WHAT IF Check report

This file was created 2011-12-18 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 pdb2yzm.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 9.788
CA-only RMS fit for the two chains : 8.797

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and C

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.

 943 DAL   ( 401-)  A  -
 944 DAL   ( 402-)  B  -
 945 DAL   ( 403-)  C  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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

Warning: What type of B-factor?

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

Note: B-factor plot

Chain identifier: C

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  26 ARG   (  26-)  A
  42 ARG   (  42-)  A
 121 ARG   ( 121-)  A
 137 ARG   ( 137-)  A
 217 ARG   ( 217-)  A
 233 ARG   ( 233-)  A
 268 ARG   ( 268-)  A
 297 ARG   ( 297-)  A
 312 ARG   ( 312-)  A
 321 ARG   (   2-)  B
 345 ARG   (  26-)  B
 403 ARG   (  84-)  B
 440 ARG   ( 121-)  B
 456 ARG   ( 137-)  B
 487 ARG   ( 168-)  B
 500 ARG   ( 181-)  B
 515 ARG   ( 196-)  B
 536 ARG   ( 217-)  B
 545 ARG   ( 233-)  B
 580 ARG   ( 268-)  B
 623 ARG   ( 311-)  B
 657 ARG   (  26-)  C
 704 ARG   (  73-)  C
 768 ARG   ( 137-)  C
 827 ARG   ( 196-)  C
 848 ARG   ( 217-)  C
 888 ARG   ( 268-)  C

Warning: Tyrosine convention problem

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

  74 TYR   (  74-)  A
 218 TYR   ( 218-)  A
 229 TYR   ( 229-)  A
 279 TYR   ( 279-)  A
 295 TYR   ( 295-)  A
 393 TYR   (  74-)  B
 607 TYR   ( 295-)  B
 915 TYR   ( 295-)  C

Warning: Phenylalanine convention problem

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

  30 PHE   (  30-)  A
  85 PHE   (  85-)  A
  94 PHE   (  94-)  A
 169 PHE   ( 169-)  A
 222 PHE   ( 222-)  A
 289 PHE   ( 289-)  A
 349 PHE   (  30-)  B
 413 PHE   (  94-)  B
 469 PHE   ( 150-)  B
 499 PHE   ( 180-)  B
 526 PHE   ( 207-)  B
 661 PHE   (  30-)  C
 725 PHE   (  94-)  C
 781 PHE   ( 150-)  C
 800 PHE   ( 169-)  C
 811 PHE   ( 180-)  C
 838 PHE   ( 207-)  C

Warning: Aspartic acid convention problem

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

  33 ASP   (  33-)  A
  75 ASP   (  75-)  A
  88 ASP   (  88-)  A
 115 ASP   ( 115-)  A
 147 ASP   ( 147-)  A
 171 ASP   ( 171-)  A
 270 ASP   ( 270-)  A
 434 ASP   ( 115-)  B
 502 ASP   ( 183-)  B
 582 ASP   ( 270-)  B
 664 ASP   (  33-)  C
 671 ASP   (  40-)  C
 719 ASP   (  88-)  C
 746 ASP   ( 115-)  C
 778 ASP   ( 147-)  C
 814 ASP   ( 183-)  C
 890 ASP   ( 270-)  C

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  15 GLU   (  15-)  A
  54 GLU   (  54-)  A
  60 GLU   (  60-)  A
  72 GLU   (  72-)  A
  87 GLU   (  87-)  A
  96 GLU   (  96-)  A
 173 GLU   ( 173-)  A
 215 GLU   ( 215-)  A
 226 GLU   ( 226-)  A
 277 GLU   ( 277-)  A
 282 GLU   ( 282-)  A
 300 GLU   ( 300-)  A
 308 GLU   ( 308-)  A
 315 GLU   ( 315-)  A
 334 GLU   (  15-)  B
 341 GLU   (  22-)  B
 366 GLU   (  47-)  B
 373 GLU   (  54-)  B
 379 GLU   (  60-)  B
 381 GLU   (  62-)  B
 406 GLU   (  87-)  B
 486 GLU   ( 167-)  B
 503 GLU   ( 184-)  B
 508 GLU   ( 189-)  B
 516 GLU   ( 197-)  B
 518 GLU   ( 199-)  B
 534 GLU   ( 215-)  B
 589 GLU   ( 277-)  B
 594 GLU   ( 282-)  B
 620 GLU   ( 308-)  B
 646 GLU   (  15-)  C
 693 GLU   (  62-)  C
 718 GLU   (  87-)  C
 846 GLU   ( 215-)  C
 872 GLU   ( 252-)  C
 928 GLU   ( 308-)  C

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

 |  0.998976 -0.000105 -0.000421|
 | -0.000105  0.998613 -0.000035|
 | -0.000421 -0.000035  0.998567|
Proposed new scale matrix

 |  0.006006  0.000000  0.002111|
 |  0.000002  0.017930  0.000000|
 |  0.000003  0.000000  0.007507|
With corresponding cell

    A    = 166.524  B   =  55.773  C    = 141.220
    Alpha=  89.999  Beta= 109.386  Gamma=  90.007

The CRYST1 cell dimensions

    A    = 166.705  B   =  55.849  C    = 141.387
    Alpha=  90.000  Beta= 109.340  Gamma=  90.000

Variance: 51.817
(Under-)estimated Z-score: 5.305

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.

 264 ARG   ( 264-)  A      N    CA   C   124.15    4.6
 268 ARG   ( 268-)  A      N    CA   C    99.82   -4.1
 576 ARG   ( 264-)  B      N    CA   C   122.44    4.0
 884 ARG   ( 264-)  C      N    CA   C   122.76    4.1
 888 ARG   ( 268-)  C      N    CA   C    99.75   -4.1

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.

  15 GLU   (  15-)  A
  26 ARG   (  26-)  A
  33 ASP   (  33-)  A
  42 ARG   (  42-)  A
  54 GLU   (  54-)  A
  60 GLU   (  60-)  A
  72 GLU   (  72-)  A
  75 ASP   (  75-)  A
  87 GLU   (  87-)  A
  88 ASP   (  88-)  A
  96 GLU   (  96-)  A
 115 ASP   ( 115-)  A
 121 ARG   ( 121-)  A
 137 ARG   ( 137-)  A
 147 ASP   ( 147-)  A
 171 ASP   ( 171-)  A
 173 GLU   ( 173-)  A
 215 GLU   ( 215-)  A
 217 ARG   ( 217-)  A
 226 GLU   ( 226-)  A
 233 ARG   ( 233-)  A
 268 ARG   ( 268-)  A
 270 ASP   ( 270-)  A
 277 GLU   ( 277-)  A
 282 GLU   ( 282-)  A
And so on for a total of 80 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 264 ARG   ( 264-)  A    4.81
 888 ARG   ( 268-)  C    4.48
 268 ARG   ( 268-)  A    4.44
 884 ARG   ( 264-)  C    4.29
 576 ARG   ( 264-)  B    4.17
 612 GLU   ( 300-)  B    4.15

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.

 275 GLU   ( 275-)  A    -2.5
  56 LYS   (  56-)  A    -2.4
 228 LYS   ( 228-)  A    -2.4
 886 MET   ( 266-)  C    -2.3
 595 LEU   ( 283-)  B    -2.2
 266 MET   ( 266-)  A    -2.2
 796 ARG   ( 165-)  C    -2.2
 699 PRO   (  68-)  C    -2.2
 134 VAL   ( 134-)  A    -2.2
 536 ARG   ( 217-)  B    -2.2
 717 GLY   (  86-)  C    -2.2
  86 GLY   (  86-)  A    -2.2
 469 PHE   ( 150-)  B    -2.1
 150 PHE   ( 150-)  A    -2.1
 765 VAL   ( 134-)  C    -2.1
 781 PHE   ( 150-)  C    -2.1
 826 VAL   ( 195-)  C    -2.1
 405 GLY   (  86-)  B    -2.1
 903 LEU   ( 283-)  C    -2.0
 397 PHE   (  78-)  B    -2.0
 399 LEU   (  80-)  B    -2.0
 912 THR   ( 292-)  C    -2.0
  85 PHE   (  85-)  A    -2.0
 660 PRO   (  29-)  C    -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.

  56 LYS   (  56-)  A  Poor phi/psi
  57 ALA   (  57-)  A  Poor phi/psi
  65 PHE   (  65-)  A  PRO omega poor
  85 PHE   (  85-)  A  Poor phi/psi
 148 PRO   ( 148-)  A  PRO omega poor
 193 SER   ( 193-)  A  PRO omega poor
 206 VAL   ( 206-)  A  Poor phi/psi
 228 LYS   ( 228-)  A  Poor phi/psi
 238 ILE   ( 238-)  A  PRO omega poor
 267 ALA   ( 267-)  A  Poor phi/psi
 275 GLU   ( 275-)  A  Poor phi/psi
 348 PRO   (  29-)  B  Poor phi/psi
 375 LYS   (  56-)  B  Poor phi/psi
 384 PHE   (  65-)  B  PRO omega poor
 404 PHE   (  85-)  B  Poor phi/psi
 467 PRO   ( 148-)  B  PRO omega poor
 502 ASP   ( 183-)  B  Poor phi/psi
 512 SER   ( 193-)  B  PRO omega poor
 525 VAL   ( 206-)  B  Poor phi/psi
 550 ILE   ( 238-)  B  PRO omega poor
 579 ALA   ( 267-)  B  Poor phi/psi
 587 GLU   ( 275-)  B  Poor phi/psi
 658 HIS   (  27-)  C  Poor phi/psi
 687 LYS   (  56-)  C  Poor phi/psi
 696 PHE   (  65-)  C  PRO omega poor
 779 PRO   ( 148-)  C  PRO omega poor
 790 SER   ( 159-)  C  Poor phi/psi
 824 SER   ( 193-)  C  PRO omega poor
 837 VAL   ( 206-)  C  Poor phi/psi
 858 ILE   ( 238-)  C  PRO omega poor
 887 ALA   ( 267-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.140

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.

 741 SER   ( 110-)  C    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!

   7 ALA   (   7-)  A      0
  10 VAL   (  10-)  A      0
  27 HIS   (  27-)  A      0
  29 PRO   (  29-)  A      0
  31 PRO   (  31-)  A      0
  45 LEU   (  45-)  A      0
  47 GLU   (  47-)  A      0
  55 ALA   (  55-)  A      0
  56 LYS   (  56-)  A      0
  57 ALA   (  57-)  A      0
  63 HIS   (  63-)  A      0
  65 PHE   (  65-)  A      0
  67 PRO   (  67-)  A      0
  68 PRO   (  68-)  A      0
  70 SER   (  70-)  A      0
  79 PRO   (  79-)  A      0
  82 HIS   (  82-)  A      0
  84 ARG   (  84-)  A      0
  85 PHE   (  85-)  A      0
  87 GLU   (  87-)  A      0
  88 ASP   (  88-)  A      0
  90 THR   (  90-)  A      0
 103 VAL   ( 103-)  A      0
 105 ALA   ( 105-)  A      0
 114 MET   ( 114-)  A      0
And so on for a total of 326 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 : 1.201

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].

 473 PRO   ( 154-)  B  -112.7 envelop C-gamma (-108 degrees)
 785 PRO   ( 154-)  C  -112.2 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 116 LYS   ( 116-)  A      NZ  <->  156 ASN   ( 156-)  A      C      0.35    2.75  INTRA
 116 LYS   ( 116-)  A      NZ  <->  156 ASN   ( 156-)  A      O      0.29    2.41  INTRA
 718 GLU   (  87-)  C      OE1 <->  945 DAL   ( 403-)  C      N      0.21    2.49  INTRA BL
 388 LEU   (  69-)  B      CD2 <->  389 SER   (  70-)  B      N      0.20    2.80  INTRA
 456 ARG   ( 137-)  B      N   <->  459 GLU   ( 140-)  B      OE2    0.19    2.51  INTRA BF
 373 GLU   (  54-)  B      OE2 <->  812 ARG   ( 181-)  C      NH1    0.18    2.52  INTRA BF
 867 GLN   ( 247-)  C      NE2 <->  948 HOH   ( 404 )  C      O      0.17    2.53  INTRA
 606 MET   ( 294-)  B      SD  <->  610 LEU   ( 298-)  B      CD1    0.17    3.23  INTRA
  27 HIS   (  27-)  A      ND1 <->  946 HOH   ( 445 )  A      O      0.16    2.54  INTRA
 408 GLY   (  89-)  B      CA  <->  411 GLN   (  92-)  B      NE2    0.16    2.94  INTRA BL
 284 ASN   ( 284-)  A      ND2 <->  946 HOH   ( 459 )  A      O      0.16    2.54  INTRA BL
 205 ASN   ( 205-)  A      O   <->  207 PHE   ( 207-)  A      N      0.15    2.55  INTRA BL
 721 THR   (  90-)  C      CG2 <->  722 VAL   (  91-)  C      N      0.15    2.85  INTRA BL
 224 ASP   ( 224-)  A      N   <->  228 LYS   ( 228-)  A      O      0.15    2.55  INTRA
 524 ASN   ( 205-)  B      O   <->  526 PHE   ( 207-)  B      N      0.15    2.55  INTRA BL
  74 TYR   (  74-)  A      O   <->  100 LYS   ( 100-)  A      NZ     0.14    2.56  INTRA BL
 524 ASN   ( 205-)  B      N   <->  947 HOH   ( 454 )  B      O      0.14    2.56  INTRA BL
 435 LYS   ( 116-)  B      NZ  <->  947 HOH   ( 409 )  B      O      0.14    2.56  INTRA
  14 HIS   (  14-)  A      CE1 <->   58 ALA   (  58-)  A      N      0.13    2.97  INTRA BL
 116 LYS   ( 116-)  A      NZ  <->  157 THR   ( 157-)  A      CA     0.13    2.97  INTRA
 731 LYS   ( 100-)  C      NZ  <->  948 HOH   ( 472 )  C      O      0.12    2.58  INTRA
 290 THR   ( 290-)  A      CG2 <->  292 THR   ( 292-)  A      N      0.12    2.98  INTRA
 523 GLY   ( 204-)  B      O   <->  576 ARG   ( 264-)  B      O      0.12    2.13  INTRA
 256 LYS   ( 256-)  A      NZ  <->  946 HOH   ( 496 )  A      O      0.11    2.59  INTRA
 487 ARG   ( 168-)  B      C   <->  489 GLN   ( 170-)  B      N      0.10    2.80  INTRA BF
And so on for a total of 110 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

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.

  84 ARG   (  84-)  A      -7.25
 225 TYR   ( 225-)  A      -7.24
 715 ARG   (  84-)  C      -6.44
 696 PHE   (  65-)  C      -6.15
  27 HIS   (  27-)  A      -6.12
 346 HIS   (  27-)  B      -6.06
 403 ARG   (  84-)  B      -5.89
  73 ARG   (  73-)  A      -5.67
 392 ARG   (  73-)  B      -5.66
 704 ARG   (  73-)  C      -5.58
 756 GLN   ( 125-)  C      -5.57
 444 GLN   ( 125-)  B      -5.35
 125 GLN   ( 125-)  A      -5.31
 229 TYR   ( 229-)  A      -5.28
  26 ARG   (  26-)  A      -5.22
 657 ARG   (  26-)  C      -5.15
 462 VAL   ( 143-)  B      -5.12
 143 VAL   ( 143-)  A      -5.11
 774 VAL   ( 143-)  C      -5.10

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

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.

 433 MET   ( 114-)  B   -2.67

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

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.

  14 HIS   (  14-)  A
 251 GLN   ( 251-)  A
 284 ASN   ( 284-)  A
 333 HIS   (  14-)  B
 411 GLN   (  92-)  B
 559 GLN   ( 247-)  B
 596 ASN   ( 284-)  B
 867 GLN   ( 247-)  C
 871 GLN   ( 251-)  C
 904 ASN   ( 284-)  C

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  11 SER   (  11-)  A      N
  26 ARG   (  26-)  A      NE
  81 LEU   (  81-)  A      N
 116 LYS   ( 116-)  A      NZ
 146 PHE   ( 146-)  A      N
 168 ARG   ( 168-)  A      N
 181 ARG   ( 181-)  A      NE
 217 ARG   ( 217-)  A      NE
 217 ARG   ( 217-)  A      NH2
 232 GLY   ( 232-)  A      N
 238 ILE   ( 238-)  A      N
 264 ARG   ( 264-)  A      N
 266 MET   ( 266-)  A      N
 292 THR   ( 292-)  A      N
 380 GLY   (  61-)  B      N
 391 GLU   (  72-)  B      N
 400 LEU   (  81-)  B      N
 407 ASP   (  88-)  B      N
 456 ARG   ( 137-)  B      NH1
 465 PHE   ( 146-)  B      N
 476 THR   ( 157-)  B      N
 478 SER   ( 159-)  B      N
 491 LEU   ( 172-)  B      N
 492 GLU   ( 173-)  B      N
 537 TYR   ( 218-)  B      N
 576 ARG   ( 264-)  B      N
 578 MET   ( 266-)  B      N
 601 PHE   ( 289-)  B      N
 646 GLU   (  15-)  C      N
 647 VAL   (  16-)  C      N
 703 GLU   (  72-)  C      N
 712 LEU   (  81-)  C      N
 715 ARG   (  84-)  C      N
 719 ASP   (  88-)  C      N
 722 VAL   (  91-)  C      N
 777 PHE   ( 146-)  C      N
 792 VAL   ( 161-)  C      N
 796 ARG   ( 165-)  C      NE
 803 LEU   ( 172-)  C      N
 884 ARG   ( 264-)  C      N
 886 MET   ( 266-)  C      N
 912 THR   ( 292-)  C      N

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.

 235 GLU   ( 235-)  A      OE1
 713 HIS   (  82-)  C      ND1

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  13 GLU   (  13-)  A   H-bonding suggests Gln; Ligand-contact
  87 GLU   (  87-)  A   H-bonding suggests Gln; Ligand-contact
 183 ASP   ( 183-)  A   H-bonding suggests Asn; but Alt-Rotamer
 332 GLU   (  13-)  B   H-bonding suggests Gln; Ligand-contact
 406 GLU   (  87-)  B   H-bonding suggests Gln; Ligand-contact
 502 ASP   ( 183-)  B   H-bonding suggests Asn
 644 GLU   (  13-)  C   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 646 GLU   (  15-)  C   H-bonding suggests Gln
 718 GLU   (  87-)  C   H-bonding suggests Gln; Ligand-contact
 814 ASP   ( 183-)  C   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.003
  2nd generation packing quality :  -0.591
  Ramachandran plot appearance   :  -0.576
  chi-1/chi-2 rotamer normality  :  -1.140
  Backbone conformation          :   0.915

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.292 (tight)
  Bond angles                    :   0.607 (tight)
  Omega angle restraints         :   0.218 (tight)
  Side chain planarity           :   0.215 (tight)
  Improper dihedral distribution :   0.607
  B-factor distribution          :   0.505
  Inside/Outside distribution    :   0.988

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 : 2.21


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.292 (tight)
  Bond angles                    :   0.607 (tight)
  Omega angle restraints         :   0.218 (tight)
  Side chain planarity           :   0.215 (tight)
  Improper dihedral distribution :   0.607
  B-factor distribution          :   0.505
  Inside/Outside distribution    :   0.988
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      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,
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    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.