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 pdb2f29.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: A and B

All-atom RMS fit for the two chains : 0.640
CA-only RMS fit for the two chains : 0.364

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: A and B

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.

 741 DAN   ( 381-)  A  -
 742 EPE   ( 382-)  A  -
 743 EPE   ( 383-)  A  -
 744 EPE   ( 382-)  B  -
 745 EPE   ( 383-)  B  -
 746 DAN   ( 381-)  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: 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: Arginine nomenclature problem

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

  41 ARG   (  41-)  A
  78 ARG   (  78-)  A
  83 ARG   (  83-)  A
 123 ARG   ( 123-)  A
 134 ARG   ( 134-)  A
 140 ARG   ( 140-)  A
 152 ARG   ( 152-)  A
 189 ARG   ( 189-)  A
 204 ARG   ( 204-)  A
 208 ARG   ( 208-)  A
 280 ARG   ( 283-)  A
 297 ARG   ( 304-)  A
 307 ARG   ( 314-)  A
 391 ARG   (  21-)  B
 411 ARG   (  41-)  B
 425 ARG   (  55-)  B
 453 ARG   (  83-)  B
 493 ARG   ( 123-)  B
 504 ARG   ( 134-)  B
 542 ARG   ( 172-)  B
 559 ARG   ( 189-)  B
 574 ARG   ( 204-)  B
 604 ARG   ( 237-)  B

Warning: Tyrosine convention problem

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

  20 TYR   (  20-)  A
  59 TYR   (  59-)  A
 179 TYR   ( 179-)  A
 390 TYR   (  20-)  B
 429 TYR   (  59-)  B
 549 TYR   ( 179-)  B

Warning: Phenylalanine convention problem

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

 102 PHE   ( 102-)  A
 157 PHE   ( 157-)  A
 195 PHE   ( 195-)  A
 211 PHE   ( 211-)  A
 276 PHE   ( 279-)  A
 360 PHE   ( 367-)  A
 407 PHE   (  37-)  B
 472 PHE   ( 102-)  B
 527 PHE   ( 157-)  B
 565 PHE   ( 195-)  B
 730 PHE   ( 367-)  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.

 141 ASP   ( 141-)  A
 215 ASP   ( 215-)  A
 248 ASP   ( 251-)  A
 299 ASP   ( 306-)  A
 329 ASP   ( 336-)  A
 351 ASP   ( 358-)  A
 511 ASP   ( 141-)  B
 514 ASP   ( 144-)  B
 585 ASP   ( 215-)  B
 618 ASP   ( 251-)  B
 669 ASP   ( 306-)  B
 699 ASP   ( 336-)  B
 721 ASP   ( 358-)  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.

 153 GLU   ( 153-)  A
 225 GLU   ( 225-)  A
 263 GLU   ( 266-)  A
 312 GLU   ( 319-)  A
 354 GLU   ( 361-)  A
 523 GLU   ( 153-)  B
 595 GLU   ( 225-)  B
 633 GLU   ( 266-)  B
 724 GLU   ( 361-)  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.

 236 HIS   ( 239-)  A      CB   CG    1.56    4.2

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.

 147 ILE   ( 147-)  A     -C    N    CA  114.08   -4.2
 446 GLN   (  76-)  B      CG   CD   NE2 126.61    6.8
 446 GLN   (  76-)  B      NE2  CD   OE1 113.15   -9.5
 584 GLN   ( 214-)  B     -C    N    CA  129.29    4.2
 635 PRO   ( 268-)  B      N    CA   C   122.75    4.4

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.

  41 ARG   (  41-)  A
  78 ARG   (  78-)  A
  83 ARG   (  83-)  A
 123 ARG   ( 123-)  A
 134 ARG   ( 134-)  A
 140 ARG   ( 140-)  A
 141 ASP   ( 141-)  A
 152 ARG   ( 152-)  A
 153 GLU   ( 153-)  A
 189 ARG   ( 189-)  A
 204 ARG   ( 204-)  A
 208 ARG   ( 208-)  A
 215 ASP   ( 215-)  A
 225 GLU   ( 225-)  A
 248 ASP   ( 251-)  A
 263 GLU   ( 266-)  A
 280 ARG   ( 283-)  A
 297 ARG   ( 304-)  A
 299 ASP   ( 306-)  A
 307 ARG   ( 314-)  A
 312 GLU   ( 319-)  A
 329 ASP   ( 336-)  A
 351 ASP   ( 358-)  A
 354 GLU   ( 361-)  A
 391 ARG   (  21-)  B
 411 ARG   (  41-)  B
 425 ARG   (  55-)  B
 453 ARG   (  83-)  B
 493 ARG   ( 123-)  B
 504 ARG   ( 134-)  B
 511 ASP   ( 141-)  B
 514 ASP   ( 144-)  B
 523 GLU   ( 153-)  B
 542 ARG   ( 172-)  B
 559 ARG   ( 189-)  B
 574 ARG   ( 204-)  B
 585 ASP   ( 215-)  B
 595 GLU   ( 225-)  B
 604 ARG   ( 237-)  B
 618 ASP   ( 251-)  B
 633 GLU   ( 266-)  B
 669 ASP   ( 306-)  B
 699 ASP   ( 336-)  B
 721 ASP   ( 358-)  B
 724 GLU   ( 361-)  B

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.

 111 GLU   ( 111-)  A    4.48
 607 LEU   ( 240-)  B    4.44
 567 PHE   ( 197-)  B    4.10
 481 GLU   ( 111-)  B    4.09

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 : -3.376

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.

 265 PRO   ( 268-)  A    -3.1
 309 PRO   ( 316-)  A    -3.0
 679 PRO   ( 316-)  B    -3.0
 635 PRO   ( 268-)  B    -3.0
 156 THR   ( 156-)  A    -2.9
 448 ARG   (  78-)  B    -2.7
  22 ILE   (  22-)  A    -2.7
 519 PRO   ( 149-)  B    -2.6
 647 PRO   ( 280-)  B    -2.6
 594 VAL   ( 224-)  B    -2.5
 411 ARG   (  41-)  B    -2.5
 392 ILE   (  22-)  B    -2.4
 565 PHE   ( 195-)  B    -2.4
 526 THR   ( 156-)  B    -2.3
 434 HIS   (  64-)  B    -2.2
 157 PHE   ( 157-)  A    -2.2
 254 GLU   ( 257-)  A    -2.2
  32 GLN   (  32-)  A    -2.2
 352 TYR   ( 359-)  A    -2.2
 380 GLU   (  10-)  B    -2.2
 274 ILE   ( 277-)  A    -2.2
 386 GLY   (  16-)  B    -2.1
  41 ARG   (  41-)  A    -2.1
 632 VAL   ( 265-)  B    -2.1
 518 GLY   ( 148-)  B    -2.1
 149 PRO   ( 149-)  A    -2.1
 195 PHE   ( 195-)  A    -2.1
 358 LEU   ( 365-)  A    -2.1
 644 ILE   ( 277-)  B    -2.1
 266 PRO   ( 269-)  A    -2.0
  16 GLY   (  16-)  A    -2.0
 107 GLY   ( 107-)  A    -2.0
  47 GLU   (  47-)  A    -2.0
 304 LEU   ( 311-)  A    -2.0
  43 SER   (  43-)  A    -2.0
 477 GLY   ( 107-)  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.

  32 GLN   (  32-)  A  Poor phi/psi
  43 SER   (  43-)  A  Poor phi/psi
  78 ARG   (  78-)  A  Poor phi/psi
  86 ASN   (  86-)  A  Poor phi/psi
 107 GLY   ( 107-)  A  Poor phi/psi
 118 ARG   ( 118-)  A  Poor phi/psi
 147 ILE   ( 147-)  A  Poor phi/psi
 160 GLY   ( 160-)  A  PRO omega poor
 164 CYS   ( 164-)  A  Poor phi/psi
 170 ARG   ( 170-)  A  Poor phi/psi
 202 HIS   ( 202-)  A  Poor phi/psi
 207 ALA   ( 207-)  A  Poor phi/psi
 212 VAL   ( 212-)  A  Poor phi/psi
 215 ASP   ( 215-)  A  Poor phi/psi
 217 LEU   ( 217-)  A  Poor phi/psi
 239 ALA   ( 242-)  A  Poor phi/psi
 248 ASP   ( 251-)  A  Poor phi/psi
 265 PRO   ( 268-)  A  Poor phi/psi
 266 PRO   ( 269-)  A  Poor phi/psi
 308 PRO   ( 315-)  A  PRO omega poor
 326 ALA   ( 333-)  A  Poor phi/psi
 351 ASP   ( 358-)  A  Poor phi/psi
 352 TYR   ( 359-)  A  Poor phi/psi
 354 GLU   ( 361-)  A  Poor phi/psi
 369 GLU   ( 376-)  A  Poor phi/psi
 392 ILE   (  22-)  B  Poor phi/psi
 413 SER   (  43-)  B  Poor phi/psi
 448 ARG   (  78-)  B  Poor phi/psi
 450 ASP   (  80-)  B  Poor phi/psi
 456 ASN   (  86-)  B  Poor phi/psi
 477 GLY   ( 107-)  B  Poor phi/psi
 526 THR   ( 156-)  B  Poor phi/psi
 530 GLY   ( 160-)  B  PRO omega poor
 565 PHE   ( 195-)  B  Poor phi/psi
 572 HIS   ( 202-)  B  Poor phi/psi
 583 ALA   ( 213-)  B  Poor phi/psi
 584 GLN   ( 214-)  B  Poor phi/psi
 585 ASP   ( 215-)  B  Poor phi/psi
 587 LEU   ( 217-)  B  Poor phi/psi
 618 ASP   ( 251-)  B  Poor phi/psi
 636 PRO   ( 269-)  B  Poor phi/psi
 660 HIS   ( 297-)  B  Poor phi/psi
 669 ASP   ( 306-)  B  Poor phi/psi
 678 PRO   ( 315-)  B  PRO omega poor
 696 ALA   ( 333-)  B  Poor phi/psi
 722 TYR   ( 359-)  B  Poor phi/psi
 724 GLU   ( 361-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.055

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 : -3.055

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!

   4 LEU   (   4-)  A      0
   6 VAL   (   6-)  A      0
   7 LEU   (   7-)  A      0
   8 GLN   (   8-)  A      0
  12 VAL   (  12-)  A      0
  13 PHE   (  13-)  A      0
  15 SER   (  15-)  A      0
  17 ALA   (  17-)  A      0
  21 ARG   (  21-)  A      0
  22 ILE   (  22-)  A      0
  32 GLN   (  32-)  A      0
  41 ARG   (  41-)  A      0
  42 ALA   (  42-)  A      0
  44 LYS   (  44-)  A      0
  49 ALA   (  49-)  A      0
  50 GLU   (  50-)  A      0
  51 LEU   (  51-)  A      0
  64 HIS   (  64-)  A      0
  69 GLN   (  69-)  A      0
  77 ALA   (  77-)  A      0
  78 ARG   (  78-)  A      0
  79 LEU   (  79-)  A      0
  80 ASP   (  80-)  A      0
  84 SER   (  84-)  A      0
  85 MET   (  85-)  A      0
And so on for a total of 360 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 : 1.333

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]

  23 PRO   (  23-)  A    0.45 HIGH

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.

 397 TYR   (  27-)  B      N   <->  701 GLN   ( 338-)  B      NE2    0.45    2.40  INTRA BL
  83 ARG   (  83-)  A      NH1 <->   85 MET   (  85-)  A      SD     0.42    2.88  INTRA
 555 HIS   ( 185-)  B      ND1 <->  557 ILE   ( 187-)  B      N      0.38    2.62  INTRA
 720 ASN   ( 357-)  B      ND2 <->  724 GLU   ( 361-)  B      OE2    0.36    2.34  INTRA
 453 ARG   (  83-)  B      NH1 <->  455 MET   (  85-)  B      SD     0.36    2.94  INTRA
 143 THR   ( 143-)  A      O   <->  147 ILE   ( 147-)  A      N      0.33    2.37  INTRA
 558 GLN   ( 188-)  B      NE2 <->  559 ARG   ( 189-)  B      NH1    0.32    2.53  INTRA BF
 651 SER   ( 288-)  B      N   <->  652 PRO   ( 289-)  B      CD     0.28    2.72  INTRA BF
 224 VAL   ( 224-)  A      CG1 <->  225 GLU   ( 225-)  A      N      0.27    2.73  INTRA
 625 SER   ( 258-)  B      C   <->  626 GLN   ( 259-)  B      CD     0.25    2.85  INTRA BF
 409 GLU   (  39-)  B      OE1 <->  411 ARG   (  41-)  B      NH1    0.24    2.46  INTRA BL
 387 ALA   (  17-)  B      N   <->  744 EPE   ( 382-)  B      O1S    0.24    2.46  INTRA BL
 433 THR   (  63-)  B      C   <->  434 HIS   (  64-)  B      ND1    0.22    2.78  INTRA BL
 449 LEU   (  79-)  B      O   <->  452 HIS   (  82-)  B      N      0.22    2.48  INTRA
  41 ARG   (  41-)  A      NH2 <->   46 ASP   (  46-)  A      OD1    0.21    2.49  INTRA
  46 ASP   (  46-)  A      O   <->   48 HIS   (  48-)  A      N      0.21    2.49  INTRA
 708 ASP   ( 345-)  B      OD1 <->  710 SER   ( 347-)  B      CB     0.21    2.59  INTRA BL
 350 ASN   ( 357-)  A      ND2 <->  354 GLU   ( 361-)  A      OE2    0.21    2.49  INTRA
 510 ARG   ( 140-)  B      NH1 <->  512 LEU   ( 142-)  B      CD2    0.21    2.89  INTRA BF
 414 LYS   (  44-)  B      NZ  <->  721 ASP   ( 358-)  B      O      0.21    2.49  INTRA BL
 201 ASP   ( 201-)  A      OD1 <->  205 THR   ( 205-)  A      N      0.20    2.50  INTRA
 226 GLN   ( 229-)  A      N   <->  747 HOH   ( 389 )  A      O      0.20    2.50  INTRA
  17 ALA   (  17-)  A      N   <->  742 EPE   ( 382-)  A      O1S    0.20    2.50  INTRA
 720 ASN   ( 357-)  B      ND2 <->  724 GLU   ( 361-)  B      CD     0.20    2.90  INTRA
  27 TYR   (  27-)  A      N   <->  331 GLN   ( 338-)  A      NE2    0.19    2.66  INTRA BL
And so on for a total of 202 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.

 170 ARG   ( 170-)  A      -6.80
 238 ARG   ( 241-)  A      -6.53
 558 GLN   ( 188-)  B      -6.45
 677 ARG   ( 314-)  B      -6.36
 559 ARG   ( 189-)  B      -6.34
 554 LEU   ( 184-)  B      -6.32
 184 LEU   ( 184-)  A      -6.26
 574 ARG   ( 204-)  B      -6.21
 267 GLN   ( 270-)  A      -6.10
 637 GLN   ( 270-)  B      -6.04
 307 ARG   ( 314-)  A      -6.03
 188 GLN   ( 188-)  A      -6.00
 204 ARG   ( 204-)  A      -5.96
 608 ARG   ( 241-)  B      -5.85
 189 ARG   ( 189-)  A      -5.84
  94 GLN   (  94-)  A      -5.71
 464 GLN   (  94-)  B      -5.61
 504 ARG   ( 134-)  B      -5.46
 295 TRP   ( 302-)  A      -5.42
 665 TRP   ( 302-)  B      -5.34
 418 HIS   (  48-)  B      -5.31
  48 HIS   (  48-)  A      -5.31
 401 GLN   (  31-)  B      -5.12
 134 ARG   ( 134-)  A      -5.11
 322 LYS   ( 329-)  A      -5.04
 739 GLU   ( 376-)  B      -5.02

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.

 187 ILE   ( 187-)  A       189 - ARG    189- ( A)         -5.56
 557 ILE   ( 187-)  B       559 - ARG    189- ( B)         -5.88

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

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.

 313 ALA   ( 320-)  A   -2.84
 683 ALA   ( 320-)  B   -2.62

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

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.

 747 HOH   ( 385 )  A      O
 747 HOH   ( 386 )  A      O
 747 HOH   ( 392 )  A      O
 747 HOH   ( 394 )  A      O
 747 HOH   ( 397 )  A      O
 747 HOH   ( 407 )  A      O
 747 HOH   ( 409 )  A      O
 747 HOH   ( 413 )  A      O
 747 HOH   ( 414 )  A      O
 747 HOH   ( 418 )  A      O
 747 HOH   ( 420 )  A      O
 748 HOH   ( 386 )  B      O
 748 HOH   ( 387 )  B      O
 748 HOH   ( 390 )  B      O
 748 HOH   ( 391 )  B      O
 748 HOH   ( 395 )  B      O
 748 HOH   ( 397 )  B      O
 748 HOH   ( 399 )  B      O
 748 HOH   ( 407 )  B      O
 748 HOH   ( 417 )  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.

  69 GLN   (  69-)  A
  71 GLN   (  71-)  A
 168 ASN   ( 168-)  A
 210 HIS   ( 210-)  A
 226 GLN   ( 229-)  A
 242 GLN   ( 245-)  A
 253 GLN   ( 256-)  A
 256 GLN   ( 259-)  A
 331 GLN   ( 338-)  A
 439 GLN   (  69-)  B
 482 GLN   ( 112-)  B
 502 HIS   ( 132-)  B
 596 GLN   ( 229-)  B
 612 GLN   ( 245-)  B
 614 GLN   ( 247-)  B
 617 ASN   ( 250-)  B
 701 GLN   ( 338-)  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 LYS   (   9-)  A      N
  14 GLN   (  14-)  A      N
  18 HIS   (  18-)  A      N
  20 TYR   (  20-)  A      OH
  21 ARG   (  21-)  A      NH1
  21 ARG   (  21-)  A      NH2
  33 SER   (  33-)  A      OG
  41 ARG   (  41-)  A      NH1
  43 SER   (  43-)  A      N
  52 ILE   (  52-)  A      N
  68 TRP   (  68-)  A      NE1
  79 LEU   (  79-)  A      N
  83 ARG   (  83-)  A      NH1
  86 ASN   (  86-)  A      ND2
 120 ASN   ( 120-)  A      ND2
 132 HIS   ( 132-)  A      ND1
 152 ARG   ( 152-)  A      N
 153 GLU   ( 153-)  A      N
 155 SER   ( 155-)  A      OG
 159 VAL   ( 159-)  A      N
 196 CYS   ( 196-)  A      N
 218 GLU   ( 218-)  A      N
 234 ARG   ( 237-)  A      NH2
 242 GLN   ( 245-)  A      NE2
 246 THR   ( 249-)  A      N
And so on for a total of 72 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.

  86 ASN   (  86-)  A      OD1
 126 GLN   ( 126-)  A      OE1
 218 GLU   ( 218-)  A      OE2
 244 GLN   ( 247-)  A      OE1
 496 GLN   ( 126-)  B      OE1
 588 GLU   ( 218-)  B      OE2
 686 GLU   ( 323-)  B      OE1

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.

  50 GLU   (  50-)  A   H-bonding suggests Gln
 141 ASP   ( 141-)  A   H-bonding suggests Asn; but Alt-Rotamer
 201 ASP   ( 201-)  A   H-bonding suggests Asn; but Alt-Rotamer
 380 GLU   (  10-)  B   H-bonding suggests Gln
 420 GLU   (  50-)  B   H-bonding suggests Gln
 501 ASP   ( 131-)  B   H-bonding suggests Asn; but Alt-Rotamer
 571 ASP   ( 201-)  B   H-bonding suggests Asn; but Alt-Rotamer
 621 ASP   ( 254-)  B   H-bonding suggests Asn
 633 GLU   ( 266-)  B   H-bonding suggests Gln; but Alt-Rotamer
 686 GLU   ( 323-)  B   H-bonding suggests Gln; but Alt-Rotamer

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 :  -0.621
  2nd generation packing quality :  -1.639
  Ramachandran plot appearance   :  -3.376 (poor)
  chi-1/chi-2 rotamer normality  :  -3.055 (poor)
  Backbone conformation          :  -1.088

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.335 (tight)
  Bond angles                    :   0.710
  Omega angle restraints         :   0.242 (tight)
  Side chain planarity           :   0.218 (tight)
  Improper dihedral distribution :   0.627
  B-factor distribution          :   0.467
  Inside/Outside distribution    :   0.990

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 : 2.92


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.335 (tight)
  Bond angles                    :   0.710
  Omega angle restraints         :   0.242 (tight)
  Side chain planarity           :   0.218 (tight)
  Improper dihedral distribution :   0.627
  B-factor distribution          :   0.467
  Inside/Outside distribution    :   0.990
==============

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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    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,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      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.