WHAT IF Check report

This file was created 2012-01-25 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 pdb2iux.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 583 NXA   (1624-)  A  -
 584 ACT   (1620-)  A  -

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 112 VAL   ( 151-)  A
 301 MET   ( 340-)  A

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'.

  25 GLU   (  64-)  A      CG
  25 GLU   (  64-)  A      CD
  25 GLU   (  64-)  A      OE1
  25 GLU   (  64-)  A      OE2
 259 SER   ( 298-)  A      OG
 268 LYS   ( 307-)  A      CG
 268 LYS   ( 307-)  A      CD
 268 LYS   ( 307-)  A      CE
 268 LYS   ( 307-)  A      NZ
 324 LYS   ( 363-)  A      CE
 324 LYS   ( 363-)  A      NZ
 386 LYS   ( 425-)  A      CE
 386 LYS   ( 425-)  A      NZ

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 447 SER   ( 487-)  A    0.50
 557 LYS   ( 597-)  A    0.50

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

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.

 134 ARG   ( 173-)  A
 147 ARG   ( 186-)  A
 152 ARG   ( 191-)  A
 182 ARG   ( 221-)  A
 214 ARG   ( 253-)  A
 430 ARG   ( 470-)  A
 449 ARG   ( 489-)  A

Warning: Tyrosine convention problem

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

 107 TYR   ( 146-)  A
 136 TYR   ( 175-)  A
 174 TYR   ( 213-)  A
 220 TYR   ( 259-)  A
 321 TYR   ( 360-)  A
 351 TYR   ( 390-)  A
 441 TYR   ( 481-)  A
 452 TYR   ( 492-)  A
 483 TYR   ( 523-)  A
 555 TYR   ( 595-)  A

Warning: Phenylalanine convention problem

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

 157 PHE   ( 196-)  A
 277 PHE   ( 316-)  A
 283 PHE   ( 322-)  A
 284 PHE   ( 323-)  A
 352 PHE   ( 391-)  A
 432 PHE   ( 472-)  A
 556 PHE   ( 596-)  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.

 282 ASP   ( 321-)  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.

   4 GLU   (  43-)  A
  94 GLU   ( 133-)  A
 104 GLU   ( 143-)  A
 163 GLU   ( 202-)  A
 264 GLU   ( 303-)  A
 303 GLU   ( 342-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 578 NAG   (1618-)  A      C8   C7    1.32   -4.2
 579 NAG   (1619-)  A      C8   C7    1.32   -4.2

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.

   4 GLU   (  43-)  A
  94 GLU   ( 133-)  A
 104 GLU   ( 143-)  A
 134 ARG   ( 173-)  A
 147 ARG   ( 186-)  A
 152 ARG   ( 191-)  A
 163 GLU   ( 202-)  A
 182 ARG   ( 221-)  A
 214 ARG   ( 253-)  A
 264 GLU   ( 303-)  A
 282 ASP   ( 321-)  A
 303 GLU   ( 342-)  A
 430 ARG   ( 470-)  A
 449 ARG   ( 489-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 115 PRO   ( 154-)  A      N     -6.0   -22.27    -2.48
 545 PRO   ( 585-)  A      N     -7.5   -27.23    -2.48
 577 PRO   ( 617-)  A      N     -8.2   -29.22    -2.48
The average deviation= 0.726

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.

 373 ALA   ( 412-)  A    5.77
 125 ASP   ( 164-)  A    4.76
 414 LYS   ( 454-)  A    4.74
 489 ILE   ( 529-)  A    4.73
 251 VAL   ( 290-)  A    4.63
 453 GLN   ( 493-)  A    4.62
 447 SER   ( 487-)  A    4.37
 233 ALA   ( 272-)  A    4.30
 534 TRP   ( 574-)  A    4.24
 257 ALA   ( 296-)  A    4.14
  65 VAL   ( 104-)  A    4.10
 426 GLN   ( 466-)  A    4.09

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 : 1.591

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.

 441 TYR   ( 481-)  A    -2.8
 545 PRO   ( 585-)  A    -2.7
 124 PRO   ( 163-)  A    -2.5
 481 ILE   ( 521-)  A    -2.5
 355 TYR   ( 394-)  A    -2.4
 573 LYS   ( 613-)  A    -2.4
 385 PRO   ( 424-)  A    -2.4
 186 GLU   ( 225-)  A    -2.3
 201 LEU   ( 240-)  A    -2.1
 114 HIS   ( 153-)  A    -2.1
 115 PRO   ( 154-)  A    -2.1
 398 GLY   ( 438-)  A    -2.1
 544 GLN   ( 584-)  A    -2.0
 329 LYS   ( 368-)  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.

  84 GLU   ( 123-)  A  Poor phi/psi
 114 HIS   ( 153-)  A  PRO omega poor
 115 PRO   ( 154-)  A  omega poor
 117 GLY   ( 156-)  A  Poor phi/psi, omega poor
 123 GLU   ( 162-)  A  PRO omega poor
 157 PHE   ( 196-)  A  omega poor
 241 ALA   ( 280-)  A  Poor phi/psi
 298 GLN   ( 337-)  A  omega poor
 324 LYS   ( 363-)  A  Poor phi/psi
 392 ASN   ( 431-)  A  Poor phi/psi
 514 GLN   ( 554-)  A  Poor phi/psi
 543 GLY   ( 583-)  A  omega poor
 544 GLN   ( 584-)  A  PRO omega poor
 546 GLN   ( 586-)  A  omega poor
 576 TRP   ( 616-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.341

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.

   6 SER   (  45-)  A    0.35
 421 SER   ( 461-)  A    0.38
 557 LYS   ( 597-)  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!

  32 THR   (  71-)  A      0
  33 ASN   (  72-)  A      0
  67 GLN   ( 106-)  A      0
  84 GLU   ( 123-)  A      0
  85 ARG   ( 124-)  A      0
 114 HIS   ( 153-)  A      0
 115 PRO   ( 154-)  A      0
 116 ASN   ( 155-)  A      0
 122 LEU   ( 161-)  A      0
 123 GLU   ( 162-)  A      0
 133 SER   ( 172-)  A      0
 149 LYS   ( 188-)  A      0
 174 TYR   ( 213-)  A      0
 175 VAL   ( 214-)  A      0
 220 TYR   ( 259-)  A      0
 224 HIS   ( 263-)  A      0
 234 HIS   ( 273-)  A      0
 235 LEU   ( 274-)  A      0
 240 TRP   ( 279-)  A      0
 242 GLN   ( 281-)  A      0
 243 THR   ( 282-)  A      0
 244 TRP   ( 283-)  A      0
 245 SER   ( 284-)  A      0
 247 ILE   ( 286-)  A      0
 251 VAL   ( 290-)  A      0
And so on for a total of 164 lines.

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.

 544 GLN   ( 584-)  A      CB  <->  545 PRO   ( 585-)  A      CD     0.58    2.52  INTRA BL
 314 HIS   ( 353-)  A      ND1 <->  472 PHE   ( 512-)  A      CD2    0.44    2.66  INTRA
  85 ARG   ( 124-)  A      NH1 <->   97 ASN   ( 136-)  A      OD1    0.36    2.34  INTRA
 261 ASP   ( 300-)  A      OD1 <->  264 GLU   ( 303-)  A      N      0.36    2.34  INTRA BF
 158 TYR   ( 197-)  A      N   <->  159 PRO   ( 198-)  A      CD     0.33    2.67  INTRA BL
 450 LEU   ( 490-)  A      O   <->  576 TRP   ( 616-)  A      NE1    0.27    2.43  INTRA BL
 544 GLN   ( 584-)  A      CA  <->  545 PRO   ( 585-)  A      CD     0.23    2.57  INTRA BL
 318 TRP   ( 357-)  A      N   <->  327 ARG   ( 366-)  A      O      0.21    2.49  INTRA BL
 214 ARG   ( 253-)  A      NE  <->  572 GLU   ( 612-)  A      OE2    0.21    2.49  INTRA BL
 314 HIS   ( 353-)  A      ND1 <->  472 PHE   ( 512-)  A      CG     0.21    2.89  INTRA
 534 TRP   ( 574-)  A      N   <->  535 PRO   ( 575-)  A      CD     0.21    2.79  INTRA BL
 111 THR   ( 150-)  A      O   <->  149 LYS   ( 188-)  A      CG     0.20    2.60  INTRA
  70 ASN   ( 109-)  A      CG  <->  579 NAG   (1619-)  A      N2     0.20    2.90  INTRA BF
  65 VAL   ( 104-)  A      CG2 <->   81 GLN   ( 120-)  A      NE2    0.20    2.90  INTRA
 367 ASN   ( 406-)  A      ND2 <->  370 PHE   ( 409-)  A      CE1    0.19    2.91  INTRA BL
  34 ILE   (  73-)  A      N   <->  310 GLU   ( 349-)  A      O      0.19    2.51  INTRA
 265 ALA   ( 304-)  A      O   <->  269 GLN   ( 308-)  A      CG     0.18    2.62  INTRA
  24 ALA   (  63-)  A      O   <->   28 TRP   (  67-)  A      N      0.17    2.53  INTRA
 494 HIS   ( 534-)  A      ND1 <->  585 HOH   (2024 )  A      O      0.17    2.53  INTRA BL
 367 ASN   ( 406-)  A      ND2 <->  370 PHE   ( 409-)  A      CD1    0.16    2.94  INTRA BL
 456 CYS   ( 496-)  A      SG  <->  585 HOH   (2028 )  A      O      0.15    2.85  INTRA BL
 494 HIS   ( 534-)  A      O   <->  498 CYS   ( 538-)  A      SG     0.15    2.70  INTRA
 467 ASP   ( 507-)  A      N   <->  468 PRO   ( 508-)  A      CD     0.14    2.86  INTRA BL
 189 SER   ( 228-)  A      CB  <->  192 GLN   ( 231-)  A      NE2    0.14    2.96  INTRA
  79 LYS   ( 118-)  A      NZ  <->  364 GLU   ( 403-)  A      OE2    0.13    2.57  INTRA
And so on for a total of 84 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.

 573 LYS   ( 613-)  A      -6.14
 463 GLN   ( 503-)  A      -6.02
 223 GLN   ( 262-)  A      -6.02
 219 HIS   ( 258-)  A      -5.64
 298 GLN   ( 337-)  A      -5.26
 227 LEU   ( 266-)  A      -5.13
  67 GLN   ( 106-)  A      -5.11
 453 GLN   ( 493-)  A      -5.07
 503 HIS   ( 543-)  A      -5.01
 218 ARG   ( 257-)  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.

 218 ARG   ( 257-)  A       220 - TYR    259- ( A)         -4.98

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.

 184 MET   ( 223-)  A   -3.04
  83 LEU   ( 122-)  A   -2.99
 470 ALA   ( 510-)  A   -2.58

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.

 585 HOH   (2033 )  A      O
Bound group on Asn; dont flip   33 ASN  (  72-) A
Bound to:  578 NAG  (1618-) A
Bound group on Asn; dont flip   70 ASN  ( 109-) A
Bound to:  579 NAG  (1619-) A
Marked this atom as acceptor  581  CL  (1622-) A     CL
Marked this atom as acceptor  582  CL  (1623-) A     CL
Metal-coordinating Histidine residue 344 fixed to   1
Metal-coordinating Histidine residue 348 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.

 314 HIS   ( 353-)  A
 514 GLN   ( 554-)  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.

 116 ASN   ( 155-)  A      N
 125 ASP   ( 164-)  A      N
 143 TRP   ( 182-)  A      NE1
 176 ASP   ( 215-)  A      N
 191 GLU   ( 230-)  A      N
 192 GLN   ( 231-)  A      NE2
 234 HIS   ( 273-)  A      NE2
 236 LEU   ( 275-)  A      N
 238 ASN   ( 277-)  A      N
 243 THR   ( 282-)  A      N
 245 SER   ( 284-)  A      N
 246 ASN   ( 285-)  A      N
 271 TRP   ( 310-)  A      NE1
 272 THR   ( 311-)  A      N
 356 LYS   ( 395-)  A      N
 361 ALA   ( 400-)  A      N
 367 ASN   ( 406-)  A      N
 375 GLY   ( 414-)  A      N
 401 GLU   ( 441-)  A      N
 420 PHE   ( 460-)  A      N
 425 ASP   ( 465-)  A      N
 428 ARG   ( 468-)  A      NH1
 449 ARG   ( 489-)  A      NE
 453 GLN   ( 493-)  A      NE2
 459 VAL   ( 499-)  A      N
 461 ARG   ( 501-)  A      NH2
 480 TYR   ( 520-)  A      OH
 482 ARG   ( 522-)  A      N
 483 TYR   ( 523-)  A      OH
 508 HIS   ( 548-)  A      N
 515 SER   ( 555-)  A      OG
 517 GLU   ( 557-)  A      N
 539 GLN   ( 579-)  A      NE2
 548 SER   ( 588-)  A      N
 552 MET   ( 592-)  A      N
 575 GLY   ( 615-)  A      N
Only metal coordination for  344 HIS  ( 383-) A      NE2
Only metal coordination for  372 GLU  ( 411-) A      OE1

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.

  13 ASP   (  52-)  A      OD1
 114 HIS   ( 153-)  A      ND1
 209 HIS   ( 248-)  A      ND1
 330 GLN   ( 369-)  A      OE1
 345 GLU   ( 384-)  A      OE1
 345 GLU   ( 384-)  A      OE2
 371 HIS   ( 410-)  A      ND1
 492 GLN   ( 532-)  A      OE1

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.

 102 ASP   ( 141-)  A   H-bonding suggests Asn; but Alt-Rotamer
 148 ASP   ( 187-)  A   H-bonding suggests Asn; but Alt-Rotamer
 433 ASP   ( 473-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.335
  2nd generation packing quality :  -1.102
  Ramachandran plot appearance   :  -2.028
  chi-1/chi-2 rotamer normality  :  -2.341
  Backbone conformation          :  -0.311

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.336 (tight)
  Bond angles                    :   0.634 (tight)
  Omega angle restraints         :   0.757
  Side chain planarity           :   0.263 (tight)
  Improper dihedral distribution :   0.667
  B-factor distribution          :   0.541
  Inside/Outside distribution    :   0.987

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :   0.5
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.336 (tight)
  Bond angles                    :   0.634 (tight)
  Omega angle restraints         :   0.757
  Side chain planarity           :   0.263 (tight)
  Improper dihedral distribution :   0.667
  B-factor distribution          :   0.541
  Inside/Outside distribution    :   0.987
==============

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.