WHAT IF Check report

This file was created 2012-01-30 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 pdb3l2p.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

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

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

Molecular weight of all polymer chains: 73969.445
Volume of the Unit Cell V= 2547617.8
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 4.305
Vm by authors and this calculated Vm agree reasonably well
Matthews coefficient read from REMARK 280 Vm= 4.060

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.

 579 AMP   ( 901-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 HIS   ( 168-)  A      CG
   1 HIS   ( 168-)  A      ND1
   1 HIS   ( 168-)  A      CD2
   1 HIS   ( 168-)  A      CE1
   1 HIS   ( 168-)  A      NE2
   3 ARG   ( 170-)  A      CG
   3 ARG   ( 170-)  A      CD
   3 ARG   ( 170-)  A      NE
   3 ARG   ( 170-)  A      CZ
   3 ARG   ( 170-)  A      NH1
   3 ARG   ( 170-)  A      NH2
   4 HIS   ( 171-)  A      CG
   4 HIS   ( 171-)  A      ND1
   4 HIS   ( 171-)  A      CD2
   4 HIS   ( 171-)  A      CE1
   4 HIS   ( 171-)  A      NE2
   5 LYS   ( 172-)  A      CG
   5 LYS   ( 172-)  A      CD
   5 LYS   ( 172-)  A      CE
   5 LYS   ( 172-)  A      NZ
  56 THR   ( 230-)  A      OG1
  56 THR   ( 230-)  A      CG2
  63 LYS   ( 237-)  A      CG
  63 LYS   ( 237-)  A      CD
  63 LYS   ( 237-)  A      CE
And so on for a total of 108 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 HIS   ( 168-)  A    High
   2 MET   ( 169-)  A    High
   3 ARG   ( 170-)  A    High
   4 HIS   ( 171-)  A    High
   5 LYS   ( 172-)  A    High
   6 ASP   ( 173-)  A    High
   7 CYS   ( 174-)  A    High
   8 LEU   ( 175-)  A    High
   9 LEU   ( 176-)  A    High
  10 ARG   ( 177-)  A    High
  11 GLU   ( 178-)  A    High
  12 PHE   ( 179-)  A    High
  13 ARG   ( 180-)  A    High
  14 LYS   ( 181-)  A    High
  15 LEU   ( 182-)  A    High
  17 ALA   ( 184-)  A    High
  18 MET   ( 185-)  A    High
  19 VAL   ( 186-)  A    High
  20 ALA   ( 187-)  A    High
  21 ASP   ( 188-)  A    High
  22 ASN   ( 189-)  A    High
  23 PRO   ( 190-)  A    High
  24 SER   ( 191-)  A    High
  25 TYR   ( 192-)  A    High
  26 ASN   ( 193-)  A    High
And so on for a total of 350 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: 4

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

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.

 508 ARG   ( 719-)  A

Warning: Tyrosine convention problem

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

  25 TYR   ( 192-)  A
  58 TYR   ( 232-)  A
 225 TYR   ( 407-)  A
 275 TYR   ( 457-)  A
 330 TYR   ( 512-)  A
 397 TYR   ( 579-)  A
 411 TYR   ( 593-)  A
 427 TYR   ( 612-)  A

Warning: Phenylalanine convention problem

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

  35 PHE   ( 202-)  A
  69 PHE   ( 243-)  A
  73 PHE   ( 247-)  A
 257 PHE   ( 439-)  A
 272 PHE   ( 454-)  A
 316 PHE   ( 498-)  A
 331 PHE   ( 513-)  A
 347 PHE   ( 529-)  A
 361 PHE   ( 543-)  A
 426 PHE   ( 611-)  A
 439 PHE   ( 624-)  A
 506 PHE   ( 717-)  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.

   6 ASP   ( 173-)  A
  41 ASP   ( 215-)  A
 173 ASP   ( 347-)  A
 252 ASP   ( 434-)  A
 289 ASP   ( 471-)  A
 296 ASP   ( 478-)  A
 392 ASP   ( 574-)  A
 514 ASP   ( 725-)  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.

  98 GLU   ( 272-)  A
 118 GLU   ( 292-)  A
 178 GLU   ( 352-)  A
 201 GLU   ( 375-)  A
 237 GLU   ( 419-)  A
 243 GLU   ( 425-)  A
 291 GLU   ( 473-)  A
 343 GLU   ( 525-)  A
 386 GLU   ( 568-)  A
 398 GLU   ( 580-)  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.

 144 THR   ( 318-)  A      CA   CB    1.61    4.2
 320 ASN   ( 502-)  A      CB   CG    1.68    6.5
 478 ILE   ( 663-)  A      CA   CB    1.64    5.6
 536 DCYT  (   1-)  B      C1'  N1    1.53    4.8
 545 DTHY  (  10-)  B      C4'  C3'   1.49   -4.1
 547 DGUA  (  12-)  C      P    OP1   1.58    5.5
 547 DGUA  (  12-)  C      P    O5'   1.72   12.3
 547 DGUA  (  12-)  C      O5'  C5'   1.62   11.2
 547 DGUA  (  12-)  C      C5'  C4'   1.58    8.9
 553 DCYT  (  18-)  C      O5'  C5'   1.38   -4.0
 555 DGUA  (  20-)  C      N9   C4    1.42    5.1
 557 DCYT  (  24-)  D      C3'  O3'   1.38   -4.0
 558 DCYT  (  25-)  D      C1'  N1    1.57    8.6
 561 DTHY  (  28-)  D      C3'  O3'   1.36   -5.8
 561 DTHY  (  28-)  D      O5'  C5'   1.37   -4.1
 562 DCYT  (  29-)  D      O5'  C5'   1.37   -4.5
 568 DADE  (  35-)  D      C3'  O3'   1.37   -4.6
 572 DADE  (  39-)  D      O5'  C5'   1.37   -4.2
 573 DTHY  (  40-)  D      O5'  C5'   1.37   -4.1
 576 DCYT  (  43-)  D      C3'  O3'   1.50    5.2
 576 DCYT  (  43-)  D      C4   N3    1.37    4.7

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.

 271 HIS   ( 453-)  A      CG   ND1  CE1 109.67    4.1
 536 DCYT  (   1-)  B      O4'  C1'  N1  115.42    9.5
 536 DCYT  (   1-)  B      N1   C2   O2  121.39    4.1
 537 DGUA  (   2-)  B      P   -C3* -O3* 125.40    4.8
 537 DGUA  (   2-)  B      C3'  C2'  C1'  96.41   -4.5
 537 DGUA  (   2-)  B      O5'  C5'  C4' 116.37    4.4
 537 DGUA  (   2-)  B      C5'  C4'  O4' 116.95    4.7
 537 DGUA  (   2-)  B      O4'  C1'  C2' 101.02   -4.6
 537 DGUA  (   2-)  B      O4'  C1'  N9  112.61    6.0
 537 DGUA  (   2-)  B      N9   C8   N7  113.90    5.6
 538 DGUA  (   3-)  B      O4'  C1'  N9  102.60   -6.5
 538 DGUA  (   3-)  B      N9   C8   N7  113.78    5.4
 539 DGUA  (   4-)  B      N9   C8   N7  114.13    6.1
 539 DGUA  (   4-)  B      N1   C2   N2  112.39   -4.2
 541 DTHY  (   6-)  B      C6   C5   C7  118.88   -6.7
 541 DTHY  (   6-)  B      C4   C5   C7  122.65    6.1
 542 DGUA  (   7-)  B      P   -C3* -O3* 126.41    5.6
 542 DGUA  (   7-)  B      N9   C8   N7  116.25   10.3
 542 DGUA  (   7-)  B      C8   N7   C5  100.55   -7.5
 542 DGUA  (   7-)  B      C8   N9   C4  104.66   -4.4
 542 DGUA  (   7-)  B      N7   C5   C6  127.28   -5.2
 542 DGUA  (   7-)  B      N7   C5   C4  113.83    7.6
 542 DGUA  (   7-)  B      C5   C6   O6  125.66   -4.9
 543 DCYT  (   8-)  B      C4'  C3'  C2' 107.46    4.3
 543 DCYT  (   8-)  B      N1   C2   O2  116.09   -4.7
And so on for a total of 95 lines.

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.

   6 ASP   ( 173-)  A
  41 ASP   ( 215-)  A
  98 GLU   ( 272-)  A
 118 GLU   ( 292-)  A
 173 ASP   ( 347-)  A
 178 GLU   ( 352-)  A
 201 GLU   ( 375-)  A
 237 GLU   ( 419-)  A
 243 GLU   ( 425-)  A
 252 ASP   ( 434-)  A
 289 ASP   ( 471-)  A
 291 GLU   ( 473-)  A
 296 ASP   ( 478-)  A
 343 GLU   ( 525-)  A
 386 GLU   ( 568-)  A
 392 ASP   ( 574-)  A
 398 GLU   ( 580-)  A
 508 ARG   ( 719-)  A
 514 ASP   ( 725-)  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.

 370 ALA   ( 552-)  A    4.62

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 : -3.710

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.

 506 PHE   ( 717-)  A    -3.6
 356 PRO   ( 538-)  A    -3.0
 417 THR   ( 602-)  A    -2.7
 127 THR   ( 301-)  A    -2.6
 269 VAL   ( 451-)  A    -2.6
 455 THR   ( 640-)  A    -2.5
 530 LEU   ( 741-)  A    -2.5
 368 THR   ( 550-)  A    -2.5
 307 THR   ( 489-)  A    -2.5
 518 TRP   ( 729-)  A    -2.5
  72 ILE   ( 246-)  A    -2.4
 157 HIS   ( 331-)  A    -2.3
 293 LEU   ( 475-)  A    -2.3
 110 LEU   ( 284-)  A    -2.3
 512 ILE   ( 723-)  A    -2.3
  31 ILE   ( 198-)  A    -2.2
 177 TYR   ( 351-)  A    -2.2
 184 ARG   ( 358-)  A    -2.2
 486 ILE   ( 697-)  A    -2.2
 238 ILE   ( 420-)  A    -2.2
 348 LEU   ( 530-)  A    -2.2
 152 ILE   ( 326-)  A    -2.2
 402 ARG   ( 584-)  A    -2.2
 159 LEU   ( 333-)  A    -2.2
 251 GLY   ( 433-)  A    -2.2
 524 LEU   ( 735-)  A    -2.2
 355 ILE   ( 537-)  A    -2.1
 383 GLU   ( 565-)  A    -2.1
 265 LEU   ( 447-)  A    -2.1
 503 SER   ( 714-)  A    -2.1
 502 ILE   ( 713-)  A    -2.1
 440 LEU   ( 625-)  A    -2.1
 151 ILE   ( 325-)  A    -2.1
 377 ILE   ( 559-)  A    -2.0
 323 LEU   ( 505-)  A    -2.0
  61 ASN   ( 235-)  A    -2.0
 508 ARG   ( 719-)  A    -2.0
 478 ILE   ( 663-)  A    -2.0
 160 LYS   ( 334-)  A    -2.0
 333 ASP   ( 515-)  A    -2.0
 431 SER   ( 616-)  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.

   2 MET   ( 169-)  A  omega poor
  59 ASN   ( 233-)  A  Poor phi/psi
  74 ASN   ( 248-)  A  Poor phi/psi
 127 THR   ( 301-)  A  Poor phi/psi
 145 ALA   ( 319-)  A  Poor phi/psi, omega poor
 157 HIS   ( 331-)  A  Poor phi/psi
 162 ASN   ( 336-)  A  Poor phi/psi
 173 ASP   ( 347-)  A  Poor phi/psi
 183 SER   ( 357-)  A  omega poor
 200 VAL   ( 374-)  A  Poor phi/psi
 209 MET   ( 391-)  A  Poor phi/psi
 220 CYS   ( 402-)  A  omega poor
 250 ASN   ( 432-)  A  omega poor
 255 SER   ( 437-)  A  omega poor
 261 LEU   ( 443-)  A  Poor phi/psi
 269 VAL   ( 451-)  A  Poor phi/psi
 286 MET   ( 468-)  A  Poor phi/psi
 295 ILE   ( 477-)  A  omega poor
 299 THR   ( 481-)  A  Poor phi/psi
 304 PRO   ( 486-)  A  omega poor
 318 ASP   ( 500-)  A  omega poor
 319 ALA   ( 501-)  A  omega poor
 329 ILE   ( 511-)  A  omega poor
 332 ASN   ( 514-)  A  Poor phi/psi
 333 ASP   ( 515-)  A  Poor phi/psi
 357 ASN   ( 539-)  A  Poor phi/psi
 359 ILE   ( 541-)  A  omega poor
 367 VAL   ( 549-)  A  omega poor
 368 THR   ( 550-)  A  Poor phi/psi
 384 GLY   ( 566-)  A  Poor phi/psi
 392 ASP   ( 574-)  A  omega poor
 416 ASP   ( 601-)  A  omega poor
 474 ASP   ( 659-)  A  omega poor
 482 ALA   ( 693-)  A  omega poor
 486 ILE   ( 697-)  A  omega poor
 490 GLU   ( 701-)  A  Poor phi/psi
 495 GLU   ( 706-)  A  Poor phi/psi
 496 ALA   ( 707-)  A  Poor phi/psi
 500 ASP   ( 711-)  A  Poor phi/psi
 501 GLY   ( 712-)  A  Poor phi/psi
 510 THR   ( 721-)  A  Poor phi/psi
 515 ASP   ( 726-)  A  omega poor
 518 TRP   ( 729-)  A  Poor phi/psi
 519 LYS   ( 730-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.150

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 : -5.150

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 ARG   ( 170-)  A      0
   7 CYS   ( 174-)  A      0
  23 PRO   ( 190-)  A      0
  37 ARG   ( 204-)  A      0
  38 LYS   ( 205-)  A      0
  39 GLY   ( 206-)  A      0
  40 GLY   ( 214-)  A      0
  41 ASP   ( 215-)  A      0
  50 LEU   ( 224-)  A      0
  55 LYS   ( 229-)  A      0
  58 TYR   ( 232-)  A      0
  59 ASN   ( 233-)  A      0
  60 LEU   ( 234-)  A      0
  62 ASP   ( 236-)  A      0
  74 ASN   ( 248-)  A      0
  75 CYS   ( 249-)  A      0
  76 ASN   ( 250-)  A      0
  86 GLN   ( 260-)  A      0
  96 PHE   ( 270-)  A      0
 101 LYS   ( 275-)  A      0
 103 PHE   ( 277-)  A      0
 107 ALA   ( 281-)  A      0
 109 SER   ( 283-)  A      0
 110 LEU   ( 284-)  A      0
 126 LEU   ( 300-)  A      0
And so on for a total of 258 lines.

Warning: Omega angle restraints not strong enough

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

Standard deviation of omega values : 7.060

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]

  23 PRO   ( 190-)  A    0.16 LOW
 302 PRO   ( 484-)  A    0.20 LOW

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].

 174 PRO   ( 348-)  A  -147.2 envelop C-delta (-144 degrees)
 211 PRO   ( 393-)  A   103.1 envelop C-beta (108 degrees)
 214 PRO   ( 396-)  A  -116.8 envelop C-gamma (-108 degrees)
 281 PRO   ( 463-)  A   104.9 envelop C-beta (108 degrees)
 340 PRO   ( 522-)  A    34.8 envelop C-delta (36 degrees)
 356 PRO   ( 538-)  A   155.1 half-chair C-alpha/N (162 degrees)
 446 PRO   ( 631-)  A    41.0 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 239 LYS   ( 421-)  A      NZ  <->  579 AMP   ( 901-)  A      P      1.07    2.23  INTRA BL
 209 MET   ( 391-)  A      CE  <->  248 HIS   ( 430-)  A      CB     0.65    2.55  INTRA BL
 259 ARG   ( 441-)  A      NH2 <->  547 DGUA  (  12-)  C      P      0.59    2.71  INTRA BL
 499 ALA   ( 710-)  A      O   <->  501 GLY   ( 712-)  A      N      0.50    2.20  INTRA BF
 313 LYS   ( 495-)  A      NZ  <->  320 ASN   ( 502-)  A      OD1    0.49    2.21  INTRA BL
 336 LEU   ( 518-)  A      CD2 <->  339 ARG   ( 521-)  A      NH1    0.46    2.64  INTRA BF
 297 ASN   ( 479-)  A      CB  <->  318 ASP   ( 500-)  A      O      0.40    2.40  INTRA BF
 518 TRP   ( 729-)  A      O   <->  520 SER   ( 731-)  A      N      0.35    2.35  INTRA BF
 239 LYS   ( 421-)  A      CE  <->  579 AMP   ( 901-)  A      P      0.32    3.08  INTRA BL
 494 SER   ( 705-)  A      N   <->  501 GLY   ( 712-)  A      O      0.32    2.38  INTRA BF
 341 LEU   ( 523-)  A      N   <->  395 GLY   ( 577-)  A      O      0.31    2.39  INTRA BL
 398 GLU   ( 580-)  A      OE1 <->  403 HIS   ( 585-)  A      CD2    0.29    2.51  INTRA BL
 293 LEU   ( 475-)  A      O   <->  322 CYS   ( 504-)  A      N      0.29    2.41  INTRA BL
 144 THR   ( 318-)  A      CG2 <->  147 ASP   ( 321-)  A      CG     0.28    2.92  INTRA BF
 454 VAL   ( 639-)  A      C   <->  497 HIS   ( 708-)  A      CD2    0.28    2.92  INTRA BF
 560 DGUA  (  27-)  D      C2' <->  561 DTHY  (  28-)  D      C5'    0.28    2.92  INTRA BL
 549 DCYT  (  14-)  C      N3  <->  564 DGUA  (  31-)  D      N1     0.25    2.75  INTRA BL
 543 DCYT  (   8-)  B      N3  <->  570 DGUA  (  37-)  D      N1     0.25    2.75  INTRA BL
 215 MET   ( 397-)  A      CE  <->  398 GLU   ( 580-)  A      N      0.25    2.85  INTRA BL
 537 DGUA  (   2-)  B      O6  <->  576 DCYT  (  43-)  D      N4     0.23    2.47  INTRA BL
 456 LYS   ( 641-)  A      NZ  <->  567 DGUA  (  34-)  D      OP1    0.23    2.47  INTRA BF
 295 ILE   ( 477-)  A      CD1 <->  322 CYS   ( 504-)  A      SG     0.23    3.17  INTRA BL
 546 DCYT  (  11-)  B      N3  <->  567 DGUA  (  34-)  D      N1     0.23    2.77  INTRA BL
 538 DGUA  (   3-)  B      N2  <->  575 DCYT  (  42-)  D      O2     0.22    2.48  INTRA BL
 100 SER   ( 274-)  A      C   <->  102 SER   ( 276-)  A      N      0.22    2.68  INTRA BF
And so on for a total of 151 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

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.

 475 MET   ( 660-)  A      -7.47
   2 MET   ( 169-)  A      -6.71
 429 GLN   ( 614-)  A      -6.54
  37 ARG   ( 204-)  A      -5.70
  86 GLN   ( 260-)  A      -5.61
 382 GLN   ( 564-)  A      -5.54
 478 ILE   ( 663-)  A      -5.47
  99 GLN   ( 273-)  A      -5.46
  38 LYS   ( 205-)  A      -5.46
 259 ARG   ( 441-)  A      -5.42
 449 GLN   ( 634-)  A      -5.30
 110 LEU   ( 284-)  A      -5.25
 198 GLN   ( 372-)  A      -5.21
 505 ARG   ( 716-)  A      -5.11
 162 ASN   ( 336-)  A      -5.05
 184 ARG   ( 358-)  A      -5.02

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

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.

 516 LYS   ( 727-)  A   -3.45
 450 LYS   ( 635-)  A   -2.85
 511 ARG   ( 722-)  A   -2.83
 103 PHE   ( 277-)  A   -2.75
 108 LYS   ( 282-)  A   -2.64
 493 LYS   ( 704-)  A   -2.60
   4 HIS   ( 171-)  A   -2.53
 477 LYS   ( 662-)  A   -2.52
 519 LYS   ( 730-)  A   -2.51

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.

   2 MET   ( 169-)  A     -    5 LYS   ( 172-)  A        -1.99

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  61 ASN   ( 235-)  A
  64 GLN   ( 238-)  A
  86 GLN   ( 260-)  A
 162 ASN   ( 336-)  A
 267 HIS   ( 449-)  A
 311 HIS   ( 493-)  A
 403 HIS   ( 585-)  A
 470 GLN   ( 655-)  A
 497 HIS   ( 708-)  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.

   6 ASP   ( 173-)  A      N
  13 ARG   ( 180-)  A      NH1
 102 SER   ( 276-)  A      N
 103 PHE   ( 277-)  A      N
 110 LEU   ( 284-)  A      N
 111 LEU   ( 285-)  A      N
 144 THR   ( 318-)  A      N
 145 ALA   ( 319-)  A      N
 147 ASP   ( 321-)  A      N
 167 HIS   ( 341-)  A      N
 171 ALA   ( 345-)  A      N
 177 TYR   ( 351-)  A      N
 217 ALA   ( 399-)  A      N
 221 LYS   ( 403-)  A      N
 222 SER   ( 404-)  A      N
 246 GLN   ( 428-)  A      NE2
 259 ARG   ( 441-)  A      N
 273 LYS   ( 455-)  A      N
 285 SER   ( 467-)  A      OG
 318 ASP   ( 500-)  A      N
 330 TYR   ( 512-)  A      OH
 358 ARG   ( 540-)  A      NH1
 368 THR   ( 550-)  A      N
 369 LYS   ( 551-)  A      N
 371 LEU   ( 553-)  A      N
 387 GLY   ( 569-)  A      N
 391 LYS   ( 573-)  A      NZ
 398 GLU   ( 580-)  A      N
 408 LYS   ( 590-)  A      N
 412 LEU   ( 594-)  A      N
 416 ASP   ( 601-)  A      N
 432 LYS   ( 617-)  A      N
 433 GLY   ( 618-)  A      N
 435 MET   ( 620-)  A      N
 444 TYR   ( 629-)  A      N
 461 HIS   ( 646-)  A      N
 461 HIS   ( 646-)  A      NE2
 470 GLN   ( 655-)  A      NE2
 473 LEU   ( 658-)  A      N
 490 GLU   ( 701-)  A      N
 506 PHE   ( 717-)  A      N
 515 ASP   ( 726-)  A      N
 521 ALA   ( 732-)  A      N

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.

 147 ASP   ( 321-)  A      OD2
 291 GLU   ( 473-)  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.

  21 ASP   ( 188-)  A   H-bonding suggests Asn; but Alt-Rotamer
  34 ASP   ( 201-)  A   H-bonding suggests Asn
  85 GLU   ( 259-)  A   H-bonding suggests Gln
  98 GLU   ( 272-)  A   H-bonding suggests Gln
 201 GLU   ( 375-)  A   H-bonding suggests Gln
 291 GLU   ( 473-)  A   H-bonding suggests Gln
 333 ASP   ( 515-)  A   H-bonding suggests Asn
 386 GLU   ( 568-)  A   H-bonding suggests Gln
 514 ASP   ( 725-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.301
  2nd generation packing quality :  -2.821
  Ramachandran plot appearance   :  -3.710 (poor)
  chi-1/chi-2 rotamer normality  :  -5.150 (bad)
  Backbone conformation          :  -0.730

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.870
  Bond angles                    :   1.185
  Omega angle restraints         :   1.284 (loose)
  Side chain planarity           :   0.554 (tight)
  Improper dihedral distribution :   0.864
  B-factor distribution          :   0.413
  Inside/Outside distribution    :   1.019

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -1.1
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.870
  Bond angles                    :   1.185
  Omega angle restraints         :   1.284 (loose)
  Side chain planarity           :   0.554 (tight)
  Improper dihedral distribution :   0.864
  B-factor distribution          :   0.413
  Inside/Outside distribution    :   1.019
==============

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.