WHAT IF Check report

This file was created 2012-01-04 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 pdb1m9i.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

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   6 HIS   (  15-)  A    High
   7 ASP   (  16-)  A    High
  99 ILE   ( 108-)  A    High
 130 GLU   ( 139-)  A    High
 161 ASP   ( 170-)  A    High
 162 VAL   ( 171-)  A    High
 163 VAL   ( 172-)  A    High
 200 GLN   ( 209-)  A    High
 222 ARG   ( 231-)  A    High
 256 LYS   ( 265-)  A    High
 258 LEU   ( 267-)  A    High
 289 GLU   ( 298-)  A    High
 313 GLY   ( 322-)  A    High
 315 ASP   ( 324-)  A    High
 316 ASP   ( 325-)  A    High
 317 ASP   ( 326-)  A    High
 318 ALA   ( 327-)  A    High
 319 ALA   ( 328-)  A    High
 343 GLU   ( 352-)  A    High
 368 LYS   ( 377-)  A    High
 379 ASP   ( 388-)  A    High
 394 GLN   ( 403-)  A    High
 466 GLU   ( 475-)  A    High
 499 HIS   ( 508-)  A    High
 508 ASP   ( 517-)  A    High
 515 GLN   ( 524-)  A    High
 522 GLU   ( 531-)  A    High
 523 ILE   ( 532-)  A    High
 524 ALA   ( 533-)  A    High
 525 ASP   ( 534-)  A    High
 526 THR   ( 535-)  A    High
 527 PRO   ( 536-)  A    High
 528 SER   ( 537-)  A    High
 529 GLY   ( 538-)  A    High
 530 ASP   ( 539-)  A    High
 531 LYS   ( 540-)  A    High
 532 THR   ( 541-)  A    High
 533 SER   ( 542-)  A    High
 534 LEU   ( 543-)  A    High
 535 GLU   ( 544-)  A    High
 567 HIS   ( 576-)  A    High
 663 GLU   ( 672-)  A    High
 664 ASP   ( 673-)  A    High

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

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.

  44 ARG   (  53-)  A
  75 ARG   (  84-)  A
 131 ARG   ( 140-)  A
 349 ARG   ( 358-)  A
 364 ARG   ( 373-)  A

Warning: Tyrosine convention problem

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

  53 TYR   (  62-)  A
 125 TYR   ( 134-)  A
 129 TYR   ( 138-)  A
 176 TYR   ( 185-)  A
 192 TYR   ( 201-)  A
 246 TYR   ( 255-)  A
 472 TYR   ( 481-)  A
 547 TYR   ( 556-)  A
 600 TYR   ( 609-)  A

Warning: Phenylalanine convention problem

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

  11 PHE   (  20-)  A
 206 PHE   ( 215-)  A
 322 PHE   ( 331-)  A
 323 PHE   ( 332-)  A
 396 PHE   ( 405-)  A
 554 PHE   ( 563-)  A
 594 PHE   ( 603-)  A
 632 PHE   ( 641-)  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.

  16 ASP   (  25-)  A
  30 ASP   (  39-)  A
  88 ASP   (  97-)  A
  94 ASP   ( 103-)  A
 102 ASP   ( 111-)  A
 136 ASP   ( 145-)  A
 171 ASP   ( 180-)  A
 174 ASP   ( 183-)  A
 207 ASP   ( 216-)  A
 262 ASP   ( 271-)  A
 276 ASP   ( 285-)  A
 279 ASP   ( 288-)  A
 299 ASP   ( 308-)  A
 317 ASP   ( 326-)  A
 359 ASP   ( 368-)  A
 375 ASP   ( 384-)  A
 407 ASP   ( 416-)  A
 415 ASP   ( 424-)  A
 431 ASP   ( 440-)  A
 445 ASP   ( 454-)  A
 471 ASP   ( 480-)  A
 513 ASP   ( 522-)  A
 576 ASP   ( 585-)  A
 579 ASP   ( 588-)  A
 597 ASP   ( 606-)  A
 609 ASP   ( 618-)  A
 624 ASP   ( 633-)  A
 637 ASP   ( 646-)  A
 651 ASP   ( 660-)  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.

  18 GLU   (  27-)  A
  32 GLU   (  41-)  A
  48 GLU   (  57-)  A
  68 GLU   (  77-)  A
  74 GLU   (  83-)  A
  91 GLU   ( 100-)  A
 103 GLU   ( 112-)  A
 108 GLU   ( 117-)  A
 134 GLU   ( 143-)  A
 159 GLU   ( 168-)  A
 187 GLU   ( 196-)  A
 224 GLU   ( 233-)  A
 274 GLU   ( 283-)  A
 282 GLU   ( 291-)  A
 289 GLU   ( 298-)  A
 303 GLU   ( 312-)  A
 325 GLU   ( 334-)  A
 335 GLU   ( 344-)  A
 343 GLU   ( 352-)  A
 411 GLU   ( 420-)  A
 451 GLU   ( 460-)  A
 466 GLU   ( 475-)  A
 470 GLU   ( 479-)  A
 501 GLU   ( 510-)  A
 502 GLU   ( 511-)  A
 535 GLU   ( 544-)  A
 556 GLU   ( 565-)  A
 566 GLU   ( 575-)  A
 631 GLU   ( 640-)  A
 645 GLU   ( 654-)  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.

 292 LEU   ( 301-)  A      N    CA   C    99.86   -4.1
 562 ASN   ( 571-)  A      N    CA   C   123.72    4.5

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.

  16 ASP   (  25-)  A
  18 GLU   (  27-)  A
  30 ASP   (  39-)  A
  32 GLU   (  41-)  A
  44 ARG   (  53-)  A
  48 GLU   (  57-)  A
  68 GLU   (  77-)  A
  74 GLU   (  83-)  A
  75 ARG   (  84-)  A
  88 ASP   (  97-)  A
  91 GLU   ( 100-)  A
  94 ASP   ( 103-)  A
 102 ASP   ( 111-)  A
 103 GLU   ( 112-)  A
 108 GLU   ( 117-)  A
 131 ARG   ( 140-)  A
 134 GLU   ( 143-)  A
 136 ASP   ( 145-)  A
 159 GLU   ( 168-)  A
 171 ASP   ( 180-)  A
 174 ASP   ( 183-)  A
 187 GLU   ( 196-)  A
 207 ASP   ( 216-)  A
 224 GLU   ( 233-)  A
 262 ASP   ( 271-)  A
And so on for a total of 64 lines.

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.

 292 LEU   ( 301-)  A    7.52
 339 VAL   ( 348-)  A    5.12
 112 SER   ( 121-)  A    5.05
 453 LEU   ( 462-)  A    4.91
 544 THR   ( 553-)  A    4.73
  38 ILE   (  47-)  A    4.40
 455 THR   ( 464-)  A    4.23
 483 ASP   ( 492-)  A    4.04

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 : 1.526

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.296

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.

  11 PHE   (  20-)  A    -2.9
 427 PRO   ( 436-)  A    -2.9
  84 PRO   (  93-)  A    -2.7
 272 ARG   ( 281-)  A    -2.7
 324 PRO   ( 333-)  A    -2.7
 523 ILE   ( 532-)  A    -2.7
   8 PHE   (  17-)  A    -2.6
   6 HIS   (  15-)  A    -2.5
 663 GLU   ( 672-)  A    -2.4
 505 GLU   ( 514-)  A    -2.4
 285 ARG   ( 294-)  A    -2.3
 161 ASP   ( 170-)  A    -2.3
 372 THR   ( 381-)  A    -2.3
 162 VAL   ( 171-)  A    -2.3
 384 ARG   ( 393-)  A    -2.2
  75 ARG   (  84-)  A    -2.2
   9 PRO   (  18-)  A    -2.1
 179 GLY   ( 188-)  A    -2.1
 185 THR   ( 194-)  A    -2.1
  10 GLY   (  19-)  A    -2.1
 217 ILE   ( 226-)  A    -2.1
 531 LYS   ( 540-)  A    -2.1
 314 GLY   ( 323-)  A    -2.0
 349 ARG   ( 358-)  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.

   8 PHE   (  17-)  A  Poor phi/psi
 161 ASP   ( 170-)  A  Poor phi/psi
 225 LEU   ( 234-)  A  Poor phi/psi
 242 SER   ( 251-)  A  Poor phi/psi
 256 LYS   ( 265-)  A  Poor phi/psi
 289 GLU   ( 298-)  A  Poor phi/psi
 290 LYS   ( 299-)  A  Poor phi/psi
 291 SER   ( 300-)  A  Poor phi/psi
 315 ASP   ( 324-)  A  Poor phi/psi
 317 ASP   ( 326-)  A  Poor phi/psi
 318 ALA   ( 327-)  A  Poor phi/psi
 319 ALA   ( 328-)  A  Poor phi/psi
 474 LYS   ( 483-)  A  Poor phi/psi
 505 GLU   ( 514-)  A  Poor phi/psi
 506 ASN   ( 515-)  A  Poor phi/psi
 524 ALA   ( 533-)  A  Poor phi/psi
 525 ASP   ( 534-)  A  Poor phi/psi
 531 LYS   ( 540-)  A  Poor phi/psi
 532 THR   ( 541-)  A  Poor phi/psi
 535 GLU   ( 544-)  A  Poor phi/psi
 560 MET   ( 569-)  A  Poor phi/psi
 561 THR   ( 570-)  A  Poor phi/psi
 562 ASN   ( 571-)  A  Poor phi/psi
 606 ALA   ( 615-)  A  Poor phi/psi
 663 GLU   ( 672-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.817

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.

 294 SER   ( 303-)  A    0.36
  55 SER   (  64-)  A    0.36
 220 SER   ( 229-)  A    0.36
 337 SER   ( 346-)  A    0.36

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!

   7 ASP   (  16-)  A      0
   8 PHE   (  17-)  A      0
  11 PHE   (  20-)  A      0
  25 LYS   (  34-)  A      0
  27 PHE   (  36-)  A      0
  29 SER   (  38-)  A      0
  57 TYR   (  66-)  A      0
  70 THR   (  79-)  A      0
  72 LYS   (  81-)  A      0
  81 MET   (  90-)  A      0
  96 ILE   ( 105-)  A      0
  97 SER   ( 106-)  A      0
  99 ILE   ( 108-)  A      0
 130 GLU   ( 139-)  A      0
 131 ARG   ( 140-)  A      0
 141 THR   ( 150-)  A      0
 142 SER   ( 151-)  A      0
 144 HIS   ( 153-)  A      0
 154 GLN   ( 163-)  A      0
 156 THR   ( 165-)  A      0
 160 ASP   ( 169-)  A      0
 161 ASP   ( 170-)  A      0
 162 VAL   ( 171-)  A      0
 164 SER   ( 173-)  A      0
 180 GLU   ( 189-)  A      0
And so on for a total of 182 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 : 1.088

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!

 427 PRO   ( 436-)  A   1.80   12
  84 PRO   (  93-)  A   1.64   10

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.

 447 LYS   ( 456-)  A      NZ  <->  598 LYS   ( 607-)  A      CE     0.41    2.69  INTRA BF
 561 THR   ( 570-)  A      O   <->  563 TYR   ( 572-)  A      N      0.34    2.36  INTRA BF
   1 TYR   (  10-)  A      N   <->  671 HOH   ( 780 )  A      O      0.32    2.38  INTRA BF
 243 THR   ( 252-)  A      N   <->  244 PRO   ( 253-)  A      CD     0.30    2.70  INTRA BL
 591 LYS   ( 600-)  A      NZ  <->  671 HOH   ( 818 )  A      O      0.30    2.40  INTRA
 509 GLN   ( 518-)  A      NE2 <->  513 ASP   ( 522-)  A      OD1    0.29    2.41  INTRA BF
 509 GLN   ( 518-)  A      NE2 <->  545 ARG   ( 554-)  A      NH2    0.27    2.58  INTRA BF
 349 ARG   ( 358-)  A      N   <->  671 HOH   ( 801 )  A      O      0.25    2.45  INTRA BF
 577 VAL   ( 586-)  A      CG1 <->  578 ARG   ( 587-)  A      N      0.25    2.75  INTRA BL
 289 GLU   ( 298-)  A      OE1 <->  570 LYS   ( 579-)  A      NZ     0.24    2.46  INTRA BF
  11 PHE   (  20-)  A      CG  <->   12 ASP   (  21-)  A      N      0.24    2.76  INTRA BL
 630 ARG   ( 639-)  A      NH1 <->  671 HOH   ( 814 )  A      O      0.22    2.48  INTRA BF
 526 THR   ( 535-)  A      N   <->  527 PRO   ( 536-)  A      CD     0.22    2.78  INTRA BF
 260 THR   ( 269-)  A      CG2 <->  261 ARG   ( 270-)  A      N      0.22    2.78  INTRA
 509 GLN   ( 518-)  A      CG  <->  545 ARG   ( 554-)  A      NH2    0.22    2.88  INTRA BF
 357 ASP   ( 366-)  A      OD1 <->  361 LYS   ( 370-)  A      NZ     0.22    2.48  INTRA BF
 447 LYS   ( 456-)  A      NZ  <->  671 HOH   ( 714 )  A      O      0.21    2.49  INTRA BF
 509 GLN   ( 518-)  A      CD  <->  545 ARG   ( 554-)  A      NH2    0.21    2.89  INTRA BF
 364 ARG   ( 373-)  A      NH2 <->  402 ARG   ( 411-)  A      NH1    0.21    2.64  INTRA BF
  72 LYS   (  81-)  A      NZ  <->  262 ASP   ( 271-)  A      OD2    0.20    2.50  INTRA BF
 520 ILE   ( 529-)  A      CD1 <->  534 LEU   ( 543-)  A      CB     0.20    3.00  INTRA BF
 521 LEU   ( 530-)  A      CG  <->  568 THR   ( 577-)  A      CB     0.20    3.00  INTRA BF
 364 ARG   ( 373-)  A      NH1 <->  402 ARG   ( 411-)  A      NH1    0.20    2.65  INTRA BF
 630 ARG   ( 639-)  A      NH2 <->  671 HOH   ( 789 )  A      O      0.19    2.51  INTRA BF
 364 ARG   ( 373-)  A      O   <->  368 LYS   ( 377-)  A      N      0.19    2.51  INTRA BF
And so on for a total of 178 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.

  27 PHE   (  36-)  A      -7.89
 258 LEU   ( 267-)  A      -7.46
 370 LEU   ( 379-)  A      -6.37
 341 ARG   ( 350-)  A      -6.18
   8 PHE   (  17-)  A      -5.84
  11 PHE   (  20-)  A      -5.81
 183 TRP   ( 192-)  A      -5.67
 399 HIS   ( 408-)  A      -5.63
  82 ARG   (  91-)  A      -5.55
 527 PRO   ( 536-)  A      -5.54
 154 GLN   ( 163-)  A      -5.51
 368 LYS   ( 377-)  A      -5.46
 182 LYS   ( 191-)  A      -5.44
 349 ARG   ( 358-)  A      -5.31
 241 ARG   ( 250-)  A      -5.31
 499 HIS   ( 508-)  A      -5.20
  99 ILE   ( 108-)  A      -5.20
 502 GLU   ( 511-)  A      -5.10
 663 GLU   ( 672-)  A      -5.01
 531 LYS   ( 540-)  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.

  25 LYS   (  34-)  A        27 - PHE     36- ( A)         -5.60
 181 LEU   ( 190-)  A       183 - TRP    192- ( A)         -5.25

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: 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.

  14 ASN   (  23-)  A
 196 ASN   ( 205-)  A
 201 HIS   ( 210-)  A
 388 GLN   ( 397-)  A
 391 GLN   ( 400-)  A
 487 HIS   ( 496-)  A
 549 HIS   ( 558-)  A
 590 ASN   ( 599-)  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.

   3 GLY   (  12-)  A      N
  41 ARG   (  50-)  A      N
  42 SER   (  51-)  A      OG
  47 GLN   (  56-)  A      NE2
  59 LYS   (  68-)  A      N
 116 GLU   ( 125-)  A      N
 131 ARG   ( 140-)  A      N
 215 LYS   ( 224-)  A      N
 257 GLY   ( 266-)  A      N
 261 ARG   ( 270-)  A      NH1
 267 ARG   ( 276-)  A      NH1
 285 ARG   ( 294-)  A      NH1
 294 SER   ( 303-)  A      N
 326 ALA   ( 335-)  A      N
 346 GLY   ( 355-)  A      N
 385 SER   ( 394-)  A      OG
 386 ASN   ( 395-)  A      N
 399 HIS   ( 408-)  A      ND1
 402 ARG   ( 411-)  A      N
 417 ALA   ( 426-)  A      N
 430 TYR   ( 439-)  A      OH
 456 ARG   ( 465-)  A      NE
 456 ARG   ( 465-)  A      NH2
 511 ARG   ( 520-)  A      NE
 531 LYS   ( 540-)  A      NZ
 532 THR   ( 541-)  A      N
 533 SER   ( 542-)  A      OG
 537 ARG   ( 546-)  A      N
 538 PHE   ( 547-)  A      N
 539 MET   ( 548-)  A      N
 555 GLN   ( 564-)  A      NE2
 620 ARG   ( 629-)  A      NE
 621 SER   ( 630-)  A      OG
 638 LYS   ( 647-)  A      N
 641 HIS   ( 650-)  A      N

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.

  14 ASN   (  23-)  A      OD1
 522 GLU   ( 531-)  A      OE1
 567 HIS   ( 576-)  A      ND1
 572 GLU   ( 581-)  A      OE1
 576 ASP   ( 585-)  A      OD2

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+.

 666  CA   ( 701-)  A   -.-  -.-  Low probability ion. Occ=0.30; B=160.3
 667  CA   ( 702-)  A   -.-  -.-  Low probability ion. Occ=0.50; B=142.1
 668  CA   ( 703-)  A   -.-  -.-  Low probability ion. B= 83.6
 669  CA   ( 704-)  A   -.-  -.-  Low probability ion. Occ=0.50; B=161.1
 670  CA   ( 705-)  A   -.-  -.-  Low probability ion. Occ=0.50; B=176.5

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.

 671 HOH   ( 706 )  A      O  1.02 NA  4 Ion-B H2O-B

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.

  36 ASP   (  45-)  A   H-bonding suggests Asn
  68 GLU   (  77-)  A   H-bonding suggests Gln
  74 GLU   (  83-)  A   H-bonding suggests Gln; but Alt-Rotamer
 103 GLU   ( 112-)  A   H-bonding suggests Gln; but Alt-Rotamer
 161 ASP   ( 170-)  A   H-bonding suggests Asn
 374 GLU   ( 383-)  A   H-bonding suggests Gln
 446 GLU   ( 455-)  A   H-bonding suggests Gln
 522 GLU   ( 531-)  A   H-bonding suggests Gln
 647 ASP   ( 656-)  A   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 :  -0.297
  2nd generation packing quality :  -1.075
  Ramachandran plot appearance   :  -3.296 (poor)
  chi-1/chi-2 rotamer normality  :  -2.817
  Backbone conformation          :  -0.101

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.321 (tight)
  Bond angles                    :   0.603 (tight)
  Omega angle restraints         :   0.198 (tight)
  Side chain planarity           :   0.229 (tight)
  Improper dihedral distribution :   0.540
  B-factor distribution          :   1.368
  Inside/Outside distribution    :   0.992

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 : 2.65


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :   1.1
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.321 (tight)
  Bond angles                    :   0.603 (tight)
  Omega angle restraints         :   0.198 (tight)
  Side chain planarity           :   0.229 (tight)
  Improper dihedral distribution :   0.540
  B-factor distribution          :   1.368
  Inside/Outside distribution    :   0.992
==============

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.