WHAT IF Check report

This file was created 2011-12-18 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2yzn.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 10.258
CA-only RMS fit for the two chains : 9.022

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

Warning: Ligands for which topology could not be determined

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

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

 943 ANP   ( 401-)  A  -
 944 ANP   ( 402-)  B  -
 945 ANP   ( 403-)  C  -

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

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

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

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

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

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.

  26 ARG   (  26-)  A
  42 ARG   (  42-)  A
 121 ARG   ( 121-)  A
 137 ARG   ( 137-)  A
 166 ARG   ( 168-)  A
 215 ARG   ( 217-)  A
 231 ARG   ( 233-)  A
 266 ARG   ( 268-)  A
 295 ARG   ( 297-)  A
 319 ARG   (   2-)  B
 343 ARG   (  26-)  B
 401 ARG   (  84-)  B
 438 ARG   ( 121-)  B
 454 ARG   ( 137-)  B
 485 ARG   ( 168-)  B
 498 ARG   ( 181-)  B
 513 ARG   ( 196-)  B
 534 ARG   ( 217-)  B
 544 ARG   ( 233-)  B
 579 ARG   ( 268-)  B
 622 ARG   ( 311-)  B
 767 ARG   ( 137-)  C
 798 ARG   ( 168-)  C
 826 ARG   ( 196-)  C
 847 ARG   ( 217-)  C
 888 ARG   ( 268-)  C

Warning: Tyrosine convention problem

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

 216 TYR   ( 218-)  A
 221 TYR   ( 223-)  A
 227 TYR   ( 229-)  A
 293 TYR   ( 295-)  A
 535 TYR   ( 218-)  B
 606 TYR   ( 295-)  B
 704 TYR   (  74-)  C
 878 TYR   ( 258-)  C
 899 TYR   ( 279-)  C
 915 TYR   ( 295-)  C

Warning: Phenylalanine convention problem

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

  30 PHE   (  30-)  A
  85 PHE   (  85-)  A
  94 PHE   (  94-)  A
 167 PHE   ( 169-)  A
 220 PHE   ( 222-)  A
 347 PHE   (  30-)  B
 411 PHE   (  94-)  B
 463 PHE   ( 146-)  B
 467 PHE   ( 150-)  B
 468 PHE   ( 151-)  B
 497 PHE   ( 180-)  B
 524 PHE   ( 207-)  B
 660 PHE   (  30-)  C
 724 PHE   (  94-)  C
 780 PHE   ( 150-)  C
 781 PHE   ( 151-)  C
 810 PHE   ( 180-)  C
 837 PHE   ( 207-)  C

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.

  75 ASP   (  75-)  A
  88 ASP   (  88-)  A
 115 ASP   ( 115-)  A
 147 ASP   ( 147-)  A
 169 ASP   ( 171-)  A
 268 ASP   ( 270-)  A
 432 ASP   ( 115-)  B
 488 ASP   ( 171-)  B
 500 ASP   ( 183-)  B
 581 ASP   ( 270-)  B
 663 ASP   (  33-)  C
 670 ASP   (  40-)  C
 705 ASP   (  75-)  C
 718 ASP   (  88-)  C
 745 ASP   ( 115-)  C
 777 ASP   ( 147-)  C
 813 ASP   ( 183-)  C
 890 ASP   ( 270-)  C

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.

  13 GLU   (  13-)  A
  47 GLU   (  47-)  A
  54 GLU   (  54-)  A
  72 GLU   (  72-)  A
  96 GLU   (  96-)  A
 165 GLU   ( 167-)  A
 213 GLU   ( 215-)  A
 246 GLU   ( 248-)  A
 275 GLU   ( 277-)  A
 298 GLU   ( 300-)  A
 306 GLU   ( 308-)  A
 313 GLU   ( 315-)  A
 332 GLU   (  15-)  B
 364 GLU   (  47-)  B
 371 GLU   (  54-)  B
 377 GLU   (  60-)  B
 379 GLU   (  62-)  B
 457 GLU   ( 140-)  B
 501 GLU   ( 184-)  B
 506 GLU   ( 189-)  B
 514 GLU   ( 197-)  B
 532 GLU   ( 215-)  B
 619 GLU   ( 308-)  B
 677 GLU   (  47-)  C
 692 GLU   (  62-)  C
 845 GLU   ( 215-)  C
 902 GLU   ( 282-)  C

Geometric checks

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

 735 ALA   ( 105-)  C      N    CA   C   125.27    5.0
 888 ARG   ( 268-)  C      N    CA   C    98.50   -4.5

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.

  13 GLU   (  13-)  A
  26 ARG   (  26-)  A
  42 ARG   (  42-)  A
  47 GLU   (  47-)  A
  54 GLU   (  54-)  A
  72 GLU   (  72-)  A
  75 ASP   (  75-)  A
  88 ASP   (  88-)  A
  96 GLU   (  96-)  A
 115 ASP   ( 115-)  A
 121 ARG   ( 121-)  A
 137 ARG   ( 137-)  A
 147 ASP   ( 147-)  A
 165 GLU   ( 167-)  A
 166 ARG   ( 168-)  A
 169 ASP   ( 171-)  A
 213 GLU   ( 215-)  A
 215 ARG   ( 217-)  A
 231 ARG   ( 233-)  A
 246 GLU   ( 248-)  A
 266 ARG   ( 268-)  A
 268 ASP   ( 270-)  A
 275 GLU   ( 277-)  A
 295 ARG   ( 297-)  A
 298 GLU   ( 300-)  A
And so on for a total of 71 lines.

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.

 735 ALA   ( 105-)  C    5.76
 920 GLU   ( 300-)  C    5.73
 298 GLU   ( 300-)  A    5.36
 888 ARG   ( 268-)  C    5.06
 348 PRO   (  31-)  B    4.23
 390 ARG   (  73-)  B    4.01

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.

 467 PHE   ( 150-)  B    -3.1
 686 LYS   (  56-)  C    -2.6
 397 LEU   (  80-)  B    -2.6
 373 LYS   (  56-)  B    -2.6
 586 GLU   ( 275-)  B    -2.5
 689 PRO   (  59-)  C    -2.5
 780 PHE   ( 150-)  C    -2.4
 579 ARG   ( 268-)  B    -2.4
 273 GLU   ( 275-)  A    -2.4
 775 PRO   ( 145-)  C    -2.4
 547 LEU   ( 236-)  B    -2.3
 401 ARG   (  84-)  B    -2.3
  29 PRO   (  29-)  A    -2.3
 473 ASN   ( 156-)  B    -2.3
 284 ILE   ( 286-)  A    -2.3
 237 PRO   ( 239-)  A    -2.2
 716 GLY   (  86-)  C    -2.2
  68 PRO   (  68-)  A    -2.2
 789 SER   ( 159-)  C    -2.2
 403 GLY   (  86-)  B    -2.2
 640 VAL   (  10-)  C    -2.2
 676 GLY   (  46-)  C    -2.2
 451 VAL   ( 134-)  B    -2.1
 534 ARG   ( 217-)  B    -2.1
 266 ARG   ( 268-)  A    -2.1
 150 PHE   ( 150-)  A    -2.1
 376 PRO   (  59-)  B    -2.1
 912 THR   ( 292-)  C    -2.1
 304 TYR   ( 306-)  A    -2.1
 134 VAL   ( 134-)  A    -2.1
 825 VAL   ( 195-)  C    -2.1
 717 GLU   (  87-)  C    -2.1
 895 GLU   ( 275-)  C    -2.0
  85 PHE   (  85-)  A    -2.0
 478 VAL   ( 161-)  B    -2.0
 242 PRO   ( 244-)  A    -2.0
  46 GLY   (  46-)  A    -2.0
 708 PHE   (  78-)  C    -2.0
  78 PHE   (  78-)  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.

  46 GLY   (  46-)  A  Poor phi/psi
  56 LYS   (  56-)  A  Poor phi/psi
  57 ALA   (  57-)  A  Poor phi/psi
  65 PHE   (  65-)  A  PRO omega poor
 148 PRO   ( 148-)  A  PRO omega poor
 178 PHE   ( 180-)  A  Poor phi/psi
 191 SER   ( 193-)  A  PRO omega poor
 204 VAL   ( 206-)  A  Poor phi/psi
 226 LYS   ( 228-)  A  Poor phi/psi
 236 ILE   ( 238-)  A  PRO omega poor
 265 ALA   ( 267-)  A  Poor phi/psi
 273 GLU   ( 275-)  A  Poor phi/psi
 346 PRO   (  29-)  B  Poor phi/psi
 358 GLY   (  41-)  B  Poor phi/psi
 362 LEU   (  45-)  B  Poor phi/psi
 363 GLY   (  46-)  B  Poor phi/psi
 373 LYS   (  56-)  B  Poor phi/psi
 374 ALA   (  57-)  B  Poor phi/psi
 382 PHE   (  65-)  B  PRO omega poor
 402 PHE   (  85-)  B  Poor phi/psi
 462 PRO   ( 145-)  B  Poor phi/psi
 465 PRO   ( 148-)  B  PRO omega poor
 476 SER   ( 159-)  B  Poor phi/psi
 477 SER   ( 160-)  B  Poor phi/psi
 510 SER   ( 193-)  B  Poor phi/psi, PRO omega poor
 523 VAL   ( 206-)  B  Poor phi/psi
 549 ILE   ( 238-)  B  PRO omega poor
 614 GLY   ( 303-)  B  Poor phi/psi
 657 HIS   (  27-)  C  Poor phi/psi
 675 LEU   (  45-)  C  Poor phi/psi
 676 GLY   (  46-)  C  Poor phi/psi
 686 LYS   (  56-)  C  Poor phi/psi
 687 ALA   (  57-)  C  Poor phi/psi
 695 PHE   (  65-)  C  PRO omega poor
 778 PRO   ( 148-)  C  PRO omega poor
 789 SER   ( 159-)  C  Poor phi/psi
 823 SER   ( 193-)  C  PRO omega poor
 836 VAL   ( 206-)  C  Poor phi/psi
 858 ILE   ( 238-)  C  PRO omega poor
 861 PRO   ( 241-)  C  Poor phi/psi
 887 ALA   ( 267-)  C  Poor phi/psi
 895 GLU   ( 275-)  C  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.888

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.

 647 SER   (  17-)  C    0.34
 334 SER   (  17-)  B    0.36
 740 SER   ( 110-)  C    0.39
 110 SER   ( 110-)  A    0.39

Warning: Unusual backbone conformations

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

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

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

   7 ALA   (   7-)  A      0
  10 VAL   (  10-)  A      0
  29 PRO   (  29-)  A      0
  31 PRO   (  31-)  A      0
  45 LEU   (  45-)  A      0
  47 GLU   (  47-)  A      0
  56 LYS   (  56-)  A      0
  57 ALA   (  57-)  A      0
  62 GLU   (  62-)  A      0
  63 HIS   (  63-)  A      0
  65 PHE   (  65-)  A      0
  68 PRO   (  68-)  A      0
  70 SER   (  70-)  A      0
  71 TRP   (  71-)  A      0
  79 PRO   (  79-)  A      0
  82 HIS   (  82-)  A      0
  84 ARG   (  84-)  A      0
  85 PHE   (  85-)  A      0
  87 GLU   (  87-)  A      0
  88 ASP   (  88-)  A      0
  90 THR   (  90-)  A      0
 103 VAL   ( 103-)  A      0
 105 ALA   ( 105-)  A      0
 114 MET   ( 114-)  A      0
 132 PRO   ( 132-)  A      0
And so on for a total of 334 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.171

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 139 GLY   ( 139-)  A   1.85   80

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]

 384 PRO   (  67-)  B    0.45 HIGH
 550 PRO   ( 239-)  B    0.45 HIGH

Warning: Unusual PRO puckering phases

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

 242 PRO   ( 244-)  A  -114.9 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.

  89 GLY   (  89-)  A      CA  <->   92 GLN   (  92-)  A      NE2    0.40    2.70  INTRA BL
 932 ARG   ( 312-)  C      NE  <->  948 HOH   ( 410 )  C      O      0.34    2.36  INTRA BL
 266 ARG   ( 268-)  A      NE  <->  268 ASP   ( 270-)  A      OD1    0.27    2.43  INTRA BL
 798 ARG   ( 168-)  C      NH1 <->  800 GLN   ( 170-)  C      CG     0.25    2.85  INTRA BF
 860 ALA   ( 240-)  C      O   <->  862 LEU   ( 242-)  C      N      0.24    2.46  INTRA BF
 547 LEU   ( 236-)  B      CD2 <->  608 ARG   ( 297-)  B      NE     0.23    2.87  INTRA BF
 886 MET   ( 266-)  C      SD  <->  909 PHE   ( 289-)  C      CE2    0.23    3.17  INTRA BF
 720 THR   (  90-)  C      CG2 <->  721 VAL   (  91-)  C      N      0.22    2.78  INTRA BL
 480 ILE   ( 163-)  B      CG2 <->  481 SER   ( 164-)  B      N      0.22    2.78  INTRA BF
 516 GLU   ( 199-)  B      CG  <->  605 MET   ( 294-)  B      SD     0.22    3.18  INTRA BF
 632 ARG   (   2-)  C      NE  <->  948 HOH   ( 405 )  C      O      0.21    2.49  INTRA BF
 719 GLY   (  89-)  C      CA  <->  722 GLN   (  92-)  C      CG     0.21    2.99  INTRA BL
 433 LYS   ( 116-)  B      N   <->  472 ALA   ( 155-)  B      O      0.21    2.49  INTRA BF
 685 ALA   (  55-)  C      O   <->  686 LYS   (  56-)  C      CD     0.19    2.51  INTRA BF
 473 ASN   ( 156-)  B      ND2 <->  500 ASP   ( 183-)  B      OD2    0.19    2.51  INTRA BF
 156 ASN   ( 156-)  A      N   <->  181 ASP   ( 183-)  A      OD2    0.19    2.51  INTRA BF
 509 LEU   ( 192-)  B      N   <->  944 ANP   ( 402-)  B      N1     0.19    2.81  INTRA BF
  27 HIS   (  27-)  A      CD2 <->  304 TYR   ( 306-)  A      CE2    0.19    3.01  INTRA BF
  74 TYR   (  74-)  A      O   <->  100 LYS   ( 100-)  A      NZ     0.18    2.52  INTRA BL
 928 GLU   ( 308-)  C      OE2 <->  931 ARG   ( 311-)  C      NH1    0.18    2.52  INTRA BL
 713 GLY   (  83-)  C      N   <->  717 GLU   (  87-)  C      OE2    0.18    2.52  INTRA BF
 715 PHE   (  85-)  C      CA  <->  720 THR   (  90-)  C      CG2    0.17    3.03  INTRA BF
 321 LEU   (   4-)  B      O   <->  395 PHE   (  78-)  B      N      0.17    2.53  INTRA BL
 534 ARG   ( 217-)  B      O   <->  546 GLU   ( 235-)  B      N      0.16    2.54  INTRA BF
 617 TYR   ( 306-)  B      N   <->  618 PRO   ( 307-)  B      CD     0.16    2.84  INTRA BF
And so on for a total of 159 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

 223 TYR   ( 225-)  A      -6.96
  84 ARG   (  84-)  A      -6.68
 714 ARG   (  84-)  C      -6.35
 695 PHE   (  65-)  C      -6.29
 344 HIS   (  27-)  B      -6.21
  27 HIS   (  27-)  A      -6.07
 401 ARG   (  84-)  B      -6.03
 179 ARG   ( 181-)  A      -5.86
 227 TYR   ( 229-)  A      -5.61
 755 GLN   ( 125-)  C      -5.59
 390 ARG   (  73-)  B      -5.57
  73 ARG   (  73-)  A      -5.55
 656 ARG   (  26-)  C      -5.51
 703 ARG   (  73-)  C      -5.47
 125 GLN   ( 125-)  A      -5.36
 442 GLN   ( 125-)  B      -5.27
 837 PHE   ( 207-)  C      -5.24
 460 VAL   ( 143-)  B      -5.22
 143 VAL   ( 143-)  A      -5.19
 797 GLU   ( 167-)  C      -5.09
 773 VAL   ( 143-)  C      -5.07

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.

 849 GLU   ( 219-)  C       851 - PRO    221- ( C)         -4.25

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

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: B

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: C

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

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

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.

 948 HOH   ( 424 )  C      O

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.

  14 HIS   (  14-)  A
  92 GLN   (  92-)  A
 156 ASN   ( 156-)  A
 331 HIS   (  14-)  B
 409 GLN   (  92-)  B
 562 GLN   ( 251-)  B
 722 GLN   (  92-)  C
 755 GLN   ( 125-)  C

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.

  11 SER   (  11-)  A      N
  26 ARG   (  26-)  A      NE
  57 ALA   (  57-)  A      N
  81 LEU   (  81-)  A      N
  82 HIS   (  82-)  A      N
  88 ASP   (  88-)  A      N
 105 ALA   ( 105-)  A      N
 120 LYS   ( 120-)  A      NZ
 121 ARG   ( 121-)  A      NE
 131 VAL   ( 131-)  A      N
 146 PHE   ( 146-)  A      N
 153 LYS   ( 153-)  A      NZ
 157 THR   ( 157-)  A      N
 159 VAL   ( 161-)  A      N
 162 SER   ( 164-)  A      OG
 262 ARG   ( 264-)  A      N
 262 ARG   ( 264-)  A      NH2
 290 THR   ( 292-)  A      N
 328 SER   (  11-)  B      N
 332 GLU   (  15-)  B      N
 367 LEU   (  50-)  B      N
 373 LYS   (  56-)  B      NZ
 374 ALA   (  57-)  B      N
 386 LEU   (  69-)  B      N
 389 GLU   (  72-)  B      N
And so on for a total of 63 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  82 HIS   (  82-)  A      NE2
 125 GLN   ( 125-)  A      OE1
 670 ASP   (  40-)  C      OD2
 819 GLU   ( 189-)  C      OE1
 902 GLU   ( 282-)  C      OE2

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.

 181 ASP   ( 183-)  A   H-bonding suggests Asn; but Alt-Rotamer
 516 GLU   ( 199-)  B   H-bonding suggests Gln
 611 GLU   ( 300-)  B   H-bonding suggests Gln
 813 ASP   ( 183-)  C   H-bonding suggests Asn
 902 GLU   ( 282-)  C   H-bonding suggests Gln; Ligand-contact

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 :  -0.331
  2nd generation packing quality :  -0.884
  Ramachandran plot appearance   :  -2.159
  chi-1/chi-2 rotamer normality  :  -2.888
  Backbone conformation          :   1.011

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.344 (tight)
  Bond angles                    :   0.635 (tight)
  Omega angle restraints         :   0.213 (tight)
  Side chain planarity           :   0.225 (tight)
  Improper dihedral distribution :   0.657
  B-factor distribution          :   0.438
  Inside/Outside distribution    :   1.002

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :   0.5
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.6
  Backbone conformation          :   1.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.344 (tight)
  Bond angles                    :   0.635 (tight)
  Omega angle restraints         :   0.213 (tight)
  Side chain planarity           :   0.225 (tight)
  Improper dihedral distribution :   0.657
  B-factor distribution          :   0.438
  Inside/Outside distribution    :   1.002
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

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    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,
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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
    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.