WHAT IF Check report

This file was created 2013-12-09 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 pdb3ac0.ent

Checks that need to be done early-on in validation

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: C 1 2 1
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 3
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 16
Polymer chain multiplicity and SEQRES multiplicity disagree 3 4
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

3331 BGC   (5001-)  A  -
3332 BGC   (5002-)  B  -
3333 BGC   (5003-)  C  -
3334 BGC   (5004-)  D  -

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

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

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.

2066 ALA   ( 402-)  C    High
2067 ALA   ( 403-)  C    High
2068 LYS   ( 404-)  C    High
2069 PRO   ( 405-)  C    High
2070 GLU   ( 409-)  C    High
2917 VAL   ( 422-)  D    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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

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

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.

 250 ARG   ( 251-)  A
 262 ARG   ( 263-)  A
 273 ARG   ( 274-)  A
 424 ARG   ( 425-)  A
1090 ARG   ( 251-)  B
1102 ARG   ( 263-)  B
1113 ARG   ( 274-)  B
1261 ARG   ( 425-)  B
1915 ARG   ( 251-)  C
1927 ARG   ( 263-)  C
1938 ARG   ( 274-)  C
2086 ARG   ( 425-)  C
2746 ARG   ( 251-)  D
2758 ARG   ( 263-)  D
2769 ARG   ( 274-)  D

Warning: Tyrosine convention problem

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

 362 TYR   ( 363-)  A
 417 TYR   ( 418-)  A
 481 TYR   ( 482-)  A
 588 TYR   ( 592-)  A
 696 TYR   ( 700-)  A
 798 TYR   ( 802-)  A
 813 TYR   ( 817-)  A
1322 TYR   ( 488-)  B
1357 TYR   ( 527-)  B
1413 TYR   ( 592-)  B
1521 TYR   ( 700-)  B
1623 TYR   ( 802-)  B
1638 TYR   ( 817-)  B
2079 TYR   ( 418-)  C
2117 TYR   ( 458-)  C
2309 TYR   ( 657-)  C
2352 TYR   ( 700-)  C
2411 TYR   ( 759-)  C
2454 TYR   ( 802-)  C
2469 TYR   ( 817-)  C
2876 TYR   ( 381-)  D
2945 TYR   ( 458-)  D
2975 TYR   ( 488-)  D
3073 TYR   ( 592-)  D
3138 TYR   ( 657-)  D
3181 TYR   ( 700-)  D
3197 TYR   ( 716-)  D
3240 TYR   ( 759-)  D
3283 TYR   ( 802-)  D
3298 TYR   ( 817-)  D

Warning: Phenylalanine convention problem

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

   3 PHE   (   4-)  A
  26 PHE   (  27-)  A
  54 PHE   (  55-)  A
  63 PHE   (  64-)  A
  73 PHE   (  74-)  A
 157 PHE   ( 158-)  A
 176 PHE   ( 177-)  A
 226 PHE   ( 227-)  A
 243 PHE   ( 244-)  A
 416 PHE   ( 417-)  A
 458 PHE   ( 459-)  A
 486 PHE   ( 487-)  A
 541 PHE   ( 545-)  A
 546 PHE   ( 550-)  A
 719 PHE   ( 723-)  A
 756 PHE   ( 760-)  A
 773 PHE   ( 777-)  A
 799 PHE   ( 803-)  A
 830 PHE   ( 834-)  A
 843 PHE   (   4-)  B
 866 PHE   (  27-)  B
 903 PHE   (  64-)  B
 913 PHE   (  74-)  B
 997 PHE   ( 158-)  B
1016 PHE   ( 177-)  B
And so on for a total of 72 lines.

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 224 ASP   ( 225-)  A
 406 ASP   ( 407-)  A
 471 ASP   ( 472-)  A
 722 ASP   ( 726-)  A
 731 ASP   ( 735-)  A
 823 ASP   ( 827-)  A
1246 ASP   ( 407-)  B
1263 ASP   ( 427-)  B
1556 ASP   ( 735-)  B
1648 ASP   ( 827-)  B
2088 ASP   ( 427-)  C
2378 ASP   ( 726-)  C
2386 ASP   ( 734-)  C
2387 ASP   ( 735-)  C
2445 ASP   ( 793-)  C
2902 ASP   ( 407-)  D
2959 ASP   ( 472-)  D
3041 ASP   ( 560-)  D
3279 ASP   ( 798-)  D

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.

  16 GLU   (  17-)  A
  33 GLU   (  34-)  A
 377 GLU   ( 378-)  A
 428 GLU   ( 429-)  A
 501 GLU   ( 502-)  A
 584 GLU   ( 588-)  A
 629 GLU   ( 633-)  A
 750 GLU   ( 754-)  A
 769 GLU   ( 773-)  A
 791 GLU   ( 795-)  A
 833 GLU   ( 837-)  A
 856 GLU   (  17-)  B
 873 GLU   (  34-)  B
1266 GLU   ( 430-)  B
1326 GLU   ( 492-)  B
1336 GLU   ( 502-)  B
1454 GLU   ( 633-)  B
1575 GLU   ( 754-)  B
1626 GLU   ( 805-)  B
1658 GLU   ( 837-)  B
1681 GLU   (  17-)  C
1803 GLU   ( 139-)  C
2000 GLU   ( 336-)  C
2033 GLU   ( 369-)  C
2090 GLU   ( 429-)  C
2130 GLU   ( 471-)  C
2171 GLU   ( 514-)  C
2240 GLU   ( 588-)  C
2406 GLU   ( 754-)  C
2512 GLU   (  17-)  D
2529 GLU   (  34-)  D
2649 GLU   ( 154-)  D
2904 GLU   ( 409-)  D
2989 GLU   ( 502-)  D
3076 GLU   ( 595-)  D
3114 GLU   ( 633-)  D
3235 GLU   ( 754-)  D
3276 GLU   ( 795-)  D
3318 GLU   ( 837-)  D

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.

 241 ILE   ( 242-)  A      CA   CB    1.63    4.9
2416 ASN   ( 764-)  C      CB   CG    1.62    4.3

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

 |  0.997488  0.000238 -0.000066|
 |  0.000238  0.997670  0.000272|
 | -0.000066  0.000272  0.998083|
Proposed new scale matrix

 |  0.004078 -0.000001  0.001717|
 | -0.000002  0.006754 -0.000002|
 |  0.000000 -0.000002  0.009086|
With corresponding cell

    A    = 245.198  B   = 148.066  C    = 119.406
    Alpha=  89.982  Beta= 112.827  Gamma=  89.973

The CRYST1 cell dimensions

    A    = 245.847  B   = 148.412  C    = 119.642
    Alpha=  90.000  Beta= 112.840  Gamma=  90.000

Variance: 554.128
(Under-)estimated Z-score: 17.349

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.

 148 VAL   ( 149-)  A     -C    N    CA  129.15    4.1
 387 HIS   ( 388-)  A      CG   ND1  CE1 109.68    4.1
1333 HIS   ( 499-)  B      N    CA   C   124.42    4.7
1334 ASN   ( 500-)  B     -C    N    CA  111.22   -5.8
1396 ASP   ( 575-)  B      C    CA   CB  102.32   -4.1
1400 LEU   ( 579-)  B      CA   CB   CG  134.86    5.3
1556 ASP   ( 735-)  B      N    CA   C   124.62    4.8
1588 VAL   ( 767-)  B      N    CA   CB  103.10   -4.4
1668 PHE   (   4-)  C      N    CA   CB  103.03   -4.4
1913 ARG   ( 249-)  C      CB   CG   CD  104.92   -4.6
2196 SER   ( 539-)  C      N    CA   C    99.70   -4.1
2385 THR   ( 733-)  C      C    CA   CB   99.19   -5.7
2695 HIS   ( 200-)  D      CG   ND1  CE1 109.83    4.2
2883 HIS   ( 388-)  D      CG   ND1  CE1 109.66    4.1
3262 HIS   ( 781-)  D      CG   ND1  CE1 109.62    4.0

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.

  16 GLU   (  17-)  A
  33 GLU   (  34-)  A
 224 ASP   ( 225-)  A
 250 ARG   ( 251-)  A
 262 ARG   ( 263-)  A
 273 ARG   ( 274-)  A
 377 GLU   ( 378-)  A
 406 ASP   ( 407-)  A
 424 ARG   ( 425-)  A
 428 GLU   ( 429-)  A
 471 ASP   ( 472-)  A
 501 GLU   ( 502-)  A
 584 GLU   ( 588-)  A
 629 GLU   ( 633-)  A
 722 ASP   ( 726-)  A
 731 ASP   ( 735-)  A
 750 GLU   ( 754-)  A
 769 GLU   ( 773-)  A
 791 GLU   ( 795-)  A
 823 ASP   ( 827-)  A
 833 GLU   ( 837-)  A
 856 GLU   (  17-)  B
 873 GLU   (  34-)  B
1090 ARG   ( 251-)  B
1102 ARG   ( 263-)  B
And so on for a total of 73 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.

1929 GLN   ( 265-)  C      CA    -6.4    21.60    33.96
The average deviation= 1.079

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.

2164 CYS   ( 507-)  C    5.12
1993 ASN   ( 329-)  C    5.11
 796 ILE   ( 800-)  A    4.63
1672 GLN   (   8-)  C    4.55
2196 SER   ( 539-)  C    4.54
1556 ASP   ( 735-)  B    4.52
1621 ILE   ( 800-)  B    4.34
1333 HIS   ( 499-)  B    4.27
3023 GLY   ( 536-)  D    4.24
1316 TYR   ( 482-)  B    4.14
 123 LEU   ( 124-)  A    4.11
3165 LYS   ( 684-)  D    4.09
 843 PHE   (   4-)  B    4.07

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

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

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

1288 PRO   ( 454-)  B    -3.0
 102 THR   ( 103-)  A    -3.0
1508 PHE   ( 687-)  B    -2.8
1216 LYS   ( 377-)  B    -2.8
 683 PHE   ( 687-)  A    -2.8
3277 LEU   ( 796-)  D    -2.8
 942 THR   ( 103-)  B    -2.8
2210 ILE   ( 558-)  C    -2.7
 729 THR   ( 733-)  A    -2.7
2899 LYS   ( 404-)  D    -2.7
3168 PHE   ( 687-)  D    -2.6
2446 LEU   ( 794-)  C    -2.6
2648 LEU   ( 153-)  D    -2.6
2164 CYS   ( 507-)  C    -2.6
2994 CYS   ( 507-)  D    -2.6
 790 LEU   ( 794-)  A    -2.6
1554 THR   ( 733-)  B    -2.5
2740 PRO   ( 245-)  D    -2.5
 721 LEU   ( 725-)  A    -2.5
 506 CYS   ( 507-)  A    -2.5
1909 PRO   ( 245-)  C    -2.4
 529 ARG   ( 530-)  A    -2.4
2938 LYS   ( 451-)  D    -2.4
2377 LEU   ( 725-)  C    -2.4
2365 PRO   ( 713-)  C    -2.4
And so on for a total of 132 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.

  25 ASP   (  26-)  A  Poor phi/psi
  43 SER   (  44-)  A  omega poor
  44 ASP   (  45-)  A  omega poor
  51 GLY   (  52-)  A  omega poor
  56 ASP   (  57-)  A  Poor phi/psi
  93 ASN   (  94-)  A  Poor phi/psi
  99 GLY   ( 100-)  A  PRO omega poor
 102 THR   ( 103-)  A  omega poor
 105 GLN   ( 106-)  A  Poor phi/psi
 106 ARG   ( 107-)  A  omega poor
 108 PRO   ( 109-)  A  omega poor
 145 LYS   ( 146-)  A  omega poor
 147 PHE   ( 148-)  A  omega poor
 149 CYS   ( 150-)  A  Poor phi/psi
 151 ASP   ( 152-)  A  omega poor
 155 GLN   ( 156-)  A  Poor phi/psi
 162 ILE   ( 163-)  A  omega poor
 169 ARG   ( 170-)  A  omega poor
 171 ILE   ( 172-)  A  omega poor
 173 LEU   ( 174-)  A  omega poor
 182 HIS   ( 183-)  A  omega poor
 183 ALA   ( 184-)  A  Poor phi/psi
 206 LEU   ( 207-)  A  omega poor
 223 SER   ( 224-)  A  omega poor
 226 PHE   ( 227-)  A  Poor phi/psi
And so on for a total of 233 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 : -3.082

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.

 309 SER   ( 310-)  A    0.35
 130 SER   ( 131-)  A    0.36
1794 SER   ( 130-)  C    0.38
1754 SER   (  90-)  C    0.38
2506 SER   (  11-)  D    0.39
2626 SER   ( 131-)  D    0.40

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 PHE   (   4-)  A      0
  21 LEU   (  22-)  A      0
  24 VAL   (  25-)  A      0
  27 TRP   (  28-)  A      0
  28 HIS   (  29-)  A      0
  30 LYS   (  31-)  A      0
  44 ASP   (  45-)  A      0
  46 PRO   (  47-)  A      0
  47 ASN   (  48-)  A      0
  50 ARG   (  51-)  A      0
  52 THR   (  53-)  A      0
  53 LYS   (  54-)  A      0
  54 PHE   (  55-)  A      0
  55 PHE   (  56-)  A      0
  73 PHE   (  74-)  A      0
  95 ALA   (  96-)  A      0
  98 LEU   (  99-)  A      0
 100 PRO   ( 101-)  A      0
 101 THR   ( 102-)  A      0
 102 THR   ( 103-)  A      0
 103 ASN   ( 104-)  A      0
 104 MET   ( 105-)  A      0
 106 ARG   ( 107-)  A      0
 108 PRO   ( 109-)  A      0
 116 SER   ( 117-)  A      0
And so on for a total of 1425 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!

2200 GLY   ( 548-)  C   2.99   10
 545 GLY   ( 549-)  A   1.80   24
2191 GLY   ( 534-)  C   1.80   22
1538 GLY   ( 717-)  B   1.76   50
 713 GLY   ( 717-)  A   1.73   46
 533 GLY   ( 534-)  A   1.73   25
  66 GLY   (  67-)  A   1.67   19
3066 GLY   ( 585-)  D   1.64   15
3198 GLY   ( 717-)  D   1.63   65
3030 GLY   ( 549-)  D   1.59   23
3023 GLY   ( 536-)  D   1.58   12

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]

 100 PRO   ( 101-)  A    0.19 LOW
 468 PRO   ( 469-)  A    0.16 LOW
 626 PRO   ( 630-)  A    0.12 LOW
1206 PRO   ( 367-)  B    0.13 LOW
1447 PRO   ( 626-)  B    0.45 HIGH
1451 PRO   ( 630-)  B    0.05 LOW
1483 PRO   ( 662-)  B    0.07 LOW
1729 PRO   (  65-)  C    0.17 LOW
2617 PRO   ( 122-)  D    0.20 LOW
2671 PRO   ( 176-)  D    0.14 LOW
2681 PRO   ( 186-)  D    0.14 LOW
3111 PRO   ( 630-)  D    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].

  59 PRO   (  60-)  A   102.3 envelop C-beta (108 degrees)
 175 PRO   ( 176-)  A  -122.9 half-chair C-delta/C-gamma (-126 degrees)
 244 PRO   ( 245-)  A   -48.0 half-chair C-beta/C-alpha (-54 degrees)
 246 PRO   ( 247-)  A   -12.6 half-chair C-alpha/N (-18 degrees)
 404 PRO   ( 405-)  A   -30.2 envelop C-alpha (-36 degrees)
 420 PRO   ( 421-)  A   -61.5 half-chair C-beta/C-alpha (-54 degrees)
 658 PRO   ( 662-)  A    99.4 envelop C-beta (108 degrees)
 674 PRO   ( 678-)  A  -112.6 envelop C-gamma (-108 degrees)
 940 PRO   ( 101-)  B  -117.4 half-chair C-delta/C-gamma (-126 degrees)
1267 PRO   ( 431-)  B  -117.8 half-chair C-delta/C-gamma (-126 degrees)
1288 PRO   ( 454-)  B   125.8 half-chair C-beta/C-alpha (126 degrees)
1291 PRO   ( 457-)  B   -33.4 envelop C-alpha (-36 degrees)
1303 PRO   ( 469-)  B   103.6 envelop C-beta (108 degrees)
1367 PRO   ( 537-)  B    51.3 half-chair C-delta/C-gamma (54 degrees)
1421 PRO   ( 600-)  B    43.5 envelop C-delta (36 degrees)
1703 PRO   (  39-)  C   -40.9 envelop C-alpha (-36 degrees)
1850 PRO   ( 186-)  C     5.7 envelop N (0 degrees)
1909 PRO   ( 245-)  C   -54.3 half-chair C-beta/C-alpha (-54 degrees)
1911 PRO   ( 247-)  C   -33.1 envelop C-alpha (-36 degrees)
2113 PRO   ( 454-)  C  -112.3 envelop C-gamma (-108 degrees)
2116 PRO   ( 457-)  C    37.3 envelop C-delta (36 degrees)
2252 PRO   ( 600-)  C   -37.2 envelop C-alpha (-36 degrees)
2267 PRO   ( 615-)  C   110.6 envelop C-beta (108 degrees)
2282 PRO   ( 630-)  C    48.0 half-chair C-delta/C-gamma (54 degrees)
2534 PRO   (  39-)  D   -58.0 half-chair C-beta/C-alpha (-54 degrees)
2555 PRO   (  60-)  D  -159.2 half-chair N/C-delta (-162 degrees)
2862 PRO   ( 367-)  D    47.7 half-chair C-delta/C-gamma (54 degrees)
2918 PRO   ( 431-)  D    27.3 envelop C-delta (36 degrees)
2944 PRO   ( 457-)  D     3.3 envelop N (0 degrees)
2956 PRO   ( 469-)  D   -57.6 half-chair C-beta/C-alpha (-54 degrees)
3081 PRO   ( 600-)  D    47.0 half-chair C-delta/C-gamma (54 degrees)
3159 PRO   ( 678-)  D  -114.9 envelop C-gamma (-108 degrees)
3251 PRO   ( 770-)  D    47.7 half-chair C-delta/C-gamma (54 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.

1334 ASN   ( 500-)  B      O   <-> 1345 ARG   ( 515-)  B      NH2    0.63    2.07  INTRA BF
1648 ASP   ( 827-)  B      CB  <-> 3336 HOH   (1558 )  B      O      0.46    2.34  INTRA BL
2902 ASP   ( 407-)  D      CG  <-> 2903 ALA   ( 408-)  D      N      0.45    2.55  INTRA BF
  85 MET   (  86-)  A      CE  <-> 3335 HOH   (1538 )  A      O      0.43    2.37  INTRA BL
2512 GLU   (  17-)  D      OE1 <-> 2530 ARG   (  35-)  D      NH2    0.43    2.27  INTRA BL
1355 GLN   ( 525-)  B      NE2 <-> 3336 HOH   (1374 )  B      O      0.40    2.30  INTRA BF
2385 THR   ( 733-)  C      OG1 <-> 2387 ASP   ( 735-)  C      N      0.40    2.30  INTRA BF
1637 GLU   ( 816-)  B      OE1 <-> 1654 GLU   ( 833-)  B      OE2    0.38    2.02  INTRA BF
1699 ARG   (  35-)  C      N   <-> 3337 HOH   (1189 )  C      O      0.37    2.33  INTRA BF
2771 ARG   ( 276-)  D      NH2 <-> 3338 HOH   (1130 )  D      O      0.35    2.35  INTRA BL
3226 ASN   ( 745-)  D      ND2 <-> 3231 PHE   ( 750-)  D      O      0.34    2.36  INTRA BF
2387 ASP   ( 735-)  C      C   <-> 2388 LYS   ( 736-)  C      CG     0.33    2.77  INTRA BF
2903 ALA   ( 408-)  D      O   <-> 2923 LYS   ( 436-)  D      NZ     0.32    2.38  INTRA BF
1136 ASN   ( 297-)  B      CB  <-> 3336 HOH   ( 897 )  B      O      0.31    2.49  INTRA BL
1497 ASP   ( 676-)  B      O   <-> 1529 ARG   ( 708-)  B      NH1    0.31    2.39  INTRA BL
1554 THR   ( 733-)  B      OG1 <-> 1556 ASP   ( 735-)  B      N      0.31    2.39  INTRA BF
 482 GLY   ( 483-)  A      O   <->  500 GLN   ( 501-)  A      NE2    0.31    2.39  INTRA BF
 729 THR   ( 733-)  A      OG1 <->  730 ASP   ( 734-)  A      N      0.30    2.30  INTRA BF
1331 GLN   ( 497-)  B      O   <-> 1335 GLN   ( 501-)  B      NE2    0.29    2.41  INTRA BF
 833 GLU   ( 837-)  A      N   <-> 3335 HOH   (1167 )  A      O      0.29    2.41  INTRA BF
2081 ASN   ( 420-)  C      O   <-> 2086 ARG   ( 425-)  C      NH1    0.28    2.42  INTRA BF
2920 HIS   ( 433-)  D      ND1 <-> 3338 HOH   (1528 )  D      O      0.27    2.43  INTRA BF
3043 GLU   ( 562-)  D      CG  <-> 3338 HOH   (1448 )  D      O      0.27    2.53  INTRA BF
1815 ASN   ( 151-)  C      ND2 <-> 3337 HOH   ( 991 )  C      O      0.27    2.43  INTRA BL
2919 PHE   ( 432-)  D      CD2 <-> 2936 HIS   ( 449-)  D      ND1    0.27    2.83  INTRA BF
And so on for a total of 510 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

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.

1316 TYR   ( 482-)  B      -7.24
2160 ARG   ( 503-)  C      -6.97
 502 ARG   ( 503-)  A      -6.95
2990 ARG   ( 503-)  D      -6.74
 469 GLN   ( 470-)  A      -6.66
1337 ARG   ( 503-)  B      -6.62
2129 GLN   ( 470-)  C      -6.60
 541 PHE   ( 545-)  A      -6.37
1292 TYR   ( 458-)  B      -6.34
2957 GLN   ( 470-)  D      -6.22
1289 LYS   ( 455-)  B      -6.20
2969 TYR   ( 482-)  D      -6.18
1282 LYS   ( 448-)  B      -6.00
2109 LYS   ( 448-)  C      -5.97
2114 LYS   ( 455-)  C      -5.89
1022 HIS   ( 183-)  B      -5.86
2141 TYR   ( 482-)  C      -5.85
2942 LYS   ( 455-)  D      -5.83
1304 GLN   ( 470-)  B      -5.83
 454 LYS   ( 455-)  A      -5.79
 447 LYS   ( 448-)  A      -5.78
 182 HIS   ( 183-)  A      -5.75
2678 HIS   ( 183-)  D      -5.66
2050 TYR   ( 386-)  C      -5.64
1847 HIS   ( 183-)  C      -5.61
And so on for a total of 57 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.

 744 ASP   ( 748-)  A       746 - PHE    750- ( A)         -4.47
2084 GLU   ( 423-)  C      2086 - ARG    425- ( C)         -4.47
2400 ASP   ( 748-)  C      2402 - PHE    750- ( C)         -4.46

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

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.

2027 TYR   ( 363-)  C   -2.60

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.

 357 SER   ( 358-)  A     -  360 SER   ( 361-)  A        -1.53

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

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

3337 HOH   (1131 )  C      O     69.12   -2.75   41.33

Error: Water molecules without hydrogen bonds

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

3335 HOH   (1000 )  A      O
3335 HOH   (1138 )  A      O
3335 HOH   (1366 )  A      O
3336 HOH   ( 920 )  B      O
3336 HOH   ( 999 )  B      O
3336 HOH   (1015 )  B      O
3336 HOH   (1072 )  B      O
3336 HOH   (1231 )  B      O
3336 HOH   (1441 )  B      O
3336 HOH   (1511 )  B      O
3336 HOH   (1513 )  B      O
3337 HOH   ( 849 )  C      O
3337 HOH   ( 921 )  C      O
3337 HOH   ( 999 )  C      O
3337 HOH   (1031 )  C      O
3337 HOH   (1099 )  C      O
3337 HOH   (1417 )  C      O
3337 HOH   (1470 )  C      O
3337 HOH   (1557 )  C      O
3338 HOH   ( 913 )  D      O
3338 HOH   ( 946 )  D      O
3338 HOH   ( 950 )  D      O
3338 HOH   (1125 )  D      O
3338 HOH   (1289 )  D      O
3338 HOH   (1370 )  D      O
3338 HOH   (1448 )  D      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  47 ASN   (  48-)  A
  93 ASN   (  94-)  A
 150 ASN   ( 151-)  A
 442 HIS   ( 443-)  A
 479 GLN   ( 480-)  A
 632 ASN   ( 636-)  A
 671 GLN   ( 675-)  A
 887 ASN   (  48-)  B
 933 ASN   (  94-)  B
 990 ASN   ( 151-)  B
1227 HIS   ( 388-)  B
1259 ASN   ( 420-)  B
1314 GLN   ( 480-)  B
1355 GLN   ( 525-)  B
1712 ASN   (  48-)  C
1758 ASN   (  94-)  C
1815 ASN   ( 151-)  C
2081 ASN   ( 420-)  C
2334 ASN   ( 682-)  C
2416 ASN   ( 764-)  C
2543 ASN   (  48-)  D
2589 ASN   (  94-)  D
2646 ASN   ( 151-)  D
2680 ASN   ( 185-)  D
2883 HIS   ( 388-)  D
3117 ASN   ( 636-)  D
3262 HIS   ( 781-)  D

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.

  22 SER   (  23-)  A      N
  53 LYS   (  54-)  A      N
  56 ASP   (  57-)  A      N
  62 CYS   (  63-)  A      N
 105 GLN   ( 106-)  A      NE2
 107 GLY   ( 108-)  A      N
 112 ARG   ( 113-)  A      NH1
 150 ASN   ( 151-)  A      N
 172 TYR   ( 173-)  A      OH
 174 GLU   ( 175-)  A      N
 177 ARG   ( 178-)  A      NH1
 193 ASN   ( 194-)  A      N
 228 THR   ( 229-)  A      N
 230 THR   ( 231-)  A      N
 335 GLU   ( 336-)  A      N
 362 TYR   ( 363-)  A      N
 408 GLU   ( 409-)  A      N
 409 ASN   ( 410-)  A      N
 410 SER   ( 411-)  A      N
 422 GLU   ( 423-)  A      N
 470 GLU   ( 471-)  A      N
 548 ALA   ( 552-)  A      N
 558 GLU   ( 562-)  A      N
 580 ASN   ( 584-)  A      N
 592 ASN   ( 596-)  A      N
And so on for a total of 190 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.

 193 ASN   ( 194-)  A      OD1
 617 ASN   ( 621-)  A      OD1
 847 GLN   (   8-)  B      OE1
 986 HIS   ( 147-)  B      NE2
1033 ASN   ( 194-)  B      OD1
1039 HIS   ( 200-)  B      ND1
1331 GLN   ( 497-)  B      OE1
1442 ASN   ( 621-)  B      OD1
1654 GLU   ( 833-)  B      OE1
1654 GLU   ( 833-)  B      OE2
1709 ASP   (  45-)  C      OD1
1811 HIS   ( 147-)  C      NE2
2052 HIS   ( 388-)  C      ND1
2156 GLN   ( 497-)  C      OE1
2226 HIS   ( 574-)  C      ND1
2273 ASN   ( 621-)  C      OD1
2485 GLU   ( 833-)  C      OE1
2540 ASP   (  45-)  D      OD1
2642 HIS   ( 147-)  D      NE2
3102 ASN   ( 621-)  D      OD1
3245 ASN   ( 764-)  D      OD1
3314 GLU   ( 833-)  D      OE1

Warning: Unusual water packing

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

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

3335 HOH   (1012 )  A      O  0.97  K  4 *2
3335 HOH   (1165 )  A      O  1.04  K  4 *2
3335 HOH   (1485 )  A      O  0.84  K  6 *2 Ion-B
3336 HOH   ( 863 )  B      O  1.20  K  4 *2
3336 HOH   (1075 )  B      O  0.96  K  4 *2
3336 HOH   (1143 )  B      O  1.19  K  4 *2
3337 HOH   ( 905 )  C      O  1.10  K  4 *2
3338 HOH   (1012 )  D      O  0.91  K  4 *2 Ion-B

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.

 310 ASP   ( 311-)  A   H-bonding suggests Asn; but Alt-Rotamer
 445 ASP   ( 446-)  A   H-bonding suggests Asn
 789 ASP   ( 793-)  A   H-bonding suggests Asn
 851 GLU   (  12-)  B   H-bonding suggests Gln; but Alt-Rotamer
1038 GLU   ( 199-)  B   H-bonding suggests Gln
1614 ASP   ( 793-)  B   H-bonding suggests Asn
2001 ASP   ( 337-)  C   H-bonding suggests Asn
2107 ASP   ( 446-)  C   H-bonding suggests Asn
2130 GLU   ( 471-)  C   H-bonding suggests Gln
2891 GLU   ( 396-)  D   H-bonding suggests Gln
2933 ASP   ( 446-)  D   H-bonding suggests Asn
3274 ASP   ( 793-)  D   H-bonding suggests Asn
3308 ASP   ( 827-)  D   H-bonding suggests Asn
3314 GLU   ( 833-)  D   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 :  -0.316
  2nd generation packing quality :  -1.338
  Ramachandran plot appearance   :  -2.068
  chi-1/chi-2 rotamer normality  :  -3.082 (poor)
  Backbone conformation          :  -0.377

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.773
  Bond angles                    :   0.815
  Omega angle restraints         :   1.257
  Side chain planarity           :   0.697
  Improper dihedral distribution :   0.896
  B-factor distribution          :   0.489
  Inside/Outside distribution    :   1.007

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 : 2.54


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.773
  Bond angles                    :   0.815
  Omega angle restraints         :   1.257
  Side chain planarity           :   0.697
  Improper dihedral distribution :   0.896
  B-factor distribution          :   0.489
  Inside/Outside distribution    :   1.007
==============

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.