WHAT IF Check report

This file was created 2011-12-17 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 pdb2oyu.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.

 560 BOG   ( 750-)  P  -
 562 IMS   ( 700-)  P  -
 563 BOG   ( 751-)  P  -
 564 BMA   ( 673-)  P  -

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-)  P  -   O4  bound to  555 NAG   ( 662-)  P  -   C1
 556 NAG   ( 671-)  P  -   O4  bound to  557 NAG   ( 672-)  P  -   C1
 557 NAG   ( 672-)  P  -   O4  bound to  564 BMA   ( 673-)  P  -   C1
 558 NAG   ( 681-)  P  -   O4  bound to  559 NAG   ( 682-)  P  -   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-)  P      CG
  48 ARG   (  79-)  P      CD
  48 ARG   (  79-)  P      NE
  48 ARG   (  79-)  P      CZ
  48 ARG   (  79-)  P      NH1
  48 ARG   (  79-)  P      NH2
  52 ARG   (  83-)  P      CG
  52 ARG   (  83-)  P      CD
  52 ARG   (  83-)  P      NE
  52 ARG   (  83-)  P      CZ
  52 ARG   (  83-)  P      NH1
  52 ARG   (  83-)  P      NH2
 138 LYS   ( 169-)  P      CG
 138 LYS   ( 169-)  P      CD
 138 LYS   ( 169-)  P      CE
 138 LYS   ( 169-)  P      NZ
 139 GLN   ( 170-)  P      CG
 139 GLN   ( 170-)  P      CD
 139 GLN   ( 170-)  P      OE1
 139 GLN   ( 170-)  P      NE2
 142 ASP   ( 173-)  P      CG
 142 ASP   ( 173-)  P      OD1
 142 ASP   ( 173-)  P      OD2
 144 GLU   ( 175-)  P      CG
 144 GLU   ( 175-)  P      CD
And so on for a total of 84 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 1

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.

  66 ARG   (  97-)  P
 148 ARG   ( 179-)  P
 149 ARG   ( 180-)  P
 428 ARG   ( 459-)  P

Warning: Tyrosine convention problem

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

  33 TYR   (  64-)  P
  99 TYR   ( 130-)  P
 116 TYR   ( 147-)  P
 211 TYR   ( 242-)  P
 223 TYR   ( 254-)  P
 231 TYR   ( 262-)  P
 244 TYR   ( 275-)  P
 317 TYR   ( 348-)  P
 324 TYR   ( 355-)  P
 342 TYR   ( 373-)  P
 354 TYR   ( 385-)  P
 373 TYR   ( 404-)  P
 386 TYR   ( 417-)  P
 444 TYR   ( 475-)  P
 464 TYR   ( 495-)  P
 513 TYR   ( 544-)  P

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-)  P
  57 PHE   (  88-)  P
 150 PHE   ( 181-)  P
 156 PHE   ( 187-)  P
 167 PHE   ( 198-)  P
 170 PHE   ( 201-)  P
 178 PHE   ( 209-)  P
 189 PHE   ( 220-)  P
 216 PHE   ( 247-)  P
 336 PHE   ( 367-)  P
 378 PHE   ( 409-)  P
 439 PHE   ( 470-)  P
 447 PHE   ( 478-)  P
 487 PHE   ( 518-)  P
 498 PHE   ( 529-)  P
 519 PHE   ( 550-)  P
 549 PHE   ( 580-)  P

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-)  P
 283 ASP   ( 314-)  P
 362 ASP   ( 393-)  P
 410 ASP   ( 441-)  P
 466 ASP   ( 497-)  P
 553 ASP   ( 584-)  P

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-)  P
 208 GLU   ( 239-)  P
 229 GLU   ( 260-)  P
 237 GLU   ( 268-)  P
 277 GLU   ( 308-)  P
 288 GLU   ( 319-)  P
 308 GLU   ( 339-)  P
 333 GLU   ( 364-)  P
 449 GLU   ( 480-)  P
 459 GLU   ( 490-)  P
 461 GLU   ( 492-)  P
 471 GLU   ( 502-)  P
 479 GLU   ( 510-)  P

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.998426 -0.000100  0.000174|
 | -0.000100  0.999034  0.000532|
 |  0.000174  0.000532  0.998776|
Proposed new scale matrix

 |  0.005521  0.003187 -0.000003|
 |  0.000000  0.006371 -0.000003|
 | -0.000002 -0.000005  0.009683|
With corresponding cell

    A    = 181.128  B   = 181.227  C    = 103.275
    Alpha=  89.957  Beta=  89.980  Gamma= 119.994

The CRYST1 cell dimensions

    A    = 181.410  B   = 181.410  C    = 103.398
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 31.877
(Under-)estimated Z-score: 4.161

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.

  18 ARG   (  49-)  P      CG   CD   NE  118.17    4.5
 402 ARG   ( 433-)  P      CG   CD   NE  118.54    4.7

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-)  P
  42 GLU   (  73-)  P
  66 ARG   (  97-)  P
 148 ARG   ( 179-)  P
 149 ARG   ( 180-)  P
 208 GLU   ( 239-)  P
 229 GLU   ( 260-)  P
 237 GLU   ( 268-)  P
 277 GLU   ( 308-)  P
 283 ASP   ( 314-)  P
 288 GLU   ( 319-)  P
 308 GLU   ( 339-)  P
 333 GLU   ( 364-)  P
 362 ASP   ( 393-)  P
 410 ASP   ( 441-)  P
 428 ARG   ( 459-)  P
 449 GLU   ( 480-)  P
 459 GLU   ( 490-)  P
 461 GLU   ( 492-)  P
 466 ASP   ( 497-)  P
 471 GLU   ( 502-)  P
 479 GLU   ( 510-)  P
 553 ASP   ( 584-)  P

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.437

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.

 378 PHE   ( 409-)  P    -3.2
 250 PRO   ( 281-)  P    -3.1
 487 PHE   ( 518-)  P    -3.0
 545 PRO   ( 576-)  P    -3.0
 354 TYR   ( 385-)  P    -2.8
 532 THR   ( 563-)  P    -2.7
 199 LEU   ( 230-)  P    -2.6
  45 THR   (  76-)  P    -2.6
 135 LYS   ( 166-)  P    -2.4
  38 CYS   (  69-)  P    -2.4
 402 ARG   ( 433-)  P    -2.3
  43 ILE   (  74-)  P    -2.3
  30 ARG   (  61-)  P    -2.3
 141 PRO   ( 172-)  P    -2.2
 304 ILE   ( 335-)  P    -2.2
   8 TYR   (  39-)  P    -2.2
 118 THR   ( 149-)  P    -2.2
 133 GLY   ( 164-)  P    -2.2
  98 THR   ( 129-)  P    -2.2
 197 VAL   ( 228-)  P    -2.2
  55 PRO   (  86-)  P    -2.2
 247 GLY   ( 278-)  P    -2.2
 249 PRO   ( 280-)  P    -2.2
 154 ARG   ( 185-)  P    -2.1
 453 GLU   ( 484-)  P    -2.1
 451 THR   ( 482-)  P    -2.1
 101 ILE   ( 132-)  P    -2.1
  39 THR   (  70-)  P    -2.1
  99 TYR   ( 130-)  P    -2.0
 248 ILE   ( 279-)  P    -2.0
 240 VAL   ( 271-)  P    -2.0
 407 ARG   ( 438-)  P    -2.0
 511 PRO   ( 542-)  P    -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.

  13 GLN   (  44-)  P  Poor phi/psi
  20 GLY   (  51-)  P  Poor phi/psi
  21 LEU   (  52-)  P  omega poor
  30 ARG   (  61-)  P  Poor phi/psi
  38 CYS   (  69-)  P  Poor phi/psi
  95 SER   ( 126-)  P  PRO omega poor
  98 THR   ( 129-)  P  Poor phi/psi
 116 TYR   ( 147-)  P  omega poor
 123 SER   ( 154-)  P  omega poor
 134 THR   ( 165-)  P  Poor phi/psi
 143 ALA   ( 174-)  P  Poor phi/psi
 154 ARG   ( 185-)  P  Poor phi/psi
 178 PHE   ( 209-)  P  omega poor
 194 GLY   ( 225-)  P  omega poor
 199 LEU   ( 230-)  P  Poor phi/psi
 200 GLY   ( 231-)  P  Poor phi/psi
 216 PHE   ( 247-)  P  Poor phi/psi
 227 ASN   ( 258-)  P  Poor phi/psi
 240 VAL   ( 271-)  P  Poor phi/psi
 245 PRO   ( 276-)  P  omega poor
 247 GLY   ( 278-)  P  omega poor
 250 PRO   ( 281-)  P  Poor phi/psi
 252 SER   ( 283-)  P  Poor phi/psi
 255 ALA   ( 286-)  P  omega poor
 256 VAL   ( 287-)  P  Poor phi/psi
 260 VAL   ( 291-)  P  Poor phi/psi
 263 LEU   ( 294-)  P  Poor phi/psi
 337 GLY   ( 368-)  P  omega poor
 339 GLN   ( 370-)  P  omega poor
 342 TYR   ( 373-)  P  Poor phi/psi
 378 PHE   ( 409-)  P  Poor phi/psi
 399 PRO   ( 430-)  P  Poor phi/psi
 400 ALA   ( 431-)  P  Poor phi/psi
 401 GLY   ( 432-)  P  omega poor
 465 GLY   ( 496-)  P  Poor phi/psi
 481 CYS   ( 512-)  P  omega poor
 484 ASN   ( 515-)  P  Poor phi/psi
 537 VAL   ( 568-)  P  omega poor
 552 PRO   ( 583-)  P  omega poor
 chi-1/chi-2 correlation Z-score : -4.393

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 : -4.393

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.

 396 SER   ( 427-)  P    0.36
 499 SER   ( 530-)  P    0.36
 110 SER   ( 141-)  P    0.40

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 ASN   (  34-)  P      0
   5 CYS   (  36-)  P      0
   6 CYS   (  37-)  P      0
   8 TYR   (  39-)  P      0
   9 PRO   (  40-)  P      0
  10 CYS   (  41-)  P      0
  11 GLN   (  42-)  P      0
  12 HIS   (  43-)  P      0
  13 GLN   (  44-)  P      0
  21 LEU   (  52-)  P      0
  22 ASP   (  53-)  P      0
  28 CYS   (  59-)  P      0
  29 THR   (  60-)  P      0
  30 ARG   (  61-)  P      0
  31 THR   (  62-)  P      0
  33 TYR   (  64-)  P      0
  34 SER   (  65-)  P      0
  36 PRO   (  67-)  P      0
  37 ASN   (  68-)  P      0
  38 CYS   (  69-)  P      0
  39 THR   (  70-)  P      0
  43 ILE   (  74-)  P      0
  63 THR   (  94-)  P      0
  64 HIS   (  95-)  P      0
  66 ARG   (  97-)  P      0
And so on for a total of 222 lines.

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-)  P    44.3 envelop C-delta (36 degrees)
   9 PRO   (  40-)  P    37.4 envelop C-delta (36 degrees)
  36 PRO   (  67-)  P  -120.0 half-chair C-delta/C-gamma (-126 degrees)
  55 PRO   (  86-)  P   111.3 envelop C-beta (108 degrees)
 122 PRO   ( 153-)  P    52.8 half-chair C-delta/C-gamma (54 degrees)
 141 PRO   ( 172-)  P  -141.5 envelop C-delta (-144 degrees)
 239 PRO   ( 270-)  P  -113.8 envelop C-gamma (-108 degrees)
 249 PRO   ( 280-)  P    31.6 envelop C-delta (36 degrees)
 250 PRO   ( 281-)  P   -10.5 half-chair C-alpha/N (-18 degrees)
 511 PRO   ( 542-)  P   124.5 half-chair C-beta/C-alpha (126 degrees)
 545 PRO   ( 576-)  P   -42.3 envelop C-alpha (-36 degrees)
 552 PRO   ( 583-)  P  -112.7 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   ( 672-)  P      O4  <->  564 BMA   ( 673-)  P      C1     0.92    1.48  INTRA BF
 120 ILE   ( 151-)  P      CG2 <->  438 ARG   ( 469-)  P      NH1    0.64    2.46  INTRA BL
 557 NAG   ( 672-)  P      C4  <->  564 BMA   ( 673-)  P      C1     0.60    2.60  INTRA BF
  59 HIS   (  90-)  P      CE1 <->  562 IMS   ( 700-)  P      C20    0.31    2.89  INTRA
 259 GLU   ( 290-)  P      CB  <->  565 HOH   ( 783 )  P      O      0.25    2.55  INTRA BF
 496 ALA   ( 527-)  P      CA  <->  562 IMS   ( 700-)  P      C5     0.25    2.95  INTRA BL
 159 ASP   ( 190-)  P      N   <->  400 ALA   ( 431-)  P      O      0.25    2.45  INTRA BL
 436 ARG   ( 467-)  P      NH1 <->  490 SER   ( 521-)  P      OG     0.23    2.47  INTRA BL
   3 ASN   (  34-)  P      CB  <->  127 ASP   ( 158-)  P      OD2    0.23    2.57  INTRA BF
 360 MET   ( 391-)  P      SD  <->  561 HEM   ( 601-)  P      CAB    0.20    3.20  INTRA BF
 255 ALA   ( 286-)  P      O   <->  565 HOH   ( 786 )  P      O      0.20    2.20  INTRA BF
 373 TYR   ( 404-)  P      CG  <->  412 HIS   ( 443-)  P      CD2    0.20    3.00  INTRA BL
 177 GLN   ( 208-)  P      NE2 <->  197 VAL   ( 228-)  P      CA     0.20    2.90  INTRA BF
 248 ILE   ( 279-)  P      C   <->  250 PRO   ( 281-)  P      CD     0.19    3.01  INTRA BF
 164 ASN   ( 195-)  P      ND2 <->  548 SER   ( 579-)  P      O      0.19    2.51  INTRA BF
 451 THR   ( 482-)  P      O   <->  453 GLU   ( 484-)  P      N      0.19    2.51  INTRA BF
 557 NAG   ( 672-)  P      C4  <->  564 BMA   ( 673-)  P      O2     0.17    2.63  INTRA BF
 315 GLU   ( 346-)  P      OE2 <->  330 PHE   ( 361-)  P      N      0.17    2.53  INTRA BL
 111 PHE   ( 142-)  P      O   <->  345 ARG   ( 376-)  P      NH2    0.16    2.54  INTRA BL
 322 SER   ( 353-)  P      CB  <->  562 IMS   ( 700-)  P      C16    0.16    3.04  INTRA BL
 436 ARG   ( 467-)  P      NH1 <->  441 MET   ( 472-)  P      SD     0.15    3.15  INTRA BL
  76 PHE   ( 107-)  P      O   <->   79 ASP   ( 110-)  P      N      0.15    2.55  INTRA BF
 255 ALA   ( 286-)  P      N   <->  565 HOH   ( 786 )  P      O      0.15    2.55  INTRA BF
 233 PRO   ( 264-)  P      O   <->  565 HOH   ( 786 )  P      O      0.14    2.26  INTRA BF
 141 PRO   ( 172-)  P      O   <->  425 ARG   ( 456-)  P      NH2    0.13    2.57  INTRA BF
And so on for a total of 100 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-)  P      -8.43
  30 ARG   (  61-)  P      -7.33
 156 PHE   ( 187-)  P      -6.53
 140 LEU   ( 171-)  P      -6.37
 137 LYS   ( 168-)  P      -6.35
 154 ARG   ( 185-)  P      -6.28
  21 LEU   (  52-)  P      -6.07
 339 GLN   ( 370-)  P      -5.87
 343 ARG   ( 374-)  P      -5.84
 185 MET   ( 216-)  P      -5.73
 105 TYR   ( 136-)  P      -5.57
 243 HIS   ( 274-)  P      -5.52
 402 ARG   ( 433-)  P      -5.48
 397 ARG   ( 428-)  P      -5.36
 149 ARG   ( 180-)  P      -5.34
   2 VAL   (  33-)  P      -5.25
 542 LYS   ( 573-)  P      -5.15
 438 ARG   ( 469-)  P      -5.09
 251 GLN   ( 282-)  P      -5.06
 288 GLU   ( 319-)  P      -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-)  P       248 - ILE    279- ( P)         -5.82

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-)  P   -3.40
  52 ARG   (  83-)  P   -2.83
 365 ARG   ( 396-)  P   -2.76
 139 GLN   ( 170-)  P   -2.75
 155 LYS   ( 186-)  P   -2.70
 184 LYS   ( 215-)  P   -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.

 152 LEU   ( 183-)  P     -  155 LYS   ( 186-)  P        -1.93

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.

 565 HOH   ( 758 )  P      O
 565 HOH   ( 763 )  P      O
 565 HOH   ( 771 )  P      O
 565 HOH   ( 802 )  P      O
 565 HOH   ( 803 )  P      O
Bound group on Asn; dont flip   37 ASN  (  68-) P
Bound to:  554 NAG  ( 661-) P
Bound group on Asn; dont flip  113 ASN  ( 144-) P
Bound to:  556 NAG  ( 671-) P
Bound group on Asn; dont flip  379 ASN  ( 410-) P
Bound to:  558 NAG  ( 681-) P
Marked this atom as acceptor  562 IMS  ( 700-) P     CL
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.

  11 GLN   (  42-)  P
 103 HIS   ( 134-)  P
 206 ASN   ( 237-)  P
 210 GLN   ( 241-)  P
 289 HIS   ( 320-)  P
 344 ASN   ( 375-)  P
 550 HIS   ( 581-)  P

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.

   2 VAL   (  33-)  P      N
  18 ARG   (  49-)  P      NH1
  37 ASN   (  68-)  P      N
  43 ILE   (  74-)  P      N
  44 TRP   (  75-)  P      N
  89 ARG   ( 120-)  P      NE
 101 ILE   ( 132-)  P      N
 105 TYR   ( 136-)  P      N
 108 TRP   ( 139-)  P      N
 110 SER   ( 141-)  P      N
 119 ARG   ( 150-)  P      NH1
 119 ARG   ( 150-)  P      NH2
 126 ARG   ( 157-)  P      N
 127 ASP   ( 158-)  P      N
 130 THR   ( 161-)  P      N
 161 GLN   ( 192-)  P      N
 172 GLN   ( 203-)  P      NE2
 177 GLN   ( 208-)  P      NE2
 181 THR   ( 212-)  P      N
 204 GLY   ( 235-)  P      N
 205 ASP   ( 236-)  P      N
 206 ASN   ( 237-)  P      N
 209 ARG   ( 240-)  P      NH2
 214 ARG   ( 245-)  P      NE
 216 PHE   ( 247-)  P      N
And so on for a total of 65 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.

 109 GLU   ( 140-)  P      OE2
 159 ASP   ( 190-)  P      OD1
 173 HIS   ( 204-)  P      NE2
 177 GLN   ( 208-)  P      OE1
 308 GLU   ( 339-)  P      OE1
 352 GLN   ( 383-)  P      OE1
 482 HIS   ( 513-)  P      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.

  70 ASP   ( 101-)  P   H-bonding suggests Asn
 419 ASP   ( 450-)  P   H-bonding suggests Asn; but Alt-Rotamer
 423 GLU   ( 454-)  P   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 :  -2.209
  2nd generation packing quality :  -2.646
  Ramachandran plot appearance   :  -3.437 (poor)
  chi-1/chi-2 rotamer normality  :  -4.393 (bad)
  Backbone conformation          :  -0.841

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.477 (tight)
  Bond angles                    :   0.695
  Omega angle restraints         :   1.167
  Side chain planarity           :   0.404 (tight)
  Improper dihedral distribution :   0.657
  B-factor distribution          :   0.327
  Inside/Outside distribution    :   1.103

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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.4
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.477 (tight)
  Bond angles                    :   0.695
  Omega angle restraints         :   1.167
  Side chain planarity           :   0.404 (tight)
  Improper dihedral distribution :   0.657
  B-factor distribution          :   0.327
  Inside/Outside distribution    :   1.103
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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    Acta Crystallogr. D52, 57--64 (1996).

DSSP
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      Dictionary of protein secondary structure: pattern
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Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
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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.