WHAT IF Check report

This file was created 2012-01-12 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 pdb1r5i.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 138.286  B   = 178.814  C    = 179.554
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 138.286  B   = 144.341  C    = 144.341
    Alpha=  76.922  Beta= 118.622  Gamma= 118.622

Dimensions of the conventional cell

    A    = 179.554  B   = 178.814  C    = 138.286
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  0.000000 -1.000000|
 |  0.000000 -1.000000  0.000000|
 |  1.000000  0.000000  0.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: I 2 2 2

Bravais type of conventional cell is: I

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.789
CA-only RMS fit for the two chains : 0.253

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and F

All-atom RMS fit for the two chains : 0.517
CA-only RMS fit for the two chains : 0.161

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 G

All-atom RMS fit for the two chains : 0.945
CA-only RMS fit for the two chains : 0.261

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: C and G

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 H

All-atom RMS fit for the two chains : 0.845
CA-only RMS fit for the two chains : 0.093

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

1205 PO4   ( 202-)  D  C

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.

1205 PO4   ( 202-)  D  C
1206 PO4   ( 214-)  D  -
1207 PO4   ( 204-)  E  -
1208 PO4   ( 214-)  H  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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'.

 971 LYS   ( 307-)  G      CG
 971 LYS   ( 307-)  G      CD
 971 LYS   ( 307-)  G      CE
 971 LYS   ( 307-)  G      NZ

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.

 288 GLN   ( 107-)  B    High
 289 PRO   ( 108-)  B    High
 290 LEU   ( 109-)  B    High
 291 GLN   ( 110-)  B    High
 292 HIS   ( 111-)  B    High
 293 HIS   ( 112-)  B    High
 886 GLN   ( 107-)  F    High
 887 PRO   ( 108-)  F    High
 888 LEU   ( 109-)  F    High
 889 GLN   ( 110-)  F    High
 890 HIS   ( 111-)  F    High

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: G

Note: B-factor plot

Chain identifier: H

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 123 ARG   ( 123-)  A
 187 ARG   (   6-)  B
 206 ARG   (  25-)  B
 236 ARG   (  55-)  B
 253 ARG   (  72-)  B
 314 ARG   ( 133-)  B
 370 ARG   ( 189-)  B
 539 ARG   ( 154-)  D
 648 ARG   (  50-)  E
 721 ARG   ( 123-)  E
 785 ARG   (   6-)  F
 804 ARG   (  25-)  F
 834 ARG   (  55-)  F
 850 ARG   (  71-)  F
 851 ARG   (  72-)  F
 872 ARG   (  93-)  F
 909 ARG   ( 130-)  F
 968 ARG   ( 189-)  F
1040 ARG   (  57-)  H

Warning: Tyrosine convention problem

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

 150 TYR   ( 150-)  A
 228 TYR   (  47-)  B
 374 TYR   ( 308-)  C
 418 TYR   (  33-)  D
 457 TYR   (  72-)  D
 579 TYR   ( 194-)  D
 881 TYR   ( 102-)  F
1016 TYR   (  33-)  H
1055 TYR   (  72-)  H
1177 TYR   ( 194-)  H

Warning: Phenylalanine convention problem

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

 112 PHE   ( 112-)  A
 221 PHE   (  40-)  B
 445 PHE   (  60-)  D
 506 PHE   ( 121-)  D
 552 PHE   ( 167-)  D
 596 PHE   ( 211-)  D
 624 PHE   (  26-)  E
 706 PHE   ( 108-)  E
 710 PHE   ( 112-)  E
 778 PHE   ( 180-)  E
1038 PHE   (  55-)  H
1043 PHE   (  60-)  H
1104 PHE   ( 121-)  H

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.

  25 ASP   (  25-)  A
  35 ASP   (  35-)  A
 159 ASP   ( 159-)  A
 162 ASP   ( 162-)  A
 181 ASP   ( 181-)  A
 183 ASP   (   2-)  B
 257 ASP   (  76-)  B
 333 ASP   ( 152-)  B
 500 ASP   ( 115-)  D
 502 ASP   ( 117-)  D
 598 ASP   ( 213-)  D
 615 ASP   (  17-)  E
 623 ASP   (  25-)  E
 708 ASP   ( 110-)  E
 781 ASP   (   2-)  F
 931 ASP   ( 152-)  F
1116 ASP   ( 133-)  H
1138 ASP   ( 155-)  H
1196 ASP   ( 213-)  H

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.

  21 GLU   (  21-)  A
  30 GLU   (  30-)  A
  40 GLU   (  40-)  A
  46 GLU   (  46-)  A
  55 GLU   (  55-)  A
  71 GLU   (  71-)  A
  88 GLU   (  88-)  A
  98 GLU   (  98-)  A
 158 GLU   ( 158-)  A
 172 GLU   ( 172-)  A
 179 GLU   ( 179-)  A
 233 GLU   (  52-)  B
 268 GLU   (  87-)  B
 318 GLU   ( 137-)  B
 319 GLU   ( 138-)  B
 343 GLU   ( 162-)  B
 357 GLU   ( 176-)  B
 424 GLU   (  39-)  D
 456 GLU   (  71-)  D
 459 GLU   (  74-)  D
 483 GLU   (  98-)  D
 515 GLU   ( 130-)  D
 619 GLU   (  21-)  E
 628 GLU   (  30-)  E
 696 GLU   (  98-)  E
 699 GLU   ( 101-)  E
 764 GLU   ( 166-)  E
 770 GLU   ( 172-)  E
 793 GLU   (  14-)  F
 848 GLU   (  69-)  F
 866 GLU   (  87-)  F
 916 GLU   ( 137-)  F
 941 GLU   ( 162-)  F
 955 GLU   ( 176-)  F
 989 GLU   (   6-)  H
1013 GLU   (  30-)  H
1022 GLU   (  39-)  H
1023 GLU   (  40-)  H
1026 GLU   (  43-)  H
1057 GLU   (  74-)  H
1092 GLU   ( 109-)  H
1124 GLU   ( 141-)  H
1140 GLU   ( 157-)  H

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

 |  0.998405 -0.000007 -0.000123|
 | -0.000007  0.998046  0.000061|
 | -0.000123  0.000061  0.997765|
Proposed new scale matrix

 |  0.007243  0.000000  0.000000|
 |  0.000000  0.005603  0.000000|
 |  0.000000  0.000000  0.005581|
With corresponding cell

    A    = 138.073  B   = 178.477  C    = 179.164
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 138.286  B   = 178.814  C    = 179.554
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 154.520
(Under-)estimated Z-score: 9.161

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.

 294 ASN   ( 113-)  B      N    CA   C   122.51    4.0
 892 ASN   ( 113-)  F      N    CA   C   123.07    4.2

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.

  21 GLU   (  21-)  A
  25 ASP   (  25-)  A
  30 GLU   (  30-)  A
  35 ASP   (  35-)  A
  40 GLU   (  40-)  A
  46 GLU   (  46-)  A
  55 GLU   (  55-)  A
  71 GLU   (  71-)  A
  88 GLU   (  88-)  A
  98 GLU   (  98-)  A
 123 ARG   ( 123-)  A
 158 GLU   ( 158-)  A
 159 ASP   ( 159-)  A
 162 ASP   ( 162-)  A
 172 GLU   ( 172-)  A
 179 GLU   ( 179-)  A
 181 ASP   ( 181-)  A
 183 ASP   (   2-)  B
 187 ARG   (   6-)  B
 206 ARG   (  25-)  B
 233 GLU   (  52-)  B
 236 ARG   (  55-)  B
 253 ARG   (  72-)  B
 257 ASP   (  76-)  B
 268 GLU   (  87-)  B
And so on for a total of 81 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.

 585 LEU   ( 200-)  D    6.18
1183 LEU   ( 200-)  H    5.81
 560 GLU   ( 175-)  D    5.52
1158 GLU   ( 175-)  H    5.48
 742 LEU   ( 144-)  E    4.39
 210 ARG   (  29-)  B    4.37
1168 LYS   ( 185-)  H    4.31
 570 LYS   ( 185-)  D    4.17
 295 LEU   ( 114-)  B    4.12
 644 GLU   (  46-)  E    4.09
 144 LEU   ( 144-)  A    4.06

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 936 THR   ( 157-)  F    -2.6
 113 THR   ( 113-)  A    -2.5
 711 THR   ( 113-)  E    -2.5
 338 THR   ( 157-)  B    -2.4
 281 THR   ( 100-)  B    -2.4
 180 PHE   ( 180-)  A    -2.4
 690 LEU   (  92-)  E    -2.4
  92 LEU   (  92-)  A    -2.4
 210 ARG   (  29-)  B    -2.4
 100 ARG   ( 100-)  A    -2.4
 290 LEU   ( 109-)  B    -2.3
 208 LEU   (  27-)  B    -2.3
 269 SER   (  88-)  B    -2.3
 614 PRO   (  16-)  E    -2.3
 806 LEU   (  27-)  F    -2.3
 964 THR   ( 185-)  F    -2.3
 136 VAL   ( 136-)  A    -2.3
 867 SER   (  88-)  F    -2.2
 143 HIS   ( 143-)  A    -2.2
 697 LEU   (  99-)  E    -2.2
 715 VAL   ( 117-)  E    -2.2
  16 PRO   (  16-)  A    -2.2
 974 LYS   ( 310-)  G    -2.2
 117 VAL   ( 117-)  A    -2.2
 184 THR   (   3-)  B    -2.2
 256 VAL   (  75-)  B    -2.1
 756 GLU   ( 158-)  E    -2.1
 912 ARG   ( 133-)  F    -2.1
 154 LEU   ( 154-)  A    -2.1
  90 THR   (  90-)  A    -2.1
 179 GLU   ( 179-)  A    -2.1
1181 ILE   ( 198-)  H    -2.1
 345 VAL   ( 164-)  B    -2.1
1183 LEU   ( 200-)  H    -2.1
 782 THR   (   3-)  F    -2.1

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.

  15 ASN   (  15-)  A  PRO omega poor
  18 GLN   (  18-)  A  Poor phi/psi
  51 PHE   (  51-)  A  Poor phi/psi
  78 ASN   (  78-)  A  Poor phi/psi
  79 TYR   (  79-)  A  Poor phi/psi
 100 ARG   ( 100-)  A  Poor phi/psi
 113 THR   ( 113-)  A  Poor phi/psi, PRO omega poor
 115 PRO   ( 115-)  A  Poor phi/psi
 125 GLY   ( 125-)  A  Poor phi/psi
 143 HIS   ( 143-)  A  Poor phi/psi
 180 PHE   ( 180-)  A  Poor phi/psi
 214 ASN   (  33-)  B  Poor phi/psi
 271 THR   (  90-)  B  Poor phi/psi
 292 HIS   ( 111-)  B  Poor phi/psi
 294 ASN   ( 113-)  B  Poor phi/psi
 304 TYR   ( 123-)  B  PRO omega poor
 315 ASN   ( 134-)  B  Poor phi/psi
 334 TRP   ( 153-)  B  Poor phi/psi
 554 SER   ( 169-)  D  Poor phi/psi
 613 ASN   (  15-)  E  PRO omega poor
 616 GLN   (  18-)  E  Poor phi/psi
 649 PHE   (  51-)  E  Poor phi/psi
 676 ASN   (  78-)  E  Poor phi/psi
 677 TYR   (  79-)  E  Poor phi/psi
 698 ARG   ( 100-)  E  Poor phi/psi
 711 THR   ( 113-)  E  Poor phi/psi, PRO omega poor
 713 PRO   ( 115-)  E  Poor phi/psi
 723 GLY   ( 125-)  E  Poor phi/psi
 741 HIS   ( 143-)  E  Poor phi/psi
 778 PHE   ( 180-)  E  Poor phi/psi
 812 ASN   (  33-)  F  Poor phi/psi
 869 THR   (  90-)  F  Poor phi/psi
 890 HIS   ( 111-)  F  Poor phi/psi
 892 ASN   ( 113-)  F  Poor phi/psi
 902 TYR   ( 123-)  F  PRO omega poor
 913 ASN   ( 134-)  F  Poor phi/psi
 932 TRP   ( 153-)  F  Poor phi/psi
1152 SER   ( 169-)  H  Poor phi/psi
1183 LEU   ( 200-)  H  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.845

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.

 469 SER   (  84-)  D    0.34
1067 SER   (  84-)  H    0.34
 645 GLU   (  47-)  E    0.36
1102 SER   ( 119-)  H    0.36

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!

  11 GLU   (  11-)  A      0
  14 LEU   (  14-)  A      0
  15 ASN   (  15-)  A      0
  17 ASP   (  17-)  A      0
  18 GLN   (  18-)  A      0
  23 MSE   (  23-)  A      0
  26 PHE   (  26-)  A      0
  32 PHE   (  32-)  A      0
  33 HIS   (  33-)  A      0
  36 MSE   (  36-)  A      0
  39 LYS   (  39-)  A      0
  44 ARG   (  44-)  A      0
  51 PHE   (  51-)  A      0
  73 MSE   (  73-)  A      0
  77 SER   (  77-)  A      0
  78 ASN   (  78-)  A      0
  79 TYR   (  79-)  A      0
  99 LEU   (  99-)  A      0
 100 ARG   ( 100-)  A      0
 110 ASP   ( 110-)  A      0
 111 LYS   ( 111-)  A      0
 112 PHE   ( 112-)  A      0
 113 THR   ( 113-)  A      0
 115 PRO   ( 115-)  A      0
 116 VAL   ( 116-)  A      0
And so on for a total of 411 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 : 1.277

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]

 700 PRO   ( 102-)  E    0.46 HIGH

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].

 305 PRO   ( 124-)  B    50.3 half-chair C-delta/C-gamma (54 degrees)
 694 PRO   (  96-)  E  -122.4 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 202 THR   (  21-)  B      O   <->  261 ARG   (  80-)  B      NH1    0.47    2.23  INTRA BF
 781 ASP   (   2-)  F      CG  <->  785 ARG   (   6-)  F      NH2    0.46    2.64  INTRA BF
 777 GLU   ( 179-)  E      O   <->  779 ASP   ( 181-)  E      N      0.37    2.33  INTRA BF
 183 ASP   (   2-)  B      CG  <->  187 ARG   (   6-)  B      NH2    0.35    2.75  INTRA BF
  17 ASP   (  17-)  A      CG  <->  187 ARG   (   6-)  B      NH1    0.32    2.78  INTRA BF
 997 HIS   (  14-)  H      N   <-> 1057 GLU   (  74-)  H      OE2    0.32    2.38  INTRA BL
 843 GLN   (  64-)  F      CG  <->  998 PHE   (  15-)  H      CE2    0.31    2.89  INTRA BF
 800 THR   (  21-)  F      O   <->  859 ARG   (  80-)  F      NH1    0.30    2.40  INTRA BF
 831 GLU   (  52-)  F      CD  <->  834 ARG   (  55-)  F      NH1    0.30    2.80  INTRA BF
1096 LYS   ( 113-)  H      NZ  <-> 1100 ASP   ( 117-)  H      OD1    0.27    2.43  INTRA BL
 956 HIS   ( 177-)  F      ND1 <->  958 SER   ( 179-)  F      N      0.27    2.73  INTRA BF
 781 ASP   (   2-)  F      OD2 <->  785 ARG   (   6-)  F      NH2    0.26    2.44  INTRA BF
 110 ASP   ( 110-)  A      OD1 <->  111 LYS   ( 111-)  A      N      0.26    2.34  INTRA BL
 637 LYS   (  39-)  E      NZ  <-> 1092 GLU   ( 109-)  H      OE1    0.26    2.44  INTRA BF
 399 HIS   (  14-)  D      CD2 <->  463 MET   (  78-)  D      SD     0.26    3.14  INTRA BL
 984 MET   (   1-)  H      CE  <-> 1115 TRP   ( 132-)  H      CB     0.25    2.95  INTRA BF
 831 GLU   (  52-)  F      OE2 <->  834 ARG   (  55-)  F      NH1    0.24    2.46  INTRA BF
 825 GLU   (  46-)  F      OE2 <->  827 ARG   (  48-)  F      NH2    0.24    2.46  INTRA BF
 288 GLN   ( 107-)  B      NE2 <->  290 LEU   ( 109-)  B      CD1    0.23    2.87  INTRA BF
 804 ARG   (  25-)  F      NH2 <->  820 ASP   (  41-)  F      OD2    0.22    2.48  INTRA BF
 578 TYR   ( 193-)  D      CE1 <-> 1037 GLN   (  54-)  H      NE2    0.22    2.88  INTRA BL
  99 LEU   (  99-)  A      CD2 <->  100 ARG   ( 100-)  A      N      0.22    2.78  INTRA BL
  67 LYS   (  67-)  A      NZ  <->  473 ASP   (  88-)  D      OD1    0.22    2.48  INTRA BL
 293 HIS   ( 112-)  B      ND1 <-> 1210 HOH   ( 198 )  B      O      0.21    2.49  INTRA BF
1024 THR   (  41-)  H      OG1 <-> 1078 ASN   (  95-)  H      ND2    0.20    2.50  INTRA BF
And so on for a total of 210 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

1137 ARG   ( 154-)  H      -7.61
 370 ARG   ( 189-)  B      -6.24
 100 ARG   ( 100-)  A      -6.16
 698 ARG   ( 100-)  E      -5.81
 968 ARG   ( 189-)  F      -5.77
 888 LEU   ( 109-)  F      -5.70
 945 ARG   ( 166-)  F      -5.59
 985 LYS   (   2-)  H      -5.51
 347 ARG   ( 166-)  B      -5.49
 648 ARG   (  50-)  E      -5.44
 395 LYS   (  10-)  D      -5.44
 778 PHE   ( 180-)  E      -5.44
 290 LEU   ( 109-)  B      -5.39
 387 LYS   (   2-)  D      -5.38
 993 LYS   (  10-)  H      -5.25
 539 ARG   ( 154-)  D      -5.21
  99 LEU   (  99-)  A      -5.09
 154 LEU   ( 154-)  A      -5.08

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

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.

 455 LEU   (  70-)  D   -2.63
1053 LEU   (  70-)  H   -2.63

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.

 582 ASP   ( 197-)  D     -  585 LEU   ( 200-)  D        -1.41

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Water, ion, and hydrogenbond related checks

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.

1212 HOH   ( 206 )  E      O
1212 HOH   ( 215 )  E      O

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.

 315 ASN   ( 134-)  B
 403 ASN   (  18-)  D
 747 HIS   ( 149-)  E
 915 GLN   ( 136-)  F
 935 GLN   ( 156-)  F
1078 ASN   (  95-)  H
1155 ASN   ( 172-)  H

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.

  38 LYS   (  38-)  A      N
  39 LYS   (  39-)  A      NZ
  45 LEU   (  45-)  A      N
  55 GLU   (  55-)  A      N
 121 TRP   ( 121-)  A      NE1
 156 SER   ( 156-)  A      OG
 180 PHE   ( 180-)  A      N
 181 ASP   ( 181-)  A      N
 187 ARG   (   6-)  B      NH2
 200 ASN   (  19-)  B      N
 218 SER   (  37-)  B      OG
 227 GLU   (  46-)  B      N
 251 GLN   (  70-)  B      NE2
 256 VAL   (  75-)  B      N
 263 ASN   (  82-)  B      ND2
 287 THR   ( 106-)  B      N
 288 GLN   ( 107-)  B      N
 290 LEU   ( 109-)  B      N
 332 GLY   ( 151-)  B      N
 335 THR   ( 154-)  B      N
 376 LYS   ( 310-)  C      NZ
 381 LYS   ( 315-)  C      NZ
 391 GLU   (   6-)  D      N
 396 ALA   (  11-)  D      N
 397 GLN   (  12-)  D      N
And so on for a total of 79 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.

  66 ASP   (  66-)  A      OD2
 149 HIS   ( 149-)  A      ND1
 197 HIS   (  16-)  B      ND1
 399 HIS   (  14-)  D      NE2
 615 ASP   (  17-)  E      OD2
 815 GLU   (  36-)  F      OE2
 997 HIS   (  14-)  H      NE2
1041 HIS   (  58-)  H      NE2

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.

1212 HOH   ( 226 )  E      O  0.94  K  5 *2
1214 HOH   ( 221 )  H      O  1.16  K  4 *2

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.

  21 GLU   (  21-)  A   H-bonding suggests Gln
  25 ASP   (  25-)  A   H-bonding suggests Asn; but Alt-Rotamer
  66 ASP   (  66-)  A   H-bonding suggests Asn
 159 ASP   ( 159-)  A   H-bonding suggests Asn; but Alt-Rotamer
 416 ASP   (  31-)  D   H-bonding suggests Asn
 478 GLU   (  93-)  D   H-bonding suggests Gln
 518 ASP   ( 133-)  D   H-bonding suggests Asn
 550 GLU   ( 165-)  D   H-bonding suggests Gln; but Alt-Rotamer
 619 GLU   (  21-)  E   H-bonding suggests Gln
 664 ASP   (  66-)  E   H-bonding suggests Asn
 757 ASP   ( 159-)  E   H-bonding suggests Asn; but Alt-Rotamer
1076 GLU   (  93-)  H   H-bonding suggests Gln
1148 GLU   ( 165-)  H   H-bonding suggests Gln; but Alt-Rotamer

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 :   0.243
  2nd generation packing quality :  -0.723
  Ramachandran plot appearance   :  -1.722
  chi-1/chi-2 rotamer normality  :  -2.845
  Backbone conformation          :   0.384

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.377 (tight)
  Bond angles                    :   0.661 (tight)
  Omega angle restraints         :   0.232 (tight)
  Side chain planarity           :   0.255 (tight)
  Improper dihedral distribution :   0.652
  B-factor distribution          :   0.417
  Inside/Outside distribution    :   1.044

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.5
  2nd generation packing quality :   0.7
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.377 (tight)
  Bond angles                    :   0.661 (tight)
  Omega angle restraints         :   0.232 (tight)
  Side chain planarity           :   0.255 (tight)
  Improper dihedral distribution :   0.652
  B-factor distribution          :   0.417
  Inside/Outside distribution    :   1.044
==============

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.