934.313
Volume of the Unit Cell V= 12048084.0
Space group multiplicity: 3
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.176
Vm by authors and this calculated Vm agree only marginally
Matthews coefficient read from REMARK 280 Vm= 4.710

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.

7185 G4P   (9100-)  N  -
7186 G4P   (9101-)  N  -

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

6870  MG   (9202-)  N  -
6933  MG   (9438-)  C  -
6969  MG   (9214-)  N  -

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

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

Warning: Missing atoms

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

1793 LYS   ( 217-)  D      CG
1793 LYS   ( 217-)  D      CD
1793 LYS   ( 217-)  D      CE
1793 LYS   ( 217-)  D      NZ
1794 LYS   ( 218-)  D      CB
1794 LYS   ( 218-)  D      CG
1794 LYS   ( 218-)  D      CD
1794 LYS   ( 218-)  D      CE
1794 LYS   ( 218-)  D      NZ
1795 GLU   ( 219-)  D      CG
1795 GLU   ( 219-)  D      CD
1795 GLU   ( 219-)  D      OE1
1795 GLU   ( 219-)  D      OE2
1796 ARG   ( 220-)  D      CG
1796 ARG   ( 220-)  D      CD
1796 ARG   ( 220-)  D      NE
1796 ARG   ( 220-)  D      CZ
1796 ARG   ( 220-)  D      NH1
1796 ARG   ( 220-)  D      NH2
1799 LEU   ( 223-)  D      CB
1799 LEU   ( 223-)  D      CG
1799 LEU   ( 223-)  D      CD1
1799 LEU   ( 223-)  D      CD2
1800 ARG   ( 224-)  D      CG
1800 ARG   ( 224-)  D      CD
And so on for a total of 400 lines.

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 MET   (   1-)  A    High
   2 LEU   (   2-)  A    High
   3 ASP   (   3-)  A    High
   4 SER   (   4-)  A    High
   5 LYS   (   5-)  A    High
 189 ARG   ( 189-)  A    High
 230 MET   (   1-)  B    High
 231 LEU   (   2-)  B    High
 232 ASP   (   3-)  B    High
 233 SER   (   4-)  B    High
 234 LYS   (   5-)  B    High
 235 LEU   (   6-)  B    High
 236 LYS   (   7-)  B    High
 291 LEU   (  62-)  B    High
 292 HIS   (  63-)  B    High
 293 GLU   (  64-)  B    High
 298 PRO   (  69-)  B    High
 324 GLN   (  95-)  B    High
 325 THR   (  96-)  B    High
 326 VAL   (  97-)  B    High
 327 THR   (  98-)  B    High
 331 LYS   ( 102-)  B    High
 332 ALA   ( 103-)  B    High
 333 GLU   ( 104-)  B    High
 334 GLY   ( 105-)  B    High
And so on for a total of 999 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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

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
 150 TYR   ( 150-)  A
 249 TYR   (  20-)  B
 529 TYR   (  71-)  C
 605 TYR   ( 147-)  C
 716 TYR   ( 258-)  C
 725 TYR   ( 267-)  C
 929 TYR   ( 471-)  C
 943 TYR   ( 485-)  C
1073 TYR   ( 615-)  C
1081 TYR   ( 623-)  C
1359 TYR   ( 901-)  C
1501 TYR   (1043-)  C
1664 TYR   (  88-)  D
2305 TYR   ( 841-)  D
2380 TYR   ( 916-)  D
2400 TYR   ( 936-)  D
2485 TYR   (1021-)  D
2609 TYR   (1145-)  D
2662 TYR   (1198-)  D
2671 TYR   (1207-)  D
2767 TYR   (1303-)  D
2842 TYR   (1378-)  D
3429 TYR   (  20-)  K
3658 TYR   (  20-)  L
And so on for a total of 52 lines.

Warning: Phenylalanine convention problem

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

  11 PHE   (  11-)  A
 454 PHE   ( 225-)  B
 585 PHE   ( 127-)  C
 685 PHE   ( 227-)  C
 697 PHE   ( 239-)  C
 769 PHE   ( 311-)  C
 852 PHE   ( 394-)  C
 883 PHE   ( 425-)  C
1123 PHE   ( 665-)  C
1236 PHE   ( 778-)  C
1364 PHE   ( 906-)  C
1451 PHE   ( 993-)  C
1570 PHE   (1112-)  C
1626 PHE   (  50-)  D
1680 PHE   ( 104-)  D
1783 PHE   ( 207-)  D
1966 PHE   ( 502-)  D
2204 PHE   ( 740-)  D
2307 PHE   ( 843-)  D
2403 PHE   ( 939-)  D
2405 PHE   ( 941-)  D
2535 PHE   (1071-)  D
2705 PHE   (1241-)  D
2978 PHE   (  10-)  E
3003 PHE   (  35-)  E
And so on for a total of 55 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.

 126 ASP   ( 126-)  A
 202 ASP   ( 202-)  A
 491 ASP   (  33-)  C
 539 ASP   (  81-)  C
 591 ASP   ( 133-)  C
 721 ASP   ( 263-)  C
 753 ASP   ( 295-)  C
 781 ASP   ( 323-)  C
 950 ASP   ( 492-)  C
1011 ASP   ( 553-)  C
1111 ASP   ( 653-)  C
1138 ASP   ( 680-)  C
1144 ASP   ( 686-)  C
1172 ASP   ( 714-)  C
1183 ASP   ( 725-)  C
1194 ASP   ( 736-)  C
1242 ASP   ( 784-)  C
1295 ASP   ( 837-)  C
1315 ASP   ( 857-)  C
1516 ASP   (1058-)  C
1533 ASP   (1075-)  C
1731 ASP   ( 155-)  D
1877 ASP   ( 413-)  D
2003 ASP   ( 539-)  D
2006 ASP   ( 542-)  D
And so on for a total of 70 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.

  19 GLU   (  19-)  A
  73 GLU   (  73-)  A
  77 GLU   (  77-)  A
 108 GLU   ( 108-)  A
 182 GLU   ( 182-)  A
 216 GLU   ( 216-)  A
 220 GLU   ( 220-)  A
 248 GLU   (  19-)  B
 302 GLU   (  73-)  B
 337 GLU   ( 108-)  B
 362 GLU   ( 133-)  B
 363 GLU   ( 134-)  B
 383 GLU   ( 154-)  B
 411 GLU   ( 182-)  B
 445 GLU   ( 216-)  B
 508 GLU   (  50-)  C
 515 GLU   (  57-)  C
 533 GLU   (  75-)  C
 568 GLU   ( 110-)  C
 581 GLU   ( 123-)  C
 737 GLU   ( 279-)  C
 779 GLU   ( 321-)  C
 796 GLU   ( 338-)  C
 900 GLU   ( 442-)  C
 949 GLU   ( 491-)  C
And so on for a total of 162 lines.

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

 |  0.998402  0.000056  0.000107|
 |  0.000056  0.998360 -0.000071|
 |  0.000107 -0.000071  0.998701|
Proposed new scale matrix

 |  0.004238  0.002447  0.000000|
 |  0.000000  0.004894  0.000000|
 |  0.000000  0.000000  0.004020|
With corresponding cell

    A    = 235.983  B   = 235.948  C    = 248.742
    Alpha=  90.001  Beta=  90.002  Gamma= 120.003

The CRYST1 cell dimensions

    A    = 236.350  B   = 236.350  C    = 249.040
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 516.684
(Under-)estimated Z-score: 16.752

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.

 385 HIS   ( 156-)  B      CG   ND1  CE1 109.61    4.0
 517 LYS   (  59-)  C     -C    N    CA  129.01    4.1
 702 PRO   ( 244-)  C     -C    N    CD  104.70   -5.0
 702 PRO   ( 244-)  C      CD   N    CA  105.20   -4.9
 720 ALA   ( 262-)  C     -C    N    CA  129.93    4.6
 777 GLY   ( 319-)  C     -CA  -C    N   107.97   -4.1
 777 GLY   ( 319-)  C     -C    N    CA  129.83    5.4
 877 THR   ( 419-)  C     -C    N    CA  129.11    4.1
 930 ARG   ( 472-)  C      CB   CG   CD  105.30   -4.4
1186 HIS   ( 728-)  C     -C    N    CA  112.81   -4.9
1186 HIS   ( 728-)  C      N    CA   C   124.02    4.6
1187 LEU   ( 729-)  C     -CA  -C    N   125.67    4.7
1187 LEU   ( 729-)  C     -C    N    CA  111.69   -5.6
1187 LEU   ( 729-)  C      N    CA   C   122.40    4.0
1457 HIS   ( 999-)  C      CG   ND1  CE1 109.61    4.0
1466 ARG   (1008-)  C      CB   CG   CD  104.25   -4.9
1515 SER   (1057-)  C     -C    N    CA  113.48   -4.6
1577 ARG   (1119-)  C     -C    N    CA  129.18    4.2
1657 THR   (  81-)  D     -CA  -C    N   107.23   -4.5
1657 THR   (  81-)  D     -C    N    CA  133.78    6.7
1659 SER   (  83-)  D     -C    N    CA  130.92    5.1
1696 ALA   ( 120-)  D     -C    N    CA  129.22    4.2
1708 TYR   ( 132-)  D      CA   CB   CG  104.75   -4.7
1775 LEU   ( 199-)  D     -C    N    CA  113.49   -4.6
1775 LEU   ( 199-)  D      CA   CB   CG   94.72   -6.2
And so on for a total of 86 lines.

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.

  19 GLU   (  19-)  A
  73 GLU   (  73-)  A
  77 GLU   (  77-)  A
 108 GLU   ( 108-)  A
 126 ASP   ( 126-)  A
 182 GLU   ( 182-)  A
 202 ASP   ( 202-)  A
 216 GLU   ( 216-)  A
 220 GLU   ( 220-)  A
 248 GLU   (  19-)  B
 302 GLU   (  73-)  B
 337 GLU   ( 108-)  B
 362 GLU   ( 133-)  B
 363 GLU   ( 134-)  B
 383 GLU   ( 154-)  B
 411 GLU   ( 182-)  B
 445 GLU   ( 216-)  B
 491 ASP   (  33-)  C
 508 GLU   (  50-)  C
 515 GLU   (  57-)  C
 533 GLU   (  75-)  C
 539 ASP   (  81-)  C
 568 GLU   ( 110-)  C
 581 GLU   ( 123-)  C
 591 ASP   ( 133-)  C
And so on for a total of 232 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.

 622 PRO   ( 164-)  C      N     -6.2   -22.70    -2.48
 702 PRO   ( 244-)  C      N    -10.1   -35.76    -2.48
2589 PRO   (1125-)  D      N     -6.5   -23.78    -2.48
3277 PRO   ( 286-)  F      N      6.5    18.93    -2.48
4031 PRO   ( 164-)  M      N     -6.8   -24.81    -2.48
4111 PRO   ( 244-)  M      N    -12.1   -42.24    -2.48
6686 PRO   ( 286-)  P      N      6.7    19.35    -2.48
The average deviation= 0.779

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.

6082 LEU   (1209-)  N    5.78
2673 LEU   (1209-)  D    5.70
4596 LEU   ( 729-)  M    4.68
1187 LEU   ( 729-)  C    4.51
6430 GLY   (  53-)  O    4.18
1973 PRO   ( 509-)  D    4.14
1186 HIS   ( 728-)  C    4.14
 777 GLY   ( 319-)  C    4.10
3021 GLY   (  53-)  E    4.10
2574 ALA   (1110-)  D    4.09

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 : -5.530

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.

2593 THR   (1129-)  D    -3.6
6002 THR   (1129-)  N    -3.5
4134 TYR   ( 267-)  M    -3.5
 196 THR   ( 196-)  A    -3.4
3834 THR   ( 196-)  L    -3.4
 425 THR   ( 196-)  B    -3.3
3605 THR   ( 196-)  K    -3.3
 725 TYR   ( 267-)  C    -3.1
5193 PRO   ( 208-)  N    -3.1
1784 PRO   ( 208-)  D    -3.1
6419 PRO   (  42-)  O    -3.1
3010 PRO   (  42-)  E    -3.1
6080 TYR   (1207-)  N    -3.1
5998 PRO   (1125-)  N    -3.1
2589 PRO   (1125-)  D    -3.1
6553 PRO   ( 153-)  P    -3.1
3144 PRO   ( 153-)  F    -3.1
2671 TYR   (1207-)  D    -3.1
4031 PRO   ( 164-)  M    -3.0
 622 PRO   ( 164-)  C    -3.0
5813 THR   ( 940-)  N    -3.0
6477 THR   (  77-)  P    -3.0
 610 PRO   ( 152-)  C    -3.0
6317 THR   (1444-)  N    -3.0
3288 PRO   ( 297-)  F    -3.0
And so on for a total of 449 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.

   3 ASP   (   3-)  A  Poor phi/psi
  26 GLU   (  26-)  A  PRO omega poor
  59 GLU   (  59-)  A  Poor phi/psi
 118 ALA   ( 118-)  A  Poor phi/psi
 130 ALA   ( 130-)  A  Poor phi/psi
 133 GLU   ( 133-)  A  Poor phi/psi
 187 GLY   ( 187-)  A  Poor phi/psi
 188 GLN   ( 188-)  A  Poor phi/psi
 232 ASP   (   3-)  B  Poor phi/psi
 255 GLU   (  26-)  B  PRO omega poor
 288 GLU   (  59-)  B  Poor phi/psi
 347 ALA   ( 118-)  B  Poor phi/psi
 359 ALA   ( 130-)  B  Poor phi/psi
 362 GLU   ( 133-)  B  Poor phi/psi
 465 GLY   (   7-)  C  Poor phi/psi
 481 VAL   (  23-)  C  Poor phi/psi
 489 GLN   (  31-)  C  Poor phi/psi
 515 GLU   (  57-)  C  Poor phi/psi
 517 LYS   (  59-)  C  Poor phi/psi
 527 LEU   (  69-)  C  Poor phi/psi
 557 GLN   (  99-)  C  Poor phi/psi
 562 ASP   ( 104-)  C  Poor phi/psi
 569 ASP   ( 111-)  C  Poor phi/psi
 587 ILE   ( 129-)  C  Poor phi/psi
 588 ASN   ( 130-)  C  Poor phi/psi
And so on for a total of 445 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 : -4.978

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.

4429 SER   ( 562-)  M    0.33
6517 SER   ( 117-)  P    0.35
1661 VAL   (  85-)  D    0.35
6751 SER   ( 351-)  P    0.36
4269 SER   ( 402-)  M    0.36
3342 SER   ( 351-)  F    0.36
1009 GLU   ( 551-)  C    0.36
4418 GLU   ( 551-)  M    0.36
4488 VAL   ( 621-)  M    0.36
5370 GLU   ( 497-)  N    0.36
6374 GLU   (1501-)  N    0.36
5783 SER   ( 910-)  N    0.37
2900 SER   (1436-)  D    0.37
 483 SER   (  25-)  C    0.37
3892 SER   (  25-)  M    0.37
2374 SER   ( 910-)  D    0.38
6309 SER   (1436-)  N    0.38
3108 SER   ( 117-)  F    0.38
6748 SER   ( 348-)  P    0.39

Warning: Unusual backbone conformations

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

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

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

   3 ASP   (   3-)  A      0
   4 SER   (   4-)  A      0
   7 LYS   (   7-)  A      0
  16 GLN   (  16-)  A      0
  18 ARG   (  18-)  A      0
  19 GLU   (  19-)  A      0
  20 TYR   (  20-)  A      0
  25 LEU   (  25-)  A      0
  26 GLU   (  26-)  A      0
  29 GLU   (  29-)  A      0
  30 ARG   (  30-)  A      0
  32 PHE   (  32-)  A      0
  46 SER   (  46-)  A      0
  47 SER   (  47-)  A      0
  52 ALA   (  52-)  A      0
  53 VAL   (  53-)  A      0
  54 THR   (  54-)  A      0
  59 GLU   (  59-)  A      0
  60 ASP   (  60-)  A      0
  62 LEU   (  62-)  A      0
  69 PRO   (  69-)  A      0
  72 LYS   (  72-)  A      0
  73 GLU   (  73-)  A      0
  90 LEU   (  90-)  A      0
  95 GLN   (  95-)  A      0
And so on for a total of 2793 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.874

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!

5704 GLY   ( 831-)  N   2.63   10
4731 GLY   ( 864-)  M   2.08   18
1322 GLY   ( 864-)  C   2.04   21
1443 GLY   ( 985-)  C   1.97   11
4852 GLY   ( 985-)  M   1.96   11
2341 PRO   ( 877-)  D   1.83   16
1480 GLY   (1022-)  C   1.79   29
5750 PRO   ( 877-)  N   1.76   17
2161 GLY   ( 697-)  D   1.73   62
4889 GLY   (1022-)  M   1.72   32
5570 GLY   ( 697-)  N   1.67   63
2645 GLY   (1181-)  D   1.59   49
1256 GLY   ( 798-)  C   1.56   11
5923 GLY   (1050-)  N   1.56   67
2514 GLY   (1050-)  D   1.56   59
6054 GLY   (1181-)  N   1.56   52
4012 GLY   ( 145-)  M   1.55   14
5173 GLY   ( 188-)  N   1.55   12
1764 GLY   ( 188-)  D   1.54   12

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 719 ILE   ( 261-)  C   2.37
4127 LEU   ( 260-)  M   1.73
4128 ILE   ( 261-)  M   2.26
6261 ARG   (1388-)  N   1.71

Warning: Unusual PRO puckering amplitudes

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

 381 PRO   ( 152-)  B    0.45 HIGH
 636 PRO   ( 178-)  C    0.46 HIGH
 763 PRO   ( 305-)  C    0.45 HIGH
 835 PRO   ( 377-)  C    0.45 HIGH
 928 PRO   ( 470-)  C    0.45 HIGH
1713 PRO   ( 137-)  D    0.47 HIGH
1784 PRO   ( 208-)  D    0.47 HIGH
1802 PRO   ( 226-)  D    0.00 LOW
1814 PRO   ( 238-)  D    0.00 LOW
1822 PRO   ( 246-)  D    0.00 LOW
1824 PRO   ( 248-)  D    0.00 LOW
1837 PRO   ( 373-)  D    0.00 LOW
1973 PRO   ( 509-)  D    0.46 HIGH
2054 PRO   ( 590-)  D    0.46 HIGH
2099 PRO   ( 635-)  D    0.48 HIGH
2170 PRO   ( 706-)  D    0.48 HIGH
2194 PRO   ( 730-)  D    0.46 HIGH
2236 PRO   ( 772-)  D    0.47 HIGH
2245 PRO   ( 781-)  D    0.45 HIGH
2721 PRO   (1257-)  D    0.46 HIGH
2770 PRO   (1306-)  D    0.46 HIGH
3026 PRO   (  58-)  E    0.47 HIGH
3071 PRO   (  80-)  F    0.47 HIGH
3277 PRO   ( 286-)  F    0.47 HIGH
3332 PRO   ( 341-)  F    0.47 HIGH
And so on for a total of 56 lines.

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].

   9 PRO   (   9-)  A   106.0 envelop C-beta (108 degrees)
  92 PRO   (  92-)  A   105.5 envelop C-beta (108 degrees)
 474 PRO   (  16-)  C    25.6 half-chair N/C-delta (18 degrees)
 610 PRO   ( 152-)  C   100.0 envelop C-beta (108 degrees)
 702 PRO   ( 244-)  C    12.2 half-chair N/C-delta (18 degrees)
 979 PRO   ( 521-)  C    46.9 half-chair C-delta/C-gamma (54 degrees)
1136 PRO   ( 678-)  C    41.5 envelop C-delta (36 degrees)
1177 PRO   ( 719-)  C    99.1 envelop C-beta (108 degrees)
1185 PRO   ( 727-)  C   103.9 envelop C-beta (108 degrees)
1269 PRO   ( 811-)  C    41.9 envelop C-delta (36 degrees)
1312 PRO   ( 854-)  C    44.4 envelop C-delta (36 degrees)
1320 PRO   ( 862-)  C   104.5 envelop C-beta (108 degrees)
1324 PRO   ( 866-)  C    29.2 envelop C-delta (36 degrees)
1605 PRO   (  29-)  D    30.0 envelop C-delta (36 degrees)
1674 PRO   (  98-)  D   100.9 envelop C-beta (108 degrees)
1685 PRO   ( 109-)  D    47.7 half-chair C-delta/C-gamma (54 degrees)
1749 PRO   ( 173-)  D    40.6 envelop C-delta (36 degrees)
1784 PRO   ( 208-)  D   113.0 envelop C-beta (108 degrees)
1985 PRO   ( 521-)  D   109.6 envelop C-beta (108 degrees)
2027 PRO   ( 563-)  D  -112.3 envelop C-gamma (-108 degrees)
2058 PRO   ( 594-)  D   100.2 envelop C-beta (108 degrees)
2273 PRO   ( 809-)  D    52.7 half-chair C-delta/C-gamma (54 degrees)
2520 PRO   (1056-)  D   -28.0 envelop C-alpha (-36 degrees)
3010 PRO   (  42-)  E    99.9 envelop C-beta (108 degrees)
3014 PRO   (  46-)  E   114.0 envelop C-beta (108 degrees)
3144 PRO   ( 153-)  F   -50.0 half-chair C-beta/C-alpha (-54 degrees)
3288 PRO   ( 297-)  F   101.6 envelop C-beta (108 degrees)
3332 PRO   ( 341-)  F   118.1 half-chair C-beta/C-alpha (126 degrees)
3458 PRO   (  49-)  K    51.5 half-chair C-delta/C-gamma (54 degrees)
3883 PRO   (  16-)  M    35.6 envelop C-delta (36 degrees)
4019 PRO   ( 152-)  M    99.1 envelop C-beta (108 degrees)
4111 PRO   ( 244-)  M    36.9 envelop C-delta (36 degrees)
4131 PRO   ( 264-)  M    36.9 envelop C-delta (36 degrees)
4415 PRO   ( 548-)  M    99.8 envelop C-beta (108 degrees)
4545 PRO   ( 678-)  M    30.5 envelop C-delta (36 degrees)
4733 PRO   ( 866-)  M    47.1 half-chair C-delta/C-gamma (54 degrees)
4879 PRO   (1012-)  M    50.8 half-chair C-delta/C-gamma (54 degrees)
5094 PRO   ( 109-)  N    30.3 envelop C-delta (36 degrees)
5158 PRO   ( 173-)  N    36.3 envelop C-delta (36 degrees)
5193 PRO   ( 208-)  N   141.8 envelop C-alpha (144 degrees)
5394 PRO   ( 521-)  N   117.4 half-chair C-beta/C-alpha (126 degrees)
5467 PRO   ( 594-)  N    99.5 envelop C-beta (108 degrees)
5579 PRO   ( 706-)  N    36.6 envelop C-delta (36 degrees)
5998 PRO   (1125-)  N    50.4 half-chair C-delta/C-gamma (54 degrees)
6419 PRO   (  42-)  O   106.0 envelop C-beta (108 degrees)
6423 PRO   (  46-)  O   104.0 envelop C-beta (108 degrees)
6492 PRO   (  92-)  P    52.8 half-chair C-delta/C-gamma (54 degrees)
6553 PRO   ( 153-)  P   -42.1 envelop C-alpha (-36 degrees)
6734 PRO   ( 334-)  P    11.7 half-chair N/C-delta (18 degrees)
6741 PRO   ( 341-)  P   121.0 half-chair C-beta/C-alpha (126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

6907  MG   (9345-)  C     MG   <-> 6955  MG   (9534-)  C     MG      0.69    2.51  INTRA BL
6990  MG   (9261-)  D     MG   <-> 7107  MG   (9546-)  D     MG      0.67    2.53  INTRA BL
6828  MG   (9327-)  A     MG   <-> 6838  MG   (9464-)  A     MG      0.66    2.54  INTRA BL
6896  MG   (9299-)  C     MG   <-> 6925  MG   (9397-)  C     MG      0.59    2.61  INTRA BL
7019  MG   (9336-)  D     MG   <-> 7036  MG   (9372-)  D     MG      0.58    2.62  INTRA BL
7094  MG   (9512-)  D     MG   <-> 7101  MG   (9529-)  D     MG      0.57    2.63  INTRA BL
6908  MG   (9346-)  C     MG   <-> 6918  MG   (9378-)  C     MG      0.56    2.64  INTRA BL
7114  MG   (9249-)  E     MG   <-> 7127  MG   (9484-)  E     MG      0.55    2.65  INTRA BL
2836 VAL   (1372-)  D      CA  <-> 6967  MG   (9208-)  D     MG      0.53    2.67  INTRA BL
6982  MG   (9241-)  D     MG   <-> 6992  MG   (9265-)  D     MG      0.53    2.67  INTRA BL
6884  MG   (9259-)  P     MG   <-> 6951  MG   (9519-)  P     MG      0.51    2.69  INTRA BL
1632 TYR   (  56-)  D      CD1 <-> 7083  MG   (9481-)  D     MG      0.48    2.72  INTRA BF
1896 TYR   ( 432-)  D      CD2 <-> 6973  MG   (9220-)  D     MG      0.48    2.72  INTRA BF
6865  MG   (9488-)  B     MG   <-> 6869  MG   (9560-)  B     MG      0.48    2.72  INTRA BL
7134  MG   (9250-)  F     MG   <-> 7155  MG   (9407-)  F     MG      0.43    2.77  INTRA BL
2839 MET   (1375-)  D      CE  <-> 6967  MG   (9208-)  D     MG      0.42    2.78  INTRA BL
1796 ARG   ( 220-)  D      C   <-> 7111  MG   (9557-)  D     MG      0.40    2.80  INTRA BF
2200 PHE   ( 736-)  D      CA  <-> 6988  MG   (9253-)  D     MG      0.40    2.80  INTRA BL
2332 TYR   ( 868-)  D      CD1 <-> 7072  MG   (9460-)  D     MG      0.40    2.80  INTRA BF
 836 LEU   ( 378-)  C      CB  <-> 6924  MG   (9396-)  C     MG      0.40    2.80  INTRA BF
1974 GLU   ( 510-)  D      C   <-> 6972  MG   (9218-)  D     MG      0.39    2.81  INTRA BF
2527 GLU   (1063-)  D      CB  <-> 6977  MG   (9233-)  D     MG      0.39    2.81  INTRA BL
2270 PHE   ( 806-)  D      O   <-> 2272 THR   ( 808-)  D      N      0.39    2.31  INTRA BF
7045  MG   (9392-)  D     MG   <-> 7095  MG   (9515-)  D     MG      0.39    2.81  INTRA BL
2103 LEU   ( 639-)  D      CB  <-> 6980  MG   (9237-)  D     MG      0.39    2.81  INTRA BL
And so on for a total of 3131 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

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.

 701 ARG   ( 243-)  C      -8.57
4110 ARG   ( 243-)  M      -8.40
4021 ARG   ( 154-)  M      -8.28
5060 ARG   (  75-)  N      -8.07
1651 ARG   (  75-)  D      -7.96
4289 ARG   ( 422-)  M      -7.91
6112 ARG   (1239-)  N      -7.76
 185 ARG   ( 185-)  A      -7.73
5460 ARG   ( 587-)  N      -7.72
6684 ARG   ( 284-)  P      -7.67
 880 ARG   ( 422-)  C      -7.65
6191 TYR   (1318-)  N      -7.64
3275 ARG   ( 284-)  F      -7.64
1739 TYR   ( 163-)  D      -7.55
 612 ARG   ( 154-)  C      -7.54
1266 ARG   ( 808-)  C      -7.52
2703 ARG   (1239-)  D      -7.47
6200 ARG   (1327-)  N      -7.23
2791 ARG   (1327-)  D      -7.22
2051 ARG   ( 587-)  D      -7.19
3594 ARG   ( 185-)  K      -7.16
3939 ARG   (  72-)  M      -6.99
 626 ARG   ( 168-)  C      -6.99
4675 ARG   ( 808-)  M      -6.97
2730 ARG   (1266-)  D      -6.92
And so on for a total of 292 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.

 466 ARG   (   8-)  C       468 - ARG     10- ( C)         -5.07
 515 GLU   (  57-)  C       519 - LYS     61- ( C)         -5.11
 530 ARG   (  72-)  C       533 - GLU     75- ( C)         -5.34
 561 LYS   ( 103-)  C       563 - THR    105- ( C)         -4.83
 750 ARG   ( 292-)  C       752 - GLU    294- ( C)         -4.95
1222 GLU   ( 764-)  C      1224 - GLU    766- ( C)         -4.69
1265 ARG   ( 807-)  C      1267 - GLY    809- ( C)         -5.79
1638 LYS   (  62-)  D      1640 - LYS     64- ( D)         -4.84
1790 GLU   ( 214-)  D      1792 - VAL    216- ( D)         -5.33
2263 LYS   ( 799-)  D      2265 - GLY    801- ( D)         -4.56
2752 GLU   (1288-)  D      2754 - LEU   1290- ( D)         -4.46
2851 SER   (1387-)  D      2854 - LEU   1390- ( D)         -4.47
3017 GLN   (  49-)  E      3019 - LEU     51- ( E)         -5.09
3059 ARG   (  91-)  E      3061 - TYR     93- ( E)         -4.41
3271 GLN   ( 280-)  F      3273 - LEU    282- ( F)         -4.98
3925 ASP   (  58-)  M      3928 - LYS     61- ( M)         -5.37
3939 ARG   (  72-)  M      3942 - GLU     75- ( M)         -5.33
3970 LYS   ( 103-)  M      3972 - THR    105- ( M)         -4.82
4159 ARG   ( 292-)  M      4161 - GLU    294- ( M)         -4.89
4253 PHE   ( 386-)  M      4255 - ARG    388- ( M)         -4.10
4631 GLU   ( 764-)  M      4633 - GLU    766- ( M)         -4.82
4674 ARG   ( 807-)  M      4676 - GLY    809- ( M)         -5.66
5199 GLU   ( 214-)  N      5201 - VAL    216- ( N)         -5.07
6426 GLN   (  49-)  O      6428 - LEU     51- ( O)         -4.63

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 6818 : -1.436

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: 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

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: M

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: N

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: O

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: P

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.

1794 LYS   ( 218-)  D   -4.06
1793 LYS   ( 217-)  D   -3.80
5202 LYS   ( 217-)  N   -3.73
5205 ARG   ( 220-)  N   -3.71
4186 GLY   ( 319-)  M   -3.59
1796 ARG   ( 220-)  D   -3.55
1800 ARG   ( 224-)  D   -3.51
 878 ARG   ( 420-)  C   -3.49
5209 ARG   ( 224-)  N   -3.42
5203 LYS   ( 218-)  N   -3.42
1851 LEU   ( 387-)  D   -3.38
1186 HIS   ( 728-)  C   -3.37
5212 LEU   ( 227-)  N   -3.33
1814 PRO   ( 238-)  D   -3.31
1799 LEU   ( 223-)  D   -3.26
5260 LEU   ( 387-)  N   -3.25
1850 HIS   ( 386-)  D   -3.24
5208 LEU   ( 223-)  N   -3.16
5234 TYR   ( 249-)  N   -3.13
6737 HIS   ( 337-)  P   -3.11
5229 GLU   ( 244-)  N   -3.11
1820 GLU   ( 244-)  D   -3.10
 934 GLY   ( 476-)  C   -3.07
1795 GLU   ( 219-)  D   -3.05
1852 HIS   ( 388-)  D   -3.03
And so on for a total of 101 lines.

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.

 154 GLU   ( 154-)  A     -  157 GLY   ( 157-)  A        -1.57
 383 GLU   ( 154-)  B     -  386 GLY   ( 157-)  B        -1.60
 463 ARG   (   5-)  C     -  468 ARG   (  10-)  C        -2.16
 476 LEU   (  18-)  C     -  479 ILE   (  21-)  C        -1.90
 623 LEU   ( 165-)  C     -  627 GLY   ( 169-)  C        -2.24
 671 ALA   ( 213-)  C     -  675 LEU   ( 217-)  C        -1.91
 816 ARG   ( 358-)  C     -  820 GLY   ( 362-)  C        -2.17
1219 PHE   ( 761-)  C     - 1222 GLU   ( 764-)  C        -1.41
1718 LEU   ( 142-)  D     - 1721 VAL   ( 145-)  D        -1.74
1790 GLU   ( 214-)  D     - 1796 ARG   ( 220-)  D        -2.91
1798 GLY   ( 222-)  D     - 1803 LEU   ( 227-)  D        -2.63
1805 ALA   ( 229-)  D     - 1814 PRO   ( 238-)  D        -2.34
1815 GLY   ( 239-)  D     - 1818 LEU   ( 242-)  D        -2.19
1824 PRO   ( 248-)  D     - 1827 PHE   ( 251-)  D        -2.19
1828 GLY   ( 364-)  D     - 1838 GLU   ( 374-)  D        -2.23
1839 GLU   ( 375-)  D     - 1844 GLU   ( 380-)  D        -2.29
1845 ALA   ( 381-)  D     - 1852 HIS   ( 388-)  D        -2.51
1880 ALA   ( 416-)  D     - 1883 ASP   ( 419-)  D        -1.79
2049 GLY   ( 585-)  D     - 2052 GLY   ( 588-)  D        -1.71
2196 VAL   ( 732-)  D     - 2199 ALA   ( 735-)  D        -1.95
2731 ARG   (1267-)  D     - 2736 ALA   (1272-)  D        -1.84
2965 GLU   (1501-)  D     - 2969 ALA   (1505-)  D        -1.97
3021 GLY   (  53-)  E     - 3024 ASP   (  56-)  E        -1.84
3244 ASP   ( 253-)  F     - 3247 ARG   ( 256-)  F        -1.79
3326 ASP   ( 335-)  F     - 3329 LEU   ( 338-)  F        -2.07
3369 GLY   ( 378-)  F     - 3373 GLY   ( 387-)  F        -2.07
3564 LYS   ( 155-)  K     - 3568 LYS   ( 159-)  K        -2.08
3593 THR   ( 184-)  K     - 3597 GLN   ( 188-)  K        -1.93
4032 LEU   ( 165-)  M     - 4036 GLY   ( 169-)  M        -2.11
4160 PHE   ( 293-)  M     - 4164 GLU   ( 297-)  M        -1.80
4284 GLY   ( 417-)  M     - 4287 ARG   ( 420-)  M        -2.00
4593 ILE   ( 726-)  M     - 4596 LEU   ( 729-)  M        -1.69
4865 TYR   ( 998-)  M     - 4868 VAL   (1001-)  M        -2.12
5111 VAL   ( 126-)  N     - 5114 PHE   ( 129-)  N        -1.68
5199 GLU   ( 214-)  N     - 5205 ARG   ( 220-)  N        -2.81
5207 GLY   ( 222-)  N     - 5210 LEU   ( 225-)  N        -2.39
5214 ALA   ( 229-)  N     - 5223 PRO   ( 238-)  N        -2.21
5224 GLY   ( 239-)  N     - 5227 LEU   ( 242-)  N        -1.97
5233 PRO   ( 248-)  N     - 5236 PHE   ( 251-)  N        -2.42
5237 GLY   ( 364-)  N     - 5241 VAL   ( 368-)  N        -2.16
5242 ALA   ( 369-)  N     - 5251 ILE   ( 378-)  N        -2.17
5256 GLY   ( 383-)  N     - 5261 HIS   ( 388-)  N        -2.21
5311 ASP   ( 438-)  N     - 5315 ASN   ( 442-)  N        -1.66
5580 THR   ( 707-)  N     - 5584 LEU   ( 711-)  N        -1.76
5693 GLU   ( 820-)  N     - 5696 LEU   ( 823-)  N        -1.89
5739 VAL   ( 866-)  N     - 5742 MET   ( 869-)  N        -1.46
6159 THR   (1286-)  N     - 6162 LYS   (1289-)  N        -1.71
6782 GLY   ( 387-)  P     - 6785 PHE   ( 390-)  P        -2.14

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

7187 HOH   (9693 )  A      O    214.97   15.15   48.58
7187 HOH   (9781 )  A      O      8.78   15.71   36.41
7187 HOH   (9822 )  A      O     30.00   26.47   16.58
7187 HOH   (9824 )  A      O     12.91   13.43   24.99
7187 HOH   (9829 )  A      O     26.06   19.16   17.52
7187 HOH   (9835 )  A      O     22.16   33.81   38.02
7187 HOH   (9846 )  A      O    205.20    4.75   41.68
7188 HOH   (9666 )  B      O    192.25   -7.97   75.57
7188 HOH   (9673 )  B      O    207.81    1.44   63.37
7188 HOH   (9712 )  B      O    200.83   10.73   78.73
7188 HOH   (9747 )  B      O    197.80  -11.98   65.86
7188 HOH   (9753 )  B      O    192.92  -15.19   90.54
7188 HOH   (9781 )  B      O    196.02   -7.97   72.48
7188 HOH   (9794 )  B      O    190.63  -13.55   93.80
7188 HOH   (9807 )  B      O    193.55  -32.26   84.25
7188 HOH   (9840 )  B      O     -1.65   15.83   31.49
7188 HOH   (9853 )  B      O    196.19   -8.47   62.35
7188 HOH   (9858 )  B      O    197.31  -20.34   71.27
7189 HOH   (2090 )  C      O    160.72   24.19   17.60
7189 HOH   (2097 )  C      O    187.18   44.06   47.38
7189 HOH   (2103 )  C      O    189.74   31.58   37.99
7189 HOH   (2104 )  C      O    164.71   24.08   21.91
7189 HOH   (2164 )  C      O    176.05   31.45   41.99
7189 HOH   (2252 )  C      O    185.25   46.58   47.42
7189 HOH   (2361 )  C      O    166.43   25.77   17.69
And so on for a total of 290 lines.

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

7187 HOH   (9579 )  A      O
7187 HOH   (9584 )  A      O
7187 HOH   (9609 )  A      O
7187 HOH   (9632 )  A      O
7187 HOH   (9646 )  A      O
7187 HOH   (9660 )  A      O
7187 HOH   (9672 )  A      O
7187 HOH   (9687 )  A      O
7187 HOH   (9695 )  A      O
7187 HOH   (9725 )  A      O
7187 HOH   (9736 )  A      O
7187 HOH   (9747 )  A      O
7187 HOH   (9756 )  A      O
7187 HOH   (9768 )  A      O
7187 HOH   (9773 )  A      O
7187 HOH   (9782 )  A      O
7187 HOH   (9792 )  A      O
7187 HOH   (9804 )  A      O
7187 HOH   (9822 )  A      O
7187 HOH   (9825 )  A      O
7187 HOH   (9827 )  A      O
7187 HOH   (9829 )  A      O
7187 HOH   (9832 )  A      O
7187 HOH   (9838 )  A      O
7188 HOH   (9572 )  B      O
And so on for a total of 574 lines.

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.

  16 GLN   (  16-)  A
  63 HIS   (  63-)  A
  91 ASN   (  91-)  A
 128 HIS   ( 128-)  A
 139 ASN   ( 139-)  A
 212 ASN   ( 212-)  A
 245 GLN   (  16-)  B
 267 ASN   (  38-)  B
 409 GLN   ( 180-)  B
 499 ASN   (  41-)  C
 637 ASN   ( 179-)  C
 864 HIS   ( 406-)  C
 964 ASN   ( 506-)  C
 996 GLN   ( 538-)  C
1121 ASN   ( 663-)  C
1129 ASN   ( 671-)  C
1162 HIS   ( 704-)  C
1299 ASN   ( 841-)  C
1301 HIS   ( 843-)  C
1330 ASN   ( 872-)  C
1339 ASN   ( 881-)  C
1701 GLN   ( 125-)  D
1719 ASN   ( 143-)  D
1926 GLN   ( 462-)  D
2024 GLN   ( 560-)  D
And so on for a total of 85 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.

   6 LEU   (   6-)  A      N
  18 ARG   (  18-)  A      NE
  18 ARG   (  18-)  A      NH1
  26 GLU   (  26-)  A      N
  38 ASN   (  38-)  A      ND2
  41 ARG   (  41-)  A      NE
  41 ARG   (  41-)  A      NH2
  42 ARG   (  42-)  A      NH1
  51 THR   (  51-)  A      N
  51 THR   (  51-)  A      OG1
  55 SER   (  55-)  A      N
  60 ASP   (  60-)  A      N
  61 VAL   (  61-)  A      N
  63 HIS   (  63-)  A      N
  68 ILE   (  68-)  A      N
  86 VAL   (  86-)  A      N
  87 VAL   (  87-)  A      N
  88 ARG   (  88-)  A      NE
  89 PHE   (  89-)  A      N
 100 LEU   ( 100-)  A      N
 124 ASN   ( 124-)  A      N
 149 GLY   ( 149-)  A      N
 154 GLU   ( 154-)  A      N
 161 ARG   ( 161-)  A      N
 163 ASN   ( 163-)  A      N
And so on for a total of 1086 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.

  64 GLU   (  64-)  A      OE2
 121 GLU   ( 121-)  A      OE1
 212 ASN   ( 212-)  A      OD1
 480 GLN   (  22-)  C      OE1
 489 GLN   (  31-)  C      OE1
 514 GLU   (  56-)  C      OE1
 597 GLN   ( 139-)  C      OE1
 900 GLU   ( 442-)  C      OE2
1001 ASN   ( 543-)  C      OD1
1003 ASN   ( 545-)  C      OD1
1009 GLU   ( 551-)  C      OE1
1023 GLN   ( 565-)  C      OE1
1042 GLU   ( 584-)  C      OE2
1065 ASP   ( 607-)  C      OD1
1128 GLN   ( 670-)  C      OE1
1129 ASN   ( 671-)  C      OD1
1242 ASP   ( 784-)  C      OD1
1345 GLU   ( 887-)  C      OE1
1395 ASP   ( 937-)  C      OD1
1427 GLN   ( 969-)  C      OE1
1457 HIS   ( 999-)  C      ND1
1461 ASP   (1003-)  C      OD1
1492 GLU   (1034-)  C      OE1
1541 GLU   (1083-)  C      OE1
1541 GLU   (1083-)  C      OE2
And so on for a total of 117 lines.

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

6819  MG   (9209-)  A   -.-  -.-  Too few ligands (3)
6820  MG   (9212-)  A     0.26   1.00 Is perhaps  K
6821  MG   (9224-)  C   -.-  -.-  Too few ligands (3)
6822  MG   (9227-)  A   -.-  -.-  Too few ligands (2)
6823  MG   (9254-)  A   -.-  -.-  Too few ligands (2)
6824  MG   (9268-)  A   -.-  -.-  Part of ionic cluster
6824  MG   (9268-)  A   -.-  -.-  Too few ligands (2)
6825  MG   (9273-)  A     0.34   1.50 Scores about as good as  K (Few ligands (4) )
6826  MG   (9295-)  A   -.-  -.-  Too few ligands (0)
6827  MG   (9318-)  A   -.-  -.-  Too few ligands (0)
6828  MG   (9327-)  A   -.-  -.-  Part of ionic cluster
6828  MG   (9327-)  A   -.-  -.-  Too few ligands (0)
6829  MG   (9329-)  P   -.-  -.-  Too few ligands (1)
6830  MG   (9334-)  A   -.-  -.-  Too few ligands (2)
6831  MG   (9365-)  A   -.-  -.-  Too few ligands (1)
6832  MG   (9368-)  A   -.-  -.-  Too few ligands (1)
6833  MG   (9394-)  A   -.-  -.-  Part of ionic cluster
6833  MG   (9394-)  A   -.-  -.-  Too few ligands (1)
6834  MG   (9423-)  A   -.-  -.-  Part of ionic cluster
6834  MG   (9423-)  A   -.-  -.-  Too few ligands (3)
6835  MG   (9437-)  A   -.-  -.-  Part of ionic cluster
6835  MG   (9437-)  A   -.-  -.-  Too few ligands (1)
6836  MG   (9442-)  A   -.-  -.-  Too few ligands (2)
6837  MG   (9462-)  A   -.-  -.-  Too few ligands (2)
6838  MG   (9464-)  A   -.-  -.-  Part of ionic cluster
And so on for a total of 463 lines.

Warning: Unusual water packing

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

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

7188 HOH   (9595 )  B      O  0.98  K  5 Ion-B
7189 HOH   (2172 )  C      O  1.05  K  4 H2O-B
7189 HOH   (2297 )  C      O  0.88  K  4 Ion-B H2O-B
7189 HOH   (2461 )  C      O  0.94  K  5 ION-B
7189 HOH   (2683 )  C      O  1.06  K  4 ION-B H2O-B
7189 HOH   (9670 )  C      O  1.11  K  5
7189 HOH   (9692 )  C      O  0.86  K  6
7189 HOH   (9707 )  C      O  0.91  K  4 H2O-B
7189 HOH   (9889 )  C      O  1.08  K  6
7190 HOH   (2095 )  D      O  0.85  K  6 Ion-B
7190 HOH   (2247 )  D      O  1.07  K  4
7190 HOH   (2333 )  D      O  1.14  K  4
7190 HOH   (2347 )  D      O  1.06  K  4 Ion-B H2O-B
7190 HOH   (2580 )  D      O  0.94  K  4
7190 HOH   (3307 )  D      O  1.09  K  4 Ion-B H2O-B
7190 HOH   (9731 )  D      O  0.91  K  5 Ion-B
7190 HOH   (9834 )  D      O  0.92  K  4 H2O-B
7190 HOH   (9920 )  D      O  0.96  K  4
7191 HOH   (9586 )  E      O  0.94  K  4 H2O-B
7191 HOH   (9603 )  E      O  1.05  K  4 H2O-B
7192 HOH   (9812 )  F      O  1.15  K  6
7193 HOH   (1230 )  K      O  0.94  K  4 H2O-B
7194 HOH   (1055 )  L      O  0.87  K  5 H2O-B
7194 HOH   (1604 )  L      O  1.09  K  5
7194 HOH   (3023 )  L      O  1.00  K  7 H2O-B
And so on for a total of 53 lines.

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.

  59 GLU   (  59-)  A   H-bonding suggests Gln
 133 GLU   ( 133-)  A   H-bonding suggests Gln
 288 GLU   (  59-)  B   H-bonding suggests Gln
 303 ASP   (  74-)  B   H-bonding suggests Asn
 431 ASP   ( 202-)  B   H-bonding suggests Asn; but Alt-Rotamer
 469 GLU   (  11-)  C   H-bonding suggests Gln; but Alt-Rotamer
 570 GLU   ( 112-)  C   H-bonding suggests Gln
 631 ASP   ( 173-)  C   H-bonding suggests Asn
 661 ASP   ( 203-)  C   H-bonding suggests Asn
 721 ASP   ( 263-)  C   H-bonding suggests Asn
 729 GLU   ( 271-)  C   H-bonding suggests Gln
 784 ASP   ( 326-)  C   H-bonding suggests Asn; but Alt-Rotamer
 887 ASP   ( 429-)  C   H-bonding suggests Asn; but Alt-Rotamer
 991 ASP   ( 533-)  C   H-bonding suggests Asn
1011 ASP   ( 553-)  C   H-bonding suggests Asn
1058 ASP   ( 600-)  C   H-bonding suggests Asn; but Alt-Rotamer
1111 ASP   ( 653-)  C   H-bonding suggests Asn; but Alt-Rotamer
1115 ASP   ( 657-)  C   H-bonding suggests Asn; but Alt-Rotamer
1144 ASP   ( 686-)  C   H-bonding suggests Asn; but Alt-Rotamer
1254 GLU   ( 796-)  C   H-bonding suggests Gln
1268 ASP   ( 810-)  C   H-bonding suggests Asn
1272 GLU   ( 814-)  C   H-bonding suggests Gln
1314 GLU   ( 856-)  C   H-bonding suggests Gln
1315 ASP   ( 857-)  C   H-bonding suggests Asn
1326 ASP   ( 868-)  C   H-bonding suggests Asn
And so on for a total of 155 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 :  -2.339
  2nd generation packing quality :  -4.022 (bad)
  Ramachandran plot appearance   :  -5.530 (bad)
  chi-1/chi-2 rotamer normality  :  -4.978 (bad)
  Backbone conformation          :  -0.632

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.572 (tight)
  Bond angles                    :   0.783
  Omega angle restraints         :   0.341 (tight)
  Side chain planarity           :   0.135 (tight)
  Improper dihedral distribution :   0.699
  B-factor distribution          :   0.407
  Inside/Outside distribution    :   1.074

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.5
  2nd generation packing quality :  -2.2
  Ramachandran plot appearance   :  -2.4
  chi-1/chi-2 rotamer normality  :  -2.5
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.572 (tight)
  Bond angles                    :   0.783
  Omega angle restraints         :   0.341 (tight)
  Side chain planarity           :   0.135 (tight)
  Improper dihedral distribution :   0.699
  B-factor distribution          :   0.407
  Inside/Outside distribution    :   1.074
==============

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.