WHAT IF Check report

This file was created 2011-12-17 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 pdb1oy6.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 108651.016
Volume of the Unit Cell V= 9276699.0
Space group multiplicity: 18
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.743
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.820

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

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.

   1 ASP   (   7-)  A    High
   2 ARG   (   8-)  A    High
   3 PRO   (   9-)  A    High
   4 ILE   (  10-)  A    High
   5 PHE   (  11-)  A    High
   6 ALA   (  12-)  A    High
   7 TRP   (  13-)  A    High
   8 VAL   (  14-)  A    High
   9 ILE   (  15-)  A    High
  10 ALA   (  16-)  A    High
  11 ILE   (  17-)  A    High
  12 ILE   (  18-)  A    High
  13 ILE   (  19-)  A    High
  14 MET   (  20-)  A    High
  15 LEU   (  21-)  A    High
  16 ALA   (  22-)  A    High
  17 GLY   (  23-)  A    High
  18 GLY   (  24-)  A    High
  19 LEU   (  25-)  A    High
  20 ALA   (  26-)  A    High
  21 ILE   (  27-)  A    High
  22 LEU   (  28-)  A    High
  23 LYS   (  29-)  A    High
  24 LEU   (  30-)  A    High
  25 PRO   (  31-)  A    High
And so on for a total of 816 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. 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

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

  43 TYR   (  49-)  A
 321 TYR   ( 327-)  A
 461 TYR   ( 467-)  A
 737 TYR   ( 758-)  A
 758 TYR   ( 779-)  A
 847 TYR   ( 877-)  A
 896 TYR   ( 926-)  A

Warning: Phenylalanine convention problem

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

   5 PHE   (  11-)  A
 130 PHE   ( 136-)  A
 240 PHE   ( 246-)  A
 346 PHE   ( 352-)  A
 374 PHE   ( 380-)  A
 380 PHE   ( 386-)  A
 382 PHE   ( 388-)  A
 390 PHE   ( 396-)  A
 464 PHE   ( 470-)  A
 536 PHE   ( 556-)  A
 552 PHE   ( 572-)  A
 590 PHE   ( 610-)  A
 595 PHE   ( 615-)  A
 741 PHE   ( 762-)  A
 783 PHE   ( 804-)  A
 918 PHE   ( 948-)  A
 952 PHE   ( 982-)  A
 990 PHE   (1020-)  A
 991 PHE   (1021-)  A
 995 PHE   (1025-)  A

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.

   1 ASP   (   7-)  A
  53 ASP   (  59-)  A
 140 ASP   ( 146-)  A
 150 ASP   ( 156-)  A
 168 ASP   ( 174-)  A
 196 ASP   ( 202-)  A
 401 ASP   ( 407-)  A
 548 ASP   ( 568-)  A
 702 ASP   ( 723-)  A
 774 ASP   ( 795-)  A
 837 ASP   ( 858-)  A
 936 ASP   ( 966-)  A

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.

 186 GLU   ( 192-)  A
 274 GLU   ( 280-)  A
 408 GLU   ( 414-)  A
 411 GLU   ( 417-)  A
 423 GLU   ( 429-)  A
 501 GLU   ( 521-)  A
 620 GLU   ( 640-)  A
 685 GLU   ( 705-)  A
 713 GLU   ( 734-)  A
 796 GLU   ( 817-)  A
 805 GLU   ( 826-)  A
 818 GLU   ( 839-)  A
 917 GLU   ( 947-)  A

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.996087  0.000178 -0.000050|
 |  0.000178  0.996468  0.000054|
 | -0.000050  0.000054  0.997380|
Proposed new scale matrix

 |  0.006993  0.004035  0.000000|
 | -0.000001  0.008072  0.000000|
 |  0.000000  0.000000  0.001929|
With corresponding cell

    A    = 142.993  B   = 143.025  C    = 518.389
    Alpha=  90.001  Beta=  90.003  Gamma= 119.976

The CRYST1 cell dimensions

    A    = 143.554  B   = 143.567  C    = 519.751
    Alpha=  90.000  Beta=  90.000  Gamma= 120.001

Variance: 349.863
(Under-)estimated Z-score: 13.785

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.

1002 ARG   (1032-)  A      CG   CD   NE  118.54    4.7

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.

   1 ASP   (   7-)  A
  53 ASP   (  59-)  A
 140 ASP   ( 146-)  A
 150 ASP   ( 156-)  A
 168 ASP   ( 174-)  A
 186 GLU   ( 192-)  A
 196 ASP   ( 202-)  A
 274 GLU   ( 280-)  A
 401 ASP   ( 407-)  A
 408 GLU   ( 414-)  A
 411 GLU   ( 417-)  A
 423 GLU   ( 429-)  A
 501 GLU   ( 521-)  A
 548 ASP   ( 568-)  A
 620 GLU   ( 640-)  A
 685 GLU   ( 705-)  A
 702 ASP   ( 723-)  A
 713 GLU   ( 734-)  A
 774 ASP   ( 795-)  A
 796 GLU   ( 817-)  A
 805 GLU   ( 826-)  A
 818 GLU   ( 839-)  A
 837 ASP   ( 858-)  A
 917 GLU   ( 947-)  A
 936 ASP   ( 966-)  A

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.

   4 ILE   (  10-)  A    6.48
 366 VAL   ( 372-)  A    4.46

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 : -5.338

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.

 993 PRO   (1023-)  A    -3.1
 217 PRO   ( 223-)  A    -3.0
 518 THR   ( 538-)  A    -2.9
 990 PHE   (1020-)  A    -2.9
 324 THR   ( 330-)  A    -2.8
  43 TYR   (  49-)  A    -2.8
 606 ILE   ( 626-)  A    -2.8
   4 ILE   (  10-)  A    -2.8
 321 TYR   ( 327-)  A    -2.8
1004 SER   (1034-)  A    -2.7
 693 THR   ( 714-)  A    -2.7
 131 LEU   ( 137-)  A    -2.7
 218 PRO   ( 224-)  A    -2.7
 216 THR   ( 222-)  A    -2.6
 761 LEU   ( 782-)  A    -2.6
 790 TYR   ( 811-)  A    -2.6
 359 THR   ( 365-)  A    -2.6
 994 VAL   (1024-)  A    -2.6
 128 SER   ( 134-)  A    -2.6
 457 THR   ( 463-)  A    -2.5
 582 GLU   ( 602-)  A    -2.5
 421 PRO   ( 427-)  A    -2.5
 554 THR   ( 574-)  A    -2.5
 875 VAL   ( 905-)  A    -2.5
 915 ILE   ( 945-)  A    -2.5
And so on for a total of 79 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.

   3 PRO   (   9-)  A  Poor phi/psi
   4 ILE   (  10-)  A  Poor phi/psi
  28 GLN   (  34-)  A  Poor phi/psi
  29 TYR   (  35-)  A  Poor phi/psi
  68 ASN   (  74-)  A  Poor phi/psi
  69 LEU   (  75-)  A  Poor phi/psi
 104 LYS   ( 110-)  A  omega poor
 127 SER   ( 133-)  A  Poor phi/psi
 128 SER   ( 134-)  A  Poor phi/psi
 140 ASP   ( 146-)  A  Poor phi/psi
 141 GLY   ( 147-)  A  omega poor
 146 GLU   ( 152-)  A  Poor phi/psi
 165 GLY   ( 171-)  A  Poor phi/psi
 191 GLN   ( 197-)  A  Poor phi/psi
 203 ALA   ( 209-)  A  Poor phi/psi
 211 GLY   ( 217-)  A  Poor phi/psi
 230 ALA   ( 236-)  A  Poor phi/psi
 249 GLN   ( 255-)  A  Poor phi/psi
 251 GLY   ( 257-)  A  Poor phi/psi
 276 ASN   ( 282-)  A  Poor phi/psi
 289 THR   ( 295-)  A  Poor phi/psi
 293 ALA   ( 299-)  A  Poor phi/psi
 321 TYR   ( 327-)  A  Poor phi/psi
 421 PRO   ( 427-)  A  Poor phi/psi
 427 LYS   ( 433-)  A  omega poor
And so on for a total of 65 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 : -5.622

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.

 465 SER   ( 471-)  A    0.36

Warning: Unusual backbone conformations

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

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

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

   3 PRO   (   9-)  A      0
   4 ILE   (  10-)  A      0
  23 LYS   (  29-)  A      0
  26 VAL   (  32-)  A      0
  28 GLN   (  34-)  A      0
  29 TYR   (  35-)  A      0
  32 ILE   (  38-)  A      0
  40 SER   (  46-)  A      0
  44 PRO   (  50-)  A      0
  53 ASP   (  59-)  A      0
  54 THR   (  60-)  A      0
  62 ASN   (  68-)  A      0
  63 MET   (  69-)  A      0
  64 ASN   (  70-)  A      0
  67 ASP   (  73-)  A      0
  68 ASN   (  74-)  A      0
  70 MET   (  76-)  A      0
  71 TYR   (  77-)  A      0
  79 THR   (  85-)  A      0
  90 SER   (  96-)  A      0
 108 ALA   ( 114-)  A      0
 111 LEU   ( 117-)  A      0
 118 GLN   ( 124-)  A      0
 119 GLN   ( 125-)  A      0
 125 LYS   ( 131-)  A      0
And so on for a total of 353 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!

 454 GLY   ( 460-)  A   2.21   13
 211 GLY   ( 217-)  A   2.04   14
 858 LEU   ( 888-)  A   1.78   41
 791 GLY   ( 812-)  A   1.68   29
 745 GLY   ( 766-)  A   1.66   43
  45 GLY   (  51-)  A   1.53   80

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]

  44 PRO   (  50-)  A    0.14 LOW
 420 PRO   ( 426-)  A    0.08 LOW
 449 PRO   ( 455-)  A    0.14 LOW
 649 PRO   ( 669-)  A    0.13 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].

 110 PRO   ( 116-)  A    50.8 half-chair C-delta/C-gamma (54 degrees)
 113 PRO   ( 119-)  A   102.4 envelop C-beta (108 degrees)
 184 PRO   ( 190-)  A    44.7 envelop C-delta (36 degrees)
 217 PRO   ( 223-)  A   -31.9 envelop C-alpha (-36 degrees)
 218 PRO   ( 224-)  A   -53.9 half-chair C-beta/C-alpha (-54 degrees)
 320 PRO   ( 326-)  A   -56.4 half-chair C-beta/C-alpha (-54 degrees)
 362 PRO   ( 368-)  A    50.2 half-chair C-delta/C-gamma (54 degrees)
 367 PRO   ( 373-)  A  -141.3 envelop C-delta (-144 degrees)
 421 PRO   ( 427-)  A   106.4 envelop C-beta (108 degrees)
 690 PRO   ( 710-)  A   -10.1 half-chair C-alpha/N (-18 degrees)
 793 PRO   ( 814-)  A   -49.4 half-chair C-beta/C-alpha (-54 degrees)
 844 PRO   ( 874-)  A   130.3 half-chair C-beta/C-alpha (126 degrees)
 876 PRO   ( 906-)  A    45.8 half-chair C-delta/C-gamma (54 degrees)
 958 PRO   ( 988-)  A   110.2 envelop C-beta (108 degrees)
 993 PRO   (1023-)  A   161.2 half-chair C-alpha/N (162 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.

 505 HIS   ( 525-)  A      O   <->  507 TYR   ( 527-)  A      N      0.31    2.39  INTRA BF
 867 ILE   ( 897-)  A      N   <->  868 PRO   ( 898-)  A      CD     0.22    2.78  INTRA BF
1003 PHE   (1033-)  A      O   <-> 1005 ARG   (1035-)  A      N      0.19    2.51  INTRA BF
 138 ASN   ( 144-)  A      ND2 <->  143 MET   ( 149-)  A      SD     0.18    3.12  INTRA BL
 109 MET   ( 115-)  A      N   <->  110 PRO   ( 116-)  A      CD     0.17    2.83  INTRA BF
 920 LYS   ( 950-)  A      NZ  <->  998 VAL   (1028-)  A      CG1    0.17    2.93  INTRA BL
 503 SER   ( 523-)  A      O   <->  508 THR   ( 528-)  A      OG1    0.17    2.23  INTRA BL
   3 PRO   (   9-)  A      C   <->    4 ILE   (  10-)  A      CD1    0.16    2.94  INTRA BF
  15 LEU   (  21-)  A      O   <->   19 LEU   (  25-)  A      N      0.15    2.55  INTRA BL
 985 THR   (1015-)  A      O   <->  987 LEU   (1017-)  A      N      0.14    2.56  INTRA BL
 248 ASN   ( 254-)  A      O   <->  250 ASP   ( 256-)  A      N      0.13    2.57  INTRA BF
 420 PRO   ( 426-)  A      N   <->  421 PRO   ( 427-)  A      CD     0.12    2.88  INTRA BF
 450 MET   ( 456-)  A      SD  <->  902 LEU   ( 932-)  A      CD1    0.11    3.29  INTRA BF
 448 VAL   ( 454-)  A      N   <->  449 PRO   ( 455-)  A      CD     0.11    2.89  INTRA BF
 308 GLU   ( 314-)  A      N   <->  309 PRO   ( 315-)  A      CD     0.11    2.89  INTRA BL
 507 TYR   ( 527-)  A      OH  <->  989 ILE   (1019-)  A      O      0.11    2.29  INTRA BL
 772 ALA   ( 793-)  A      O   <->  774 ASP   ( 795-)  A      N      0.10    2.60  INTRA BL
 675 LEU   ( 695-)  A      CD2 <->  804 MET   ( 825-)  A      SD     0.10    3.30  INTRA BL
 948 THR   ( 978-)  A      O   <->  952 PHE   ( 982-)  A      N      0.10    2.60  INTRA BF
 320 PRO   ( 326-)  A      O   <->  321 TYR   ( 327-)  A      C      0.10    2.50  INTRA BL
 761 LEU   ( 782-)  A      CB  <->  762 PRO   ( 783-)  A      CD     0.09    3.01  INTRA BL
 366 VAL   ( 372-)  A      N   <->  367 PRO   ( 373-)  A      CD     0.09    2.91  INTRA BL
   4 ILE   (  10-)  A      O   <->    8 VAL   (  14-)  A      N      0.09    2.61  INTRA BF
 288 ALA   ( 294-)  A      O   <->  289 THR   ( 295-)  A      C      0.08    2.52  INTRA BF
 501 GLU   ( 521-)  A      O   <->  505 HIS   ( 525-)  A      N      0.08    2.62  INTRA BF
And so on for a total of 61 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

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.

 600 ARG   ( 620-)  A      -8.00
1005 ARG   (1035-)  A      -7.85
 790 TYR   ( 811-)  A      -7.11
 744 ARG   ( 765-)  A      -7.00
 319 TYR   ( 325-)  A      -6.67
 220 LYS   ( 226-)  A      -6.58
 249 GLN   ( 255-)  A      -6.43
 667 GLN   ( 687-)  A      -6.20
  29 TYR   (  35-)  A      -6.05
 223 GLN   ( 229-)  A      -6.00
 597 PHE   ( 617-)  A      -5.77
 516 ARG   ( 536-)  A      -5.76
 733 TRP   ( 754-)  A      -5.64
 653 GLU   ( 673-)  A      -5.54
 760 MET   ( 781-)  A      -5.52
 229 ILE   ( 235-)  A      -5.46
 692 LEU   ( 713-)  A      -5.44
 930 LEU   ( 960-)  A      -5.41
 538 ARG   ( 558-)  A      -5.40
 617 ARG   ( 637-)  A      -5.40
 925 LYS   ( 955-)  A      -5.37
 453 PHE   ( 459-)  A      -5.34
 269 TYR   ( 275-)  A      -5.25
 222 GLN   ( 228-)  A      -5.23
 654 LEU   ( 674-)  A      -5.21
1002 ARG   (1032-)  A      -5.20
 799 ASN   ( 820-)  A      -5.18
 888 PHE   ( 918-)  A      -5.15
 310 PHE   ( 316-)  A      -5.07
 939 ARG   ( 969-)  A      -5.01
 991 PHE   (1021-)  A      -5.00

Warning: Abnormal packing environment for sequential residues

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

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

 222 GLN   ( 228-)  A       224 - LEU    230- ( A)         -5.27

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: 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

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.

  75 ASN   (  81-)  A
 100 GLN   ( 106-)  A
 118 GLN   ( 124-)  A
 175 GLN   ( 181-)  A
 222 GLN   ( 228-)  A
 231 GLN   ( 237-)  A
 385 ASN   ( 391-)  A
 549 GLN   ( 569-)  A
 593 ASN   ( 613-)  A
 602 GLN   ( 622-)  A

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.

   5 PHE   (  11-)  A      N
   7 TRP   (  13-)  A      NE1
  22 LEU   (  28-)  A      N
  26 VAL   (  32-)  A      N
  27 ALA   (  33-)  A      N
  28 GLN   (  34-)  A      N
  29 TYR   (  35-)  A      N
  48 ALA   (  54-)  A      N
  58 VAL   (  64-)  A      N
  63 MET   (  69-)  A      N
  64 ASN   (  70-)  A      N
  66 ILE   (  72-)  A      N
  72 MET   (  78-)  A      N
  74 SER   (  80-)  A      OG
  81 THR   (  87-)  A      N
  89 GLU   (  95-)  A      N
 103 ASN   ( 109-)  A      ND2
 104 LYS   ( 110-)  A      N
 106 GLN   ( 112-)  A      NE2
 107 LEU   ( 113-)  A      N
 115 GLU   ( 121-)  A      N
 119 GLN   ( 125-)  A      NE2
 127 SER   ( 133-)  A      N
 129 SER   ( 135-)  A      N
 132 MET   ( 138-)  A      N
And so on for a total of 149 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.

  53 ASP   (  59-)  A      OD1
  60 GLU   (  66-)  A      OE2
  61 GLN   (  67-)  A      OE1
 138 ASN   ( 144-)  A      OD1
 145 GLN   ( 151-)  A      OE1
 146 GLU   ( 152-)  A      OE2
 248 ASN   ( 254-)  A      OD1
 276 ASN   ( 282-)  A      OD1
 402 ASP   ( 408-)  A      OD1
 409 ASN   ( 415-)  A      OD1
 463 GLN   ( 469-)  A      OE1
 565 GLU   ( 585-)  A      OE2
 576 HIS   ( 596-)  A      ND1
 582 GLU   ( 602-)  A      OE1
 661 ASP   ( 681-)  A      OD1
 702 ASP   ( 723-)  A      OD1
 712 GLN   ( 733-)  A      OE1
 898 GLN   ( 928-)  A      OE1
 970 GLN   (1000-)  A      OE1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  53 ASP   (  59-)  A   H-bonding suggests Asn; but Alt-Rotamer
  77 ASP   (  83-)  A   H-bonding suggests Asn
 124 GLU   ( 130-)  A   H-bonding suggests Gln; but Alt-Rotamer
 146 GLU   ( 152-)  A   H-bonding suggests Gln
 186 GLU   ( 192-)  A   H-bonding suggests Gln; but Alt-Rotamer
 340 GLU   ( 346-)  A   H-bonding suggests Gln
 509 ASP   ( 529-)  A   H-bonding suggests Asn
 582 GLU   ( 602-)  A   H-bonding suggests Gln
 666 ASP   ( 686-)  A   H-bonding suggests Asn; but Alt-Rotamer
 701 GLU   ( 722-)  A   H-bonding suggests Gln
 740 ASP   ( 761-)  A   H-bonding suggests Asn
 894 ASP   ( 924-)  A   H-bonding suggests Asn; but Alt-Rotamer
 917 GLU   ( 947-)  A   H-bonding suggests Gln; but Alt-Rotamer
 921 ASP   ( 951-)  A   H-bonding suggests Asn
 924 ASP   ( 954-)  A   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 :  -1.957
  2nd generation packing quality :  -2.246
  Ramachandran plot appearance   :  -5.338 (bad)
  chi-1/chi-2 rotamer normality  :  -5.622 (bad)
  Backbone conformation          :  -1.178

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.568 (tight)
  Omega angle restraints         :   0.959
  Side chain planarity           :   0.149 (tight)
  Improper dihedral distribution :   0.477
  B-factor distribution          :   0.866
  Inside/Outside distribution    :   1.077

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 : 3.68


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -2.2
  chi-1/chi-2 rotamer normality  :  -3.0 (poor)
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.349 (tight)
  Bond angles                    :   0.568 (tight)
  Omega angle restraints         :   0.959
  Side chain planarity           :   0.149 (tight)
  Improper dihedral distribution :   0.477
  B-factor distribution          :   0.866
  Inside/Outside distribution    :   1.077
==============

WHAT IF
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      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.