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 pdb1w0p.ent

Checks that need to be done early-on in validation

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.

 759 SIA   (1784-)  A  -
 760 TRS   (1783-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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

Warning: 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 : 3.33

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 154 ARG   ( 178-)  A

Warning: Tyrosine convention problem

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

 284 TYR   ( 308-)  A

Warning: Phenylalanine convention problem

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

 454 PHE   ( 478-)  A

Warning: Aspartic acid convention problem

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

  14 ASP   (  38-)  A
 366 ASP   ( 390-)  A
 497 ASP   ( 521-)  A
 565 ASP   ( 589-)  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.

 251 GLU   ( 275-)  A
 342 GLU   ( 366-)  A
 409 GLU   ( 433-)  A
 420 GLU   ( 444-)  A
 449 GLU   ( 473-)  A
 665 GLU   ( 689-)  A
 699 GLU   ( 723-)  A

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.255
RMS-deviation in bond distances: 0.006

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.998725 -0.000325  0.000010|
 | -0.000325  0.999363 -0.000007|
 |  0.000010 -0.000007  0.998731|
Proposed new scale matrix

 |  0.014241  0.000005  0.000000|
 |  0.000004  0.013358  0.000000|
 |  0.000000  0.000000  0.006604|
With corresponding cell

    A    =  70.219  B   =  74.864  C    = 151.415
    Alpha=  90.001  Beta=  90.001  Gamma=  90.037

The CRYST1 cell dimensions

    A    =  70.310  B   =  74.910  C    = 151.615
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 29.090
(Under-)estimated Z-score: 3.975

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.

 288 PRO   ( 312-)  A      N    CA   C    99.78   -4.8
 457 ALA   ( 481-)  A      N    CA   C   123.08    4.2
 516 GLY   ( 540-)  A     -C    N    CA  127.45    4.0
 561 ILE   ( 585-)  A      N    CA   C    98.88   -4.4
 707 ILE   ( 731-)  A      N    CA   C    99.48   -4.2

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.604
RMS-deviation in bond angles: 1.377

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.

  14 ASP   (  38-)  A
 154 ARG   ( 178-)  A
 251 GLU   ( 275-)  A
 342 GLU   ( 366-)  A
 366 ASP   ( 390-)  A
 409 GLU   ( 433-)  A
 420 GLU   ( 444-)  A
 449 GLU   ( 473-)  A
 497 ASP   ( 521-)  A
 565 ASP   ( 589-)  A
 665 GLU   ( 689-)  A
 699 GLU   ( 723-)  A

Error: Tau angle problems

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

 288 PRO   ( 312-)  A    5.36
 457 ALA   ( 481-)  A    4.85
 328 VAL   ( 352-)  A    4.47
 561 ILE   ( 585-)  A    4.34
 371 GLN   ( 395-)  A    4.24
 743 MET   ( 767-)  A    4.10
 707 ILE   ( 731-)  A    4.08

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 590 THR   ( 614-)  A    -2.9
 547 PRO   ( 571-)  A    -2.8
 514 LEU   ( 538-)  A    -2.7
 201 ILE   ( 225-)  A    -2.7
 440 THR   ( 464-)  A    -2.5
 662 THR   ( 686-)  A    -2.5
 584 SER   ( 608-)  A    -2.4
 657 VAL   ( 681-)  A    -2.3
 624 SER   ( 648-)  A    -2.2
 699 GLU   ( 723-)  A    -2.2
  32 VAL   (  56-)  A    -2.1
  87 TYR   ( 111-)  A    -2.1
  93 GLN   ( 117-)  A    -2.1
 205 VAL   ( 229-)  A    -2.1
 524 PRO   ( 548-)  A    -2.0
   8 THR   (  32-)  A    -2.0
 451 ASN   ( 475-)  A    -2.0
 744 PRO   ( 768-)  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.

  27 ASN   (  51-)  A  Poor phi/psi
  30 SER   (  54-)  A  Poor phi/psi
  36 ALA   (  60-)  A  Poor phi/psi
  91 GLY   ( 115-)  A  Poor phi/psi
 166 MET   ( 190-)  A  Poor phi/psi
 197 GLY   ( 221-)  A  PRO omega poor
 201 ILE   ( 225-)  A  Poor phi/psi
 278 ASN   ( 302-)  A  Poor phi/psi
 292 ALA   ( 316-)  A  Poor phi/psi
 303 PRO   ( 327-)  A  Poor phi/psi
 369 ALA   ( 393-)  A  Poor phi/psi
 435 ASP   ( 459-)  A  Poor phi/psi
 516 GLY   ( 540-)  A  Poor phi/psi
 584 SER   ( 608-)  A  Poor phi/psi
 594 SER   ( 618-)  A  Poor phi/psi
 614 PHE   ( 638-)  A  Poor phi/psi
 624 SER   ( 648-)  A  Poor phi/psi
 643 ALA   ( 667-)  A  Poor phi/psi
 645 ASN   ( 669-)  A  Poor phi/psi
 651 ASN   ( 675-)  A  Poor phi/psi
 681 ASN   ( 705-)  A  PRO omega poor
 699 GLU   ( 723-)  A  Poor phi/psi
 705 GLY   ( 729-)  A  Poor phi/psi
 715 ALA   ( 739-)  A  Poor phi/psi
 733 THR   ( 757-)  A  Poor phi/psi
 736 SER   ( 760-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.494

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 PHE   (  27-)  A      0
   4 ASP   (  28-)  A      0
   7 ALA   (  31-)  A      0
  13 PHE   (  37-)  A      0
  14 ASP   (  38-)  A      0
  19 GLN   (  43-)  A      0
  21 TRP   (  45-)  A      0
  25 ASN   (  49-)  A      0
  26 THR   (  50-)  A      0
  27 ASN   (  51-)  A      0
  30 SER   (  54-)  A      0
  35 ASN   (  59-)  A      0
  36 ALA   (  60-)  A      0
  37 ASP   (  61-)  A      0
  45 GLN   (  69-)  A      0
  47 ILE   (  71-)  A      0
  50 ARG   (  74-)  A      0
  51 ALA   (  75-)  A      0
  52 GLN   (  76-)  A      0
  67 SER   (  91-)  A      0
  70 TRP   (  94-)  A      0
  76 MET   ( 100-)  A      0
  80 SER   ( 104-)  A      0
  83 MET   ( 107-)  A      0
  85 THR   ( 109-)  A      0
And so on for a total of 342 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 : 1.598

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.

 332 SER   ( 356-)  A      O   <->  516 GLY   ( 540-)  A      N      0.49    2.21  INTRA BL
 171 ASN   ( 195-)  A      ND2 <->  761 HOH   (2132 )  A      O      0.41    2.29  INTRA BL
 456 ASN   ( 480-)  A      ND2 <->  761 HOH   (2343 )  A      O      0.41    2.29  INTRA BL
 489 GLN   ( 513-)  A      NE2 <->  761 HOH   (2364 )  A      O      0.29    2.41  INTRA
 663 ARG   ( 687-)  A      NE  <->  761 HOH   (2518 )  A      O      0.28    2.42  INTRA
 281 LEU   ( 305-)  A      CD2 <->  308 TYR   ( 332-)  A      CD1    0.28    2.92  INTRA BL
 602 GLN   ( 626-)  A      NE2 <->  663 ARG   ( 687-)  A      NH2    0.26    2.59  INTRA
 602 GLN   ( 626-)  A      N   <->  699 GLU   ( 723-)  A      OE2    0.21    2.49  INTRA
  71 ARG   (  95-)  A      NH1 <->  726 ASN   ( 750-)  A      ND2    0.17    2.68  INTRA
 584 SER   ( 608-)  A      OG  <->  585 SER   ( 609-)  A      N      0.17    2.43  INTRA
  50 ARG   (  74-)  A      NH1 <->  759 SIA   (1784-)  A      O1A    0.16    2.54  INTRA
 582 TRP   ( 606-)  A      C   <->  584 SER   ( 608-)  A      N      0.15    2.75  INTRA
 388 ASP   ( 412-)  A      OD1 <->  390 SER   ( 414-)  A      N      0.13    2.57  INTRA
 228 GLY   ( 252-)  A      O   <->  297 ARG   ( 321-)  A      NH2    0.13    2.57  INTRA BL
  90 ASN   ( 114-)  A      O   <->   92 THR   ( 116-)  A      N      0.12    2.58  INTRA
 584 SER   ( 608-)  A      C   <->  586 SER   ( 610-)  A      N      0.11    2.79  INTRA
 354 GLN   ( 378-)  A      NE2 <->  475 GLN   ( 499-)  A      CD     0.11    2.99  INTRA
 429 THR   ( 453-)  A      OG1 <->  441 THR   ( 465-)  A      CG2    0.11    2.69  INTRA
 490 GLN   ( 514-)  A      O   <->  496 LYS   ( 520-)  A      NZ     0.11    2.59  INTRA BL
 113 GLY   ( 137-)  A      N   <->  761 HOH   (2093 )  A      O      0.10    2.60  INTRA
   6 ASN   (  30-)  A      ND2 <->  184 ASP   ( 208-)  A      OD2    0.10    2.60  INTRA
 472 LEU   ( 496-)  A      CB  <->  480 VAL   ( 504-)  A      CG2    0.10    3.10  INTRA
  71 ARG   (  95-)  A      NH1 <->  761 HOH   (2063 )  A      O      0.09    2.61  INTRA
 356 TRP   ( 380-)  A      C   <->  357 GLN   ( 381-)  A      CD     0.09    3.01  INTRA
 246 ILE   ( 270-)  A      CD1 <->  742 ARG   ( 766-)  A      CZ     0.09    3.11  INTRA
And so on for a total of 78 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 242 ARG   ( 266-)  A      -6.09
  39 MET   (  63-)  A      -5.98
 389 GLU   ( 413-)  A      -5.71
 114 GLN   ( 138-)  A      -5.70
 319 GLN   ( 343-)  A      -5.52
 475 GLN   ( 499-)  A      -5.49
 602 GLN   ( 626-)  A      -5.44
 735 ASN   ( 759-)  A      -5.30
  19 GLN   (  43-)  A      -5.28
 196 ARG   ( 220-)  A      -5.17
 632 LYS   ( 656-)  A      -5.13
 353 GLN   ( 377-)  A      -5.04
 742 ARG   ( 766-)  A      -5.00

Warning: Abnormal packing environment for sequential residues

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

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

 293 GLN   ( 317-)  A       295 - GLY    319- ( A)         -4.37

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

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.

 402 ALA   ( 426-)  A   -3.21
 701 VAL   ( 725-)  A   -2.66
 514 LEU   ( 538-)  A   -2.61

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  35 ASN   (  59-)  A
  45 GLN   (  69-)  A
  52 GLN   (  76-)  A
  62 HIS   (  86-)  A
 158 GLN   ( 182-)  A
 171 ASN   ( 195-)  A
 293 GLN   ( 317-)  A
 304 ASN   ( 328-)  A
 370 ASN   ( 394-)  A
 373 GLN   ( 397-)  A
 410 HIS   ( 434-)  A
 414 HIS   ( 438-)  A
 450 ASN   ( 474-)  A
 451 ASN   ( 475-)  A
 453 GLN   ( 477-)  A
 466 HIS   ( 490-)  A
 602 GLN   ( 626-)  A
 644 ASN   ( 668-)  A
 671 HIS   ( 695-)  A
 681 ASN   ( 705-)  A
 726 ASN   ( 750-)  A

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  15 SER   (  39-)  A      N
  37 ASP   (  61-)  A      N
  39 MET   (  63-)  A      N
  47 ILE   (  71-)  A      N
 124 THR   ( 148-)  A      OG1
 156 ASN   ( 180-)  A      N
 169 TRP   ( 193-)  A      NE1
 173 SER   ( 197-)  A      N
 174 SER   ( 198-)  A      N
 183 ARG   ( 207-)  A      NH2
 206 ALA   ( 230-)  A      N
 229 ALA   ( 253-)  A      N
 257 GLN   ( 281-)  A      NE2
 270 ARG   ( 294-)  A      NE
 301 TRP   ( 325-)  A      N
 315 SER   ( 339-)  A      N
 319 GLN   ( 343-)  A      NE2
 332 SER   ( 356-)  A      N
 338 TRP   ( 362-)  A      N
 345 ARG   ( 369-)  A      NE
 458 ASP   ( 482-)  A      N
 586 SER   ( 610-)  A      N
 626 ARG   ( 650-)  A      NH1
 658 ASP   ( 682-)  A      N
 711 ASN   ( 735-)  A      N
 717 SER   ( 741-)  A      N
 742 ARG   ( 766-)  A      NH2
Only metal coordination for  232 ASN  ( 256-) A      OD1
Only metal coordination for  262 ASP  ( 286-) A      OD1
Only metal coordination for  658 ASP  ( 682-) A      OD1

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.

 234 ASN   ( 258-)  A      OD1
 370 ASN   ( 394-)  A      OD1
 417 HIS   ( 441-)  A      NE2
 456 ASN   ( 480-)  A      OD1
 628 GLN   ( 652-)  A      OE1

Warning: No crystallisation information

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

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 755  CA   (1780-)  A     0.85   1.09 Scores about as good as NA
 756  CA   (1781-)  A     0.78   1.02 Scores about as good as NA
 757  CA   (1782-)  A   -.-  -.-  Too few ligands (2)

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.

 761 HOH   (2005 )  A      O  1.05  K  6
 761 HOH   (2160 )  A      O  0.90  K  4
 761 HOH   (2254 )  A      O  0.94  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.

   4 ASP   (  28-)  A   H-bonding suggests Asn
 552 ASP   ( 576-)  A   H-bonding suggests Asn
 589 GLU   ( 613-)  A   H-bonding suggests Gln
 698 ASP   ( 722-)  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 :   0.455
  2nd generation packing quality :  -0.987
  Ramachandran plot appearance   :  -0.907
  chi-1/chi-2 rotamer normality  :  -0.494
  Backbone conformation          :  -0.506

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.255 (tight)
  Bond angles                    :   0.604 (tight)
  Omega angle restraints         :   0.290 (tight)
  Side chain planarity           :   0.266 (tight)
  Improper dihedral distribution :   0.597
  B-factor distribution          :   0.645
  Inside/Outside distribution    :   1.016

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 : 1.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -1.3
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.255 (tight)
  Bond angles                    :   0.604 (tight)
  Omega angle restraints         :   0.290 (tight)
  Side chain planarity           :   0.266 (tight)
  Improper dihedral distribution :   0.597
  B-factor distribution          :   0.645
  Inside/Outside distribution    :   1.016
==============

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.