WHAT IF Check report

This file was created 2012-01-25 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2dpy.ent

Checks that need to be done early-on in validation

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.

 851 ADP   ( 600-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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.

 111 PRO   ( 145-)  A    High
 112 PRO   ( 146-)  A    High
 113 PHE   ( 147-)  A    High
 369 ASP   ( 403-)  A    High
 370 LEU   ( 404-)  A    High
 371 VAL   ( 405-)  A    High
 372 SER   ( 406-)  A    High
 373 VAL   ( 407-)  A    High
 374 GLY   ( 408-)  A    High
 375 ALA   ( 409-)  A    High
 376 TYR   ( 410-)  A    High
 377 ALA   ( 411-)  A    High
 378 LYS   ( 412-)  A    High
 379 GLY   ( 413-)  A    High
 380 SER   ( 414-)  A    High
 381 ASP   ( 415-)  A    High
 423 PRO   (  23-)  B    High
 424 ALA   (  24-)  B    High
 425 VAL   (  25-)  B    High
 426 ARG   (  26-)  B    High
 427 ARG   (  27-)  B    High
 428 TYR   (  28-)  B    High
 457 GLN   (  57-)  B    High
 458 ASP   (  58-)  B    High
 459 GLY   (  59-)  B    High
 460 PRO   (  60-)  B    High
 461 GLU   (  61-)  B    High
 462 THR   (  62-)  B    High
 484 GLU   (  84-)  B    High
 485 VAL   (  85-)  B    High

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

 164 TYR   ( 198-)  A
 218 TYR   ( 252-)  A
 292 TYR   ( 326-)  A
 329 TYR   ( 363-)  A
 428 TYR   (  28-)  B
 590 TYR   ( 198-)  B
 644 TYR   ( 252-)  B
 689 TYR   ( 297-)  B
 718 TYR   ( 326-)  B
 755 TYR   ( 363-)  B

Warning: Phenylalanine convention problem

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

  54 PHE   (  78-)  A
 147 PHE   ( 181-)  A
 226 PHE   ( 260-)  A
 268 PHE   ( 302-)  A
 357 PHE   ( 391-)  A
 397 PHE   ( 431-)  A
 403 PHE   ( 437-)  A
 472 PHE   (  72-)  B
 478 PHE   (  78-)  B
 573 PHE   ( 181-)  B
 652 PHE   ( 260-)  B
 694 PHE   ( 302-)  B
 783 PHE   ( 391-)  B

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.

 101 ASP   ( 135-)  A
 168 ASP   ( 202-)  A
 299 ASP   ( 333-)  A
 303 ASP   ( 337-)  A
 307 ASP   ( 341-)  A
 333 ASP   ( 367-)  A
 410 ASP   ( 444-)  A
 521 ASP   ( 129-)  B
 552 ASP   ( 160-)  B
 610 ASP   ( 218-)  B
 726 ASP   ( 334-)  B

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.

 249 GLU   ( 283-)  A
 276 GLU   ( 310-)  A
 325 GLU   ( 359-)  A
 335 GLU   ( 369-)  A
 348 GLU   ( 382-)  A
 486 GLU   (  86-)  B
 650 GLU   ( 258-)  B
 675 GLU   ( 283-)  B
 702 GLU   ( 310-)  B
 751 GLU   ( 359-)  B

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.

  74 LYS   ( 108-)  A      N    CA    1.36   -5.1
 498 SER   ( 106-)  B      N    CA    1.36   -5.1

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

 |  0.998641 -0.000209 -0.000047|
 | -0.000209  0.999109 -0.000132|
 | -0.000047 -0.000132  0.998950|
Proposed new scale matrix

 |  0.020792  0.000005  0.001502|
 |  0.000003  0.013758  0.000002|
 |  0.000000  0.000001  0.007982|
With corresponding cell

    A    =  48.095  B   =  72.684  C    = 125.602
    Alpha=  90.013  Beta=  94.131  Gamma=  90.024

The CRYST1 cell dimensions

    A    =  48.160  B   =  72.750  C    = 125.740
    Alpha=  90.000  Beta=  94.130  Gamma=  90.000

Variance: 33.951
(Under-)estimated Z-score: 4.294

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.

   5 GLY   (  29-)  A      N    CA   C    98.28   -4.9
 238 ASP   ( 272-)  A      CA   C    O   113.11   -4.5
 239 SER   ( 273-)  A      N    CA   CB  124.24    8.1
 284 GLY   ( 318-)  A      N    CA   C    90.53   -7.6
 665 SER   ( 273-)  B      N    CA   CB  121.81    6.7
 765 SER   ( 373-)  B      N    CA   C    99.47   -4.2

Error: Nomenclature error(s)

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

 101 ASP   ( 135-)  A
 168 ASP   ( 202-)  A
 249 GLU   ( 283-)  A
 276 GLU   ( 310-)  A
 299 ASP   ( 333-)  A
 303 ASP   ( 337-)  A
 307 ASP   ( 341-)  A
 325 GLU   ( 359-)  A
 333 ASP   ( 367-)  A
 335 GLU   ( 369-)  A
 348 GLU   ( 382-)  A
 410 ASP   ( 444-)  A
 486 GLU   (  86-)  B
 521 ASP   ( 129-)  B
 552 ASP   ( 160-)  B
 610 ASP   ( 218-)  B
 650 GLU   ( 258-)  B
 675 GLU   ( 283-)  B
 702 GLU   ( 310-)  B
 726 ASP   ( 334-)  B
 751 GLU   ( 359-)  B

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.

 238 ASP   ( 272-)  A      C    -17.5   -27.00    -0.01
 664 ASP   ( 272-)  B      C    -14.9   -23.00    -0.01
 846 PRO   ( 454-)  B      N      7.7    22.81    -2.48
The average deviation= 0.772

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.

 284 GLY   ( 318-)  A    8.27
   5 GLY   (  29-)  A    5.74
 134 ALA   ( 168-)  A    4.92
 164 TYR   ( 198-)  A    4.68
 135 LEU   ( 169-)  A    4.67
 765 SER   ( 373-)  B    4.62
 269 ALA   ( 303-)  A    4.56
 238 ASP   ( 272-)  A    4.53
 459 GLY   (  59-)  B    4.52
 601 ILE   ( 209-)  B    4.42
 614 ASN   ( 222-)  B    4.37
 187 GLU   ( 221-)  A    4.24
 771 LEU   ( 379-)  B    4.22
 508 LEU   ( 116-)  B    4.13
 560 ALA   ( 168-)  B    4.10
 419 PHE   ( 453-)  A    4.00

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.569

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.014

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.

 420 PRO   ( 454-)  A    -3.1
 730 PRO   ( 338-)  B    -2.8
 419 PHE   ( 453-)  A    -2.7
 462 THR   (  62-)  B    -2.6
 103 LEU   ( 137-)  A    -2.6
 764 ILE   ( 372-)  B    -2.6
 102 THR   ( 136-)  A    -2.6
  52 ARG   (  76-)  A    -2.5
 680 ILE   ( 288-)  B    -2.5
 847 THR   ( 455-)  B    -2.4
 738 ILE   ( 346-)  B    -2.4
  78 LEU   ( 112-)  A    -2.4
 109 ILE   ( 143-)  A    -2.4
 504 LEU   ( 112-)  B    -2.4
 421 THR   ( 455-)  A    -2.3
 260 THR   ( 294-)  A    -2.3
 433 ARG   (  33-)  B    -2.3
 207 VAL   ( 241-)  A    -2.2
 254 ILE   ( 288-)  A    -2.2
 799 VAL   ( 407-)  B    -2.2
 542 LEU   ( 150-)  B    -2.1
 490 PRO   (  90-)  B    -2.1
  47 GLY   (  71-)  A    -2.1
 563 THR   ( 171-)  B    -2.1
  46 VAL   (  70-)  A    -2.1
 446 LEU   (  46-)  B    -2.1
 724 GLY   ( 332-)  B    -2.1
 739 LEU   ( 347-)  B    -2.0
 815 THR   ( 423-)  B    -2.0
 548 GLU   ( 156-)  B    -2.0
 660 LEU   ( 268-)  B    -2.0

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.

  50 GLY   (  74-)  A  Poor phi/psi
  51 GLN   (  75-)  A  Poor phi/psi
  52 ARG   (  76-)  A  Poor phi/psi
 102 THR   ( 136-)  A  Poor phi/psi
 103 LEU   ( 137-)  A  Poor phi/psi
 105 THR   ( 139-)  A  Poor phi/psi
 109 ILE   ( 143-)  A  Poor phi/psi
 110 THR   ( 144-)  A  Poor phi/psi
 115 PRO   ( 149-)  A  Poor phi/psi
 238 ASP   ( 272-)  A  omega poor
 260 THR   ( 294-)  A  Poor phi/psi
 261 LYS   ( 295-)  A  Poor phi/psi
 299 ASP   ( 333-)  A  Poor phi/psi
 329 TYR   ( 363-)  A  PRO omega poor
 331 ALA   ( 365-)  A  Poor phi/psi
 419 PHE   ( 453-)  A  Poor phi/psi
 420 PRO   ( 454-)  A  Poor phi/psi
 434 ALA   (  34-)  B  Poor phi/psi
 435 THR   (  35-)  B  Poor phi/psi
 458 ASP   (  58-)  B  Poor phi/psi
 467 SER   (  67-)  B  Poor phi/psi
 483 GLU   (  83-)  B  Poor phi/psi
 496 ALA   (  96-)  B  Poor phi/psi
 499 GLY   ( 107-)  B  Poor phi/psi
 504 LEU   ( 112-)  B  Poor phi/psi
 522 GLY   ( 130-)  B  Poor phi/psi
 664 ASP   ( 272-)  B  omega poor
 685 ALA   ( 293-)  B  Poor phi/psi
 687 LYS   ( 295-)  B  Poor phi/psi
 688 GLY   ( 296-)  B  Poor phi/psi
 708 ILE   ( 316-)  B  Poor phi/psi
 709 HIS   ( 317-)  B  Poor phi/psi
 723 GLU   ( 331-)  B  Poor phi/psi
 725 ASP   ( 333-)  B  Poor phi/psi
 728 GLN   ( 336-)  B  Poor phi/psi
 755 TYR   ( 363-)  B  PRO omega poor
 804 LYS   ( 412-)  B  Poor phi/psi
 845 PHE   ( 453-)  B  Poor phi/psi
 846 PRO   ( 454-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.441

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 : -3.441

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.

 837 SER   ( 445-)  B    0.35
 310 ARG   ( 344-)  A    0.36
 411 SER   ( 445-)  A    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!

  10 ALA   (  34-)  A      0
  11 THR   (  35-)  A      0
  13 LEU   (  37-)  A      0
  18 THR   (  42-)  A      0
  20 LEU   (  44-)  A      0
  24 LEU   (  48-)  A      0
  34 ASP   (  58-)  A      0
  36 PRO   (  60-)  A      0
  46 VAL   (  70-)  A      0
  48 PHE   (  72-)  A      0
  49 ASN   (  73-)  A      0
  51 GLN   (  75-)  A      0
  52 ARG   (  76-)  A      0
  57 PRO   (  81-)  A      0
  62 GLU   (  86-)  A      0
  68 ALA   (  92-)  A      0
  69 ARG   (  93-)  A      0
  72 ALA   (  96-)  A      0
  73 ARG   (  97-)  A      0
  74 LYS   ( 108-)  A      0
  75 GLN   ( 109-)  A      0
  77 PRO   ( 111-)  A      0
  78 LEU   ( 112-)  A      0
  83 LEU   ( 117-)  A      0
  92 LYS   ( 126-)  A      0
And so on for a total of 287 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 : 1.222

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!

  25 GLY   (  49-)  A   2.49   29
  15 LEU   (  39-)  A   1.66   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]

 846 PRO   ( 454-)  B    0.46 HIGH

Warning: Unusual PRO puckering phases

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

  57 PRO   (  81-)  A    50.6 half-chair C-delta/C-gamma (54 degrees)
 204 PRO   ( 238-)  A    48.6 half-chair C-delta/C-gamma (54 degrees)
 209 PRO   ( 243-)  A  -117.2 half-chair C-delta/C-gamma (-126 degrees)
 420 PRO   ( 454-)  A   -58.7 half-chair C-beta/C-alpha (-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.

 284 GLY   ( 318-)  A      N   <->  285 GLY   ( 319-)  A      N      0.50    2.10  INTRA BF
 586 MET   ( 194-)  B      SD  <->  853 HOH   ( 625 )  B      O      0.42    2.58  INTRA BF
  49 ASN   (  73-)  A      O   <->   51 GLN   (  75-)  A      N      0.36    2.34  INTRA BF
 576 SER   ( 184-)  B      O   <->  747 ARG   ( 355-)  B      NH2    0.36    2.34  INTRA BL
 114 ASN   ( 148-)  A      O   <->  116 LEU   ( 150-)  A      N      0.36    2.34  INTRA BF
 227 ARG   ( 261-)  A      NH1 <->  228 ASP   ( 262-)  A      OD1    0.35    2.35  INTRA BL
 114 ASN   ( 148-)  A      ND2 <->  117 GLN   ( 151-)  A      NE2    0.35    2.50  INTRA BF
  18 THR   (  42-)  A      OG1 <->   52 ARG   (  76-)  A      NE     0.34    2.36  INTRA BF
 184 ASP   ( 218-)  A      OD1 <->  188 ASN   ( 222-)  A      ND2    0.34    2.36  INTRA BL
 457 GLN   (  57-)  B      NE2 <->  461 GLU   (  61-)  B      O      0.34    2.36  INTRA BF
 171 VAL   ( 205-)  A      CG2 <->  235 LEU   ( 269-)  A      CD1    0.32    2.88  INTRA BL
 496 ALA   (  96-)  B      N   <->  853 HOH   ( 640 )  B      O      0.30    2.40  INTRA BF
 130 ARG   ( 164-)  A      NH2 <->  399 GLN   ( 433-)  A      O      0.30    2.40  INTRA BL
  85 ARG   ( 119-)  A      NH2 <->   98 PRO   ( 132-)  A      O      0.30    2.40  INTRA BL
  40 GLU   (  64-)  A      OE1 <->   73 ARG   (  97-)  A      NH2    0.30    2.40  INTRA BF
 328 HIS   ( 362-)  A      NE2 <->  852 HOH   ( 465 )  A      O      0.28    2.42  INTRA BL
 349 GLN   ( 383-)  A      CG  <->  353 ARG   ( 387-)  A      NH1    0.26    2.84  INTRA BF
 727 GLN   ( 335-)  B      O   <->  729 ASP   ( 337-)  B      N      0.26    2.44  INTRA BF
 166 ARG   ( 200-)  A      NE  <->  405 ARG   ( 439-)  A      NH2    0.25    2.60  INTRA BF
 320 SER   ( 354-)  A      OG  <->  322 ARG   ( 356-)  A      NE     0.25    2.45  INTRA BF
  88 ASP   ( 122-)  A      OD1 <->   90 GLY   ( 124-)  A      N      0.25    2.45  INTRA BL
 114 ASN   ( 148-)  A      C   <->  116 LEU   ( 150-)  A      N      0.24    2.66  INTRA BF
 260 THR   ( 294-)  A      O   <->  262 GLY   ( 296-)  A      N      0.24    2.46  INTRA BF
   9 ARG   (  33-)  A      NH1 <->   11 THR   (  35-)  A      CG2    0.23    2.87  INTRA BF
 811 ASP   ( 419-)  B      O   <->  815 THR   ( 423-)  B      CG2    0.23    2.57  INTRA BL
And so on for a total of 228 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

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.

   3 ARG   (  27-)  A      -7.45
 445 GLN   (  45-)  B      -7.21
 539 PHE   ( 147-)  B      -6.94
  21 GLN   (  45-)  A      -6.92
 728 GLN   ( 336-)  B      -6.66
 709 HIS   ( 317-)  B      -6.54
  51 GLN   (  75-)  A      -6.32
 544 ARG   ( 152-)  B      -6.19
 592 ARG   ( 200-)  B      -6.18
 283 HIS   ( 317-)  A      -6.10
 118 ARG   ( 152-)  A      -5.97
 113 PHE   ( 147-)  A      -5.90
 166 ARG   ( 200-)  A      -5.85
 302 GLN   ( 336-)  A      -5.75
 804 LYS   ( 412-)  B      -5.62
 708 ILE   ( 316-)  B      -5.60
 723 GLU   ( 331-)  B      -5.37
 378 LYS   ( 412-)  A      -5.35
 109 ILE   ( 143-)  A      -5.32
  48 PHE   (  72-)  A      -5.26
 329 TYR   ( 363-)  A      -5.22
 523 LEU   ( 131-)  B      -5.20
 489 LEU   (  89-)  B      -5.19
 282 ILE   ( 316-)  A      -5.18
 755 TYR   ( 363-)  B      -5.17
 301 GLN   ( 335-)  A      -5.16
 277 ARG   ( 311-)  A      -5.15
 792 ARG   ( 400-)  B      -5.14
 829 PHE   ( 437-)  B      -5.06
  75 GLN   ( 109-)  A      -5.05
 427 ARG   (  27-)  B      -5.04
 687 LYS   ( 295-)  B      -5.03
 727 GLN   ( 335-)  B      -5.01

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.

 282 ILE   ( 316-)  A       284 - GLY    318- ( A)         -5.18
 542 LEU   ( 150-)  B       544 - ARG    152- ( B)         -4.87
 708 ILE   ( 316-)  B       710 - GLY    318- ( B)         -5.54

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: 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

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.

 852 HOH   ( 519 )  A      O     44.63   40.09  -19.11

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.

 852 HOH   ( 458 )  A      O
 853 HOH   ( 611 )  B      O
 853 HOH   ( 633 )  B      O
 853 HOH   ( 636 )  B      O
 853 HOH   ( 651 )  B      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.

  75 GLN   ( 109-)  A
 117 GLN   ( 151-)  A
 247 GLN   ( 281-)  A
 280 ASN   ( 314-)  A
 283 HIS   ( 317-)  A
 302 GLN   ( 336-)  A
 316 HIS   ( 350-)  A
 365 GLN   ( 399-)  A
 706 ASN   ( 314-)  B
 728 GLN   ( 336-)  B

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.

   9 ARG   (  33-)  A      NH1
  21 GLN   (  45-)  A      N
  33 GLN   (  57-)  A      N
  37 GLU   (  61-)  A      N
  38 THR   (  62-)  A      N
  40 GLU   (  64-)  A      N
  47 GLY   (  71-)  A      N
  59 GLU   (  83-)  A      N
  95 ASP   ( 129-)  A      N
 109 ILE   ( 143-)  A      N
 114 ASN   ( 148-)  A      N
 116 LEU   ( 150-)  A      N
 143 ARG   ( 177-)  A      NE
 149 GLY   ( 183-)  A      N
 152 VAL   ( 186-)  A      N
 163 ARG   ( 197-)  A      NH2
 177 GLU   ( 211-)  A      N
 178 ARG   ( 212-)  A      N
 191 GLY   ( 225-)  A      N
 193 ASP   ( 227-)  A      N
 197 ARG   ( 231-)  A      N
 227 ARG   ( 261-)  A      NE
 239 SER   ( 273-)  A      N
 241 THR   ( 275-)  A      OG1
 263 TYR   ( 297-)  A      N
And so on for a total of 79 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 280 ASN   ( 314-)  A      OD1
 316 HIS   ( 350-)  A      ND1
 367 ASN   ( 401-)  A      OD1
 811 ASP   ( 419-)  B      OD2

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.

 122 GLU   ( 156-)  A   H-bonding suggests Gln
 228 ASP   ( 262-)  A   H-bonding suggests Asn; but Alt-Rotamer
 300 ASP   ( 334-)  A   H-bonding suggests Asn; but Alt-Rotamer
 307 ASP   ( 341-)  A   H-bonding suggests Asn
 369 ASP   ( 403-)  A   H-bonding suggests Asn
 385 ASP   ( 419-)  A   H-bonding suggests Asn
 486 GLU   (  86-)  B   H-bonding suggests Gln
 514 ASP   ( 122-)  B   H-bonding suggests Asn; but Alt-Rotamer
 654 ASP   ( 262-)  B   H-bonding suggests Asn; but Alt-Rotamer
 723 GLU   ( 331-)  B   H-bonding suggests Gln
 725 ASP   ( 333-)  B   H-bonding suggests Asn
 726 ASP   ( 334-)  B   H-bonding suggests Asn
 729 ASP   ( 337-)  B   H-bonding suggests Asn; but Alt-Rotamer
 811 ASP   ( 419-)  B   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 :  -0.945
  2nd generation packing quality :  -1.206
  Ramachandran plot appearance   :  -3.014 (poor)
  chi-1/chi-2 rotamer normality  :  -3.441 (poor)
  Backbone conformation          :   0.991

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.363 (tight)
  Bond angles                    :   0.684
  Omega angle restraints         :   0.222 (tight)
  Side chain planarity           :   0.240 (tight)
  Improper dihedral distribution :   0.818
  B-factor distribution          :   0.504
  Inside/Outside distribution    :   0.989

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.363 (tight)
  Bond angles                    :   0.684
  Omega angle restraints         :   0.222 (tight)
  Side chain planarity           :   0.240 (tight)
  Improper dihedral distribution :   0.818
  B-factor distribution          :   0.504
  Inside/Outside distribution    :   0.989
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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      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.