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 pdb2xn9.ent

Checks that need to be done early-on in validation

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

1036 GOL   (1201-)  B  A

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.

1036 GOL   (1201-)  B  A
1037 GOL   (1245-)  B  -
1038 GOL   (1246-)  B  -
1040 GOL   (1247-)  B  -

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

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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 GLN   (   2-)  A      CG
   1 GLN   (   2-)  A      CD
   1 GLN   (   2-)  A      OE1
   1 GLN   (   2-)  A      NE2
   2 LEU   (   3-)  A      CG
   2 LEU   (   3-)  A      CD1
   2 LEU   (   3-)  A      CD2
  94 GLN   (  95-)  A      CG
  94 GLN   (  95-)  A      CD
  94 GLN   (  95-)  A      OE1
  94 GLN   (  95-)  A      NE2
 112 GLN   ( 113-)  A      CG
 112 GLN   ( 113-)  A      CD
 112 GLN   ( 113-)  A      OE1
 112 GLN   ( 113-)  A      NE2
 128 ASP   ( 129-)  A      CG
 128 ASP   ( 129-)  A      OD1
 128 ASP   ( 129-)  A      OD2
 214 GLU   (  17-)  B      CG
 214 GLU   (  17-)  B      CD
 214 GLU   (  17-)  B      OE1
 214 GLU   (  17-)  B      OE2
 386 SER   ( 189-)  B      OG
 415 SER   ( 218-)  B      OG
 416 GLU   ( 219-)  B      CG
And so on for a total of 79 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: 0

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

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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.

 406 ARG   ( 209-)  B
 753 ARG   ( 100-)  D
 776 ARG   ( 123-)  D

Warning: Tyrosine convention problem

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

 234 TYR   (  37-)  B
 247 TYR   (  50-)  B
 263 TYR   (  66-)  B
 301 TYR   ( 104-)  B
 459 TYR   (  18-)  C
 462 TYR   (  21-)  C
 515 TYR   (  74-)  C
 520 TYR   (  79-)  C
 535 TYR   (  94-)  C
 591 TYR   ( 150-)  C
 594 TYR   ( 153-)  C
 620 TYR   ( 179-)  C
 628 TYR   ( 187-)  C
 634 TYR   ( 193-)  C
 653 TYR   ( 212-)  C
 803 TYR   ( 150-)  D
 814 TYR   ( 161-)  D

Warning: Phenylalanine convention problem

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

 180 PHE   ( 181-)  A
 197 PHE   ( 198-)  A
 254 PHE   (  57-)  B
 287 PHE   (  90-)  B
 347 PHE   ( 150-)  B
 405 PHE   ( 208-)  B
 498 PHE   (  57-)  C
 507 PHE   (  66-)  C
 519 PHE   (  78-)  C
 617 PHE   ( 176-)  C
 704 PHE   (  51-)  D
 833 PHE   ( 180-)  D
 846 PHE   (  13-)  E
 851 PHE   (  18-)  E
 873 PHE   (  40-)  E
 965 PHE   ( 132-)  E

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.

  70 ASP   (  71-)  A
 138 ASP   ( 139-)  A
 155 ASP   ( 156-)  A
 179 ASP   ( 180-)  A
 194 ASP   ( 195-)  A
 253 ASP   (  56-)  B
 350 ASP   ( 153-)  B
 446 ASP   (   5-)  C
 452 ASP   (  11-)  C
 502 ASP   (  61-)  C
 627 ASP   ( 186-)  C
 835 ASP   (   2-)  E
 909 ASP   (  76-)  E

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.

  14 GLU   (  15-)  A
  16 GLU   (  17-)  A
  37 GLU   (  38-)  A
  53 GLU   (  54-)  A
 326 GLU   ( 129-)  B
 329 GLU   ( 132-)  B
 331 GLU   ( 134-)  B
 362 GLU   ( 165-)  B
 419 GLU   ( 222-)  B
 442 GLU   (   1-)  C
 524 GLU   (  83-)  C
 528 GLU   (  87-)  C
 543 GLU   ( 102-)  C
 563 GLU   ( 122-)  C
 599 GLU   ( 158-)  C
 606 GLU   ( 165-)  C
 635 GLU   ( 194-)  C
 700 GLU   (  47-)  D
 708 GLU   (  55-)  D
 724 GLU   (  71-)  D
 751 GLU   (  98-)  D
 787 GLU   ( 134-)  D
 794 GLU   ( 141-)  D
 811 GLU   ( 158-)  D
 819 GLU   ( 166-)  D
 832 GLU   ( 179-)  D
 885 GLU   (  52-)  E
 892 GLU   (  59-)  E
 971 GLU   ( 138-)  E
1009 GLU   ( 176-)  E

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

 |  0.996890 -0.000226 -0.000225|
 | -0.000226  0.996793 -0.000282|
 | -0.000225 -0.000282  0.996889|
Proposed new scale matrix

 |  0.005248  0.000002  0.002288|
 |  0.000005  0.020520  0.000006|
 |  0.000001  0.000002  0.006563|
With corresponding cell

    A    = 190.573  B   =  48.733  C    = 166.231
    Alpha=  90.019  Beta= 113.572  Gamma=  90.026

The CRYST1 cell dimensions

    A    = 191.180  B   =  48.890  C    = 166.720
    Alpha=  90.000  Beta= 113.550  Gamma=  90.000

Variance: 343.446
(Under-)estimated Z-score: 13.658

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.

  74 HIS   (  75-)  A      CG   ND1  CE1 109.73    4.1
 334 HIS   ( 137-)  B      CG   ND1  CE1 109.63    4.0
 351 HIS   ( 154-)  B      CG   ND1  CE1 109.64    4.0
 354 LEU   ( 157-)  B      CA   CB   CG  131.77    4.4
 404 HIS   ( 207-)  B      CG   ND1  CE1 109.66    4.1
 985 ASP   ( 152-)  E      N    CA   C   123.64    4.4

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  14 GLU   (  15-)  A
  16 GLU   (  17-)  A
  37 GLU   (  38-)  A
  53 GLU   (  54-)  A
  70 ASP   (  71-)  A
 138 ASP   ( 139-)  A
 155 ASP   ( 156-)  A
 179 ASP   ( 180-)  A
 194 ASP   ( 195-)  A
 253 ASP   (  56-)  B
 326 GLU   ( 129-)  B
 329 GLU   ( 132-)  B
 331 GLU   ( 134-)  B
 350 ASP   ( 153-)  B
 362 GLU   ( 165-)  B
 406 ARG   ( 209-)  B
 419 GLU   ( 222-)  B
 442 GLU   (   1-)  C
 446 ASP   (   5-)  C
 452 ASP   (  11-)  C
 502 ASP   (  61-)  C
 524 GLU   (  83-)  C
 528 GLU   (  87-)  C
 543 GLU   ( 102-)  C
 563 GLU   ( 122-)  C
 599 GLU   ( 158-)  C
 606 GLU   ( 165-)  C
 627 ASP   ( 186-)  C
 635 GLU   ( 194-)  C
 700 GLU   (  47-)  D
 708 GLU   (  55-)  D
 724 GLU   (  71-)  D
 751 GLU   (  98-)  D
 753 ARG   ( 100-)  D
 776 ARG   ( 123-)  D
 787 GLU   ( 134-)  D
 794 GLU   ( 141-)  D
 811 GLU   ( 158-)  D
 819 GLU   ( 166-)  D
 832 GLU   ( 179-)  D
 835 ASP   (   2-)  E
 885 GLU   (  52-)  E
 892 GLU   (  59-)  E
 909 ASP   (  76-)  E
 971 GLU   ( 138-)  E
1009 GLU   ( 176-)  E

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.

 985 ASP   ( 152-)  E    4.19

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.

 939 THR   ( 106-)  E    -3.1
 836 THR   (   3-)  E    -3.0
 957 PRO   ( 124-)  E    -2.9
 273 PHE   (  76-)  B    -2.7
 766 THR   ( 113-)  D    -2.7
 592 LYS   ( 151-)  C    -2.7
 515 TYR   (  74-)  C    -2.6
  18 LEU   (  19-)  A    -2.6
 439 ARG   ( 242-)  B    -2.5
 747 ASN   (  94-)  D    -2.5
 703 ARG   (  50-)  D    -2.5
 806 PHE   ( 153-)  D    -2.4
 745 LEU   (  92-)  D    -2.4
 669 PRO   (  16-)  D    -2.4
  46 VAL   (  47-)  A    -2.3
  56 LYS   (  57-)  A    -2.3
  69 LYS   (  70-)  A    -2.3
 755 PRO   ( 102-)  D    -2.3
 933 THR   ( 100-)  E    -2.3
 569 THR   ( 128-)  C    -2.3
 796 HIS   ( 143-)  D    -2.3
 854 THR   (  21-)  E    -2.3
  64 PHE   (  65-)  A    -2.3
  12 ILE   (  13-)  A    -2.3
 122 ARG   ( 123-)  A    -2.3
 238 PRO   (  41-)  B    -2.2
 749 PRO   (  96-)  D    -2.2
 789 VAL   ( 136-)  D    -2.2
 313 ASP   ( 116-)  B    -2.2
 908 VAL   (  75-)  E    -2.2
 826 PRO   ( 173-)  D    -2.2
 751 GLU   (  98-)  D    -2.2
 839 ARG   (   6-)  E    -2.1
 871 VAL   (  38-)  E    -2.1
 823 LEU   ( 170-)  D    -2.1
 792 PRO   ( 139-)  D    -2.1
 990 THR   ( 157-)  E    -2.1
 768 PRO   ( 115-)  D    -2.1
 804 LEU   ( 151-)  D    -2.1
 108 LYS   ( 109-)  A    -2.1
 248 SER   (  51-)  B    -2.1
 941 PRO   ( 108-)  E    -2.1
 810 THR   ( 157-)  D    -2.1
  95 GLY   (  96-)  A    -2.0
 534 LEU   (  93-)  C    -2.0
 775 LEU   ( 122-)  D    -2.0
 159 LEU   ( 160-)  A    -2.0
 940 GLN   ( 107-)  E    -2.0
 807 LEU   ( 154-)  D    -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.

   6 SER   (   7-)  A  PRO omega poor
  58 LYS   (  59-)  A  Poor phi/psi
  68 ARG   (  69-)  A  Poor phi/psi
  91 ALA   (  92-)  A  omega poor
  94 GLN   (  95-)  A  omega poor
  95 GLY   (  96-)  A  omega poor
  96 ASN   (  97-)  A  Poor phi/psi
  97 LEU   (  98-)  A  omega poor
 102 GLY   ( 103-)  A  omega poor
 136 ASP   ( 137-)  A  Poor phi/psi
 169 ASN   ( 170-)  A  omega poor
 175 SER   ( 176-)  A  omega poor
 176 ASN   ( 177-)  A  omega poor
 206 SER   (   9-)  B  PRO omega poor
 227 ASN   (  30-)  B  Poor phi/psi
 234 TYR   (  37-)  B  omega poor
 252 ASN   (  55-)  B  Poor phi/psi
 265 VAL   (  68-)  B  omega poor
 271 GLU   (  74-)  B  omega poor
 299 GLU   ( 102-)  B  omega poor
 320 PRO   ( 123-)  B  omega poor
 336 GLN   ( 139-)  B  Poor phi/psi
 348 TYR   ( 151-)  B  PRO omega poor
 416 GLU   ( 219-)  B  Poor phi/psi
 417 ASN   ( 220-)  B  Poor phi/psi
And so on for a total of 66 lines.

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

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

chi-1/chi-2 correlation Z-score : -3.114

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.

 773 THR   ( 120-)  D    0.36
 588 SER   ( 147-)  C    0.37

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!

   6 SER   (   7-)  A      0
   8 GLN   (   9-)  A      0
   9 PHE   (  10-)  A      0
  14 GLU   (  15-)  A      0
  24 SER   (  25-)  A      0
  26 SER   (  27-)  A      0
  38 PRO   (  39-)  A      0
  46 VAL   (  47-)  A      0
  49 VAL   (  50-)  A      0
  57 LEU   (  58-)  A      0
  58 LYS   (  59-)  A      0
  68 ARG   (  69-)  A      0
  69 LYS   (  70-)  A      0
  70 ASP   (  71-)  A      0
  76 THR   (  77-)  A      0
  77 ALA   (  78-)  A      0
  78 ALA   (  79-)  A      0
  79 GLN   (  80-)  A      0
  83 THR   (  84-)  A      0
  93 SER   (  94-)  A      0
  94 GLN   (  95-)  A      0
  96 ASN   (  97-)  A      0
 101 LYS   ( 102-)  A      0
 114 PRO   ( 115-)  A      0
 116 PRO   ( 117-)  A      0
And so on for a total of 435 lines.

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]

  38 PRO   (  39-)  A    0.46 HIGH
 114 PRO   ( 115-)  A    0.07 LOW
 284 PRO   (  87-)  B    0.18 LOW
 327 PRO   ( 130-)  B    0.18 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].

  42 PRO   (  43-)  A   101.7 envelop C-beta (108 degrees)
 274 PRO   (  77-)  B  -133.1 half-chair C-delta/C-gamma (-126 degrees)
 319 PRO   ( 122-)  B   -54.3 half-chair C-beta/C-alpha (-54 degrees)
 669 PRO   (  16-)  D   -61.2 half-chair C-beta/C-alpha (-54 degrees)
 749 PRO   (  96-)  D  -167.2 half-chair N/C-delta (-162 degrees)
 826 PRO   ( 173-)  D   164.8 half-chair C-alpha/N (162 degrees)
 838 PRO   (   5-)  E   -59.5 half-chair C-beta/C-alpha (-54 degrees)
 941 PRO   ( 108-)  E   -20.6 half-chair C-alpha/N (-18 degrees)
 957 PRO   ( 124-)  E   -64.6 envelop C-beta (-72 degrees)
 998 PRO   ( 165-)  E    18.6 half-chair N/C-delta (18 degrees)
1023 PRO   (   1-)  F   -27.3 envelop C-alpha (-36 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 370 ASP   ( 173-)  B      OD1  <->   390 ARG   ( 193-)  B      NH2  0.41    2.29  INTRA BL
 984 GLY   ( 151-)  E      O    <->   986 TRP   ( 153-)  E      N    0.41    2.29  INTRA BF
 227 ASN   (  30-)  B      OD1  <->   270 LYS   (  73-)  B      NZ   0.34    2.36  INTRA BF
 513 ASP   (  72-)  C      OD2  <->   544 LYS   ( 103-)  C      NZ   0.33    2.37  INTRA
 787 GLU   ( 134-)  D      OE1  <->   800 LYS   ( 147-)  D      NZ   0.33    2.37  INTRA BF
 549 ARG   ( 108-)  C      NH2  <->   645 ILE   ( 204-)  C      O    0.28    2.42  INTRA
 835 ASP   (   2-)  E      OD1  <->   839 ARG   (   6-)  E      NH2  0.25    2.45  INTRA BF
 940 GLN   ( 107-)  E      OE1  <->   947 LEU   ( 114-)  E      N    0.25    2.45  INTRA BF
 372 GLN   ( 175-)  B      NE2  <->  1038 GOL   (1246-)  B      O2   0.21    2.49  INTRA BF
 549 ARG   ( 108-)  C      NH1  <->  1043 HOH   (2035 )  C      O    0.21    2.49  INTRA
 852 ASN   (  19-)  E      ND2  <->   855 GLU   (  22-)  E      OE1  0.21    2.49  INTRA BF
  25 SER   (  26-)  A      N    <->  1041 HOH   (2017 )  A      O    0.20    2.50  INTRA BF
 815 ASP   ( 162-)  D      OD1  <->   830 HIS   ( 177-)  D      ND1  0.20    2.50  INTRA BF
 654 THR   ( 213-)  C      CG2  <->   655 LYS   ( 214-)  C      N    0.20    2.80  INTRA BF
 267 ARG   (  70-)  B      NH2  <->   270 LYS   (  73-)  B      O    0.19    2.51  INTRA BL
 835 ASP   (   2-)  E      CG   <->   839 ARG   (   6-)  E      NH2  0.18    2.92  INTRA BF
  91 ALA   (  92-)  A      O    <->  1041 HOH   (2050 )  A      O    0.18    2.22  INTRA
 962 VAL   ( 129-)  E      CG1  <->   992 VAL   ( 159-)  E      CG2  0.17    3.03  INTRA BF
 316 ASN   ( 119-)  B      ND2  <->   382 ASP   ( 185-)  B      OD2  0.16    2.54  INTRA BF
 847 GLU   (  14-)  E      N    <->   860 LEU   (  27-)  E      O    0.15    2.55  INTRA BL
 963 ARG   ( 130-)  E      O    <->  1007 GLN   ( 174-)  E      N    0.15    2.55  INTRA BF
 265 VAL   (  68-)  B      O    <->  1042 HOH   (2018 )  B      O    0.15    2.25  INTRA BL
 568 ARG   ( 127-)  C      NH2  <->   902 GLU   (  69-)  E      OE1  0.15    2.55  INTRA BF
 170 SER   ( 171-)  A      OG   <->   390 ARG   ( 193-)  B      CD   0.15    2.65  INTRA BL
 326 GLU   ( 129-)  B      OE1  <->   439 ARG   ( 242-)  B      NH1  0.14    2.56  INTRA
And so on for a total of 130 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

 753 ARG   ( 100-)  D      -7.67
 298 TYR   ( 101-)  B      -6.31
 940 GLN   ( 107-)  E      -6.13
 282 LYS   (  85-)  B      -6.06
 999 ARG   ( 166-)  E      -5.88
 295 ARG   (  98-)  B      -5.82
 833 PHE   ( 180-)  D      -5.75
 190 ILE   ( 191-)  A      -5.69
 147 LYS   ( 148-)  A      -5.63
 938 LYS   ( 105-)  E      -5.56
 334 HIS   ( 137-)  B      -5.54
 521 TYR   (  80-)  C      -5.53
 671 GLN   (  18-)  D      -5.53
 101 LYS   ( 102-)  A      -5.39
 945 HIS   ( 112-)  E      -5.30
 623 LYS   ( 182-)  C      -5.22
 927 ARG   (  94-)  E      -5.19
   9 PHE   (  10-)  A      -5.17
 463 ASN   (  22-)  C      -5.16
 485 ARG   (  44-)  C      -5.08
 316 ASN   ( 119-)  B      -5.06
 449 GLU   (   8-)  C      -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.

 938 LYS   ( 105-)  E       941 - PRO    108- ( E)         -4.98

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: 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: D

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: E

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: F

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.

 943 GLN   ( 110-)  E   -2.95
 837 ARG   (   4-)  E   -2.90
  94 GLN   (  95-)  A   -2.86
 572 LYS   ( 131-)  C   -2.77
 825 GLU   ( 172-)  D   -2.70
 942 LEU   ( 109-)  E   -2.54

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.

 941 PRO   ( 108-)  E     -  944 HIS   ( 111-)  E        -2.17

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

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

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.

 224 GLN   (  27-)  B
 225 ASN   (  28-)  B
 240 GLN   (  43-)  B
 364 HIS   ( 167-)  B
 372 GLN   ( 175-)  B
 430 GLN   ( 233-)  B
 486 ASN   (  45-)  C
 577 GLN   ( 136-)  C
 989 GLN   ( 156-)  E
1028 GLN   (   6-)  F
1029 ASN   (   7-)  F

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.

  32 GLN   (  33-)  A      NE2
  54 VAL   (  55-)  A      N
  70 ASP   (  71-)  A      N
  88 CYS   (  89-)  A      N
 101 LYS   ( 102-)  A      N
 129 LYS   ( 130-)  A      N
 137 PHE   ( 138-)  A      N
 156 LYS   ( 157-)  A      NZ
 175 SER   ( 176-)  A      N
 217 ASN   (  20-)  B      N
 229 ASP   (  32-)  B      N
 242 LEU   (  45-)  B      N
 243 ARG   (  46-)  B      NH2
 250 ILE   (  53-)  B      N
 251 VAL   (  54-)  B      N
 267 ARG   (  70-)  B      N
 271 GLU   (  74-)  B      N
 282 LYS   (  85-)  B      N
 292 SER   (  95-)  B      OG
 294 SER   (  97-)  B      OG
 300 GLN   ( 103-)  B      NE2
 313 ASP   ( 116-)  B      N
 328 SER   ( 131-)  B      OG
 390 ARG   ( 193-)  B      NH2
 394 SER   ( 197-)  B      N
And so on for a total of 56 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.

 481 ASP   (  40-)  C      OD1
 627 ASP   ( 186-)  C      OD1
 631 ASP   ( 190-)  C      OD1
 664 GLU   (  11-)  D      OE1
 719 ASP   (  66-)  D      OD2
 802 HIS   ( 149-)  D      ND1
 869 GLU   (  36-)  E      OE2
 909 ASP   (  76-)  E      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1043 HOH   (2013 )  C      O  0.96  K  5

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.

 614 ASP   ( 173-)  C   H-bonding suggests Asn
 631 ASP   ( 190-)  C   H-bonding suggests Asn
 649 ASP   ( 208-)  C   H-bonding suggests Asn; but Alt-Rotamer
 682 ASP   (  29-)  D   H-bonding suggests Asn; but Alt-Rotamer
 719 ASP   (  66-)  D   H-bonding suggests Asn; but Alt-Rotamer
 751 GLU   (  98-)  D   H-bonding suggests Gln
 812 ASP   ( 159-)  D   H-bonding suggests Asn; but Alt-Rotamer
1002 GLU   ( 169-)  E   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 :  -0.263
  2nd generation packing quality :  -1.474
  Ramachandran plot appearance   :  -0.759
  chi-1/chi-2 rotamer normality  :  -3.114 (poor)
  Backbone conformation          :  -0.227

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.580 (tight)
  Bond angles                    :   0.709
  Omega angle restraints         :   1.195
  Side chain planarity           :   0.513 (tight)
  Improper dihedral distribution :   0.750
  B-factor distribution          :   0.432
  Inside/Outside distribution    :   1.033

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   0.6
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.580 (tight)
  Bond angles                    :   0.709
  Omega angle restraints         :   1.195
  Side chain planarity           :   0.513 (tight)
  Improper dihedral distribution :   0.750
  B-factor distribution          :   0.432
  Inside/Outside distribution    :   1.033
==============

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.