WHAT IF Check report

This file was created 2011-12-18 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 pdb2v5y.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

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

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

Molecular weight of all polymer chains: 62740.781
Volume of the Unit Cell V= 1036955.1
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z a bit high: Vm= 4.132
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.070

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'.

   1 THR   (   2-)  A      OG1
   1 THR   (   2-)  A      CG2

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 6

Crystal temperature (K) :100.000

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.

 169 ARG   ( 170-)  A
 363 ARG   ( 364-)  A
 514 ARG   ( 518-)  A
 540 ARG   ( 544-)  A

Warning: Tyrosine convention problem

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

  80 TYR   (  81-)  A
 148 TYR   ( 149-)  A
 237 TYR   ( 238-)  A
 276 TYR   ( 277-)  A
 328 TYR   ( 329-)  A
 392 TYR   ( 393-)  A
 398 TYR   ( 399-)  A
 400 TYR   ( 401-)  A
 489 TYR   ( 490-)  A
 495 TYR   ( 496-)  A
 499 TYR   ( 500-)  A
 530 TYR   ( 534-)  A
 535 TYR   ( 539-)  A

Warning: Phenylalanine convention problem

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

   8 PHE   (   9-)  A
  25 PHE   (  26-)  A
  78 PHE   (  79-)  A
 129 PHE   ( 130-)  A
 133 PHE   ( 134-)  A
 183 PHE   ( 184-)  A
 220 PHE   ( 221-)  A
 224 PHE   ( 225-)  A
 382 PHE   ( 383-)  A
 524 PHE   ( 528-)  A
 526 PHE   ( 530-)  A
 537 PHE   ( 541-)  A
 547 PHE   ( 551-)  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.

  39 ASP   (  40-)  A
  72 ASP   (  73-)  A
  77 ASP   (  78-)  A
 195 ASP   ( 196-)  A
 233 ASP   ( 234-)  A
 289 ASP   ( 290-)  A
 308 ASP   ( 309-)  A
 457 ASP   ( 458-)  A
 506 ASP   ( 507-)  A
 507 ASP   ( 511-)  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.

  28 GLU   (  29-)  A
 211 GLU   ( 212-)  A
 296 GLU   ( 297-)  A
 369 GLU   ( 370-)  A
 380 GLU   ( 381-)  A
 410 GLU   ( 411-)  A
 411 GLU   ( 412-)  A
 417 GLU   ( 418-)  A
 444 GLU   ( 445-)  A
 458 GLU   ( 459-)  A
 521 GLU   ( 525-)  A

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.998680  0.000117  0.000131|
 |  0.000117  0.998317 -0.000125|
 |  0.000131 -0.000125  0.998496|
Proposed new scale matrix

 |  0.005984  0.000000  0.002604|
 | -0.000002  0.014449  0.000002|
 | -0.000001  0.000001  0.011204|
With corresponding cell

    A    = 167.115  B   =  69.207  C    =  97.336
    Alpha=  90.017  Beta= 113.512  Gamma=  89.991

The CRYST1 cell dimensions

    A    = 167.336  B   =  69.325  C    =  97.487
    Alpha=  90.000  Beta= 113.520  Gamma=  90.000

Variance: 43.409
(Under-)estimated Z-score: 4.856

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.

  85 LYS   (  86-)  A     -C    N    CA  130.59    4.9

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.

  28 GLU   (  29-)  A
  39 ASP   (  40-)  A
  72 ASP   (  73-)  A
  77 ASP   (  78-)  A
 169 ARG   ( 170-)  A
 195 ASP   ( 196-)  A
 211 GLU   ( 212-)  A
 233 ASP   ( 234-)  A
 289 ASP   ( 290-)  A
 296 GLU   ( 297-)  A
 308 ASP   ( 309-)  A
 363 ARG   ( 364-)  A
 369 GLU   ( 370-)  A
 380 GLU   ( 381-)  A
 410 GLU   ( 411-)  A
 411 GLU   ( 412-)  A
 417 GLU   ( 418-)  A
 444 GLU   ( 445-)  A
 457 ASP   ( 458-)  A
 458 GLU   ( 459-)  A
 506 ASP   ( 507-)  A
 507 ASP   ( 511-)  A
 514 ARG   ( 518-)  A
 521 GLU   ( 525-)  A
 540 ARG   ( 544-)  A

Error: Tau angle problems

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

  84 SER   (  85-)  A    4.31
 477 LYS   ( 478-)  A    4.11

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.

 420 HIS   ( 421-)  A    -3.0
 486 THR   ( 487-)  A    -2.8
 489 TYR   ( 490-)  A    -2.7
 552 THR   ( 556-)  A    -2.6
 324 PRO   ( 325-)  A    -2.5
 511 GLN   ( 515-)  A    -2.4
 437 LYS   ( 438-)  A    -2.4
 378 ARG   ( 379-)  A    -2.4
 375 ILE   ( 376-)  A    -2.4
 208 PRO   ( 209-)  A    -2.4
 351 THR   ( 352-)  A    -2.4
 277 LEU   ( 278-)  A    -2.4
 402 VAL   ( 403-)  A    -2.4
 559 ILE   ( 563-)  A    -2.3
 219 ARG   ( 220-)  A    -2.2
 528 GLY   ( 532-)  A    -2.2
 382 PHE   ( 383-)  A    -2.2
 214 VAL   ( 215-)  A    -2.2
  37 THR   (  38-)  A    -2.1
  63 LEU   (  64-)  A    -2.1
 550 PRO   ( 554-)  A    -2.1
 117 ARG   ( 118-)  A    -2.1
 431 TYR   ( 432-)  A    -2.1
 487 GLN   ( 488-)  A    -2.1
 151 ILE   ( 152-)  A    -2.1
  43 PRO   (  44-)  A    -2.1
 197 LEU   ( 198-)  A    -2.1
 204 VAL   ( 205-)  A    -2.1
 514 ARG   ( 518-)  A    -2.1
 113 GLY   ( 114-)  A    -2.1
 307 ASN   ( 308-)  A    -2.1
 417 GLU   ( 418-)  A    -2.1
 111 ILE   ( 112-)  A    -2.1
 360 ARG   ( 361-)  A    -2.1
 175 VAL   ( 176-)  A    -2.0
 494 LEU   ( 495-)  A    -2.0
 518 LEU   ( 522-)  A    -2.0
 369 GLU   ( 370-)  A    -2.0
 418 ASN   ( 419-)  A    -2.0
 477 LYS   ( 478-)  A    -2.0
 427 ASN   ( 428-)  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 SER   (   4-)  A  omega poor
   8 PHE   (   9-)  A  Poor phi/psi
  23 ASP   (  24-)  A  Poor phi/psi
  33 LEU   (  34-)  A  omega poor
  49 LEU   (  50-)  A  omega poor
  64 LEU   (  65-)  A  omega poor
  83 SER   (  84-)  A  omega poor
  84 SER   (  85-)  A  omega poor
  85 LYS   (  86-)  A  Poor phi/psi, omega poor
  86 SER   (  87-)  A  Poor phi/psi, omega poor
 111 ILE   ( 112-)  A  omega poor
 112 SER   ( 113-)  A  omega poor
 116 THR   ( 117-)  A  Poor phi/psi
 117 ARG   ( 118-)  A  Poor phi/psi
 128 THR   ( 129-)  A  omega poor
 130 TRP   ( 131-)  A  PRO omega poor
 145 HIS   ( 146-)  A  omega poor
 151 ILE   ( 152-)  A  omega poor
 152 ASP   ( 153-)  A  Poor phi/psi
 226 VAL   ( 227-)  A  omega poor
 283 ALA   ( 284-)  A  Poor phi/psi
 305 SER   ( 306-)  A  Poor phi/psi
 306 TRP   ( 307-)  A  omega poor
 321 HIS   ( 322-)  A  Poor phi/psi
 324 PRO   ( 325-)  A  Poor phi/psi
 325 ASP   ( 326-)  A  Poor phi/psi, omega poor
 338 GLY   ( 339-)  A  omega poor
 340 GLY   ( 341-)  A  omega poor
 343 GLY   ( 344-)  A  omega poor
 359 MET   ( 360-)  A  omega poor
 364 LYS   ( 365-)  A  Poor phi/psi
 366 GLU   ( 367-)  A  omega poor
 389 CYS   ( 390-)  A  Poor phi/psi
 402 VAL   ( 403-)  A  omega poor
 415 ASP   ( 416-)  A  Poor phi/psi
 420 HIS   ( 421-)  A  Poor phi/psi
 427 ASN   ( 428-)  A  Poor phi/psi
 441 MET   ( 442-)  A  omega poor
 474 PHE   ( 475-)  A  omega poor
 476 GLU   ( 477-)  A  Poor phi/psi
 489 TYR   ( 490-)  A  Poor phi/psi
 494 LEU   ( 495-)  A  omega poor
 504 SER   ( 505-)  A  omega poor
 505 PHE   ( 506-)  A  omega poor
 510 ASN   ( 514-)  A  omega poor
 526 PHE   ( 530-)  A  omega poor
 527 PHE   ( 531-)  A  omega poor
 550 PRO   ( 554-)  A  omega poor
 563 SER   ( 567-)  A  omega poor
 chi-1/chi-2 correlation Z-score : -4.352

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

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

chi-1/chi-2 correlation Z-score : -4.352

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 SER   (   4-)  A      0
   7 LEU   (   8-)  A      0
   8 PHE   (   9-)  A      0
   9 ASP   (  10-)  A      0
  10 GLU   (  11-)  A      0
  15 CYS   (  16-)  A      0
  21 GLU   (  22-)  A      0
  23 ASP   (  24-)  A      0
  24 ASP   (  25-)  A      0
  27 TRP   (  28-)  A      0
  31 ASN   (  32-)  A      0
  34 THR   (  35-)  A      0
  41 TRP   (  42-)  A      0
  46 SER   (  47-)  A      0
  52 ALA   (  53-)  A      0
  53 SER   (  54-)  A      0
  57 GLU   (  58-)  A      0
  69 LYS   (  70-)  A      0
  72 ASP   (  73-)  A      0
  81 PHE   (  82-)  A      0
  84 SER   (  85-)  A      0
  85 LYS   (  86-)  A      0
  86 SER   (  87-)  A      0
  87 ASN   (  88-)  A      0
  90 PRO   (  91-)  A      0
And so on for a total of 264 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.454

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!

 443 PRO   ( 444-)  A   1.73   13
 304 GLY   ( 305-)  A   1.73   57

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].

  43 PRO   (  44-)  A   -62.6 half-chair C-beta/C-alpha (-54 degrees)
  56 PRO   (  57-)  A    39.7 envelop C-delta (36 degrees)
 107 PRO   ( 108-)  A    42.9 envelop C-delta (36 degrees)
 165 PRO   ( 166-)  A    42.7 envelop C-delta (36 degrees)
 208 PRO   ( 209-)  A   -54.5 half-chair C-beta/C-alpha (-54 degrees)
 261 PRO   ( 262-)  A    52.1 half-chair C-delta/C-gamma (54 degrees)
 263 PRO   ( 264-)  A    39.0 envelop C-delta (36 degrees)
 345 PRO   ( 346-)  A   -61.8 half-chair C-beta/C-alpha (-54 degrees)
 430 PRO   ( 431-)  A    48.7 half-chair C-delta/C-gamma (54 degrees)
 549 PRO   ( 553-)  A   -63.5 envelop C-beta (-72 degrees)
 550 PRO   ( 554-)  A   -33.4 envelop C-alpha (-36 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.

 480 LEU   ( 481-)  A      CD2 <->  497 ILE   ( 498-)  A      CD1    0.33    2.87  INTRA BL
 282 ASN   ( 283-)  A      O   <->  284 ASN   ( 285-)  A      N      0.28    2.42  INTRA BF
 520 ASN   ( 524-)  A      ND2 <->  571 NAG   (1575-)  A      C7     0.25    2.85  INTRA BF
 543 THR   ( 547-)  A      CG2 <->  544 ALA   ( 548-)  A      N      0.22    2.78  INTRA BL
 515 VAL   ( 519-)  A      CG2 <->  524 PHE   ( 528-)  A      CZ     0.22    2.98  INTRA BL
 358 PRO   ( 359-)  A      O   <->  447 LYS   ( 448-)  A      NZ     0.19    2.51  INTRA BF
 211 GLU   ( 212-)  A      OE1 <->  213 LYS   ( 214-)  A      NZ     0.17    2.53  INTRA
 100 ASN   ( 101-)  A      ND2 <->  132 ASN   ( 133-)  A      OD1    0.15    2.55  INTRA BL
 268 GLN   ( 269-)  A      O   <->  280 GLN   ( 281-)  A      N      0.14    2.56  INTRA
  28 GLU   (  29-)  A      N   <->   49 LEU   (  50-)  A      O      0.14    2.56  INTRA
  32 THR   (  33-)  A      OG1 <->   45 GLY   (  46-)  A      N      0.13    2.57  INTRA BF
 187 ALA   ( 188-)  A      CB  <->  220 PHE   ( 221-)  A      CE1    0.13    3.07  INTRA BL
 437 LYS   ( 438-)  A      NZ  <->  448 GLU   ( 449-)  A      OE1    0.12    2.58  INTRA BF
  94 ASN   (  95-)  A      N   <->  139 GLU   ( 140-)  A      O      0.11    2.59  INTRA BL
 537 PHE   ( 541-)  A      N   <->  553 ASN   ( 557-)  A      O      0.11    2.59  INTRA BL
 411 GLU   ( 412-)  A      OE1 <->  423 HIS   ( 424-)  A      NE2    0.11    2.59  INTRA BF
 262 VAL   ( 263-)  A      O   <->  287 ASN   ( 288-)  A      N      0.11    2.59  INTRA
 324 PRO   ( 325-)  A      O   <->  326 THR   ( 327-)  A      N      0.11    2.59  INTRA BL
  12 TYR   (  13-)  A      CD2 <->   48 MET   (  49-)  A      SD     0.11    3.29  INTRA
 401 GLN   ( 402-)  A      C   <->  402 VAL   ( 403-)  A      CG2    0.10    3.00  INTRA BF
 182 THR   ( 183-)  A      OG1 <->  225 ASN   ( 226-)  A      OD1    0.10    2.30  INTRA BL
 351 THR   ( 352-)  A      CG2 <->  352 ARG   ( 353-)  A      N      0.09    2.91  INTRA
  83 SER   (  84-)  A      O   <->  148 TYR   ( 149-)  A      N      0.09    2.61  INTRA BL
 304 GLY   ( 305-)  A      O   <->  306 TRP   ( 307-)  A      N      0.09    2.61  INTRA BF
 281 LEU   ( 282-)  A      CD1 <->  312 VAL   ( 313-)  A      CG2    0.08    3.12  INTRA
And so on for a total of 64 lines.

Packing, accessibility and threading

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.

 505 PHE   ( 506-)  A      -7.46
 530 TYR   ( 534-)  A      -6.53
 163 ARG   ( 164-)  A      -6.44
 244 GLU   ( 245-)  A      -6.23
 360 ARG   ( 361-)  A      -6.12
 190 ARG   ( 191-)  A      -5.91
 359 MET   ( 360-)  A      -5.90
 460 LEU   ( 461-)  A      -5.68
 559 ILE   ( 563-)  A      -5.62
 420 HIS   ( 421-)  A      -5.59
 218 ARG   ( 219-)  A      -5.56
 117 ARG   ( 118-)  A      -5.54
 483 ARG   ( 484-)  A      -5.47
  33 LEU   (  34-)  A      -5.43
 339 GLU   ( 340-)  A      -5.41
 146 GLN   ( 147-)  A      -5.33
 508 LEU   ( 512-)  A      -5.31
 205 ARG   ( 206-)  A      -5.22
 431 TYR   ( 432-)  A      -5.11
 336 ARG   ( 337-)  A      -5.09
 321 HIS   ( 322-)  A      -5.09
 563 SER   ( 567-)  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.

 558 LYS   ( 562-)  A       560 - SER    564- ( A)         -4.67

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.

 225 ASN   ( 226-)  A
 228 ASN   ( 229-)  A
 284 ASN   ( 285-)  A
 287 ASN   ( 288-)  A
 455 GLN   ( 456-)  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.

   9 ASP   (  10-)  A      N
  60 ARG   (  61-)  A      N
  70 GLU   (  71-)  A      N
  79 HIS   (  80-)  A      N
  84 SER   (  85-)  A      N
  85 LYS   (  86-)  A      N
  86 SER   (  87-)  A      OG
  91 GLY   (  92-)  A      N
  97 VAL   (  98-)  A      N
 106 ASN   ( 107-)  A      N
 110 ASN   ( 111-)  A      N
 118 THR   ( 119-)  A      N
 128 THR   ( 129-)  A      N
 136 VAL   ( 137-)  A      N
 144 GLY   ( 145-)  A      N
 147 GLY   ( 148-)  A      N
 153 GLU   ( 154-)  A      N
 167 PHE   ( 168-)  A      N
 190 ARG   ( 191-)  A      NE
 232 ARG   ( 233-)  A      N
 242 ARG   ( 243-)  A      NH1
 262 VAL   ( 263-)  A      N
 276 TYR   ( 277-)  A      N
 278 TRP   ( 279-)  A      NE1
 284 ASN   ( 285-)  A      N
And so on for a total of 51 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  71 ASN   (  72-)  A      OD1
  79 HIS   (  80-)  A      ND1
 289 ASP   ( 290-)  A      OD1
 393 ASN   ( 394-)  A      OD1
 523 HIS   ( 527-)  A      ND1

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+.

 572  NA   (1576-)  A     0.69   1.62 Scores about as good as  K *2
 573  NA   (1577-)  A     0.66   1.32 Scores about as good as  K *2
Since there are no waters, the water check has been skipped.

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.

 259 GLU   ( 260-)  A   H-bonding suggests Gln
 308 ASP   ( 309-)  A   H-bonding suggests Asn; but Alt-Rotamer
 417 GLU   ( 418-)  A   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.303
  2nd generation packing quality :  -1.426
  Ramachandran plot appearance   :  -2.839
  chi-1/chi-2 rotamer normality  :  -4.352 (bad)
  Backbone conformation          :  -0.031

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.369 (tight)
  Bond angles                    :   0.612 (tight)
  Omega angle restraints         :   1.355 (loose)
  Side chain planarity           :   0.325 (tight)
  Improper dihedral distribution :   0.561
  B-factor distribution          :   0.351
  Inside/Outside distribution    :   1.035

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :   0.5
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.369 (tight)
  Bond angles                    :   0.612 (tight)
  Omega angle restraints         :   1.355 (loose)
  Side chain planarity           :   0.325 (tight)
  Improper dihedral distribution :   0.561
  B-factor distribution          :   0.351
  Inside/Outside distribution    :   1.035
==============

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.