WHAT IF Check report

This file was created 2012-01-13 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 pdb1vcu.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 157.650  B   =  74.000  C    =  77.190
    Alpha=  90.000  Beta=  90.640  Gamma=  90.000

Dimensions of a reduced cell

    A    =  77.190  B   =  74.000  C    =  87.077
    Alpha= 115.145  Beta=  89.421  Gamma=  90.000

Dimensions of the conventional cell

    A    =  74.000  B   = 157.650  C    =  77.190
    Alpha=  90.640  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  1.000000  0.000000|
 | -1.000000  0.000000  0.000000|
 |  0.000000  0.000000 -1.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: C 1 2 1

Bravais type of conventional cell is: C

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

 744 DAN   ( 381-)  A  -
 745 EPE   ( 382-)  A  -
 746 EPE   ( 383-)  A  -
 747 EPE   ( 382-)  B  -
 748 EPE   ( 383-)  B  -
 749 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

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 3.91

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.

  21 ARG   (  21-)  A
  78 ARG   (  78-)  A
  83 ARG   (  83-)  A
 152 ARG   ( 152-)  A
 182 ARG   ( 182-)  A
 189 ARG   ( 189-)  A
 204 ARG   ( 204-)  A
 208 ARG   ( 208-)  A
 240 ARG   ( 243-)  A
 280 ARG   ( 283-)  A
 297 ARG   ( 304-)  A
 391 ARG   (  21-)  B
 426 ARG   (  56-)  B
 493 ARG   ( 123-)  B
 559 ARG   ( 189-)  B
 613 ARG   ( 243-)  B
 653 ARG   ( 283-)  B
 670 ARG   ( 304-)  B
 680 ARG   ( 314-)  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
 179 TYR   ( 179-)  A
 390 TYR   (  20-)  B
 551 TYR   ( 181-)  B

Warning: Phenylalanine convention problem

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

  37 PHE   (  37-)  A
  99 PHE   (  99-)  A
 102 PHE   ( 102-)  A
 157 PHE   ( 157-)  A
 195 PHE   ( 195-)  A
 276 PHE   ( 279-)  A
 360 PHE   ( 367-)  A
 407 PHE   (  37-)  B
 527 PHE   ( 157-)  B
 565 PHE   ( 195-)  B
 733 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
 144 ASP   ( 144-)  A
 215 ASP   ( 215-)  A
 248 ASP   ( 251-)  A
 299 ASP   ( 306-)  A
 329 ASP   ( 336-)  A
 351 ASP   ( 358-)  A
 514 ASP   ( 144-)  B
 585 ASP   ( 215-)  B
 672 ASP   ( 306-)  B
 724 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
 595 GLU   ( 225-)  B
 636 GLU   ( 266-)  B
 689 GLU   ( 323-)  B
 727 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.

  86 ASN   (  86-)  A      CG   OD1   1.32    4.5
  86 ASN   (  86-)  A      CG   ND2   1.23   -4.7
 456 ASN   (  86-)  B      CG   OD1   1.33    4.7
 456 ASN   (  86-)  B      CG   ND2   1.23   -4.5

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.

 172 ARG   ( 172-)  A      C    CA   CB  119.14    4.8

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.

  21 ARG   (  21-)  A
  78 ARG   (  78-)  A
  83 ARG   (  83-)  A
 141 ASP   ( 141-)  A
 144 ASP   ( 144-)  A
 152 ARG   ( 152-)  A
 153 GLU   ( 153-)  A
 182 ARG   ( 182-)  A
 189 ARG   ( 189-)  A
 204 ARG   ( 204-)  A
 208 ARG   ( 208-)  A
 215 ASP   ( 215-)  A
 225 GLU   ( 225-)  A
 240 ARG   ( 243-)  A
 248 ASP   ( 251-)  A
 263 GLU   ( 266-)  A
 280 ARG   ( 283-)  A
 297 ARG   ( 304-)  A
 299 ASP   ( 306-)  A
 312 GLU   ( 319-)  A
 329 ASP   ( 336-)  A
 351 ASP   ( 358-)  A
 354 GLU   ( 361-)  A
 391 ARG   (  21-)  B
 426 ARG   (  56-)  B
 493 ARG   ( 123-)  B
 514 ASP   ( 144-)  B
 559 ARG   ( 189-)  B
 585 ASP   ( 215-)  B
 595 GLU   ( 225-)  B
 613 ARG   ( 243-)  B
 636 GLU   ( 266-)  B
 653 ARG   ( 283-)  B
 670 ARG   ( 304-)  B
 672 ASP   ( 306-)  B
 680 ARG   ( 314-)  B
 689 GLU   ( 323-)  B
 724 ASP   ( 358-)  B
 727 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.

 552 ARG   ( 182-)  B    4.93
 111 GLU   ( 111-)  A    4.22
 635 VAL   ( 265-)  B    4.18

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 : -3.055

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.

 309 PRO   ( 316-)  A    -3.0
 265 PRO   ( 268-)  A    -3.0
 526 THR   ( 156-)  B    -2.9
  22 ILE   (  22-)  A    -2.7
 392 ILE   (  22-)  B    -2.6
 611 ARG   ( 241-)  B    -2.6
 680 ARG   ( 314-)  B    -2.5
 266 PRO   ( 269-)  A    -2.5
 682 PRO   ( 316-)  B    -2.4
 518 GLY   ( 148-)  B    -2.4
 224 VAL   ( 224-)  A    -2.4
 106 PRO   ( 106-)  A    -2.4
 156 THR   ( 156-)  A    -2.4
  83 ARG   (  83-)  A    -2.3
 477 GLY   ( 107-)  B    -2.3
 421 LEU   (  51-)  B    -2.2
 725 TYR   ( 359-)  B    -2.2
 380 GLU   (  10-)  B    -2.2
  41 ARG   (  41-)  A    -2.2
 434 HIS   (  64-)  B    -2.1
 598 GLU   ( 228-)  B    -2.1
 148 GLY   ( 148-)  A    -2.1
 157 PHE   ( 157-)  A    -2.1
 358 LEU   ( 365-)  A    -2.1
 311 PRO   ( 318-)  A    -2.1
  12 VAL   (  12-)  A    -2.1
 296 GLN   ( 303-)  A    -2.1
 386 GLY   (  16-)  B    -2.1
 107 GLY   ( 107-)  A    -2.0
  16 GLY   (  16-)  A    -2.0
 255 SER   ( 258-)  A    -2.0
 527 PHE   ( 157-)  B    -2.0
 149 PRO   ( 149-)  A    -2.0
  78 ARG   (  78-)  A    -2.0
 195 PHE   ( 195-)  A    -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.

  22 ILE   (  22-)  A  Poor phi/psi
  32 GLN   (  32-)  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
 160 GLY   ( 160-)  A  PRO omega poor
 164 CYS   ( 164-)  A  Poor phi/psi
 195 PHE   ( 195-)  A  Poor phi/psi
 202 HIS   ( 202-)  A  Poor phi/psi
 214 GLN   ( 214-)  A  Poor phi/psi
 215 ASP   ( 215-)  A  Poor phi/psi
 217 LEU   ( 217-)  A  Poor phi/psi
 237 LEU   ( 240-)  A  Poor phi/psi
 266 PRO   ( 269-)  A  Poor phi/psi
 290 HIS   ( 297-)  A  Poor phi/psi
 299 ASP   ( 306-)  A  Poor phi/psi
 308 PRO   ( 315-)  A  PRO omega poor
 326 ALA   ( 333-)  A  Poor phi/psi
 376 VAL   (   6-)  B  Poor phi/psi
 392 ILE   (  22-)  B  Poor phi/psi
 402 GLN   (  32-)  B  Poor phi/psi
 420 GLU   (  50-)  B  Poor phi/psi
 447 ALA   (  77-)  B  Poor phi/psi
 448 ARG   (  78-)  B  Poor phi/psi
 456 ASN   (  86-)  B  Poor phi/psi
 477 GLY   ( 107-)  B  Poor phi/psi
 502 HIS   ( 132-)  B  Poor phi/psi
 518 GLY   ( 148-)  B  Poor phi/psi
 530 GLY   ( 160-)  B  PRO omega poor
 534 CYS   ( 164-)  B  Poor phi/psi
 572 HIS   ( 202-)  B  Poor phi/psi
 582 VAL   ( 212-)  B  Poor phi/psi
 585 ASP   ( 215-)  B  Poor phi/psi
 587 LEU   ( 217-)  B  Poor phi/psi
 611 ARG   ( 241-)  B  Poor phi/psi
 621 ASP   ( 251-)  B  Poor phi/psi
 626 GLN   ( 256-)  B  Poor phi/psi
 627 GLU   ( 257-)  B  Poor phi/psi
 638 PRO   ( 268-)  B  PRO omega poor
 663 HIS   ( 297-)  B  Poor phi/psi
 672 ASP   ( 306-)  B  Poor phi/psi
 681 PRO   ( 315-)  B  PRO omega poor
 699 ALA   ( 333-)  B  Poor phi/psi
 724 ASP   ( 358-)  B  Poor phi/psi
 725 TYR   ( 359-)  B  Poor phi/psi
 727 GLU   ( 361-)  B  Poor phi/psi
 742 GLU   ( 376-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.661

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!

   8 GLN   (   8-)  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
  31 GLN   (  31-)  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
  74 VAL   (  74-)  A      0
  75 ALA   (  75-)  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
  86 ASN   (  86-)  A      0
And so on for a total of 356 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 : 1.308

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!

 641 GLY   ( 271-)  B   1.88   23
 707 GLY   ( 341-)  B   1.58   19

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    0.46 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.

 453 ARG   (  83-)  B      NH1 <->  455 MET   (  85-)  B      SD     0.44    2.86  INTRA BL
 555 HIS   ( 185-)  B      CD2 <->  558 GLN   ( 188-)  B      N      0.44    2.66  INTRA
 395 LEU   (  25-)  B      N   <->  702 ASP   ( 336-)  B      OD2    0.34    2.36  INTRA BL
 626 GLN   ( 256-)  B      O   <->  628 SER   ( 258-)  B      N      0.34    2.36  INTRA BF
  27 TYR   (  27-)  A      N   <->  331 GLN   ( 338-)  A      NE2    0.33    2.52  INTRA BL
 185 HIS   ( 185-)  A      ND1 <->  187 ILE   ( 187-)  A      N      0.33    2.67  INTRA
  41 ARG   (  41-)  A      NH2 <->   46 ASP   (  46-)  A      OD1    0.25    2.45  INTRA
  31 GLN   (  31-)  A      NE2 <->  132 HIS   ( 132-)  A      NE2    0.24    2.76  INTRA
 118 ARG   ( 118-)  A      O   <->  183 LYS   ( 183-)  A      NZ     0.24    2.46  INTRA
 501 ASP   ( 131-)  B      CB  <->  504 ARG   ( 134-)  B      NH2    0.24    2.86  INTRA
 460 LEU   (  90-)  B      N   <->  469 PHE   (  99-)  B      O      0.24    2.46  INTRA BL
 334 GLY   ( 341-)  A      O   <->  342 LEU   ( 349-)  A      N      0.23    2.47  INTRA BL
 378 GLN   (   8-)  B      OE1 <->  436 VAL   (  66-)  B      N      0.23    2.47  INTRA BL
 539 ASP   ( 169-)  B      CB  <->  600 ARG   ( 230-)  B      NH2    0.23    2.87  INTRA
  83 ARG   (  83-)  A      NH1 <->  105 ILE   ( 105-)  A      CB     0.22    2.88  INTRA
 118 ARG   ( 118-)  A      NH2 <->  185 HIS   ( 185-)  A      O      0.21    2.49  INTRA
 185 HIS   ( 185-)  A      ND1 <->  188 GLN   ( 188-)  A      N      0.21    2.79  INTRA
 493 ARG   ( 123-)  B      NH2 <->  513 THR   ( 143-)  B      CG2    0.21    2.89  INTRA
 120 ASN   ( 120-)  A      ND2 <->  151 TYR   ( 151-)  A      CE1    0.20    2.90  INTRA
 636 GLU   ( 266-)  B      OE1 <->  663 HIS   ( 297-)  B      NE2    0.19    2.51  INTRA BL
 605 ASN   ( 235-)  B      OD1 <->  613 ARG   ( 243-)  B      NE     0.19    2.51  INTRA BL
 401 GLN   (  31-)  B      NE2 <->  502 HIS   ( 132-)  B      CD2    0.19    2.91  INTRA
 283 ALA   ( 290-)  A      CB  <->  284 GLN   ( 291-)  A      NE2    0.19    2.81  INTRA
 561 ILE   ( 191-)  B      CD1 <->  585 ASP   ( 215-)  B      N      0.18    2.92  INTRA
  86 ASN   (  86-)  A      ND2 <->  750 HOH   ( 395 )  A      O      0.18    2.52  INTRA BL
And so on for a total of 173 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.

 504 ARG   ( 134-)  B      -6.64
 184 LEU   ( 184-)  A      -6.43
 189 ARG   ( 189-)  A      -6.35
 574 ARG   ( 204-)  B      -6.34
 307 ARG   ( 314-)  A      -6.28
 188 GLN   ( 188-)  A      -6.19
 238 ARG   ( 241-)  A      -6.12
 204 ARG   ( 204-)  A      -6.11
 558 GLN   ( 188-)  B      -6.03
 680 ARG   ( 314-)  B      -6.01
 267 GLN   ( 270-)  A      -5.86
 559 ARG   ( 189-)  B      -5.81
 640 GLN   ( 270-)  B      -5.78
 554 LEU   ( 184-)  B      -5.74
  94 GLN   (  94-)  A      -5.68
 464 GLN   (  94-)  B      -5.68
 611 ARG   ( 241-)  B      -5.45
 134 ARG   ( 134-)  A      -5.42
 668 TRP   ( 302-)  B      -5.42
 418 HIS   (  48-)  B      -5.41
 295 TRP   ( 302-)  A      -5.40
  48 HIS   (  48-)  A      -5.34
 401 GLN   (  31-)  B      -5.04
 322 LYS   ( 329-)  A      -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)         -5.72
 557 ILE   ( 187-)  B       559 - ARG    189- ( B)         -5.55

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   -2.76
 686 ALA   ( 320-)  B   -2.70
 561 ILE   ( 191-)  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

Warning: Water molecules need moving

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

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

 750 HOH   ( 392 )  A      O     62.96   24.35   33.73

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.

 750 HOH   ( 394 )  A      O
 750 HOH   ( 411 )  A      O
 750 HOH   ( 412 )  A      O
 750 HOH   ( 416 )  A      O
 750 HOH   ( 426 )  A      O
 750 HOH   ( 428 )  A      O
 750 HOH   ( 443 )  A      O
 751 HOH   ( 395 )  B      O
 751 HOH   ( 401 )  B      O
 751 HOH   ( 405 )  B      O
 751 HOH   ( 406 )  B      O
 751 HOH   ( 409 )  B      O
 751 HOH   ( 410 )  B      O
 751 HOH   ( 415 )  B      O
 751 HOH   ( 416 )  B      O
 751 HOH   ( 426 )  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.

  86 ASN   (  86-)  A
 242 GLN   ( 245-)  A
 331 GLN   ( 338-)  A
 456 ASN   (  86-)  B
 502 HIS   ( 132-)  B
 538 ASN   ( 168-)  B
 580 HIS   ( 210-)  B
 590 GLN   ( 220-)  B
 615 GLN   ( 245-)  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.

  14 GLN   (  14-)  A      N
  15 SER   (  15-)  A      OG
  18 HIS   (  18-)  A      N
  20 TYR   (  20-)  A      OH
  21 ARG   (  21-)  A      NH1
  21 ARG   (  21-)  A      NH2
  41 ARG   (  41-)  A      NE
  43 SER   (  43-)  A      N
  68 TRP   (  68-)  A      NE1
 120 ASN   ( 120-)  A      ND2
 144 ASP   ( 144-)  A      N
 156 THR   ( 156-)  A      N
 157 PHE   ( 157-)  A      N
 159 VAL   ( 159-)  A      N
 166 GLN   ( 166-)  A      NE2
 193 SER   ( 193-)  A      OG
 200 HIS   ( 200-)  A      N
 206 TRP   ( 206-)  A      N
 206 TRP   ( 206-)  A      NE1
 218 GLU   ( 218-)  A      N
 234 ARG   ( 237-)  A      NH2
 236 HIS   ( 239-)  A      N
 239 ALA   ( 242-)  A      N
 242 GLN   ( 245-)  A      NE2
 256 GLN   ( 259-)  A      NE2
And so on for a total of 81 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.

  10 GLU   (  10-)  A      OE1
 126 GLN   ( 126-)  A      OE1
 236 HIS   ( 239-)  A      ND1
 456 ASN   (  86-)  B      OD1
 496 GLN   ( 126-)  B      OE1

Warning: Unusual water packing

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

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

 750 HOH   ( 406 )  A      O  1.00  K  4

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
 131 ASP   ( 131-)  A   H-bonding suggests Asn
 141 ASP   ( 141-)  A   H-bonding suggests Asn; but Alt-Rotamer
 201 ASP   ( 201-)  A   H-bonding suggests Asn
 251 ASP   ( 254-)  A   H-bonding suggests Asn; 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 :  -0.623
  2nd generation packing quality :  -1.704
  Ramachandran plot appearance   :  -3.055 (poor)
  chi-1/chi-2 rotamer normality  :  -2.661
  Backbone conformation          :  -1.053

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.680
  Omega angle restraints         :   0.238 (tight)
  Side chain planarity           :   0.231 (tight)
  Improper dihedral distribution :   0.602
  B-factor distribution          :   0.677
  Inside/Outside distribution    :   0.976

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 : 2.85


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.333 (tight)
  Bond angles                    :   0.680
  Omega angle restraints         :   0.238 (tight)
  Side chain planarity           :   0.231 (tight)
  Improper dihedral distribution :   0.602
  B-factor distribution          :   0.677
  Inside/Outside distribution    :   0.976
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.