WHAT IF Check report

This file was created 2011-12-21 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 pdb1bf2.ent

Checks that need to be done early-on in validation

Warning: Unconventional orthorhombic cell

The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length.

The CRYST1 cell dimensions

    A    = 138.900  B   = 152.400  C    =  53.500
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    = 138.900  B   = 152.400  C    =  53.500
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  53.500  B   = 138.900  C    = 152.400
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  53.500  B   = 138.900  C    = 152.400
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

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) :298.000

Note: B-factor plot

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

Chain identifier: A

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.

 225 LEU   ( 225-)  A      N    CA   C    99.69   -4.1
 297 HIS   ( 297-)  A      CG   ND1  CE1 109.69    4.1
 345 PHE   ( 345-)  A      N    CA   C    97.59   -4.9
 435 GLU   ( 435-)  A      N    CA   C    92.69   -6.6
 492 PHE   ( 492-)  A      N    CA   C   123.57    4.4
 536 GLY   ( 536-)  A      N    CA   C   126.40    4.8
 556 VAL   ( 556-)  A      C    CA   CB  101.92   -4.3
 603 TRP   ( 603-)  A      CA   CB   CG  122.22    4.5
 744 LEU   ( 744-)  A      CA   CB   CG  132.94    4.8

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.

 492 PHE   ( 492-)  A    6.56
 435 GLU   ( 435-)  A    6.40
 345 PHE   ( 345-)  A    5.26
 225 LEU   ( 225-)  A    4.69
 493 GLN   ( 493-)  A    4.69
 536 GLY   ( 536-)  A    4.60
 325 TYR   ( 325-)  A    4.47
 516 ASP   ( 516-)  A    4.37
 680 SER   ( 680-)  A    4.12
 465 ARG   ( 465-)  A    4.12

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 : 1.545

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.

 530 PRO   ( 530-)  A    -2.9
 666 ILE   ( 666-)  A    -2.6
   6 SER   (   6-)  A    -2.5
 588 LEU   ( 588-)  A    -2.5
 226 PRO   ( 226-)  A    -2.5
 390 THR   ( 390-)  A    -2.4
 152 GLY   ( 152-)  A    -2.3
  54 SER   (  54-)  A    -2.3
 681 ILE   ( 681-)  A    -2.3
 709 THR   ( 709-)  A    -2.3
 747 LEU   ( 747-)  A    -2.3
 184 VAL   ( 184-)  A    -2.2
  86 TRP   (  86-)  A    -2.2
 488 SER   ( 488-)  A    -2.1
 577 LEU   ( 577-)  A    -2.1
 165 THR   ( 165-)  A    -2.1
 508 VAL   ( 508-)  A    -2.1
 131 ASN   ( 131-)  A    -2.1
 536 GLY   ( 536-)  A    -2.1
 309 PRO   ( 309-)  A    -2.1
 697 PRO   ( 697-)  A    -2.1
 571 LEU   ( 571-)  A    -2.0
  59 VAL   (  59-)  A    -2.0
 746 LEU   ( 746-)  A    -2.0
  22 VAL   (  22-)  A    -2.0
 546 GLN   ( 546-)  A    -2.0
 542 TYR   ( 542-)  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.

   3 ASN   (   3-)  A  Poor phi/psi
  15 GLN   (  15-)  A  Poor phi/psi
  54 SER   (  54-)  A  Poor phi/psi
 152 GLY   ( 152-)  A  Poor phi/psi
 232 ASN   ( 232-)  A  Poor phi/psi
 315 TYR   ( 315-)  A  Poor phi/psi
 316 SER   ( 316-)  A  Poor phi/psi
 332 ASN   ( 332-)  A  Poor phi/psi
 436 PRO   ( 436-)  A  Poor phi/psi
 438 ALA   ( 438-)  A  Poor phi/psi
 529 TRP   ( 529-)  A  PRO omega poor
 532 GLY   ( 532-)  A  PRO omega poor
 536 GLY   ( 536-)  A  Poor phi/psi
 542 TYR   ( 542-)  A  Poor phi/psi
 546 GLN   ( 546-)  A  Poor phi/psi
 585 LEU   ( 585-)  A  Poor phi/psi
 590 CYS   ( 590-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.637

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 ASN   (   3-)  A      0
   4 SER   (   4-)  A      0
   6 SER   (   6-)  A      0
   7 LEU   (   7-)  A      0
   9 ALA   (   9-)  A      0
  16 ALA   (  16-)  A      0
  17 ASN   (  17-)  A      0
  25 SER   (  25-)  A      0
  39 TYR   (  39-)  A      0
  52 ALA   (  52-)  A      0
  54 SER   (  54-)  A      0
  71 ILE   (  71-)  A      0
  74 ALA   (  74-)  A      0
  77 TYR   (  77-)  A      0
  82 TRP   (  82-)  A      0
  86 TRP   (  86-)  A      0
  88 TYR   (  88-)  A      0
  92 TRP   (  92-)  A      0
  94 LYS   (  94-)  A      0
  98 ALA   (  98-)  A      0
 100 PHE   ( 100-)  A      0
 101 VAL   ( 101-)  A      0
 102 SER   ( 102-)  A      0
 103 ASP   ( 103-)  A      0
 109 ASP   ( 109-)  A      0
And so on for a total of 334 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 : 1.680

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!

 537 GLY   ( 537-)  A   1.75   10

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]

 673 PRO   ( 673-)  A    0.46 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 156 PRO   ( 156-)  A  -113.9 envelop C-gamma (-108 degrees)
 499 PRO   ( 499-)  A  -114.2 envelop C-gamma (-108 degrees)
 530 PRO   ( 530-)  A   -59.5 half-chair C-beta/C-alpha (-54 degrees)
 576 PRO   ( 576-)  A    50.6 half-chair C-delta/C-gamma (54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 572 SER   ( 572-)  A      O   <->  626 ARG   ( 626-)  A      NH2    0.34    2.36  INTRA
   5 MET   (   5-)  A      O   <->   21 ARG   (  21-)  A      NH1    0.31    2.39  INTRA
 598 ASP   ( 598-)  A      OD1 <->  603 TRP   ( 603-)  A      CZ3    0.18    2.62  INTRA BL
 283 HIS   ( 283-)  A      CE1 <->  370 ASP   ( 370-)  A      OD2    0.14    2.66  INTRA BL
 535 ASP   ( 535-)  A      O   <->  593 ASN   ( 593-)  A      ND2    0.14    2.56  INTRA
 298 THR   ( 298-)  A      CG2 <->  299 ALA   ( 299-)  A      N      0.13    2.87  INTRA BL
 559 ARG   ( 559-)  A      NH1 <->  716 ASP   ( 716-)  A      OD2    0.12    2.58  INTRA
 168 THR   ( 168-)  A      O   <->  283 HIS   ( 283-)  A      CD2    0.12    2.68  INTRA
 298 THR   ( 298-)  A      CG2 <->  300 GLU   ( 300-)  A      N      0.11    2.99  INTRA BL
 559 ARG   ( 559-)  A      NH1 <->  716 ASP   ( 716-)  A      CG     0.09    3.01  INTRA
 260 ARG   ( 260-)  A      NH2 <->  267 ALA   ( 267-)  A      O      0.09    2.61  INTRA
 396 CYS   ( 396-)  A      SG  <->  399 GLY   ( 399-)  A      CA     0.08    3.32  INTRA BL
 298 THR   ( 298-)  A      CG2 <->  317 TRP   ( 317-)  A      CZ3    0.08    3.12  INTRA BL
   3 ASN   (   3-)  A      N   <->  358 ASP   ( 358-)  A      OD1    0.08    2.62  INTRA
 715 ASN   ( 715-)  A      O   <->  720 THR   ( 720-)  A      CB     0.06    2.74  INTRA
 126 SER   ( 126-)  A      OG  <->  127 GLN   ( 127-)  A      NE2    0.06    2.64  INTRA BL
 192 GLN   ( 192-)  A      CD  <->  603 TRP   ( 603-)  A      CD1    0.06    3.14  INTRA
 179 ASP   ( 179-)  A      OD2 <->  288 LYS   ( 288-)  A      NZ     0.06    2.64  INTRA BL
  39 TYR   (  39-)  A      CD1 <->   40 GLY   (  40-)  A      N      0.06    2.94  INTRA
 588 LEU   ( 588-)  A      N   <->  589 GLN   ( 589-)  A      N      0.05    2.55  INTRA BL
 291 MET   ( 291-)  A      SD  <->  363 TRP   ( 363-)  A      CE3    0.05    3.35  INTRA BL
 254 ASN   ( 254-)  A      ND2 <->  256 PHE   ( 256-)  A      N      0.04    2.81  INTRA BL
  28 THR   (  28-)  A      CG2 <->  753 HOH   (1131 )  A      O      0.04    2.76  INTRA
 300 GLU   ( 300-)  A      O   <->  318 ARG   ( 318-)  A      NH2    0.04    2.66  INTRA BL
 660 ASN   ( 660-)  A      CB  <->  663 ASN   ( 663-)  A      ND2    0.04    3.06  INTRA
 447 GLY   ( 447-)  A      N   <->  455 GLU   ( 455-)  A      OE1    0.04    2.66  INTRA BL
 408 SER   ( 408-)  A      O   <->  417 ARG   ( 417-)  A      NH2    0.04    2.66  INTRA
 710 ASP   ( 710-)  A      OD1 <->  712 CYS   ( 712-)  A      SG     0.03    2.97  INTRA
  52 ALA   (  52-)  A      N   <->   56 VAL   (  56-)  A      O      0.03    2.67  INTRA
 408 SER   ( 408-)  A      O   <->  417 ARG   ( 417-)  A      NH1    0.03    2.67  INTRA
 742 GLN   ( 742-)  A      CG  <->  753 HOH   ( 847 )  A      O      0.03    2.77  INTRA
 138 ASN   ( 138-)  A      ND2 <->  304 TRP   ( 304-)  A      CH2    0.02    3.08  INTRA
 639 SER   ( 639-)  A      N   <->  642 GLN   ( 642-)  A      NE2    0.02    2.83  INTRA
 193 ASP   ( 193-)  A      OD2 <->  210 LYS   ( 210-)  A      NZ     0.02    2.68  INTRA BL
 650 GLY   ( 650-)  A      N   <->  651 ALA   ( 651-)  A      N      0.02    2.58  INTRA B3
 501 ASN   ( 501-)  A      N   <->  502 SER   ( 502-)  A      N      0.02    2.58  INTRA BL
 250 TYR   ( 250-)  A      O   <->  297 HIS   ( 297-)  A      NE2    0.02    2.68  INTRA BL
 436 PRO   ( 436-)  A      O   <->  445 GLN   ( 445-)  A      N      0.02    2.68  INTRA BL
 183 GLU   ( 183-)  A      OE2 <->  509 HIS   ( 509-)  A      CD2    0.01    2.79  INTRA BL
 354 ASN   ( 354-)  A      OD1 <->  414 ARG   ( 414-)  A      NH2    0.01    2.69  INTRA BL

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.

 389 TYR   ( 389-)  A      -5.65
 451 GLN   ( 451-)  A      -5.50
 398 ASN   ( 398-)  A      -5.50
 284 ASN   ( 284-)  A      -5.28
 715 ASN   ( 715-)  A      -5.15
 490 ASN   ( 490-)  A      -5.11

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.

 225 LEU   ( 225-)  A   -2.77
 139 VAL   ( 139-)  A   -2.55

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: 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.

 753 HOH   ( 864 )  A      O
 753 HOH   (1042 )  A      O
 753 HOH   (1057 )  A      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.

  17 ASN   (  17-)  A
  85 ASN   (  85-)  A
 127 GLN   ( 127-)  A
 135 GLN   ( 135-)  A
 192 GLN   ( 192-)  A
 231 GLN   ( 231-)  A
 235 ASN   ( 235-)  A
 245 GLN   ( 245-)  A
 246 ASN   ( 246-)  A
 254 ASN   ( 254-)  A
 332 ASN   ( 332-)  A
 333 GLN   ( 333-)  A
 346 ASN   ( 346-)  A
 349 ASN   ( 349-)  A
 386 ASN   ( 386-)  A
 480 GLN   ( 480-)  A
 483 ASN   ( 483-)  A
 509 HIS   ( 509-)  A
 527 GLN   ( 527-)  A
 546 GLN   ( 546-)  A
 558 GLN   ( 558-)  A
 579 GLN   ( 579-)  A
 589 GLN   ( 589-)  A
 620 GLN   ( 620-)  A
 642 GLN   ( 642-)  A
 659 ASN   ( 659-)  A
 686 ASN   ( 686-)  A
 739 GLN   ( 739-)  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.

  14 GLN   (  14-)  A      N
  37 ALA   (  37-)  A      N
  80 ARG   (  80-)  A      NE
 119 ASP   ( 119-)  A      N
 124 GLU   ( 124-)  A      N
 134 ASN   ( 134-)  A      ND2
 135 GLN   ( 135-)  A      NE2
 151 SER   ( 151-)  A      OG
 192 GLN   ( 192-)  A      N
 251 MET   ( 251-)  A      N
 254 ASN   ( 254-)  A      N
 261 ARG   ( 261-)  A      NE
 276 GLN   ( 276-)  A      NE2
 296 ASN   ( 296-)  A      N
 297 HIS   ( 297-)  A      N
 300 GLU   ( 300-)  A      N
 311 THR   ( 311-)  A      N
 317 TRP   ( 317-)  A      NE1
 339 THR   ( 339-)  A      N
 343 ALA   ( 343-)  A      N
 368 GLY   ( 368-)  A      N
 373 ARG   ( 373-)  A      NE
 378 SER   ( 378-)  A      N
 504 ASN   ( 504-)  A      ND2
 505 PHE   ( 505-)  A      N
 510 ASP   ( 510-)  A      N
 546 GLN   ( 546-)  A      N
 626 ARG   ( 626-)  A      NH1
 626 ARG   ( 626-)  A      NH2
 636 SER   ( 636-)  A      N
 654 ASP   ( 654-)  A      N
 690 SER   ( 690-)  A      N
 701 SER   ( 701-)  A      N
 742 GLN   ( 742-)  A      NE2
Only metal coordination for  229 GLU  ( 229-) A      OE1

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.

 242 ASP   ( 242-)  A      OD2
 253 GLU   ( 253-)  A      OE2
 327 GLU   ( 327-)  A      OE2
 484 ASP   ( 484-)  A      OD2
 739 GLN   ( 739-)  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+.

 752  CA   ( 751-)  A     0.71   0.93 Scores about as good as NA

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.

 753 HOH   (1118 )  A      O  1.01  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.

 242 ASP   ( 242-)  A   H-bonding suggests Asn
 327 GLU   ( 327-)  A   H-bonding suggests Gln
 358 ASP   ( 358-)  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 :  -0.718
  2nd generation packing quality :  -1.622
  Ramachandran plot appearance   :  -1.183
  chi-1/chi-2 rotamer normality  :  -1.637
  Backbone conformation          :  -0.480

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.439 (tight)
  Bond angles                    :   0.707
  Omega angle restraints         :   0.305 (tight)
  Side chain planarity           :   0.500 (tight)
  Improper dihedral distribution :   0.918
  B-factor distribution          :   1.042
  Inside/Outside distribution    :   1.040

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.439 (tight)
  Bond angles                    :   0.707
  Omega angle restraints         :   0.305 (tight)
  Side chain planarity           :   0.500 (tight)
  Improper dihedral distribution :   0.918
  B-factor distribution          :   1.042
  Inside/Outside distribution    :   1.040
==============

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Quality Control
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    M.Nayal and E.Di Cera,
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    P.Mueller, S.Koepke and G.M.Sheldrick,
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Checking checks
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