WHAT IF Check report

This file was created 2011-12-28 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 pdb1hxy.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

  44 GLU   (  46-)  A      CG
  44 GLU   (  46-)  A      CD
  44 GLU   (  46-)  A      OE1
  44 GLU   (  46-)  A      OE2
 200 GLU   (  22-)  B      CG
 200 GLU   (  22-)  B      CD
 200 GLU   (  22-)  B      OE1
 200 GLU   (  22-)  B      OE2
 308 GLU   ( 138-)  B      CG
 308 GLU   ( 138-)  B      CD
 308 GLU   ( 138-)  B      OE1
 308 GLU   ( 138-)  B      OE2
 334 VAL   ( 164-)  B      CG1
 334 VAL   ( 164-)  B      CG2
 336 ARG   ( 166-)  B      CG
 336 ARG   ( 166-)  B      CD
 336 ARG   ( 166-)  B      NE
 336 ARG   ( 166-)  B      CZ
 336 ARG   ( 166-)  B      NH1
 336 ARG   ( 166-)  B      NH2
 337 SER   ( 167-)  B      OG
 399 LYS   (  27-)  D      CG
 399 LYS   (  27-)  D      CD
 399 LYS   (  27-)  D      CE
 399 LYS   (  27-)  D      NZ
And so on for a total of 56 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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.

 121 ARG   ( 123-)  A

Warning: Tyrosine convention problem

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

 390 TYR   (  18-)  D
 393 TYR   (  21-)  D
 446 TYR   (  74-)  D
 522 TYR   ( 150-)  D
 525 TYR   ( 153-)  D
 551 TYR   ( 179-)  D
 565 TYR   ( 193-)  D

Warning: Phenylalanine convention problem

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

  49 PHE   (  51-)  A
 135 PHE   ( 137-)  A
 178 PHE   ( 180-)  A
 450 PHE   (  78-)  D
 548 PHE   ( 176-)  D

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.

 254 ASP   (  76-)  B
 383 ASP   (  11-)  D
 539 ASP   ( 167-)  D
 545 ASP   ( 173-)  D

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.

   2 GLU   (   4-)  A
  69 GLU   (  71-)  A
 237 GLU   (  59-)  B
 400 GLU   (  28-)  D
 455 GLU   (  83-)  D
 459 GLU   (  87-)  D
 494 GLU   ( 122-)  D
 530 GLU   ( 158-)  D
 537 GLU   ( 165-)  D
 556 GLU   ( 184-)  D
 566 GLU   ( 194-)  D

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.

  86 GLU   (  88-)  A      N    CA   C    99.73   -4.1
  96 GLU   (  98-)  A      N    CA   C    99.78   -4.1
 549 ASP   ( 177-)  D      N    CA   C    97.90   -4.8

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

   2 GLU   (   4-)  A
  69 GLU   (  71-)  A
 121 ARG   ( 123-)  A
 237 GLU   (  59-)  B
 254 ASP   (  76-)  B
 383 ASP   (  11-)  D
 400 GLU   (  28-)  D
 455 GLU   (  83-)  D
 459 GLU   (  87-)  D
 494 GLU   ( 122-)  D
 530 GLU   ( 158-)  D
 537 GLU   ( 165-)  D
 539 ASP   ( 167-)  D
 545 ASP   ( 173-)  D
 556 GLU   ( 184-)  D
 566 GLU   ( 194-)  D

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.

 562 ASP   ( 190-)  D    4.49
 553 LEU   ( 181-)  D    4.31
  86 GLU   (  88-)  A    4.18
 549 ASP   ( 177-)  D    4.15
 247 GLU   (  69-)  B    4.13

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.

 111 THR   ( 113-)  A    -2.6
 327 THR   ( 157-)  B    -2.5
 500 THR   ( 128-)  D    -2.4
 199 THR   (  21-)  B    -2.4
 217 ARG   (  39-)  B    -2.4
  90 LEU   (  92-)  A    -2.4
 151 PHE   ( 153-)  A    -2.3
 153 PRO   ( 155-)  A    -2.3
 216 VAL   (  38-)  B    -2.2
 272 ARG   (  94-)  B    -2.2
 457 ILE   (  85-)  D    -2.2
 115 VAL   ( 117-)  A    -2.2
 228 VAL   (  50-)  B    -2.1
  96 GLU   (  98-)  A    -2.1
 474 GLU   ( 102-)  D    -2.0
 168 LEU   ( 170-)  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.

   2 GLU   (   4-)  A  Poor phi/psi
  13 ASN   (  15-)  A  PRO omega poor
  16 GLN   (  18-)  A  Poor phi/psi
  37 LYS   (  39-)  A  Poor phi/psi
  76 ASN   (  78-)  A  Poor phi/psi
  77 TYR   (  79-)  A  Poor phi/psi
  98 ARG   ( 100-)  A  Poor phi/psi
 111 THR   ( 113-)  A  Poor phi/psi, PRO omega poor
 127 THR   ( 129-)  A  Poor phi/psi
 141 HIS   ( 143-)  A  Poor phi/psi
 197 ASN   (  19-)  B  Poor phi/psi
 211 ASN   (  33-)  B  Poor phi/psi
 293 TYR   ( 123-)  B  PRO omega poor
 304 ASN   ( 134-)  B  Poor phi/psi
 323 TRP   ( 153-)  B  Poor phi/psi
 401 ASN   (  29-)  D  Poor phi/psi
 410 GLU   (  38-)  D  Poor phi/psi
 417 ASN   (  45-)  D  Poor phi/psi
 440 ASN   (  68-)  D  Poor phi/psi
 453 LYS   (  81-)  D  Poor phi/psi
 458 SER   (  86-)  D  Poor phi/psi
 489 ASP   ( 117-)  D  Poor phi/psi
 523 LYS   ( 151-)  D  Poor phi/psi
 543 PRO   ( 171-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.286

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 519 SER   ( 147-)  D    0.33

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 HIS   (   5-)  A      0
   9 GLU   (  11-)  A      0
  13 ASN   (  15-)  A      0
  15 ASP   (  17-)  A      0
  16 GLN   (  18-)  A      0
  17 SER   (  19-)  A      0
  20 PHE   (  22-)  A      0
  24 PHE   (  26-)  A      0
  30 PHE   (  32-)  A      0
  31 HIS   (  33-)  A      0
  36 LYS   (  38-)  A      0
  37 LYS   (  39-)  A      0
  42 ARG   (  44-)  A      0
  48 ARG   (  50-)  A      0
  49 PHE   (  51-)  A      0
  50 ALA   (  52-)  A      0
  75 SER   (  77-)  A      0
  76 ASN   (  78-)  A      0
  77 TYR   (  79-)  A      0
  97 LEU   (  99-)  A      0
  98 ARG   ( 100-)  A      0
 108 ASP   ( 110-)  A      0
 109 LYS   ( 111-)  A      0
 110 PHE   ( 112-)  A      0
 111 THR   ( 113-)  A      0
And so on for a total of 242 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 : 1.413

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]

 171 PRO   ( 173-)  A    0.47 HIGH
 335 PRO   ( 165-)  B    0.48 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].

  14 PRO   (  16-)  A   -62.1 half-chair C-beta/C-alpha (-54 degrees)
 361 PRO   ( 306-)  C  -116.8 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 249 ARG   (  71-)  B      NH1  <->   366 GLN   ( 311-)  C      CG   0.35    2.75  INTRA BF
 181 THR   (   3-)  B      CG2  <->   592 HOH   ( 216 )  B      O    0.34    2.46  INTRA BF
 378 LYS   (   6-)  D      NZ   <->   529 SER   ( 157-)  D      OG   0.32    2.38  INTRA
  75 SER   (  77-)  A      O    <->    78 THR   (  80-)  A      CG2  0.32    2.48  INTRA BL
  74 ARG   (  76-)  A      NH1  <->   235 ASP   (  57-)  B      OD2  0.31    2.39  INTRA
 437 LYS   (  65-)  D      O    <->   441 LYS   (  69-)  D      NZ   0.29    2.41  INTRA BF
 145 LYS   ( 147-)  A      NZ   <->   147 HIS   ( 149-)  A      CE1  0.29    2.81  INTRA BL
 214 GLU   (  36-)  B      O    <->   228 VAL   (  50-)  B      CG2  0.27    2.53  INTRA BL
 447 GLY   (  75-)  D      CA   <->   508 GLN   ( 136-)  D      NE2  0.26    2.84  INTRA BF
 448 ALA   (  76-)  D      N    <->   508 GLN   ( 136-)  D      NE2  0.26    2.59  INTRA BF
 365 LYS   ( 310-)  C      NZ   <->   367 ASN   ( 312-)  C      OD1  0.25    2.45  INTRA BL
 207 ARG   (  29-)  B      NH1  <->   214 GLU   (  36-)  B      CD   0.23    2.87  INTRA BF
  15 ASP   (  17-)  A      CG   <->   184 ARG   (   6-)  B      NH1  0.23    2.87  INTRA BF
 542 THR   ( 170-)  D      O    <->   544 ARG   ( 172-)  D      N    0.23    2.47  INTRA BF
 259 HIS   (  81-)  B      CD2  <->   364 VAL   ( 309-)  C      CG2  0.22    2.98  INTRA BL
 249 ARG   (  71-)  B      NH2  <->   367 ASN   ( 312-)  C      O    0.20    2.50  INTRA BL
 480 ARG   ( 108-)  D      NH2  <->   576 ILE   ( 204-)  D      O    0.20    2.50  INTRA
 362 LYS   ( 307-)  C      CE   <->   594 HOH   ( 611 )  D      O    0.20    2.60  INTRA BF
 214 GLU   (  36-)  B      OE2  <->   217 ARG   (  39-)  B      NH1  0.20    2.50  INTRA BL
 426 ARG   (  54-)  D      NH2  <->   457 ILE   (  85-)  D      CG2  0.20    2.90  INTRA BF
 182 ARG   (   4-)  B      NH1  <->   592 HOH   ( 216 )  B      O    0.18    2.52  INTRA BF
 233 ARG   (  55-)  B      N    <->   234 PRO   (  56-)  B      CD   0.18    2.82  INTRA BF
 283 ASN   ( 113-)  B      ND2  <->   284 LEU   ( 114-)  B      N    0.17    2.58  INTRA BF
 109 LYS   ( 111-)  A      CG   <->   138 ARG   ( 140-)  A      NH2  0.17    2.93  INTRA BL
  88 THR   (  90-)  A      CB   <->   591 HOH   ( 193 )  A      O    0.17    2.63  INTRA BF
And so on for a total of 131 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 359 ARG   ( 189-)  B      -6.64
 452 TYR   (  80-)  D      -6.59
 459 GLU   (  87-)  D      -6.12
  98 ARG   ( 100-)  A      -5.97
 554 LYS   ( 182-)  D      -5.89
 309 LYS   ( 139-)  B      -5.59
  49 PHE   (  51-)  A      -5.55
 478 GLN   ( 106-)  D      -5.44
  16 GLN   (  18-)  A      -5.34
 280 TYR   ( 102-)  B      -5.31
  48 ARG   (  50-)  A      -5.25
 394 ASN   (  22-)  D      -5.09
  42 ARG   (  44-)  A      -5.06

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

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: C

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: D

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.

 439 LYS   (  67-)  D   -3.14
 503 LYS   ( 131-)  D   -2.95
 559 TYR   ( 187-)  D   -2.56

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 563 LYS   ( 191-)  D     -  566 GLU   ( 194-)  D        -1.52

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

 591 HOH   ( 197 )  A      O
 592 HOH   ( 217 )  B      O
 594 HOH   ( 623 )  D      O
Metal-coordinating Histidine residue 259 fixed to   1
Metal-coordinating Histidine residue 578 fixed to   1

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.

 141 HIS   ( 143-)  A
 147 HIS   ( 149-)  A
 188 GLN   (  10-)  B
 282 HIS   ( 112-)  B
 326 GLN   ( 156-)  B
 417 ASN   (  45-)  D
 423 ASN   (  51-)  D
 508 GLN   ( 136-)  D

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.

  20 PHE   (  22-)  A      N
  43 LEU   (  45-)  A      N
  49 PHE   (  51-)  A      N
 128 THR   ( 130-)  A      N
 154 SER   ( 156-)  A      N
 170 GLU   ( 172-)  A      N
 188 GLN   (  10-)  B      NE2
 207 ARG   (  29-)  B      NE
 207 ARG   (  29-)  B      NH1
 224 GLU   (  46-)  B      N
 249 ARG   (  71-)  B      NE
 249 ARG   (  71-)  B      NH1
 260 ASN   (  82-)  B      ND2
 272 ARG   (  94-)  B      NH1
 300 ARG   ( 130-)  B      NH1
 333 THR   ( 163-)  B      OG1
 366 GLN   ( 311-)  C      NE2
 392 GLN   (  20-)  D      NE2
 411 LYS   (  39-)  D      N
 431 THR   (  59-)  D      N
 457 ILE   (  85-)  D      N
 504 ASN   ( 132-)  D      N
 519 SER   ( 147-)  D      OG
 531 ILE   ( 159-)  D      N
 553 LEU   ( 181-)  D      N
 554 LYS   ( 182-)  D      N
 555 GLY   ( 183-)  D      N
 556 GLU   ( 184-)  D      N
 569 LYS   ( 197-)  D      N
 574 ASP   ( 202-)  D      N
Only metal coordination for  578 HIS  ( 206-) D      NE2

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.

   1 GLU   (   3-)  A      OE1
 380 GLU   (   8-)  D      OE1
 392 GLN   (  20-)  D      OE1
 412 ASP   (  40-)  D      OD1
 558 ASP   ( 186-)  D      OD1
 562 ASP   ( 190-)  D      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.

  19 GLU   (  21-)  A   H-bonding suggests Gln
  64 ASP   (  66-)  A   H-bonding suggests Asn
 157 ASP   ( 159-)  A   H-bonding suggests Asn; but Alt-Rotamer
 179 ASP   ( 181-)  A   H-bonding suggests Asn
 412 ASP   (  40-)  D   H-bonding suggests Asn
 562 ASP   ( 190-)  D   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 :  -0.028
  2nd generation packing quality :  -1.381
  Ramachandran plot appearance   :  -1.881
  chi-1/chi-2 rotamer normality  :  -2.286
  Backbone conformation          :  -0.438

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.351 (tight)
  Bond angles                    :   0.658 (tight)
  Omega angle restraints         :   0.257 (tight)
  Side chain planarity           :   0.250 (tight)
  Improper dihedral distribution :   0.620
  B-factor distribution          :   0.462
  Inside/Outside distribution    :   1.055

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.2
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.351 (tight)
  Bond angles                    :   0.658 (tight)
  Omega angle restraints         :   0.257 (tight)
  Side chain planarity           :   0.250 (tight)
  Improper dihedral distribution :   0.620
  B-factor distribution          :   0.462
  Inside/Outside distribution    :   1.055
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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DSSP
    W.Kabsch and C.Sander,
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      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    J. Appl. Cryst. 29, 714--716 (1996).

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

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

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

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

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

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

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

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