WHAT IF Check report

This file was created 2011-12-15 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 pdb1fe2.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 560 BMA   ( 673-)  A  -         OK
 561 BMA   ( 674-)  A  -         OK
 562 BOG   ( 750-)  A  -         OK
 563 BOG   ( 751-)  A  -         OK
 564 COH   ( 601-)  A  -         Atom types
 565 LAX   ( 700-)  A  -         OK
 566 BOG   ( 752-)  A  -         OK
 567 BMA   ( 675-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 554 NAG   ( 661-)  A  -   O4  bound to  555 NAG   ( 662-)  A  -   C1
 556 NAG   ( 671-)  A  -   O4  bound to  557 NAG   ( 672-)  A  -   C1
 557 NAG   ( 672-)  A  -   O4  bound to  560 BMA   ( 673-)  A  -   C1
 558 NAG   ( 681-)  A  -   O4  bound to  559 NAG   ( 682-)  A  -   C1

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'.

  48 ARG   (  79-)  A      CG
  48 ARG   (  79-)  A      CD
  48 ARG   (  79-)  A      NE
  48 ARG   (  79-)  A      CZ
  48 ARG   (  79-)  A      NH1
  48 ARG   (  79-)  A      NH2
  52 ARG   (  83-)  A      CG
  52 ARG   (  83-)  A      CD
  52 ARG   (  83-)  A      NE
  52 ARG   (  83-)  A      CZ
  52 ARG   (  83-)  A      NH1
  52 ARG   (  83-)  A      NH2
 137 LYS   ( 168-)  A      CG
 137 LYS   ( 168-)  A      CD
 137 LYS   ( 168-)  A      CE
 137 LYS   ( 168-)  A      NZ
 138 LYS   ( 169-)  A      CG
 138 LYS   ( 169-)  A      CD
 138 LYS   ( 169-)  A      CE
 138 LYS   ( 169-)  A      NZ
 139 GLN   ( 170-)  A      CG
 139 GLN   ( 170-)  A      CD
 139 GLN   ( 170-)  A      OE1
 139 GLN   ( 170-)  A      NE2
 142 ASP   ( 173-)  A      CG
And so on for a total of 95 lines.

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.

 208 GLU   ( 239-)  A    High
 249 PRO   ( 280-)  A    High
 250 PRO   ( 281-)  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

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.529 over 3970 bonds
Average difference in B over a bond : 1.64
RMS difference in B over a bond : 5.65

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.

  66 ARG   (  97-)  A
 149 ARG   ( 180-)  A
 428 ARG   ( 459-)  A

Warning: Tyrosine convention problem

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

  24 TYR   (  55-)  A
  99 TYR   ( 130-)  A
 211 TYR   ( 242-)  A
 223 TYR   ( 254-)  A
 324 TYR   ( 355-)  A
 342 TYR   ( 373-)  A
 354 TYR   ( 385-)  A
 373 TYR   ( 404-)  A
 386 TYR   ( 417-)  A
 444 TYR   ( 475-)  A
 464 TYR   ( 495-)  A
 513 TYR   ( 544-)  A

Warning: Phenylalanine convention problem

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

  57 PHE   (  88-)  A
  71 PHE   ( 102-)  A
  76 PHE   ( 107-)  A
 150 PHE   ( 181-)  A
 156 PHE   ( 187-)  A
 170 PHE   ( 201-)  A
 336 PHE   ( 367-)  A
 439 PHE   ( 470-)  A
 487 PHE   ( 518-)  A
 498 PHE   ( 529-)  A
 549 PHE   ( 580-)  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.

  22 ASP   (  53-)  A
  70 ASP   ( 101-)  A
 205 ASP   ( 236-)  A
 283 ASP   ( 314-)  A
 362 ASP   ( 393-)  A
 385 ASP   ( 416-)  A
 410 ASP   ( 441-)  A
 466 ASP   ( 497-)  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.

  42 GLU   (  73-)  A
 259 GLU   ( 290-)  A
 277 GLU   ( 308-)  A
 288 GLU   ( 319-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 374 GLU   ( 405-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 462 GLU   ( 493-)  A
 522 GLU   ( 553-)  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.

   1 PRO   (  32-)  A      N    CA   CB  107.86    4.4
 112 SER   ( 143-)  A      N    CA   C   122.68    4.1

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.

  22 ASP   (  53-)  A
  42 GLU   (  73-)  A
  66 ARG   (  97-)  A
  70 ASP   ( 101-)  A
 149 ARG   ( 180-)  A
 205 ASP   ( 236-)  A
 259 GLU   ( 290-)  A
 277 GLU   ( 308-)  A
 283 ASP   ( 314-)  A
 288 GLU   ( 319-)  A
 308 GLU   ( 339-)  A
 333 GLU   ( 364-)  A
 362 ASP   ( 393-)  A
 374 GLU   ( 405-)  A
 385 ASP   ( 416-)  A
 410 ASP   ( 441-)  A
 428 ARG   ( 459-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 462 GLU   ( 493-)  A
 466 ASP   ( 497-)  A
 522 GLU   ( 553-)  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.

 112 SER   ( 143-)  A    6.91
 533 LEU   ( 564-)  A    5.88
  55 PRO   (  86-)  A    4.70
 306 ILE   ( 337-)  A    4.43
 144 GLU   ( 175-)  A    4.11
 117 TYR   ( 148-)  A    4.03

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 : 1.629

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 108 TRP   ( 139-)  A      CB   4.10
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -5.023

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -5.023

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.

 250 PRO   ( 281-)  A    -3.0
 354 TYR   ( 385-)  A    -2.7
 252 SER   ( 283-)  A    -2.6
 105 TYR   ( 136-)  A    -2.5
 380 THR   ( 411-)  A    -2.5
 520 GLY   ( 551-)  A    -2.4
  98 THR   ( 129-)  A    -2.4
  87 THR   ( 118-)  A    -2.4
 199 LEU   ( 230-)  A    -2.4
  38 CYS   (  69-)  A    -2.3
 223 TYR   ( 254-)  A    -2.3
 487 PHE   ( 518-)  A    -2.3
 253 GLN   ( 284-)  A    -2.2
  75 THR   ( 106-)  A    -2.2
 278 HIS   ( 309-)  A    -2.2
 416 VAL   ( 447-)  A    -2.2
 129 PRO   ( 160-)  A    -2.2
  66 ARG   (  97-)  A    -2.2
 260 VAL   ( 291-)  A    -2.1
 525 PHE   ( 556-)  A    -2.1
 366 VAL   ( 397-)  A    -2.1
 378 PHE   ( 409-)  A    -2.1
 241 LEU   ( 272-)  A    -2.1
  15 ILE   (  46-)  A    -2.1
 247 GLY   ( 278-)  A    -2.1
 402 ARG   ( 433-)  A    -2.1
 345 ARG   ( 376-)  A    -2.1
   8 TYR   (  39-)  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 TYR   (  39-)  A  Poor phi/psi
  12 HIS   (  43-)  A  Poor phi/psi
  13 GLN   (  44-)  A  Poor phi/psi
  38 CYS   (  69-)  A  Poor phi/psi
  66 ARG   (  97-)  A  Poor phi/psi
  86 LEU   ( 117-)  A  Poor phi/psi
  87 THR   ( 118-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  A  Poor phi/psi
 147 SER   ( 178-)  A  Poor phi/psi
 154 ARG   ( 185-)  A  Poor phi/psi
 195 HIS   ( 226-)  A  Poor phi/psi
 200 GLY   ( 231-)  A  Poor phi/psi
 206 ASN   ( 237-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 223 TYR   ( 254-)  A  Poor phi/psi
 227 ASN   ( 258-)  A  Poor phi/psi
 236 GLU   ( 267-)  A  Poor phi/psi
 237 GLU   ( 268-)  A  Poor phi/psi
 239 PRO   ( 270-)  A  Poor phi/psi
 242 MET   ( 273-)  A  Poor phi/psi
 250 PRO   ( 281-)  A  Poor phi/psi
 261 PHE   ( 292-)  A  Poor phi/psi
 361 PRO   ( 392-)  A  Poor phi/psi
 363 SER   ( 394-)  A  Poor phi/psi
 378 PHE   ( 409-)  A  Poor phi/psi
 400 ALA   ( 431-)  A  Poor phi/psi
 407 ARG   ( 438-)  A  Poor phi/psi
 428 ARG   ( 459-)  A  Poor phi/psi
 453 GLU   ( 484-)  A  Poor phi/psi
 454 LYS   ( 485-)  A  Poor phi/psi
 455 GLU   ( 486-)  A  Poor phi/psi
 465 GLY   ( 496-)  A  Poor phi/psi
 470 LEU   ( 501-)  A  Poor phi/psi
 484 ASN   ( 515-)  A  Poor phi/psi
 514 TRP   ( 545-)  A  Poor phi/psi
 520 GLY   ( 551-)  A  Poor phi/psi
 537 VAL   ( 568-)  A  Poor phi/psi
 545 PRO   ( 576-)  A  Poor phi/psi
 548 SER   ( 579-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.062

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 : -4.062

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.

 110 SER   ( 141-)  A    0.35
 424 SER   ( 455-)  A    0.39
  56 SER   (  87-)  A    0.39

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!

   5 CYS   (  36-)  A      0
   6 CYS   (  37-)  A      0
   7 TYR   (  38-)  A      0
   8 TYR   (  39-)  A      0
   9 PRO   (  40-)  A      0
  10 CYS   (  41-)  A      0
  11 GLN   (  42-)  A      0
  12 HIS   (  43-)  A      0
  13 GLN   (  44-)  A      0
  19 PHE   (  50-)  A      0
  21 LEU   (  52-)  A      0
  22 ASP   (  53-)  A      0
  28 CYS   (  59-)  A      0
  29 THR   (  60-)  A      0
  30 ARG   (  61-)  A      0
  31 THR   (  62-)  A      0
  34 SER   (  65-)  A      0
  36 PRO   (  67-)  A      0
  37 ASN   (  68-)  A      0
  38 CYS   (  69-)  A      0
  39 THR   (  70-)  A      0
  63 THR   (  94-)  A      0
  64 HIS   (  95-)  A      0
  74 ALA   ( 105-)  A      0
  94 PRO   ( 125-)  A      0
And so on for a total of 236 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 : 1.166

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]

 233 PRO   ( 264-)  A    0.45 HIGH
 239 PRO   ( 270-)  A    0.46 HIGH

Warning: Unusual PRO puckering phases

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

   1 PRO   (  32-)  A    51.1 half-chair C-delta/C-gamma (54 degrees)
 358 PRO   ( 389-)  A  -134.5 half-chair C-delta/C-gamma (-126 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.

 561 BMA   ( 674-)  A      O3  <->  567 BMA   ( 675-)  A      C1     0.99    1.41  INTRA BF
 561 BMA   ( 674-)  A      C3  <->  567 BMA   ( 675-)  A      C1     0.70    2.50  INTRA BF
 248 ILE   ( 279-)  A      C   <->  250 PRO   ( 281-)  A      CD     0.48    2.72  INTRA BF
 357 HIS   ( 388-)  A      NE2 <->  564 COH   ( 601-)  A      NC     0.40    2.60  INTRA BF
 381 SER   ( 412-)  A      O   <->  385 ASP   ( 416-)  A      N      0.39    2.31  INTRA
 227 ASN   ( 258-)  A      ND2 <->  384 VAL   ( 415-)  A      CG1    0.37    2.73  INTRA BF
 214 ARG   ( 245-)  A      NH2 <->  294 ASP   ( 325-)  A      OD2    0.34    2.36  INTRA BF
 173 HIS   ( 204-)  A      ND1 <->  270 TYR   ( 301-)  A      CB     0.34    2.76  INTRA BL
  65 GLY   (  96-)  A      O   <->   67 TRP   (  98-)  A      N      0.34    2.36  INTRA BF
 411 HIS   ( 442-)  A      CD2 <->  412 HIS   ( 443-)  A      N      0.34    2.66  INTRA BF
 119 ARG   ( 150-)  A      NH2 <->  348 MET   ( 379-)  A      SD     0.33    2.97  INTRA BL
 120 ILE   ( 151-)  A      CG2 <->  438 ARG   ( 469-)  A      NH1    0.32    2.78  INTRA BL
 154 ARG   ( 185-)  A      NH1 <->  407 ARG   ( 438-)  A      NH1    0.32    2.53  INTRA BF
 372 SER   ( 403-)  A      N   <->  375 GLN   ( 406-)  A      OE1    0.32    2.38  INTRA
 220 LYS   ( 251-)  A      CB  <->  279 ASN   ( 310-)  A      ND2    0.31    2.79  INTRA
 453 GLU   ( 484-)  A      OE1 <->  456 MET   ( 487-)  A      N      0.31    2.39  INTRA
 164 ASN   ( 195-)  A      ND2 <->  396 SER   ( 427-)  A      CA     0.29    2.81  INTRA
 173 HIS   ( 204-)  A      CD2 <->  201 HIS   ( 232-)  A      CD2    0.29    2.91  INTRA BF
 150 PHE   ( 181-)  A      O   <->  407 ARG   ( 438-)  A      N      0.28    2.42  INTRA
 125 PRO   ( 156-)  A      CB  <->  128 CYS   ( 159-)  A      SG     0.28    3.12  INTRA BF
 111 PHE   ( 142-)  A      O   <->  345 ARG   ( 376-)  A      NH2    0.27    2.43  INTRA BL
 211 TYR   ( 242-)  A      CD1 <->  216 PHE   ( 247-)  A      CZ     0.27    2.93  INTRA
 235 VAL   ( 266-)  A      CG2 <->  253 GLN   ( 284-)  A      NE2    0.27    2.83  INTRA BF
 461 GLU   ( 492-)  A      O   <->  465 GLY   ( 496-)  A      N      0.26    2.44  INTRA
  89 ARG   ( 120-)  A      NH1 <->  565 LAX   ( 700-)  A      O2     0.25    2.45  INTRA BL
And so on for a total of 264 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.

 246 ARG   ( 277-)  A      -8.80
  30 ARG   (  61-)  A      -7.48
 241 LEU   ( 272-)  A      -6.75
 140 LEU   ( 171-)  A      -6.65
 343 ARG   ( 374-)  A      -6.63
 156 PHE   ( 187-)  A      -6.07
  21 LEU   (  52-)  A      -6.02
   7 TYR   (  38-)  A      -5.95
 248 ILE   ( 279-)  A      -5.92
 105 TYR   ( 136-)  A      -5.62
 216 PHE   ( 247-)  A      -5.59
 154 ARG   ( 185-)  A      -5.53
 149 ARG   ( 180-)  A      -5.53
 126 ARG   ( 157-)  A      -5.46
 185 MET   ( 216-)  A      -5.46
 339 GLN   ( 370-)  A      -5.45
  66 ARG   (  97-)  A      -5.45
 244 TYR   ( 275-)  A      -5.42
 453 GLU   ( 484-)  A      -5.28
   2 VAL   (  33-)  A      -5.26
 438 ARG   ( 469-)  A      -5.16
 402 ARG   ( 433-)  A      -5.16
 106 ILE   ( 137-)  A      -5.10
 243 HIS   ( 274-)  A      -5.05
 153 ARG   ( 184-)  A      -5.03

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.

 246 ARG   ( 277-)  A       248 - ILE    279- ( A)         -6.32

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 559 : -1.528

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.

 217 LYS   ( 248-)  A   -3.35
 137 LYS   ( 168-)  A   -3.12
 105 TYR   ( 136-)  A   -2.94
 365 ARG   ( 396-)  A   -2.85
 442 LYS   ( 473-)  A   -2.83
  52 ARG   (  83-)  A   -2.82
 344 ASN   ( 375-)  A   -2.81
 155 LYS   ( 186-)  A   -2.63
 413 ILE   ( 444-)  A   -2.54
 184 LYS   ( 215-)  A   -2.52

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.

 136 GLY   ( 167-)  A     -  139 GLN   ( 170-)  A        -1.97
 333 GLU   ( 364-)  A     -  336 PHE   ( 367-)  A        -1.94

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.

 568 HOH   ( 800 )  A      O
 568 HOH   ( 849 )  A      O
 568 HOH   ( 859 )  A      O
Bound group on Asn; dont flip   37 ASN  (  68-) A
Bound to:  554 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to:  556 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to:  558 NAG  ( 681-) A
Metal-coordinating Histidine residue 357 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.

 177 GLN   ( 208-)  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.

   5 CYS   (  36-)  A      N
  10 CYS   (  41-)  A      N
  18 ARG   (  49-)  A      NH1
  37 ASN   (  68-)  A      N
  44 TRP   (  75-)  A      N
  66 ARG   (  97-)  A      NE
  67 TRP   (  98-)  A      N
  89 ARG   ( 120-)  A      NH2
 100 ASN   ( 131-)  A      ND2
 101 ILE   ( 132-)  A      N
 105 TYR   ( 136-)  A      N
 106 ILE   ( 137-)  A      N
 107 SER   ( 138-)  A      OG
 108 TRP   ( 139-)  A      N
 109 GLU   ( 140-)  A      N
 119 ARG   ( 150-)  A      NH1
 119 ARG   ( 150-)  A      NH2
 123 SER   ( 154-)  A      N
 132 MET   ( 163-)  A      N
 153 ARG   ( 184-)  A      NE
 163 THR   ( 194-)  A      OG1
 164 ASN   ( 195-)  A      ND2
 172 GLN   ( 203-)  A      NE2
 173 HIS   ( 204-)  A      NE2
 177 GLN   ( 208-)  A      NE2
And so on for a total of 63 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.

 173 HIS   ( 204-)  A      ND1
 259 GLU   ( 290-)  A      OE1
 289 HIS   ( 320-)  A      NE2
 299 GLN   ( 330-)  A      OE1
 308 GLU   ( 339-)  A      OE1
 352 GLN   ( 383-)  A      OE1
 482 HIS   ( 513-)  A      ND1

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.

 308 GLU   ( 339-)  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 :  -2.570
  2nd generation packing quality :  -2.990
  Ramachandran plot appearance   :  -5.023 (bad)
  chi-1/chi-2 rotamer normality  :  -4.062 (bad)
  Backbone conformation          :  -1.260

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.389 (tight)
  Bond angles                    :   0.703
  Omega angle restraints         :   0.212 (tight)
  Side chain planarity           :   0.262 (tight)
  Improper dihedral distribution :   0.730
  B-factor distribution          :   1.529 (loose)
  Inside/Outside distribution    :   1.104

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 : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.4
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.389 (tight)
  Bond angles                    :   0.703
  Omega angle restraints         :   0.212 (tight)
  Side chain planarity           :   0.262 (tight)
  Improper dihedral distribution :   0.730
  B-factor distribution          :   1.529 (loose)
  Inside/Outside distribution    :   1.104
==============

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.