WHAT IF Check report

This file was created 2011-12-13 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 pdb2aeq.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

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

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

Molecular weight of all polymer chains: 68313.688
Volume of the Unit Cell V= 2656769.8
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.861
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.500

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.

 620 MAN   ( 218-)  H  -
 621 MAN   ( 219-)  H  -
 622 MAN   ( 218-)  L  -
 623 MAN   ( 217-)  L  -

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: L

Note: Ramachandran plot

Chain identifier: H

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) :295.000

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.000

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: A

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: L

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: H

Nomenclature related problems

Warning: Tyrosine convention problem

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

 592 TYR   (  97-)  H
 602 TYR   ( 107-)  H
 604 TYR   ( 109-)  H

Warning: Phenylalanine convention problem

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

 175 PHE   ( 256-)  A

Warning: Glutamic acid convention problem

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

 473 GLU   (  85-)  L
 501 GLU   (   6-)  H

Geometric checks

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.

 198 SER   ( 279-)  A      N    CA   C    99.57   -4.2
 209 VAL   ( 290-)  A      N    CA   C    96.93   -5.1
 350 LYS   ( 431-)  A     -C    N    CA  129.14    4.1
 350 LYS   ( 431-)  A      N    CA   C    95.64   -5.6
 550 GLY   (  55-)  H      N    CA   C   100.83   -4.0
 556 GLU   (  61-)  H      N    CA   C    98.95   -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.

 473 GLU   (  85-)  L
 501 GLU   (   6-)  H

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.

 350 LYS   ( 431-)  A    6.03
 209 VAL   ( 290-)  A    5.37
 393 THR   (   5-)  L    4.76
 550 GLY   (  55-)  H    4.57
 198 SER   ( 279-)  A    4.57
 556 GLU   (  61-)  H    4.52
 145 GLN   ( 226-)  A    4.27
 322 ARG   ( 403-)  A    4.23
 256 CYS   ( 337-)  A    4.23

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.508

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 : -3.685

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.

 584 THR   (  89-)  H    -3.4
 582 THR   (  87-)  H    -3.4
 600 THR   ( 105-)  H    -3.3
 536 PRO   (  41-)  H    -3.0
 523 THR   (  28-)  H    -3.0
 283 ARG   ( 364-)  A    -2.9
 204 PRO   ( 285-)  A    -2.8
 358 THR   ( 439-)  A    -2.7
  57 THR   ( 138-)  A    -2.5
 378 PRO   ( 459-)  A    -2.5
 574 SER   (  79-)  H    -2.4
 406 ARG   (  18-)  L    -2.4
  67 THR   ( 148-)  A    -2.4
 129 ARG   ( 210-)  A    -2.4
 522 PHE   (  27-)  H    -2.4
 545 LEU   (  50-)  H    -2.4
 322 ARG   ( 403-)  A    -2.4
 266 HIS   ( 347-)  A    -2.4
 553 TYR   (  58-)  H    -2.3
 602 TYR   ( 107-)  H    -2.3
 256 CYS   ( 337-)  A    -2.3
   2 GLU   (  83-)  A    -2.3
 513 LEU   (  18-)  H    -2.3
  24 SER   ( 105-)  A    -2.3
 383 ILE   ( 464-)  A    -2.3
And so on for a total of 57 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   6 TRP   (  87-)  A  Poor phi/psi
  23 ASN   ( 104-)  A  Poor phi/psi
  37 ARG   ( 118-)  A  Poor phi/psi
  38 GLU   ( 119-)  A  Poor phi/psi
  40 TYR   ( 121-)  A  Poor phi/psi
  66 ASP   ( 147-)  A  Poor phi/psi
 141 ILE   ( 222-)  A  Poor phi/psi
 146 GLU   ( 227-)  A  Poor phi/psi
 153 ASN   ( 234-)  A  Poor phi/psi
 178 GLU   ( 259-)  A  Poor phi/psi
 203 TYR   ( 284-)  A  PRO omega poor
 229 TYR   ( 310-)  A  Poor phi/psi
 238 SER   ( 319-)  A  Poor phi/psi
 241 VAL   ( 322-)  A  Poor phi/psi
 244 THR   ( 325-)  A  PRO omega poor
 255 HIS   ( 336-)  A  Poor phi/psi
 256 CYS   ( 337-)  A  Poor phi/psi
 266 HIS   ( 347-)  A  Poor phi/psi
 272 ALA   ( 353-)  A  Poor phi/psi
 283 ARG   ( 364-)  A  Poor phi/psi
 292 GLY   ( 373-)  A  Poor phi/psi
 296 PHE   ( 377-)  A  Poor phi/psi
 300 GLU   ( 381-)  A  Poor phi/psi
 306 ASN   ( 387-)  A  Poor phi/psi
 323 SER   ( 404-)  A  Poor phi/psi
And so on for a total of 53 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.122

Warning: Unusual backbone conformations

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

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

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

   3 TYR   (  84-)  A      0
   4 ARG   (  85-)  A      0
   5 ASN   (  86-)  A      0
   6 TRP   (  87-)  A      0
   7 SER   (  88-)  A      0
   8 LYS   (  89-)  A      0
  13 ILE   (  94-)  A      0
  14 THR   (  95-)  A      0
  16 PHE   (  97-)  A      0
  18 PRO   (  99-)  A      0
  19 PHE   ( 100-)  A      0
  20 SER   ( 101-)  A      0
  22 ASP   ( 103-)  A      0
  32 ASP   ( 113-)  A      0
  34 TRP   ( 115-)  A      0
  35 VAL   ( 116-)  A      0
  37 ARG   ( 118-)  A      0
  38 GLU   ( 119-)  A      0
  39 PRO   ( 120-)  A      0
  46 ASP   ( 127-)  A      0
  55 GLN   ( 136-)  A      0
  61 ASN   ( 142-)  A      0
  63 HIS   ( 144-)  A      0
  65 ASN   ( 146-)  A      0
  66 ASP   ( 147-)  A      0
And so on for a total of 338 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 : 1.433

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!

 456 GLY   (  68-)  L   1.57   10

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 547 ARG   (  52-)  H   1.75

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]

  39 PRO   ( 120-)  A    0.45 HIGH
 447 PRO   (  59-)  L    0.45 HIGH
 536 PRO   (  41-)  H    0.47 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.

 526 ASP   (  31-)  H      N   <->  549 LYS   (  54-)  H      CG     0.69    2.41  INTRA
 119 ASN   ( 200-)  A      CG  <->  613 NAG   ( 215-)  L      C1     0.50    2.70  INTRA
 119 ASN   ( 200-)  A      ND2 <->  613 NAG   ( 215-)  L      C1     0.49    2.61  INTRA
 584 THR   (  89-)  H      O   <->  586 GLU   (  91-)  H      N      0.48    2.22  INTRA
 614 NAG   ( 216-)  L      O4  <->  623 MAN   ( 217-)  L      C1     0.48    2.32  INTRA
 581 ASN   (  86-)  H      ND2 <->  582 THR   (  87-)  H      CG2    0.46    2.64  INTRA
 549 LYS   (  54-)  H      CD  <->  569 ARG   (  74-)  H      NH1    0.45    2.65  INTRA
 583 LEU   (  88-)  H      O   <->  585 ALA   (  90-)  H      N      0.45    2.25  INTRA
 294 GLU   ( 375-)  A      OE1 <->  313 ARG   ( 394-)  A      NH1    0.41    2.29  INTRA
 550 GLY   (  55-)  H      O   <->  552 GLY   (  57-)  H      N      0.38    2.32  INTRA
 549 LYS   (  54-)  H      NZ  <->  569 ARG   (  74-)  H      NH1    0.37    2.48  INTRA
 581 ASN   (  86-)  H      CG  <->  582 THR   (  87-)  H      CG2    0.36    2.84  INTRA
 524 PHE   (  29-)  H      O   <->  549 LYS   (  54-)  H      CE     0.36    2.44  INTRA
 525 ILE   (  30-)  H      C   <->  549 LYS   (  54-)  H      CG     0.36    2.84  INTRA
 219 ARG   ( 300-)  A      NH1 <->  242 GLY   ( 323-)  A      C      0.35    2.75  INTRA
 526 ASP   (  31-)  H      N   <->  549 LYS   (  54-)  H      CE     0.35    2.75  INTRA
 478 GLN   (  90-)  L      NE2 <->  480 ASN   (  92-)  L      N      0.34    2.51  INTRA
 255 HIS   ( 336-)  A      C   <->  256 CYS   ( 337-)  A      SG     0.34    2.96  INTRA
 550 GLY   (  55-)  H      O   <->  551 ASN   (  56-)  H      CG     0.34    2.36  INTRA
 525 ILE   (  30-)  H      CA  <->  549 LYS   (  54-)  H      CG     0.33    2.87  INTRA
 620 MAN   ( 218-)  H      C1  <->  621 MAN   ( 219-)  H      C5     0.32    2.88  INTRA
 405 ASP   (  17-)  L      CG  <->  406 ARG   (  18-)  L      N      0.32    2.68  INTRA
  65 ASN   ( 146-)  A      ND2 <->  612 NAG   ( 501-)  A      C2     0.32    2.78  INTRA
 620 MAN   ( 218-)  H      C2  <->  621 MAN   ( 219-)  H      C5     0.32    2.88  INTRA
 429 GLY   (  41-)  L      C   <->  430 GLN   (  42-)  L      NE2    0.31    2.69  INTRA
And so on for a total of 271 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: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

 202 ARG   ( 283-)  A      -6.74
 168 ARG   ( 249-)  A      -6.67
 508 GLN   (  13-)  H      -6.57
 506 LEU   (  11-)  H      -6.53
 372 TYR   ( 453-)  A      -6.50
 481 ARG   (  93-)  L      -6.40
 203 TYR   ( 284-)  A      -6.39
 430 GLN   (  42-)  L      -6.30
  74 TYR   ( 155-)  A      -6.19
 482 TYR   (  94-)  L      -6.01
 266 HIS   ( 347-)  A      -5.85
 334 LYS   ( 415-)  A      -5.74
 522 PHE   (  27-)  H      -5.34
 257 LEU   ( 338-)  A      -5.13
 263 GLU   ( 344-)  A      -5.04
  60 ASN   ( 141-)  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.

 371 THR   ( 452-)  A       374 - THR    455- ( A)         -5.13

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: L

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: H

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.

 346 ILE   ( 427-)  A   -2.56

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: L

Note: Second generation quality Z-score plot

Chain identifier: H

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.

  23 ASN   ( 104-)  A
  50 GLN   ( 131-)  A
  61 ASN   ( 142-)  A
 145 GLN   ( 226-)  A
 193 HIS   ( 274-)  A
 338 ASN   ( 419-)  A
 416 ASN   (  28-)  L
 478 GLN   (  90-)  L

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   5 ASN   (  86-)  A      N
   6 TRP   (  87-)  A      N
  21 LYS   ( 102-)  A      NZ
  23 ASN   ( 104-)  A      N
  23 ASN   ( 104-)  A      ND2
  25 ILE   ( 106-)  A      N
  26 ARG   ( 107-)  A      N
  37 ARG   ( 118-)  A      N
  40 TYR   ( 121-)  A      OH
  41 VAL   ( 122-)  A      N
  50 GLN   ( 131-)  A      NE2
  56 GLY   ( 137-)  A      N
  57 THR   ( 138-)  A      N
  68 VAL   ( 149-)  A      N
  69 HIS   ( 150-)  A      N
  72 THR   ( 153-)  A      N
  74 TYR   ( 155-)  A      N
  86 PHE   ( 167-)  A      N
  91 LYS   ( 172-)  A      N
  92 GLN   ( 173-)  A      NE2
  94 CYS   ( 175-)  A      N
  98 SER   ( 179-)  A      N
 101 SER   ( 182-)  A      N
 103 HIS   ( 184-)  A      N
 105 GLY   ( 186-)  A      N
And so on for a total of 105 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.

  23 ASN   ( 104-)  A      OD1
  65 ASN   ( 146-)  A      OD1
 103 HIS   ( 184-)  A      ND1
 153 ASN   ( 234-)  A      OD1
 310 GLN   ( 391-)  A      OE1
 587 ASP   (  92-)  H      OD2
 603 ASP   ( 108-)  H      OD2

Warning: Possible wrong residue type

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

  44 ASP   ( 125-)  A   H-bonding suggests Asn; but Alt-Rotamer
  46 ASP   ( 127-)  A   H-bonding suggests Asn
 104 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 146 GLU   ( 227-)  A   H-bonding suggests Gln; but Alt-Rotamer
 262 GLU   ( 343-)  A   H-bonding suggests Gln
 405 ASP   (  17-)  L   H-bonding suggests Asn
 526 ASP   (  31-)  H   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.189
  2nd generation packing quality :  -1.653
  Ramachandran plot appearance   :  -3.685 (poor)
  chi-1/chi-2 rotamer normality  :  -4.122 (bad)
  Backbone conformation          :  -0.825

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.402 (tight)
  Bond angles                    :   0.723
  Omega angle restraints         :   0.261 (tight)
  Side chain planarity           :   0.276 (tight)
  Improper dihedral distribution :   0.677
  B-factor distribution          :   0.353
  Inside/Outside distribution    :   1.036

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.402 (tight)
  Bond angles                    :   0.723
  Omega angle restraints         :   0.261 (tight)
  Side chain planarity           :   0.276 (tight)
  Improper dihedral distribution :   0.677
  B-factor distribution          :   0.353
  Inside/Outside distribution    :   1.036
==============

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.