WHAT IF Check report

This file was created 2011-12-28 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 pdb1gl9.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    = 132.410  B   =  68.690  C    = 134.000
    Alpha=  90.000  Beta=  99.700  Gamma=  90.000

Dimensions of a reduced cell

    A    =  68.690  B   = 132.410  C    = 134.000
    Alpha=  99.700  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 171.783  B   = 203.635  C    =  68.690
    Alpha=  90.000  Beta=  90.000  Gamma=  89.306

Transformation to conventional cell

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

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: C

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: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
but NCS matrices (but not the unitary matrix) are found labeled `dont use`: 1
SEQRES multiplicity agrees with number of MTRIX matrices labeled `dont use`
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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.

2028 ANP   (2055-)  B  -
2030 ANP   (2055-)  C  -

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: B

Note: Ramachandran plot

Chain identifier: C

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'.

   1 ILE   (   2-)  B      CG1
   1 ILE   (   2-)  B      CG2
   1 ILE   (   2-)  B      CD1
   2 PRO   (   3-)  B      CG
   2 PRO   (   3-)  B      CD
   3 VAL   (   4-)  B      CG1
   3 VAL   (   4-)  B      CG2
   4 VAL   (   5-)  B      CG1
   4 VAL   (   5-)  B      CG2
   5 TYR   (   6-)  B      CG
   5 TYR   (   6-)  B      CD1
   5 TYR   (   6-)  B      CD2
   5 TYR   (   6-)  B      CE1
   5 TYR   (   6-)  B      CE2
   5 TYR   (   6-)  B      CZ
   5 TYR   (   6-)  B      OH
   6 PRO   (  11-)  B      CG
   6 PRO   (  11-)  B      CD
   7 VAL   (  12-)  B      CG1
   7 VAL   (  12-)  B      CG2
   8 CYS   (  13-)  B      SG
  11 LEU   (  17-)  B      CG
  11 LEU   (  17-)  B      CD1
  11 LEU   (  17-)  B      CD2
  12 GLU   (  18-)  B      CG
And so on for a total of 107 lines.

Warning: B-factors outside the range 0.0 - 100.0

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

  21 ARG   (  32-)  B    High
  30 PHE   (  41-)  B    High
  33 LYS   (  44-)  B    High
  41 LYS   (  52-)  B    High
 110 LYS   ( 121-)  B    High
 115 ALA   ( 126-)  B    High
 116 GLY   ( 127-)  B    High
 117 VAL   ( 128-)  B    High
 118 GLY   ( 129-)  B    High
 119 THR   ( 130-)  B    High
 120 GLU   ( 131-)  B    High
 121 ASN   ( 132-)  B    High
 122 LEU   ( 133-)  B    High
 128 GLY   ( 139-)  B    High
 129 ARG   ( 140-)  B    High
 130 ILE   ( 141-)  B    High
 131 PRO   ( 142-)  B    High
 132 LYS   ( 143-)  B    High
 133 ARG   ( 144-)  B    High
 134 GLU   ( 145-)  B    High
 135 LYS   ( 146-)  B    High
 136 GLU   ( 147-)  B    High
 140 GLN   ( 151-)  B    High
 157 LYS   ( 168-)  B    High
 158 HIS   ( 169-)  B    High
And so on for a total of 714 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 6.99

Note: B-factor plot

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

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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.

  90 ARG   ( 101-)  B
 324 ARG   ( 335-)  B
 331 ARG   ( 342-)  B
 366 ARG   ( 377-)  B
 427 ARG   ( 438-)  B
 658 ARG   ( 692-)  B
 693 ARG   ( 727-)  B
 814 ARG   ( 848-)  B
 884 ARG   ( 918-)  B
 888 ARG   ( 922-)  B
1041 ARG   (  32-)  C
1110 ARG   ( 101-)  C
1351 ARG   ( 342-)  C
1669 ARG   ( 692-)  C
1704 ARG   ( 727-)  C
1823 ARG   ( 848-)  C
1889 ARG   ( 918-)  C
1893 ARG   ( 922-)  C

Warning: Tyrosine convention problem

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

 301 TYR   ( 312-)  B
 363 TYR   ( 374-)  B
 740 TYR   ( 774-)  B
 846 TYR   ( 880-)  B
 942 TYR   ( 976-)  B
 954 TYR   ( 988-)  B
 959 TYR   ( 993-)  B
1321 TYR   ( 312-)  C
1383 TYR   ( 374-)  C
1749 TYR   ( 774-)  C
1855 TYR   ( 880-)  C
1947 TYR   ( 976-)  C
1959 TYR   ( 988-)  C
1964 TYR   ( 993-)  C

Warning: Phenylalanine convention problem

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

  26 PHE   (  37-)  B
  63 PHE   (  74-)  B
 138 PHE   ( 149-)  B
 145 PHE   ( 156-)  B
 169 PHE   ( 180-)  B
 192 PHE   ( 203-)  B
 225 PHE   ( 236-)  B
 231 PHE   ( 242-)  B
 288 PHE   ( 299-)  B
 304 PHE   ( 315-)  B
 343 PHE   ( 354-)  B
 412 PHE   ( 423-)  B
 843 PHE   ( 877-)  B
 850 PHE   ( 884-)  B
 861 PHE   ( 895-)  B
 922 PHE   ( 956-)  B
1046 PHE   (  37-)  C
1158 PHE   ( 149-)  C
1165 PHE   ( 156-)  C
1189 PHE   ( 180-)  C
1212 PHE   ( 203-)  C
1245 PHE   ( 236-)  C
1251 PHE   ( 242-)  C
1324 PHE   ( 315-)  C
1363 PHE   ( 354-)  C
1420 PHE   ( 423-)  C
1459 PHE   ( 462-)  C
1852 PHE   ( 877-)  C
1870 PHE   ( 895-)  C
1927 PHE   ( 956-)  C

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.

  29 ASP   (  40-)  B
 184 ASP   ( 195-)  B
 195 ASP   ( 206-)  B
 232 ASP   ( 243-)  B
 443 ASP   ( 454-)  B
 478 ASP   ( 489-)  B
 482 ASP   ( 493-)  B
 491 ASP   ( 502-)  B
 547 ASP   ( 558-)  B
 588 ASP   ( 622-)  B
 599 ASP   ( 633-)  B
 608 ASP   ( 642-)  B
 641 ASP   ( 675-)  B
 692 ASP   ( 726-)  B
 710 ASP   ( 744-)  B
 721 ASP   ( 755-)  B
 822 ASP   ( 856-)  B
 990 ASP   (1024-)  B
 996 ASP   (1030-)  B
1004 ASP   (1038-)  B
1049 ASP   (  40-)  C
1204 ASP   ( 195-)  C
1215 ASP   ( 206-)  C
1252 ASP   ( 243-)  C
1451 ASP   ( 454-)  C
1486 ASP   ( 489-)  C
1490 ASP   ( 493-)  C
1499 ASP   ( 502-)  C
1555 ASP   ( 558-)  C
1599 ASP   ( 622-)  C
1610 ASP   ( 633-)  C
1619 ASP   ( 642-)  C
1652 ASP   ( 675-)  C
1703 ASP   ( 726-)  C
1721 ASP   ( 744-)  C
1730 ASP   ( 755-)  C
1831 ASP   ( 856-)  C
1995 ASP   (1024-)  C
2001 ASP   (1030-)  C
2009 ASP   (1038-)  C

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.

  61 GLU   (  72-)  B
 106 GLU   ( 117-)  B
 136 GLU   ( 147-)  B
 161 GLU   ( 172-)  B
 223 GLU   ( 234-)  B
 278 GLU   ( 289-)  B
 279 GLU   ( 290-)  B
 282 GLU   ( 293-)  B
 302 GLU   ( 313-)  B
 396 GLU   ( 407-)  B
 409 GLU   ( 420-)  B
 442 GLU   ( 453-)  B
 453 GLU   ( 464-)  B
 461 GLU   ( 472-)  B
 476 GLU   ( 487-)  B
 501 GLU   ( 512-)  B
 528 GLU   ( 539-)  B
 590 GLU   ( 624-)  B
 601 GLU   ( 635-)  B
 634 GLU   ( 668-)  B
 670 GLU   ( 704-)  B
 718 GLU   ( 752-)  B
 729 GLU   ( 763-)  B
 732 GLU   ( 766-)  B
 743 GLU   ( 777-)  B
And so on for a total of 66 lines.

Geometric checks

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.

   2 PRO   (   3-)  B      N    CA   CB  110.23    6.6
   6 PRO   (  11-)  B      N    CA   CB  109.80    6.2
 202 VAL   ( 213-)  B      N    CA   C    99.61   -4.1
 235 SER   ( 246-)  B      N    CA   C   123.84    4.5
 242 ASN   ( 253-)  B      N    CA   C    98.90   -4.4
 294 THR   ( 305-)  B      N    CA   C   125.13    5.0
 376 PRO   ( 387-)  B     -C    N    CA  101.96   -4.1
 377 ALA   ( 388-)  B      N    CA   C    92.68   -6.6
 380 ARG   ( 391-)  B      N    CA   C    91.57   -7.0
1021 PRO   (   3-)  C      N    CA   CB  109.81    6.2
1026 PRO   (  11-)  C      N    CA   CB  109.95    6.3
1184 HIS   ( 175-)  C      CG   ND1  CE1 109.62    4.0
1313 VAL   ( 304-)  C      N    CA   C   122.89    4.2
1314 THR   ( 305-)  C     -C    N    CA  128.99    4.1
1314 THR   ( 305-)  C      N    CA   C   129.73    6.6

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  29 ASP   (  40-)  B
  61 GLU   (  72-)  B
  90 ARG   ( 101-)  B
 106 GLU   ( 117-)  B
 136 GLU   ( 147-)  B
 161 GLU   ( 172-)  B
 184 ASP   ( 195-)  B
 195 ASP   ( 206-)  B
 223 GLU   ( 234-)  B
 232 ASP   ( 243-)  B
 278 GLU   ( 289-)  B
 279 GLU   ( 290-)  B
 282 GLU   ( 293-)  B
 302 GLU   ( 313-)  B
 324 ARG   ( 335-)  B
 331 ARG   ( 342-)  B
 366 ARG   ( 377-)  B
 396 GLU   ( 407-)  B
 409 GLU   ( 420-)  B
 427 ARG   ( 438-)  B
 442 GLU   ( 453-)  B
 443 ASP   ( 454-)  B
 453 GLU   ( 464-)  B
 461 GLU   ( 472-)  B
 476 GLU   ( 487-)  B
And so on for a total of 124 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 376 PRO   ( 387-)  B      N     -6.3   -22.98    -2.48
The average deviation= 0.747

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.

 377 ALA   ( 388-)  B    7.77
 380 ARG   ( 391-)  B    7.39
1314 THR   ( 305-)  C    6.30
 844 ALA   ( 878-)  B    6.23
 978 ARG   (1012-)  B    5.93
 374 LEU   ( 385-)  B    5.13
1393 ARG   ( 384-)  C    5.06
 371 ILE   ( 382-)  B    5.01
1313 VAL   ( 304-)  C    4.96
 294 THR   ( 305-)  B    4.75
1596 LEU   ( 619-)  C    4.72
 610 LYS   ( 644-)  B    4.71
1101 SER   (  92-)  C    4.69
 235 SER   ( 246-)  B    4.66
 373 ARG   ( 384-)  B    4.63
1459 PHE   ( 462-)  C    4.55
 375 LEU   ( 386-)  B    4.51
1853 ALA   ( 878-)  C    4.43
 585 LEU   ( 619-)  B    4.39
1507 ILE   ( 510-)  C    4.37
 489 GLU   ( 500-)  B    4.37
 684 THR   ( 718-)  B    4.35
2019 ALA   (1048-)  C    4.30
 451 PHE   ( 462-)  B    4.27
1743 ARG   ( 768-)  C    4.27
1695 THR   ( 718-)  C    4.23
 612 LEU   ( 646-)  B    4.21
 242 ASN   ( 253-)  B    4.20
 753 LEU   ( 787-)  B    4.18
 934 ARG   ( 968-)  B    4.13
 200 SER   ( 211-)  B    4.10
 503 PRO   ( 514-)  B    4.10
1391 ILE   ( 382-)  C    4.09
 734 ARG   ( 768-)  B    4.06
 202 VAL   ( 213-)  B    4.03

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 672 PHE   ( 706-)  B      CB   4.55
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -5.922

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -5.922

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.

1729 PHE   ( 754-)  C    -3.4
1314 THR   ( 305-)  C    -3.4
 720 PHE   ( 754-)  B    -3.1
1170 THR   ( 161-)  C    -3.1
1151 PRO   ( 142-)  C    -3.0
1258 ILE   ( 249-)  C    -3.0
 959 TYR   ( 993-)  B    -2.9
 465 ILE   ( 476-)  B    -2.9
1276 LEU   ( 267-)  C    -2.9
 256 LEU   ( 267-)  B    -2.9
  96 PRO   ( 107-)  B    -2.8
1683 PHE   ( 706-)  C    -2.8
1273 ILE   ( 264-)  C    -2.7
1047 PRO   (  38-)  C    -2.7
 778 THR   ( 812-)  B    -2.7
 292 ILE   ( 303-)  B    -2.7
1253 ILE   ( 244-)  C    -2.7
1473 ILE   ( 476-)  C    -2.6
 529 ILE   ( 540-)  B    -2.6
 461 GLU   ( 472-)  B    -2.6
 131 PRO   ( 142-)  B    -2.6
 473 LEU   ( 484-)  B    -2.6
 253 ILE   ( 264-)  B    -2.6
 598 PRO   ( 632-)  B    -2.6
1743 ARG   ( 768-)  C    -2.6
And so on for a total of 150 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.

   4 VAL   (   5-)  B  Poor phi/psi
   7 VAL   (  12-)  B  Poor phi/psi
  17 GLU   (  23-)  B  Poor phi/psi
  18 LYS   (  24-)  B  Poor phi/psi
  21 ARG   (  32-)  B  Poor phi/psi
  60 LYS   (  71-)  B  Poor phi/psi
  70 GLY   (  81-)  B  Poor phi/psi
  77 GLY   (  88-)  B  Poor phi/psi
  90 ARG   ( 101-)  B  Poor phi/psi
 115 ALA   ( 126-)  B  Poor phi/psi
 117 VAL   ( 128-)  B  Poor phi/psi
 121 ASN   ( 132-)  B  Poor phi/psi
 128 GLY   ( 139-)  B  Poor phi/psi
 129 ARG   ( 140-)  B  Poor phi/psi
 130 ILE   ( 141-)  B  Poor phi/psi
 131 PRO   ( 142-)  B  Poor phi/psi
 143 ARG   ( 154-)  B  Poor phi/psi
 162 LEU   ( 173-)  B  Poor phi/psi
 183 VAL   ( 194-)  B  Poor phi/psi
 197 LYS   ( 208-)  B  Poor phi/psi
 199 LYS   ( 210-)  B  Poor phi/psi
 201 TRP   ( 212-)  B  Poor phi/psi
 202 VAL   ( 213-)  B  Poor phi/psi
 218 LYS   ( 229-)  B  Poor phi/psi
 233 ILE   ( 244-)  B  Poor phi/psi
And so on for a total of 205 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -5.000

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.

1676 SER   ( 699-)  C    0.33
 856 SER   ( 890-)  B    0.35
1594 ARG   ( 617-)  C    0.36
 925 SER   ( 959-)  B    0.38
1488 SER   ( 491-)  C    0.38
1482 SER   ( 485-)  C    0.38
 279 GLU   ( 290-)  B    0.38
 583 ARG   ( 617-)  B    0.38

Warning: Unusual backbone conformations

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

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

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

   3 VAL   (   4-)  B      0
   4 VAL   (   5-)  B      0
   5 TYR   (   6-)  B      0
   6 PRO   (  11-)  B      0
   7 VAL   (  12-)  B      0
   9 GLY   (  14-)  B      0
  10 GLY   (  15-)  B      0
  11 LEU   (  17-)  B      0
  12 GLU   (  18-)  B      0
  17 GLU   (  23-)  B      0
  18 LYS   (  24-)  B      0
  19 HIS   (  25-)  B      0
  20 LYS   (  31-)  B      0
  21 ARG   (  32-)  B      0
  24 CYS   (  35-)  B      0
  28 GLU   (  39-)  B      0
  29 ASP   (  40-)  B      0
  42 CYS   (  53-)  B      0
  43 VAL   (  54-)  B      0
  45 GLU   (  56-)  B      0
  67 ALA   (  78-)  B      0
  69 THR   (  80-)  B      0
  73 LYS   (  84-)  B      0
  89 LYS   ( 100-)  B      0
  90 ARG   ( 101-)  B      0
And so on for a total of 783 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 : 1.157

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!

 796 GLY   ( 830-)  B   3.15   13
1805 GLY   ( 830-)  C   3.06   16
 432 GLY   ( 443-)  B   2.03   16
1047 PRO   (  38-)  C   1.84   16
1440 GLY   ( 443-)  C   1.69   15
1952 ASP   ( 981-)  C   1.55   12
1078 LEU   (  69-)  C   1.53   13
1846 GLY   ( 871-)  C   1.52   12

Warning: Unusual peptide bond conformations

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

 734 ARG   ( 768-)  B   1.84
1313 VAL   ( 304-)  C   3.74
1713 LYS   ( 736-)  C   1.58

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]

   2 PRO   (   3-)  B    0.00 LOW
   6 PRO   (  11-)  B    0.00 LOW
1021 PRO   (   3-)  C    0.00 LOW
1026 PRO   (  11-)  C    0.00 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].

  46 PRO   (  57-)  B   105.1 envelop C-beta (108 degrees)
 376 PRO   ( 387-)  B   -44.4 envelop C-alpha (-36 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.

 379 GLU   ( 390-)  B      C   <->  381 HIS   ( 392-)  B      N      0.63    2.27  INTRA BF
  50 GLN   (  61-)  B      NE2 <-> 2028 ANP   (2055-)  B      N6     0.60    2.40  INTRA BL
 454 ARG   ( 465-)  B      NH2 <->  830 GLU   ( 864-)  B      OE2    0.58    2.12  INTRA BL
 380 ARG   ( 391-)  B      N   <->  381 HIS   ( 392-)  B      N      0.55    2.05  INTRA BF
1467 ASP   ( 470-)  C      O   <-> 1469 GLU   ( 472-)  C      N      0.54    2.16  INTRA BF
 459 ASP   ( 470-)  B      O   <->  461 GLU   ( 472-)  B      N      0.53    2.17  INTRA BL
 376 PRO   ( 387-)  B      C   <->  378 VAL   ( 389-)  B      N      0.53    2.37  INTRA BF
 377 ALA   ( 388-)  B      N   <->  378 VAL   ( 389-)  B      N      0.47    2.13  INTRA BF
 656 GLU   ( 690-)  B      OE2 <->  681 ARG   ( 715-)  B      NH1    0.47    2.23  INTRA BL
1477 ASP   ( 480-)  C      O   <-> 1479 GLU   ( 482-)  C      N      0.46    2.24  INTRA BF
1369 ASP   ( 360-)  C      O   <-> 1371 ASP   ( 362-)  C      N      0.45    2.25  INTRA BF
 469 ASP   ( 480-)  B      O   <->  471 GLU   ( 482-)  B      N      0.45    2.25  INTRA BL
 294 THR   ( 305-)  B      CG2 <->  295 ALA   ( 306-)  B      N      0.45    2.55  INTRA BF
1314 THR   ( 305-)  C      O   <-> 1316 THR   ( 307-)  C      N      0.43    2.27  INTRA BF
 750 ASN   ( 784-)  B      ND2 <->  925 SER   ( 959-)  B      N      0.43    2.42  INTRA BL
1253 ILE   ( 244-)  C      CG2 <-> 1254 GLY   ( 245-)  C      N      0.43    2.57  INTRA BL
   1 ILE   (   2-)  B      N   <->    6 PRO   (  11-)  B      N      0.42    2.43  INTRA BL
1021 PRO   (   3-)  C      O   <-> 1026 PRO   (  11-)  C      N      0.42    2.28  INTRA BF
 254 SER   ( 265-)  B      O   <->  256 LEU   ( 267-)  B      N      0.42    2.28  INTRA BF
  75 SER   (  86-)  B      N   <-> 2028 ANP   (2055-)  B      O1A    0.40    2.30  INTRA BL
 574 ASN   ( 608-)  B      ND2 <->  576 ARG   ( 610-)  B      CB     0.40    2.70  INTRA BL
 518 VAL   ( 529-)  B      CG1 <->  519 LYS   ( 530-)  B      N      0.39    2.61  INTRA BL
 402 ASP   ( 413-)  B      OD2 <->  826 ARG   ( 860-)  B      NH2    0.37    2.33  INTRA BL
1783 THR   ( 808-)  C      CG2 <-> 1823 ARG   ( 848-)  C      NE     0.37    2.73  INTRA BL
 784 SER   ( 818-)  B      N   <->  811 GLU   ( 845-)  B      OE2    0.37    2.33  INTRA BL
And so on for a total of 1138 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: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

  21 ARG   (  32-)  B      -7.79
1149 ARG   ( 140-)  C      -7.75
 129 ARG   ( 140-)  B      -7.67
1964 TYR   ( 993-)  C      -7.32
1398 ARG   ( 397-)  C      -7.26
1786 ARG   ( 811-)  C      -6.83
 777 ARG   ( 811-)  B      -6.79
1414 ARG   ( 417-)  C      -6.76
 959 TYR   ( 993-)  B      -6.73
 406 ARG   ( 417-)  B      -6.67
 399 GLN   ( 410-)  B      -6.65
 908 ARG   ( 942-)  B      -6.62
1709 ARG   ( 732-)  C      -6.53
 698 ARG   ( 732-)  B      -6.52
 218 LYS   ( 229-)  B      -6.42
1237 LYS   ( 228-)  C      -6.41
 217 LYS   ( 228-)  B      -6.36
1405 ARG   ( 408-)  C      -6.33
1238 LYS   ( 229-)  C      -6.30
1292 ARG   ( 283-)  C      -6.28
 272 ARG   ( 283-)  B      -6.21
1364 ARG   ( 355-)  C      -6.16
1686 ARG   ( 709-)  C      -6.16
1407 GLN   ( 410-)  C      -6.04
1913 ARG   ( 942-)  C      -6.03
And so on for a total of 74 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 395 LYS   ( 406-)  B       397 - ARG    408- ( B)         -4.79
1711 ARG   ( 734-)  C      1713 - LYS    736- ( C)         -4.55

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

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.

1039 LYS   (  24-)  C   -3.87
  18 LYS   (  24-)  B   -3.67
1032 LEU   (  17-)  C   -2.79
1180 ARG   ( 171-)  C   -2.73
   8 CYS   (  13-)  B   -2.65
  16 ILE   (  22-)  B   -2.55
1024 TYR   (   6-)  C   -2.54

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.

   1 ILE   (   2-)  B     -    5 TYR   (   6-)  B        -2.08
   6 PRO   (  11-)  B     -   10 GLY   (  15-)  B        -2.10
  15 GLU   (  21-)  B     -   18 LYS   (  24-)  B        -2.50
1021 PRO   (   3-)  C     - 1025 SER   (   7-)  C        -1.96
1035 LYS   (  20-)  C     - 1039 LYS   (  24-)  C        -2.34

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: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

  50 GLN   (  61-)  B
 127 HIS   ( 138-)  B
 140 GLN   ( 151-)  B
 574 ASN   ( 608-)  B
 587 HIS   ( 621-)  B
 715 HIS   ( 749-)  B
 750 ASN   ( 784-)  B
 770 ASN   ( 804-)  B
 842 HIS   ( 876-)  B
 924 GLN   ( 958-)  B
1070 GLN   (  61-)  C
1160 GLN   ( 151-)  C
1331 HIS   ( 322-)  C
1516 GLN   ( 519-)  C
1585 ASN   ( 608-)  C
1598 HIS   ( 621-)  C
1759 ASN   ( 784-)  C
1779 ASN   ( 804-)  C
1851 HIS   ( 876-)  C
1929 GLN   ( 958-)  C

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.

   7 VAL   (  12-)  B      N
  13 SER   (  19-)  B      N
  47 ARG   (  58-)  B      NE
  47 ARG   (  58-)  B      NH2
  49 ILE   (  60-)  B      N
  50 GLN   (  61-)  B      NE2
  53 TRP   (  64-)  B      NE1
  56 ARG   (  67-)  B      NE
  59 ARG   (  70-)  B      NH1
  66 THR   (  77-)  B      N
  70 GLY   (  81-)  B      N
  72 GLY   (  83-)  B      N
  75 SER   (  86-)  B      OG
  81 SER   (  92-)  B      OG
  90 ARG   ( 101-)  B      NH2
  97 THR   ( 108-)  B      N
 118 GLY   ( 129-)  B      N
 121 ASN   ( 132-)  B      N
 123 ILE   ( 134-)  B      N
 127 HIS   ( 138-)  B      N
 133 ARG   ( 144-)  B      N
 134 GLU   ( 145-)  B      N
 143 ARG   ( 154-)  B      N
 145 PHE   ( 156-)  B      N
 155 LEU   ( 166-)  B      N
And so on for a total of 284 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.

  28 GLU   (  39-)  B      OE2
  45 GLU   (  56-)  B      OE1
 158 HIS   ( 169-)  B      ND1
 188 HIS   ( 199-)  B      ND1
 311 HIS   ( 322-)  B      ND1
 478 ASP   ( 489-)  B      OD1
 488 GLN   ( 499-)  B      OE1
 857 GLN   ( 891-)  B      OE1
1048 GLU   (  39-)  C      OE2
1065 GLU   (  56-)  C      OE1
1178 HIS   ( 169-)  C      ND1
1208 HIS   ( 199-)  C      ND1
1390 GLU   ( 381-)  C      OE1
1410 ASP   ( 413-)  C      OD1
1451 ASP   ( 454-)  C      OD1
1496 GLN   ( 499-)  C      OE1
1497 GLU   ( 500-)  C      OE2
1619 ASP   ( 642-)  C      OD2
1866 GLN   ( 891-)  C      OE1
1990 GLU   (1019-)  C      OE2

Warning: Unusual ion packing

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

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

2029  MG   (2056-)  B   -.-  -.-  Too few ligands (1)
2031  MG   (2056-)  C   -.-  -.-  Too few ligands (1)
Since there are no waters, the water check has been skipped.

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.

 282 GLU   ( 293-)  B   H-bonding suggests Gln
 300 ASP   ( 311-)  B   H-bonding suggests Asn
 370 GLU   ( 381-)  B   H-bonding suggests Gln
 379 GLU   ( 390-)  B   H-bonding suggests Gln; but Alt-Rotamer
 696 GLU   ( 730-)  B   H-bonding suggests Gln
 717 GLU   ( 751-)  B   H-bonding suggests Gln
 718 GLU   ( 752-)  B   H-bonding suggests Gln
 719 GLU   ( 753-)  B   H-bonding suggests Gln
 721 ASP   ( 755-)  B   H-bonding suggests Asn; but Alt-Rotamer
 798 ASP   ( 832-)  B   H-bonding suggests Asn; but Alt-Rotamer
 891 GLU   ( 925-)  B   H-bonding suggests Gln
 957 GLU   ( 991-)  B   H-bonding suggests Gln
 990 ASP   (1024-)  B   H-bonding suggests Asn
1302 GLU   ( 293-)  C   H-bonding suggests Gln
1320 ASP   ( 311-)  C   H-bonding suggests Asn; but Alt-Rotamer
1371 ASP   ( 362-)  C   H-bonding suggests Asn
1390 GLU   ( 381-)  C   H-bonding suggests Gln
1451 ASP   ( 454-)  C   H-bonding suggests Asn; but Alt-Rotamer
1469 GLU   ( 472-)  C   H-bonding suggests Gln
1619 ASP   ( 642-)  C   H-bonding suggests Asn
1703 ASP   ( 726-)  C   H-bonding suggests Asn
1707 GLU   ( 730-)  C   H-bonding suggests Gln; but Alt-Rotamer
1710 GLU   ( 733-)  C   H-bonding suggests Gln
1726 GLU   ( 751-)  C   H-bonding suggests Gln
1727 GLU   ( 752-)  C   H-bonding suggests Gln
1728 GLU   ( 753-)  C   H-bonding suggests Gln
1730 ASP   ( 755-)  C   H-bonding suggests Asn; but Alt-Rotamer
1807 ASP   ( 832-)  C   H-bonding suggests Asn; but Alt-Rotamer
1896 GLU   ( 925-)  C   H-bonding suggests Gln
1962 GLU   ( 991-)  C   H-bonding suggests Gln; but Alt-Rotamer
1995 ASP   (1024-)  C   H-bonding suggests Asn

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 :  -1.869
  2nd generation packing quality :  -2.324
  Ramachandran plot appearance   :  -5.922 (bad)
  chi-1/chi-2 rotamer normality  :  -5.000 (bad)
  Backbone conformation          :  -0.157

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.348 (tight)
  Bond angles                    :   0.658 (tight)
  Omega angle restraints         :   0.210 (tight)
  Side chain planarity           :   0.206 (tight)
  Improper dihedral distribution :   0.670
  Inside/Outside distribution    :   1.042

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :  -2.9
  chi-1/chi-2 rotamer normality  :  -2.5
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.348 (tight)
  Bond angles                    :   0.658 (tight)
  Omega angle restraints         :   0.210 (tight)
  Side chain planarity           :   0.206 (tight)
  Improper dihedral distribution :   0.670
  Inside/Outside distribution    :   1.042
==============

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.