WHAT IF Check report

This file was created 2012-01-25 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 pdb2hv7.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    =  80.041  B   =  86.096  C    =  95.099
    Alpha=  73.910  Beta=  89.970  Gamma=  73.310

Dimensions of a reduced cell

    A    =  80.041  B   =  86.096  C    =  95.099
    Alpha= 106.090  Beta=  89.970  Gamma= 106.690

Dimensions of the conventional cell

    A    =  80.041  B   =  86.096  C    =  95.099
    Alpha= 106.090  Beta=  89.970  Gamma= 106.690

Transformation to conventional cell

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

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.014
CA-only RMS fit for the two chains : 0.668

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 B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.983
CA-only RMS fit for the two chains : 0.657

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.557
CA-only RMS fit for the two chains : 0.326

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 D

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 : 1.038
CA-only RMS fit for the two chains : 0.692

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: A and F

All-atom RMS fit for the two chains : 0.408
CA-only RMS fit for the two chains : 0.220

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 F

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

2409 ADP   ( 324-)  C  -
2410 ADP   ( 324-)  E  -
2411 ADP   ( 324-)  G  -
2412 ADP   ( 324-)  B  -

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: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 2.91

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: Tyrosine convention problem

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

  24 TYR   (  45-)  A
 130 TYR   ( 151-)  A
 211 TYR   ( 232-)  A
 431 TYR   ( 151-)  B
 732 TYR   ( 151-)  C
 927 TYR   (  45-)  D
1033 TYR   ( 151-)  D
1070 TYR   ( 188-)  D
1228 TYR   (  45-)  E
1288 TYR   ( 105-)  E
1334 TYR   ( 151-)  E
1532 TYR   (  48-)  F
1635 TYR   ( 151-)  F
1716 TYR   ( 232-)  F
1936 TYR   ( 151-)  G
2237 TYR   ( 151-)  H
2318 TYR   ( 232-)  H

Warning: Phenylalanine convention problem

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

 196 PHE   ( 217-)  A
 232 PHE   ( 253-)  A
 247 PHE   ( 268-)  A
 288 PHE   ( 309-)  A
 497 PHE   ( 217-)  B
 533 PHE   ( 253-)  B
 548 PHE   ( 268-)  B
 589 PHE   ( 309-)  B
 798 PHE   ( 217-)  C
 834 PHE   ( 253-)  C
 849 PHE   ( 268-)  C
 890 PHE   ( 309-)  C
1099 PHE   ( 217-)  D
1120 PHE   ( 238-)  D
1135 PHE   ( 253-)  D
1150 PHE   ( 268-)  D
1185 PHE   ( 303-)  D
1193 PHE   ( 311-)  D
1400 PHE   ( 217-)  E
1436 PHE   ( 253-)  E
1451 PHE   ( 268-)  E
1492 PHE   ( 309-)  E
1669 PHE   ( 185-)  F
1701 PHE   ( 217-)  F
1737 PHE   ( 253-)  F
1752 PHE   ( 268-)  F
1795 PHE   ( 311-)  F
2002 PHE   ( 217-)  G
2038 PHE   ( 253-)  G
2053 PHE   ( 268-)  G
2088 PHE   ( 303-)  G
2094 PHE   ( 309-)  G
2303 PHE   ( 217-)  H
2339 PHE   ( 253-)  H
2354 PHE   ( 268-)  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.

  64 ASP   (  85-)  A
  74 ASP   (  95-)  A
  92 ASP   ( 113-)  A
 219 ASP   ( 240-)  A
 520 ASP   ( 240-)  B
 666 ASP   (  85-)  C
 821 ASP   ( 240-)  C
 967 ASP   (  85-)  D
 977 ASP   (  95-)  D
1111 ASP   ( 229-)  D
1122 ASP   ( 240-)  D
1132 ASP   ( 250-)  D
1423 ASP   ( 240-)  E
1569 ASP   (  85-)  F
1579 ASP   (  95-)  F
1713 ASP   ( 229-)  F
2025 ASP   ( 240-)  G
2171 ASP   (  85-)  H
2181 ASP   (  95-)  H
2261 ASP   ( 175-)  H
2326 ASP   ( 240-)  H
2336 ASP   ( 250-)  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.

  51 GLU   (  72-)  A
 220 GLU   ( 241-)  A
 225 GLU   ( 246-)  A
 249 GLU   ( 270-)  A
 309 GLU   (  29-)  B
 394 GLU   ( 114-)  B
 414 GLU   ( 134-)  B
 421 GLU   ( 141-)  B
 550 GLU   ( 270-)  B
 610 GLU   (  29-)  C
 656 GLU   (  75-)  C
 827 GLU   ( 246-)  C
 851 GLU   ( 270-)  C
1123 GLU   ( 241-)  D
1212 GLU   (  29-)  E
1297 GLU   ( 114-)  E
1317 GLU   ( 134-)  E
1424 GLU   ( 241-)  E
1453 GLU   ( 270-)  E
1556 GLU   (  72-)  F
1686 GLU   ( 202-)  F
1746 GLU   ( 262-)  F
1814 GLU   (  29-)  G
1875 GLU   (  90-)  G
2055 GLU   ( 270-)  G
2153 GLU   (  67-)  H
2161 GLU   (  75-)  H
2332 GLU   ( 246-)  H
2348 GLU   ( 262-)  H
2356 GLU   ( 270-)  H

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

1058 ASP   ( 176-)  D      CG   OD1   1.41    8.7
1537 LEU   (  53-)  F      CG   CD1   1.73    6.2
1537 LEU   (  53-)  F      CG   CD2   1.76    7.4
1713 ASP   ( 229-)  F      CG   OD1   1.58   17.2
1713 ASP   ( 229-)  F      CG   OD2   1.68   22.5

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

 |  0.997154  0.000155  0.000176|
 |  0.000155  0.997892 -0.000204|
 |  0.000176 -0.000204  0.997240|
Proposed new scale matrix

 |  0.012530 -0.003756  0.001125|
 | -0.000001  0.012151 -0.003671|
 | -0.000002  0.000002  0.011015|
With corresponding cell

    A    =  79.811  B   =  85.915  C    =  94.828
    Alpha=  73.914  Beta=  89.947  Gamma=  73.305

The CRYST1 cell dimensions

    A    =  80.041  B   =  86.096  C    =  95.099
    Alpha=  73.910  Beta=  89.970  Gamma=  73.310

Variance: 543.658
(Under-)estimated Z-score: 17.184

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.

1713 ASP   ( 229-)  F      OD2  CG   OD1 132.64    4.1
2184 SER   (  98-)  H      N    CA   C   125.42    5.1
2185 ARG   (  99-)  H      N    CA   C   122.83    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.

  51 GLU   (  72-)  A
  64 ASP   (  85-)  A
  74 ASP   (  95-)  A
  92 ASP   ( 113-)  A
 219 ASP   ( 240-)  A
 220 GLU   ( 241-)  A
 225 GLU   ( 246-)  A
 249 GLU   ( 270-)  A
 309 GLU   (  29-)  B
 394 GLU   ( 114-)  B
 414 GLU   ( 134-)  B
 421 GLU   ( 141-)  B
 520 ASP   ( 240-)  B
 550 GLU   ( 270-)  B
 610 GLU   (  29-)  C
 656 GLU   (  75-)  C
 666 ASP   (  85-)  C
 821 ASP   ( 240-)  C
 827 GLU   ( 246-)  C
 851 GLU   ( 270-)  C
 967 ASP   (  85-)  D
 977 ASP   (  95-)  D
1111 ASP   ( 229-)  D
1122 ASP   ( 240-)  D
1123 GLU   ( 241-)  D
And so on for a total of 52 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.

2184 SER   (  98-)  H    5.27
1312 ALA   ( 129-)  E    4.99
2201 GLU   ( 115-)  H    4.95
 710 ALA   ( 129-)  C    4.72
  38 VAL   (  59-)  A    4.66
 226 ASN   ( 247-)  A    4.61
 313 VAL   (  33-)  B    4.33
1599 GLU   ( 115-)  F    4.33
2185 ARG   (  99-)  H    4.31
1731 ASN   ( 247-)  F    4.01

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

1713 ASP   ( 229-)  F    9.72
1058 ASP   ( 176-)  D    6.65

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.359

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.

  76 PRO   (  97-)  A    -3.0
1207 ILE   (  24-)  E    -2.7
1766 PRO   ( 282-)  F    -2.7
2151 THR   (  65-)  H    -2.7
2110 ILE   (  24-)  H    -2.6
2368 PRO   ( 282-)  H    -2.6
1805 THR   ( 321-)  F    -2.6
1395 LEU   ( 212-)  E    -2.5
1199 ILE   ( 317-)  D    -2.5
1850 THR   (  65-)  G    -2.5
 295 PRO   ( 316-)  A    -2.5
2102 ILE   ( 317-)  G    -2.5
1809 ILE   (  24-)  G    -2.5
 898 ILE   ( 317-)  C    -2.4
1876 THR   (  91-)  G    -2.4
 429 ILE   ( 149-)  B    -2.4
1188 ILE   ( 306-)  D    -2.4
1525 ARG   (  41-)  F    -2.4
1383 ARG   ( 200-)  E    -2.4
1801 ILE   ( 317-)  F    -2.4
2183 PRO   (  97-)  H    -2.4
1489 ILE   ( 306-)  E    -2.4
2091 ILE   ( 306-)  G    -2.4
 296 ILE   ( 317-)  A    -2.3
2177 THR   (  91-)  H    -2.3
And so on for a total of 78 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.

   8 GLU   (  29-)  A  Poor phi/psi
  75 GLN   (  96-)  A  PRO omega poor
  76 PRO   (  97-)  A  Poor phi/psi
  77 SER   (  98-)  A  Poor phi/psi
  79 PHE   ( 100-)  A  Poor phi/psi
 188 VAL   ( 209-)  A  Poor phi/psi
 193 ASP   ( 214-)  A  omega poor
 208 ASP   ( 229-)  A  Poor phi/psi
 225 GLU   ( 246-)  A  omega poor
 229 ASP   ( 250-)  A  omega poor
 284 VAL   ( 305-)  A  omega poor
 321 ARG   (  41-)  B  omega poor
 380 PHE   ( 100-)  B  Poor phi/psi
 421 GLU   ( 141-)  B  omega poor
 455 ASP   ( 175-)  B  omega poor
 480 ARG   ( 200-)  B  Poor phi/psi
 495 PHE   ( 215-)  B  omega poor
 509 ASP   ( 229-)  B  Poor phi/psi
 678 PRO   (  97-)  C  omega poor
 681 PHE   ( 100-)  C  Poor phi/psi
 730 ILE   ( 149-)  C  Poor phi/psi
 756 ASP   ( 175-)  C  omega poor
 778 LYS   ( 197-)  C  omega poor
 781 ARG   ( 200-)  C  Poor phi/psi
 788 GLN   ( 207-)  C  Poor phi/psi
And so on for a total of 71 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.530

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.

1604 VAL   ( 120-)  F    0.36
 504 SER   ( 224-)  B    0.37
 805 SER   ( 224-)  C    0.38
1769 SER   ( 285-)  F    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!

   7 LYS   (  28-)  A      0
   8 GLU   (  29-)  A      0
   9 ILE   (  30-)  A      0
  10 HIS   (  31-)  A      0
  20 ARG   (  41-)  A      0
  38 VAL   (  59-)  A      0
  39 LYS   (  60-)  A      0
  47 TYR   (  68-)  A      0
  70 THR   (  91-)  A      0
  75 GLN   (  96-)  A      0
  76 PRO   (  97-)  A      0
  77 SER   (  98-)  A      0
  79 PHE   ( 100-)  A      0
  81 ASN   ( 102-)  A      0
  82 LYS   ( 103-)  A      0
  94 GLU   ( 115-)  A      0
 102 VAL   ( 123-)  A      0
 122 VAL   ( 143-)  A      0
 128 ILE   ( 149-)  A      0
 129 ASP   ( 150-)  A      0
 150 VAL   ( 171-)  A      0
 152 ARG   ( 173-)  A      0
 156 GLN   ( 177-)  A      0
 161 PHE   ( 182-)  A      0
 180 MET   ( 201-)  A      0
And so on for a total of 787 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

1692 GLY   ( 208-)  F   1.64   16

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]

1878 PRO   (  93-)  G    0.18 LOW
2120 PRO   (  34-)  H    0.18 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  76 PRO   (  97-)  A   125.2 half-chair C-beta/C-alpha (126 degrees)
 210 PRO   ( 231-)  A  -120.0 half-chair C-delta/C-gamma (-126 degrees)
 214 PRO   ( 235-)  A    99.2 envelop C-beta (108 degrees)
 246 PRO   ( 267-)  A    48.6 half-chair C-delta/C-gamma (54 degrees)
 295 PRO   ( 316-)  A    15.8 half-chair N/C-delta (18 degrees)
 373 PRO   (  93-)  B  -121.2 half-chair C-delta/C-gamma (-126 degrees)
 405 PRO   ( 125-)  B  -120.8 half-chair C-delta/C-gamma (-126 degrees)
 596 PRO   ( 316-)  B    41.7 envelop C-delta (36 degrees)
 615 PRO   (  34-)  C  -114.3 envelop C-gamma (-108 degrees)
 800 PRO   ( 219-)  C  -118.8 half-chair C-delta/C-gamma (-126 degrees)
 897 PRO   ( 316-)  C   -12.0 half-chair C-alpha/N (-18 degrees)
1085 PRO   ( 203-)  D    34.4 envelop C-delta (36 degrees)
1117 PRO   ( 235-)  D   101.3 envelop C-beta (108 degrees)
1198 PRO   ( 316-)  D    40.1 envelop C-delta (36 degrees)
1217 PRO   (  34-)  E   101.2 envelop C-beta (108 degrees)
1308 PRO   ( 125-)  E  -115.5 envelop C-gamma (-108 degrees)
1499 PRO   ( 316-)  E     3.2 envelop N (0 degrees)
1609 PRO   ( 125-)  F  -114.4 envelop C-gamma (-108 degrees)
1703 PRO   ( 219-)  F  -115.9 envelop C-gamma (-108 degrees)
1719 PRO   ( 235-)  F   101.7 envelop C-beta (108 degrees)
1766 PRO   ( 282-)  F   106.1 envelop C-beta (108 degrees)
1819 PRO   (  34-)  G  -120.1 half-chair C-delta/C-gamma (-126 degrees)
1882 PRO   (  97-)  G   -45.6 half-chair C-beta/C-alpha (-54 degrees)
2101 PRO   ( 316-)  G     2.5 envelop N (0 degrees)
2289 PRO   ( 203-)  H    51.5 half-chair C-delta/C-gamma (54 degrees)
2321 PRO   ( 235-)  H   104.2 envelop C-beta (108 degrees)
2402 PRO   ( 316-)  H     6.1 envelop N (0 degrees)
2405 PRO   ( 319-)  H   105.0 envelop C-beta (108 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.

 680 ARG   (  99-)  C      O   <->  781 ARG   ( 200-)  C      NH1    0.49    2.21  INTRA BL
1990 GLY   ( 205-)  G      CA  <-> 2411 ADP   ( 324-)  G      C8     0.47    2.73  INTRA BF
2171 ASP   (  85-)  H      OD1 <-> 2280 LYS   ( 194-)  H      NZ     0.44    2.26  INTRA BL
1978 ARG   ( 193-)  G      NH2 <-> 2041 CYS   ( 256-)  G      SG     0.43    2.87  INTRA BL
 179 ARG   ( 200-)  A      NH2 <-> 1279 GLN   (  96-)  E      O      0.40    2.30  INTRA BL
 127 ARG   ( 148-)  A      NH1 <->  129 ASP   ( 150-)  A      OD2    0.38    2.32  INTRA BL
1282 ARG   (  99-)  E      O   <-> 1383 ARG   ( 200-)  E      NH1    0.34    2.36  INTRA BL
 377 PRO   (  97-)  B      CB  <-> 1145 MET   ( 263-)  D      CE     0.33    2.87  INTRA BL
2316 HIS   ( 230-)  H      CD2 <-> 2319 LEU   ( 233-)  H      N      0.33    2.77  INTRA BL
1418 PRO   ( 235-)  E      CG  <-> 1464 VAL   ( 281-)  E      O      0.33    2.47  INTRA BL
1787 PHE   ( 303-)  F      CE2 <-> 1791 GLN   ( 307-)  F      NE2    0.32    2.78  INTRA BL
 132 THR   ( 153-)  A      CG2 <->  186 GLN   ( 207-)  A      NE2    0.28    2.82  INTRA
1714 HIS   ( 230-)  F      CD2 <-> 1717 LEU   ( 233-)  F      N      0.28    2.82  INTRA BL
1747 MET   ( 263-)  F      CE  <-> 1882 PRO   (  97-)  G      CB     0.27    2.93  INTRA BL
2015 HIS   ( 230-)  G      CD2 <-> 2018 LEU   ( 233-)  G      N      0.25    2.85  INTRA BL
1992 GLN   ( 207-)  G      NE2 <-> 2411 ADP   ( 324-)  G      N7     0.25    2.75  INTRA BF
1376 ARG   ( 193-)  E      NH2 <-> 1439 CYS   ( 256-)  E      SG     0.25    3.05  INTRA BL
1884 ARG   (  99-)  G      O   <-> 1985 ARG   ( 200-)  G      NH2    0.25    2.45  INTRA BL
1093 GLY   ( 211-)  D      O   <-> 1156 GLN   ( 274-)  D      NE2    0.25    2.45  INTRA
 428 ARG   ( 148-)  B      NH1 <-> 2412 ADP   ( 324-)  B      O2B    0.24    2.46  INTRA
1718 GLU   ( 234-)  F      N   <-> 1721 HIS   ( 237-)  F      CD2    0.24    2.86  INTRA BL
 872 LEU   ( 291-)  C      O   <->  876 TYR   ( 295-)  C      N      0.23    2.47  INTRA BL
1413 HIS   ( 230-)  E      CD2 <-> 1416 LEU   ( 233-)  E      N      0.22    2.88  INTRA BL
 967 ASP   (  85-)  D      OD2 <-> 1069 ARG   ( 187-)  D      NH2    0.22    2.48  INTRA BL
1637 THR   ( 153-)  F      CG2 <-> 1691 GLN   ( 207-)  F      NE2    0.22    2.88  INTRA
And so on for a total of 258 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.

2185 ARG   (  99-)  H      -7.83
2017 TYR   ( 232-)  G      -7.66
 680 ARG   (  99-)  C      -7.53
1114 TYR   ( 232-)  D      -7.32
 512 TYR   ( 232-)  B      -7.03
 813 TYR   ( 232-)  C      -6.88
 211 TYR   ( 232-)  A      -6.79
2318 TYR   ( 232-)  H      -6.79
1415 TYR   ( 232-)  E      -6.76
1884 ARG   (  99-)  G      -6.54
 379 ARG   (  99-)  B      -6.49
1716 TYR   ( 232-)  F      -6.07
1694 TRP   ( 210-)  F      -5.94
1282 ARG   (  99-)  E      -5.60
1580 GLN   (  96-)  F      -5.50
1826 ARG   (  41-)  G      -5.48
1310 HIS   ( 127-)  E      -5.42
2182 GLN   (  96-)  H      -5.41
1583 ARG   (  99-)  F      -5.40
 551 HIS   ( 271-)  B      -5.38
1454 HIS   ( 271-)  E      -5.34
1755 HIS   ( 271-)  F      -5.33
1912 HIS   ( 127-)  G      -5.31
2056 HIS   ( 271-)  G      -5.29
1153 HIS   ( 271-)  D      -5.22
 407 HIS   ( 127-)  B      -5.21
1214 HIS   (  31-)  E      -5.21
 250 HIS   ( 271-)  A      -5.18
  78 ARG   (  99-)  A      -5.15
1224 ARG   (  41-)  E      -5.13
 681 PHE   ( 100-)  C      -5.12
  10 HIS   (  31-)  A      -5.12
2357 HIS   ( 271-)  H      -5.12
 913 HIS   (  31-)  D      -5.10
1009 HIS   ( 127-)  D      -5.08
 852 HIS   ( 271-)  C      -5.06
 622 ARG   (  41-)  C      -5.06
1816 HIS   (  31-)  G      -5.03
 612 HIS   (  31-)  C      -5.00
2153 GLU   (  67-)  H      -5.00

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.

 241 GLU   ( 262-)  A       244 - THR    265- ( A)         -4.47
 843 GLU   ( 262-)  C       846 - THR    265- ( C)         -4.44
1145 MET   ( 263-)  D      1147 - THR    265- ( D)         -4.48
1747 MET   ( 263-)  F      1749 - THR    265- ( F)         -4.52
2181 ASP   (  95-)  H      2183 - PRO     97- ( H)         -4.64
2348 GLU   ( 262-)  H      2351 - THR    265- ( H)         -4.37

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.

 301 SER   ( 322-)  A   -3.01
2093 HIS   ( 308-)  G   -2.84
 903 SER   ( 322-)  C   -2.80
1491 HIS   ( 308-)  E   -2.74
1989 ALA   ( 204-)  G   -2.73
 484 ALA   ( 204-)  B   -2.72
1387 ALA   ( 204-)  E   -2.71
  75 GLN   (  96-)  A   -2.66
 485 GLY   ( 205-)  B   -2.64
 785 ALA   ( 204-)  C   -2.63
 786 GLY   ( 205-)  C   -2.62
 889 HIS   ( 308-)  C   -2.61
 978 GLN   (  96-)  D   -2.59
2182 GLN   (  96-)  H   -2.54
2090 VAL   ( 305-)  G   -2.50

Warning: Abnormal packing Z-score for sequential residues

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

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

 908 PRO   (  26-)  D     -  911 GLU   (  29-)  D        -1.56
1510 PRO   (  26-)  F     - 1513 GLU   (  29-)  F        -1.65

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: 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.

 186 GLN   ( 207-)  A
 195 GLN   ( 216-)  A
 216 HIS   ( 237-)  A
 256 ASN   ( 277-)  A
 457 GLN   ( 177-)  B
 496 GLN   ( 216-)  B
 553 ASN   ( 273-)  B
 557 ASN   ( 277-)  B
 758 GLN   ( 177-)  C
 797 GLN   ( 216-)  C
 854 ASN   ( 273-)  C
1098 GLN   ( 216-)  D
1119 HIS   ( 237-)  D
1205 ASN   (  22-)  E
1360 GLN   ( 177-)  E
1399 GLN   ( 216-)  E
1456 ASN   ( 273-)  E
1460 ASN   ( 277-)  E
1580 GLN   (  96-)  F
1691 GLN   ( 207-)  F
1700 GLN   ( 216-)  F
1721 HIS   ( 237-)  F
1807 ASN   (  22-)  G
1903 ASN   ( 118-)  G
1962 GLN   ( 177-)  G
2001 GLN   ( 216-)  G
2058 ASN   ( 273-)  G
2062 ASN   ( 277-)  G
2182 GLN   (  96-)  H
2302 GLN   ( 216-)  H
2359 ASN   ( 273-)  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.

   8 GLU   (  29-)  A      N
   9 ILE   (  30-)  A      N
  50 SER   (  71-)  A      N
  75 GLN   (  96-)  A      NE2
  82 LYS   ( 103-)  A      N
  96 GLU   ( 117-)  A      N
 122 VAL   ( 143-)  A      N
 123 GLY   ( 144-)  A      N
 152 ARG   ( 173-)  A      NE
 157 ILE   ( 178-)  A      N
 160 VAL   ( 181-)  A      N
 175 GLN   ( 196-)  A      NE2
 189 TRP   ( 210-)  A      N
 190 GLY   ( 211-)  A      N
 194 PHE   ( 215-)  A      N
 211 TYR   ( 232-)  A      N
 212 LEU   ( 233-)  A      N
 218 VAL   ( 239-)  A      N
 228 LYS   ( 249-)  A      N
 232 PHE   ( 253-)  A      N
 254 LEU   ( 275-)  A      N
 262 SER   ( 283-)  A      N
 274 TYR   ( 295-)  A      OH
 281 LYS   ( 302-)  A      N
 287 HIS   ( 308-)  A      N
And so on for a total of 255 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.

 175 GLN   ( 196-)  A      OE1
 656 GLU   (  75-)  C      OE1
 737 GLU   ( 156-)  C      OE1
1009 HIS   ( 127-)  D      ND1
1078 GLN   ( 196-)  D      OE1
1230 ASP   (  47-)  E      OD2
1420 HIS   ( 237-)  E      ND1
1680 GLN   ( 196-)  F      OE1
1981 GLN   ( 196-)  G      OE1
2334 HIS   ( 248-)  H      ND1

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.

 113 GLU   ( 134-)  A   H-bonding suggests Gln
 309 GLU   (  29-)  B   H-bonding suggests Gln; but Alt-Rotamer
 315 ASP   (  35-)  B   H-bonding suggests Asn
 355 GLU   (  75-)  B   H-bonding suggests Gln
 414 GLU   ( 134-)  B   H-bonding suggests Gln
 542 GLU   ( 262-)  B   H-bonding suggests Gln
 656 GLU   (  75-)  C   H-bonding suggests Gln; but Alt-Rotamer
 715 GLU   ( 134-)  C   H-bonding suggests Gln
 827 GLU   ( 246-)  C   H-bonding suggests Gln
1016 GLU   ( 134-)  D   H-bonding suggests Gln
1116 GLU   ( 234-)  D   H-bonding suggests Gln; but Alt-Rotamer
1122 ASP   ( 240-)  D   H-bonding suggests Asn; but Alt-Rotamer
1137 GLU   ( 255-)  D   H-bonding suggests Gln; but Alt-Rotamer
1212 GLU   (  29-)  E   H-bonding suggests Gln; but Alt-Rotamer
1230 ASP   (  47-)  E   H-bonding suggests Asn; but Alt-Rotamer
1258 GLU   (  75-)  E   H-bonding suggests Gln
1317 GLU   ( 134-)  E   H-bonding suggests Gln
1373 GLU   ( 190-)  E   H-bonding suggests Gln
1385 GLU   ( 202-)  E   H-bonding suggests Gln
1417 GLU   ( 234-)  E   H-bonding suggests Gln; but Alt-Rotamer
1481 GLU   ( 298-)  E   H-bonding suggests Gln
1531 ASP   (  47-)  F   H-bonding suggests Asn; but Alt-Rotamer
1618 GLU   ( 134-)  F   H-bonding suggests Gln
1739 GLU   ( 255-)  F   H-bonding suggests Gln; but Alt-Rotamer
1820 ASP   (  35-)  G   H-bonding suggests Asn; but Alt-Rotamer
1860 GLU   (  75-)  G   H-bonding suggests Gln
1919 GLU   ( 134-)  G   H-bonding suggests Gln
1975 GLU   ( 190-)  G   H-bonding suggests Gln
2019 GLU   ( 234-)  G   H-bonding suggests Gln
2083 GLU   ( 298-)  G   H-bonding suggests Gln
2161 GLU   (  75-)  H   H-bonding suggests Gln
2220 GLU   ( 134-)  H   H-bonding suggests Gln
2341 GLU   ( 255-)  H   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.069
  2nd generation packing quality :  -2.195
  Ramachandran plot appearance   :  -3.359 (poor)
  chi-1/chi-2 rotamer normality  :  -3.530 (poor)
  Backbone conformation          :  -0.672

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.493 (tight)
  Bond angles                    :   0.647 (tight)
  Omega angle restraints         :   1.045
  Side chain planarity           :   0.575 (tight)
  Improper dihedral distribution :   0.646
  B-factor distribution          :   0.453
  Inside/Outside distribution    :   0.993

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -1.1
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.493 (tight)
  Bond angles                    :   0.647 (tight)
  Omega angle restraints         :   1.045
  Side chain planarity           :   0.575 (tight)
  Improper dihedral distribution :   0.646
  B-factor distribution          :   0.453
  Inside/Outside distribution    :   0.993
==============

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.