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 pdb1u67.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.

 558 NDG   ( 662-)  A  -         OK
 559 BMA   ( 673-)  A  -         OK
 560 BOG   ( 750-)  A  -         OK
 561 BOG   ( 751-)  A  -         OK
 562 BOG   ( 752-)  A  -         OK
 563 COH   ( 601-)  A  -         Atom types
 564 ACD   ( 700-)  A  -         OK
 565 BOG   ( 753-)  A  -         OK
 566 NDG   ( 682-)  A  -         OK
 567 BMA   ( 674-)  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  558 NDG   ( 662-)  A  -   C1
 555 NAG   ( 671-)  A  -   O4  bound to  556 NAG   ( 672-)  A  -   C1
 556 NAG   ( 672-)  A  -   O4  bound to  559 BMA   ( 673-)  A  -   C1
 557 NAG   ( 681-)  A  -   O4  bound to  566 NDG   ( 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'.

  31 THR   (  62-)  A      OG1
  31 THR   (  62-)  A      CG2
  34 SER   (  65-)  A      OG
  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
  54 SER   (  85-)  A      OG
  58 ILE   (  89-)  A      CG1
  58 ILE   (  89-)  A      CG2
  58 ILE   (  89-)  A      CD1
  66 ARG   (  97-)  A      CG
  66 ARG   (  97-)  A      CD
  66 ARG   (  97-)  A      NE
  66 ARG   (  97-)  A      CZ
  66 ARG   (  97-)  A      NH1
  66 ARG   (  97-)  A      NH2
And so on for a total of 180 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.

   1 PRO   (  32-)  A    High
   5 CYS   (  36-)  A    High
 187 PRO   ( 218-)  A    High
 192 ALA   ( 223-)  A    High
 218 ASP   ( 249-)  A    High
 247 GLY   ( 278-)  A    High
 249 PRO   ( 280-)  A    High
 250 PRO   ( 281-)  A    High
 251 GLN   ( 282-)  A    High
 252 SER   ( 283-)  A    High
 368 PRO   ( 399-)  A    High
 394 ALA   ( 425-)  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 : 1.845 over 3849 bonds
Average difference in B over a bond : 2.02
RMS difference in B over a bond : 7.28

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.

 149 ARG   ( 180-)  A
 154 ARG   ( 185-)  A
 402 ARG   ( 433-)  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

  99 TYR   ( 130-)  A
 211 TYR   ( 242-)  A
 223 TYR   ( 254-)  A
 244 TYR   ( 275-)  A
 324 TYR   ( 355-)  A
 342 TYR   ( 373-)  A
 354 TYR   ( 385-)  A
 371 TYR   ( 402-)  A
 373 TYR   ( 404-)  A
 386 TYR   ( 417-)  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.

  19 PHE   (  50-)  A
  57 PHE   (  88-)  A
  71 PHE   ( 102-)  A
  76 PHE   ( 107-)  A
 150 PHE   ( 181-)  A
 156 PHE   ( 187-)  A
 167 PHE   ( 198-)  A
 170 PHE   ( 201-)  A
 178 PHE   ( 209-)  A
 325 PHE   ( 356-)  A
 336 PHE   ( 367-)  A
 447 PHE   ( 478-)  A
 487 PHE   ( 518-)  A
 498 PHE   ( 529-)  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
  79 ASP   ( 110-)  A
 205 ASP   ( 236-)  A
 283 ASP   ( 314-)  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
 109 GLU   ( 140-)  A
 277 GLU   ( 308-)  A
 288 GLU   ( 319-)  A
 308 GLU   ( 339-)  A
 316 GLU   ( 347-)  A
 423 GLU   ( 454-)  A
 449 GLU   ( 480-)  A
 479 GLU   ( 510-)  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.

  98 THR   ( 129-)  A      N    CA   C   123.14    4.3
 117 TYR   ( 148-)  A      N    CA   C    96.90   -5.1
 357 HIS   ( 388-)  A      NE2  CD2  CG  110.93    4.4

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
  79 ASP   ( 110-)  A
 109 GLU   ( 140-)  A
 149 ARG   ( 180-)  A
 154 ARG   ( 185-)  A
 205 ASP   ( 236-)  A
 277 GLU   ( 308-)  A
 283 ASP   ( 314-)  A
 288 GLU   ( 319-)  A
 308 GLU   ( 339-)  A
 316 GLU   ( 347-)  A
 402 ARG   ( 433-)  A
 423 GLU   ( 454-)  A
 428 ARG   ( 459-)  A
 449 GLU   ( 480-)  A
 466 ASP   ( 497-)  A
 479 GLU   ( 510-)  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.

 533 LEU   ( 564-)  A    6.23
 117 TYR   ( 148-)  A    5.45
 112 SER   ( 143-)  A    5.32
 315 GLU   ( 346-)  A    5.15
 392 VAL   ( 423-)  A    4.59
 154 ARG   ( 185-)  A    4.16
  55 PRO   (  86-)  A    4.11
  98 THR   ( 129-)  A    4.07
 538 CYS   ( 569-)  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 : 1.620

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 : -5.089

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.

 432 PHE   ( 463-)  A    -3.0
 487 PHE   ( 518-)  A    -2.9
 105 TYR   ( 136-)  A    -2.8
 117 TYR   ( 148-)  A    -2.7
  87 THR   ( 118-)  A    -2.7
  43 ILE   (  74-)  A    -2.6
 125 PRO   ( 156-)  A    -2.6
 276 ARG   ( 307-)  A    -2.5
 291 THR   ( 322-)  A    -2.5
 345 ARG   ( 376-)  A    -2.4
  89 ARG   ( 120-)  A    -2.4
 520 GLY   ( 551-)  A    -2.4
 354 TYR   ( 385-)  A    -2.4
  45 THR   (  76-)  A    -2.3
 545 PRO   ( 576-)  A    -2.3
 190 THR   ( 221-)  A    -2.3
  63 THR   (  94-)  A    -2.3
 133 GLY   ( 164-)  A    -2.2
 114 VAL   ( 145-)  A    -2.2
 197 VAL   ( 228-)  A    -2.2
 129 PRO   ( 160-)  A    -2.2
 504 LEU   ( 535-)  A    -2.2
 253 GLN   ( 284-)  A    -2.2
  75 THR   ( 106-)  A    -2.2
 223 TYR   ( 254-)  A    -2.1
 173 HIS   ( 204-)  A    -2.1
 260 VAL   ( 291-)  A    -2.1
 453 GLU   ( 484-)  A    -2.1
 525 PHE   ( 556-)  A    -2.1
 278 HIS   ( 309-)  A    -2.1
 247 GLY   ( 278-)  A    -2.1
 146 LEU   ( 177-)  A    -2.1
  98 THR   ( 129-)  A    -2.1
 213 LEU   ( 244-)  A    -2.0
   8 TYR   (  39-)  A    -2.0
 249 PRO   ( 280-)  A    -2.0
  39 THR   (  70-)  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
  30 ARG   (  61-)  A  Poor phi/psi
  38 CYS   (  69-)  A  Poor phi/psi
  64 HIS   (  95-)  A  Poor phi/psi
  86 LEU   ( 117-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
 129 PRO   ( 160-)  A  Poor phi/psi
 134 THR   ( 165-)  A  Poor phi/psi
 138 LYS   ( 169-)  A  Poor phi/psi
 154 ARG   ( 185-)  A  Poor phi/psi
 195 HIS   ( 226-)  A  Poor phi/psi
 199 LEU   ( 230-)  A  Poor phi/psi
 200 GLY   ( 231-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 223 TYR   ( 254-)  A  Poor phi/psi
 227 ASN   ( 258-)  A  Poor phi/psi
 239 PRO   ( 270-)  A  Poor phi/psi
 246 ARG   ( 277-)  A  Poor phi/psi
 250 PRO   ( 281-)  A  Poor phi/psi
 252 SER   ( 283-)  A  Poor phi/psi
 261 PHE   ( 292-)  A  Poor phi/psi
 297 LEU   ( 328-)  A  Poor phi/psi
 361 PRO   ( 392-)  A  Poor phi/psi
 370 ASP   ( 401-)  A  Poor phi/psi
 378 PHE   ( 409-)  A  Poor phi/psi
 389 GLU   ( 420-)  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
 462 GLU   ( 493-)  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
 538 CYS   ( 569-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.942

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.942

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.

 424 SER   ( 455-)  A    0.37
 110 SER   ( 141-)  A    0.38

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
   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
  28 CYS   (  59-)  A      0
  29 THR   (  60-)  A      0
  30 ARG   (  61-)  A      0
  31 THR   (  62-)  A      0
  33 TYR   (  64-)  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
  43 ILE   (  74-)  A      0
  63 THR   (  94-)  A      0
  64 HIS   (  95-)  A      0
  66 ARG   (  97-)  A      0
  74 ALA   ( 105-)  A      0
And so on for a total of 229 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 : 1.165

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!

 297 LEU   ( 328-)  A   1.77   49

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]

 511 PRO   ( 542-)  A    0.45 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].

 358 PRO   ( 389-)  A  -116.7 envelop C-gamma (-108 degrees)
 497 PRO   ( 528-)  A  -117.0 envelop C-gamma (-108 degrees)
 507 PRO   ( 538-)  A  -112.8 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

 557 NAG   ( 681-)  A      O4  <->  566 NDG   ( 682-)  A      C1     1.01    1.39  INTRA B3
 559 BMA   ( 673-)  A      O6  <->  567 BMA   ( 674-)  A      C1     1.00    1.40  INTRA BF
 559 BMA   ( 673-)  A      C6  <->  567 BMA   ( 674-)  A      C1     0.84    2.36  INTRA BF
 557 NAG   ( 681-)  A      C4  <->  566 NDG   ( 682-)  A      C1     0.70    2.50  INTRA
 119 ARG   ( 150-)  A      NH2 <->  348 MET   ( 379-)  A      SD     0.52    2.78  INTRA BL
  82 MET   ( 113-)  A      SD  <->  329 LYS   ( 360-)  A      N      0.45    2.85  INTRA BL
  42 GLU   (  73-)  A      N   <->   45 THR   (  76-)  A      CG2    0.43    2.67  INTRA BL
 357 HIS   ( 388-)  A      NE2 <->  563 COH   ( 601-)  A      NC     0.43    2.57  INTRA BF
 245 PRO   ( 276-)  A      O   <->  247 GLY   ( 278-)  A      N      0.42    2.28  INTRA BF
 111 PHE   ( 142-)  A      O   <->  345 ARG   ( 376-)  A      NH2    0.41    2.29  INTRA BL
 119 ARG   ( 150-)  A      NE  <->  348 MET   ( 379-)  A      SD     0.37    2.93  INTRA BL
 473 TYR   ( 504-)  A      N   <->  568 HOH   ( 822 )  A      O      0.36    2.34  INTRA
 352 GLN   ( 383-)  A      NE2 <->  429 LEU   ( 460-)  A      CD1    0.36    2.74  INTRA
 411 HIS   ( 442-)  A      NE2 <->  412 HIS   ( 443-)  A      CE1    0.34    2.76  INTRA BF
 125 PRO   ( 156-)  A      CB  <->  128 CYS   ( 159-)  A      SG     0.33    3.07  INTRA
 453 GLU   ( 484-)  A      OE2 <->  456 MET   ( 487-)  A      N      0.33    2.37  INTRA BF
 173 HIS   ( 204-)  A      NE2 <->  201 HIS   ( 232-)  A      CD2    0.33    2.77  INTRA
 470 LEU   ( 501-)  A      CD2 <->  471 GLU   ( 502-)  A      N      0.33    2.67  INTRA BF
 302 ARG   ( 333-)  A      O   <->  305 LEU   ( 336-)  A      N      0.32    2.38  INTRA BL
 119 ARG   ( 150-)  A      NH2 <->  429 LEU   ( 460-)  A      CD2    0.31    2.79  INTRA BL
 248 ILE   ( 279-)  A      C   <->  250 PRO   ( 281-)  A      CD     0.31    2.89  INTRA BF
 173 HIS   ( 204-)  A      CD2 <->  201 HIS   ( 232-)  A      CD2    0.31    2.89  INTRA
  76 PHE   ( 107-)  A      C   <->   78 ARG   ( 109-)  A      N      0.30    2.60  INTRA
 173 HIS   ( 204-)  A      ND1 <->  270 TYR   ( 301-)  A      CB     0.30    2.80  INTRA BL
 377 LEU   ( 408-)  A      O   <->  379 ASN   ( 410-)  A      N      0.29    2.41  INTRA BL
And so on for a total of 260 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.

  30 ARG   (  61-)  A      -7.95
 244 TYR   ( 275-)  A      -7.42
   7 TYR   (  38-)  A      -6.67
 402 ARG   ( 433-)  A      -6.66
 339 GLN   ( 370-)  A      -6.50
 140 LEU   ( 171-)  A      -6.50
 156 PHE   ( 187-)  A      -6.33
 343 ARG   ( 374-)  A      -6.32
 241 LEU   ( 272-)  A      -6.05
 185 MET   ( 216-)  A      -5.75
 154 ARG   ( 185-)  A      -5.71
  21 LEU   (  52-)  A      -5.67
 132 MET   ( 163-)  A      -5.66
 254 MET   ( 285-)  A      -5.65
 216 PHE   ( 247-)  A      -5.46
 149 ARG   ( 180-)  A      -5.44
 105 TYR   ( 136-)  A      -5.35
   2 VAL   (  33-)  A      -5.24
 345 ARG   ( 376-)  A      -5.15
 438 ARG   ( 469-)  A      -5.13
 253 GLN   ( 284-)  A      -5.11
 106 ILE   ( 137-)  A      -5.11
 135 LYS   ( 166-)  A      -5.11
 153 ARG   ( 184-)  A      -5.08
 288 GLU   ( 319-)  A      -5.02
 222 LYS   ( 253-)  A      -5.01

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.

 343 ARG   ( 374-)  A       345 - ARG    376- ( A)         -5.27

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 - 557 : -1.759

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   -3.44
  52 ARG   (  83-)  A   -2.88
 244 TYR   ( 275-)  A   -2.72
 139 GLN   ( 170-)  A   -2.70
 365 ARG   ( 396-)  A   -2.67
 467 ILE   ( 498-)  A   -2.65
 334 LEU   ( 365-)  A   -2.58
 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        -1.87
 152 LEU   ( 183-)  A     -  155 LYS   ( 186-)  A        -1.83
 245 PRO   ( 276-)  A     -  248 ILE   ( 279-)  A        -2.04
 333 GLU   ( 364-)  A     -  336 PHE   ( 367-)  A        -1.98
 452 GLY   ( 483-)  A     -  455 GLU   ( 486-)  A        -1.71

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   ( 809 )  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:  555 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to:  557 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.

 176 HIS   ( 207-)  A
 177 GLN   ( 208-)  A
 206 ASN   ( 237-)  A
 408 ASN   ( 439-)  A
 411 HIS   ( 442-)  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.

   8 TYR   (  39-)  A      N
  10 CYS   (  41-)  A      N
  18 ARG   (  49-)  A      NH1
  32 GLY   (  63-)  A      N
  33 TYR   (  64-)  A      N
  38 CYS   (  69-)  A      N
  40 ILE   (  71-)  A      N
  43 ILE   (  74-)  A      N
  44 TRP   (  75-)  A      N
  52 ARG   (  83-)  A      N
  67 TRP   (  98-)  A      N
  89 ARG   ( 120-)  A      NE
 100 ASN   ( 131-)  A      ND2
 101 ILE   ( 132-)  A      N
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      OG
 119 ARG   ( 150-)  A      NH1
 119 ARG   ( 150-)  A      NH2
 123 SER   ( 154-)  A      N
 132 MET   ( 163-)  A      N
 154 ARG   ( 185-)  A      N
 154 ARG   ( 185-)  A      NE
 161 GLN   ( 192-)  A      N
 164 ASN   ( 195-)  A      ND2
 172 GLN   ( 203-)  A      NE2
And so on for a total of 75 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.

 159 ASP   ( 190-)  A      OD1
 258 GLN   ( 289-)  A      OE1
 277 GLU   ( 308-)  A      OE2
 289 HIS   ( 320-)  A      NE2
 308 GLU   ( 339-)  A      OE1
 355 HIS   ( 386-)  A      ND1
 482 HIS   ( 513-)  A      ND1

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 :  -3.148
  2nd generation packing quality :  -3.640 (poor)
  Ramachandran plot appearance   :  -5.089 (bad)
  chi-1/chi-2 rotamer normality  :  -3.942 (poor)
  Backbone conformation          :  -1.240

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.373 (tight)
  Bond angles                    :   0.700
  Omega angle restraints         :   0.212 (tight)
  Side chain planarity           :   0.243 (tight)
  Improper dihedral distribution :   0.656
  B-factor distribution          :   1.845 (loose)
  Inside/Outside distribution    :   1.107

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 :  -1.9
  2nd generation packing quality :  -1.4
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.373 (tight)
  Bond angles                    :   0.700
  Omega angle restraints         :   0.212 (tight)
  Side chain planarity           :   0.243 (tight)
  Improper dihedral distribution :   0.656
  B-factor distribution          :   1.845 (loose)
  Inside/Outside distribution    :   1.107
==============

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.