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 pdb3n8w.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: A and B

All-atom RMS fit for the two chains : 0.503
CA-only RMS fit for the two chains : 0.277

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: A and B

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 65
Number of matrices in space group: 6
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 1
Warning: one pair of SEQRES sequences is sneakingly different
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 6
Polymer chain multiplicity and SEQRES multiplicity disagree 2 1
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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.

1115 NDG   ( 662-)  A  -
1116 BMA   ( 683-)  A  -
1117 NDG   ( 672-)  A  -
1118 BMA   ( 673-)  A  -
1119 MAN   ( 674-)  A  -
1120 MAN   ( 675-)  A  -
1122 NDG   (1662-)  B  -
1123 NDG   (1681-)  B  -
1124 A11   (1751-)  B  -
1125 A10   (1750-)  B  -
1126 BMA   (1673-)  B  -
1127 NDG   (1672-)  B  -
1128 MAN   (1683-)  B  -
1129 BOG   ( 751-)  A  -
1130 FLP   ( 701-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1107 NAG   ( 661-)  A  -   O4  bound to 1115 NDG   ( 662-)  A  -   C1
1108 NAG   ( 681-)  A  -   O4  bound to 1109 NAG   ( 682-)  A  -   C1
1109 NAG   ( 682-)  A  -   O4  bound to 1116 BMA   ( 683-)  A  -   C1
1110 NAG   ( 671-)  A  -   O4  bound to 1117 NDG   ( 672-)  A  -   C1
1111 NAG   (1661-)  B  -   O4  bound to 1122 NDG   (1662-)  B  -   C1
1112 NAG   (1682-)  B  -   O4  bound to 1128 MAN   (1683-)  B  -   C1
1113 NAG   (1671-)  B  -   O4  bound to 1127 NDG   (1672-)  B  -   C1

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

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'.

  52 ARG   (  83-)  A      CG
  52 ARG   (  83-)  A      CD
  52 ARG   (  83-)  A      NE
  52 ARG   (  83-)  A      CZ
  52 ARG   (  83-)  A      NH1
  52 ARG   (  83-)  A      NH2
 137 LYS   ( 168-)  A      CG
 137 LYS   ( 168-)  A      CD
 137 LYS   ( 168-)  A      CE
 137 LYS   ( 168-)  A      NZ
 138 LYS   ( 169-)  A      CG
 138 LYS   ( 169-)  A      CD
 138 LYS   ( 169-)  A      CE
 138 LYS   ( 169-)  A      NZ
 139 GLN   ( 170-)  A      CG
 139 GLN   ( 170-)  A      CD
 139 GLN   ( 170-)  A      OE1
 139 GLN   ( 170-)  A      NE2
 155 LYS   ( 186-)  A      CG
 155 LYS   ( 186-)  A      CD
 155 LYS   ( 186-)  A      CE
 155 LYS   ( 186-)  A      NZ
 208 GLU   ( 239-)  A      CG
 208 GLU   ( 239-)  A      CD
 208 GLU   ( 239-)  A      OE1
And so on for a total of 132 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: 2

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

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.

 119 ARG   ( 150-)  A
 428 ARG   ( 459-)  A
 981 ARG   ( 459-)  B

Warning: Tyrosine convention problem

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

  24 TYR   (  55-)  A
  99 TYR   ( 130-)  A
 211 TYR   ( 242-)  A
 223 TYR   ( 254-)  A
 231 TYR   ( 262-)  A
 244 TYR   ( 275-)  A
 317 TYR   ( 348-)  A
 324 TYR   ( 355-)  A
 342 TYR   ( 373-)  A
 354 TYR   ( 385-)  A
 373 TYR   ( 404-)  A
 386 TYR   ( 417-)  A
 444 TYR   ( 475-)  A
 464 TYR   ( 495-)  A
 513 TYR   ( 544-)  A
 560 TYR   (  38-)  B
 577 TYR   (  55-)  B
 652 TYR   ( 130-)  B
 658 TYR   ( 136-)  B
 669 TYR   ( 147-)  B
 764 TYR   ( 242-)  B
 776 TYR   ( 254-)  B
 784 TYR   ( 262-)  B
 870 TYR   ( 348-)  B
 877 TYR   ( 355-)  B
 895 TYR   ( 373-)  B
 907 TYR   ( 385-)  B
 926 TYR   ( 404-)  B
 939 TYR   ( 417-)  B
 997 TYR   ( 475-)  B
1017 TYR   ( 495-)  B
1066 TYR   ( 544-)  B

Warning: Phenylalanine convention problem

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

  19 PHE   (  50-)  A
  57 PHE   (  88-)  A
  71 PHE   ( 102-)  A
 150 PHE   ( 181-)  A
 156 PHE   ( 187-)  A
 167 PHE   ( 198-)  A
 170 PHE   ( 201-)  A
 178 PHE   ( 209-)  A
 216 PHE   ( 247-)  A
 336 PHE   ( 367-)  A
 378 PHE   ( 409-)  A
 447 PHE   ( 478-)  A
 487 PHE   ( 518-)  A
 498 PHE   ( 529-)  A
 519 PHE   ( 550-)  A
 549 PHE   ( 580-)  A
 572 PHE   (  50-)  B
 610 PHE   (  88-)  B
 629 PHE   ( 107-)  B
 703 PHE   ( 181-)  B
 709 PHE   ( 187-)  B
 720 PHE   ( 198-)  B
 723 PHE   ( 201-)  B
 731 PHE   ( 209-)  B
 742 PHE   ( 220-)  B
 769 PHE   ( 247-)  B
 889 PHE   ( 367-)  B
 931 PHE   ( 409-)  B
1000 PHE   ( 478-)  B
1040 PHE   ( 518-)  B
1051 PHE   ( 529-)  B
1072 PHE   ( 550-)  B
1102 PHE   ( 580-)  B

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  22 ASP   (  53-)  A
 218 ASP   ( 249-)  A
 283 ASP   ( 314-)  A
 362 ASP   ( 393-)  A
 393 ASP   ( 424-)  A
 419 ASP   ( 450-)  A
 466 ASP   ( 497-)  A
 553 ASP   ( 584-)  A
 575 ASP   (  53-)  B
 632 ASP   ( 110-)  B
 771 ASP   ( 249-)  B
 836 ASP   ( 314-)  B
 915 ASP   ( 393-)  B
 972 ASP   ( 450-)  B
1019 ASP   ( 497-)  B
1106 ASP   ( 584-)  B

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  42 GLU   (  73-)  A
 144 GLU   ( 175-)  A
 237 GLU   ( 268-)  A
 277 GLU   ( 308-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 316 GLU   ( 347-)  A
 333 GLU   ( 364-)  A
 374 GLU   ( 405-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 462 GLU   ( 493-)  A
 479 GLU   ( 510-)  A
 522 GLU   ( 553-)  A
 595 GLU   (  73-)  B
 761 GLU   ( 239-)  B
 790 GLU   ( 268-)  B
 830 GLU   ( 308-)  B
 841 GLU   ( 319-)  B
 848 GLU   ( 326-)  B
 861 GLU   ( 339-)  B
 886 GLU   ( 364-)  B
 927 GLU   ( 405-)  B
 976 GLU   ( 454-)  B
1002 GLU   ( 480-)  B
1006 GLU   ( 484-)  B
1032 GLU   ( 510-)  B
1042 GLU   ( 520-)  B
1075 GLU   ( 553-)  B

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

 |  0.997464 -0.000038 -0.000038|
 | -0.000038  0.997482 -0.000132|
 | -0.000038 -0.000132  0.997628|
Proposed new scale matrix

 |  0.005494  0.003172  0.000000|
 |  0.000000  0.006344  0.000000|
 |  0.000000  0.000001  0.009723|
With corresponding cell

    A    = 182.017  B   = 182.020  C    = 102.848
    Alpha=  90.007  Beta=  90.001  Gamma= 120.002

The CRYST1 cell dimensions

    A    = 182.483  B   = 182.483  C    = 103.095
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 233.563
(Under-)estimated Z-score: 11.263

Error: Nomenclature error(s)

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

  22 ASP   (  53-)  A
  42 GLU   (  73-)  A
 119 ARG   ( 150-)  A
 144 GLU   ( 175-)  A
 218 ASP   ( 249-)  A
 237 GLU   ( 268-)  A
 277 GLU   ( 308-)  A
 283 ASP   ( 314-)  A
 295 GLU   ( 326-)  A
 308 GLU   ( 339-)  A
 316 GLU   ( 347-)  A
 333 GLU   ( 364-)  A
 362 ASP   ( 393-)  A
 374 GLU   ( 405-)  A
 393 ASP   ( 424-)  A
 419 ASP   ( 450-)  A
 428 ARG   ( 459-)  A
 449 GLU   ( 480-)  A
 453 GLU   ( 484-)  A
 462 GLU   ( 493-)  A
 466 ASP   ( 497-)  A
 479 GLU   ( 510-)  A
 522 GLU   ( 553-)  A
 553 ASP   ( 584-)  A
 575 ASP   (  53-)  B
 595 GLU   (  73-)  B
 632 ASP   ( 110-)  B
 761 GLU   ( 239-)  B
 771 ASP   ( 249-)  B
 790 GLU   ( 268-)  B
 830 GLU   ( 308-)  B
 836 ASP   ( 314-)  B
 841 GLU   ( 319-)  B
 848 GLU   ( 326-)  B
 861 GLU   ( 339-)  B
 886 GLU   ( 364-)  B
 915 ASP   ( 393-)  B
 927 GLU   ( 405-)  B
 972 ASP   ( 450-)  B
 976 GLU   ( 454-)  B
 981 ARG   ( 459-)  B
1002 GLU   ( 480-)  B
1006 GLU   ( 484-)  B
1019 ASP   ( 497-)  B
1032 GLU   ( 510-)  B
1042 GLU   ( 520-)  B
1075 GLU   ( 553-)  B
1106 ASP   ( 584-)  B

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.

1040 PHE   ( 518-)  B    -3.1
 487 PHE   ( 518-)  A    -3.0
 378 PHE   ( 409-)  A    -2.8
 931 PHE   ( 409-)  B    -2.8
 981 ARG   ( 459-)  B    -2.8
 907 TYR   ( 385-)  B    -2.7
1085 THR   ( 563-)  B    -2.7
 532 THR   ( 563-)  A    -2.7
 545 PRO   ( 576-)  A    -2.6
 354 TYR   ( 385-)  A    -2.5
 561 TYR   (  39-)  B    -2.5
 914 PRO   ( 392-)  B    -2.4
 453 GLU   ( 484-)  A    -2.4
 154 ARG   ( 185-)  A    -2.3
 483 PRO   ( 514-)  A    -2.3
1006 GLU   ( 484-)  B    -2.2
  98 THR   ( 129-)  A    -2.2
 686 GLY   ( 164-)  B    -2.2
   8 TYR   (  39-)  A    -2.2
1098 PRO   ( 576-)  B    -2.2
 133 GLY   ( 164-)  A    -2.2
 591 CYS   (  69-)  B    -2.1
 752 LEU   ( 230-)  B    -2.1
 565 HIS   (  43-)  B    -2.1
 199 LEU   ( 230-)  A    -2.1
 980 LEU   ( 458-)  B    -2.0
 630 ILE   ( 108-)  B    -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.

  12 HIS   (  43-)  A  Poor phi/psi
  13 GLN   (  44-)  A  Poor phi/psi
  30 ARG   (  61-)  A  Poor phi/psi
  38 CYS   (  69-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  A  Poor phi/psi
 116 TYR   ( 147-)  A  omega poor
 154 ARG   ( 185-)  A  Poor phi/psi
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 227 ASN   ( 258-)  A  Poor phi/psi
 378 PHE   ( 409-)  A  Poor phi/psi
 484 ASN   ( 515-)  A  Poor phi/psi
 548 SER   ( 579-)  A  Poor phi/psi
 565 HIS   (  43-)  B  Poor phi/psi
 566 GLN   (  44-)  B  Poor phi/psi
 583 ARG   (  61-)  B  Poor phi/psi
 591 CYS   (  69-)  B  Poor phi/psi
 648 SER   ( 126-)  B  PRO omega poor
 651 THR   ( 129-)  B  Poor phi/psi
 669 TYR   ( 147-)  B  omega poor
 703 PHE   ( 181-)  B  Poor phi/psi
 707 ARG   ( 185-)  B  Poor phi/psi
 726 HIS   ( 204-)  B  Poor phi/psi
 748 HIS   ( 226-)  B  Poor phi/psi
 752 LEU   ( 230-)  B  Poor phi/psi
 769 PHE   ( 247-)  B  Poor phi/psi
 780 ASN   ( 258-)  B  Poor phi/psi
 881 LEU   ( 359-)  B  omega poor
 931 PHE   ( 409-)  B  Poor phi/psi
 978 ARG   ( 456-)  B  Poor phi/psi
1018 GLY   ( 496-)  B  Poor phi/psi
1034 CYS   ( 512-)  B  omega poor
1037 ASN   ( 515-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.811

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.

1052 SER   ( 530-)  B    0.35
 110 SER   ( 141-)  A    0.36

Warning: Unusual backbone conformations

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

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

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

   3 ASN   (  34-)  A      0
   5 CYS   (  36-)  A      0
   6 CYS   (  37-)  A      0
   8 TYR   (  39-)  A      0
   9 PRO   (  40-)  A      0
  10 CYS   (  41-)  A      0
  11 GLN   (  42-)  A      0
  12 HIS   (  43-)  A      0
  13 GLN   (  44-)  A      0
  19 PHE   (  50-)  A      0
  21 LEU   (  52-)  A      0
  22 ASP   (  53-)  A      0
  28 CYS   (  59-)  A      0
  29 THR   (  60-)  A      0
  30 ARG   (  61-)  A      0
  31 THR   (  62-)  A      0
  33 TYR   (  64-)  A      0
  34 SER   (  65-)  A      0
  38 CYS   (  69-)  A      0
  39 THR   (  70-)  A      0
  43 ILE   (  74-)  A      0
  64 HIS   (  95-)  A      0
  66 ARG   (  97-)  A      0
  74 ALA   ( 105-)  A      0
  94 PRO   ( 125-)  A      0
And so on for a total of 422 lines.

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!

 131 PRO   ( 162-)  A   1.77   13

Warning: Unusual PRO puckering phases

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

   1 PRO   (  32-)  A   -61.2 half-chair C-beta/C-alpha (-54 degrees)
   9 PRO   (  40-)  A    49.3 half-chair C-delta/C-gamma (54 degrees)
  41 PRO   (  72-)  A   -39.8 envelop C-alpha (-36 degrees)
  55 PRO   (  86-)  A   102.0 envelop C-beta (108 degrees)
 249 PRO   ( 280-)  A    46.1 half-chair C-delta/C-gamma (54 degrees)
 483 PRO   ( 514-)  A   111.4 envelop C-beta (108 degrees)
 507 PRO   ( 538-)  A  -114.9 envelop C-gamma (-108 degrees)
 545 PRO   ( 576-)  A   -61.5 half-chair C-beta/C-alpha (-54 degrees)
 594 PRO   (  72-)  B   -48.0 half-chair C-beta/C-alpha (-54 degrees)
 649 PRO   ( 127-)  B  -117.8 half-chair C-delta/C-gamma (-126 degrees)
 785 PRO   ( 263-)  B  -115.7 envelop C-gamma (-108 degrees)
 914 PRO   ( 392-)  B    13.9 half-chair N/C-delta (18 degrees)
1036 PRO   ( 514-)  B  -118.4 half-chair C-delta/C-gamma (-126 degrees)
1060 PRO   ( 538-)  B  -117.2 half-chair C-delta/C-gamma (-126 degrees)
1064 PRO   ( 542-)  B   103.6 envelop C-beta (108 degrees)
1105 PRO   ( 583-)  B   105.4 envelop C-beta (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.

 932 ASN   ( 410-)  B      ND2 <-> 1123 NDG   (1681-)  B      C1     1.66    1.44  INTRA BF
1112 NAG   (1682-)  B      O4  <-> 1128 MAN   (1683-)  B      C1     0.95    1.45  INTRA BF
1113 NAG   (1671-)  B      O4  <-> 1127 NDG   (1672-)  B      C1     0.94    1.46  INTRA B3
1112 NAG   (1682-)  B      C4  <-> 1128 MAN   (1683-)  B      C1     0.86    2.34  INTRA BF
 932 ASN   ( 410-)  B      CG  <-> 1123 NDG   (1681-)  B      C1     0.86    2.34  INTRA BF
1113 NAG   (1671-)  B      C4  <-> 1127 NDG   (1672-)  B      C1     0.77    2.43  INTRA BL
 579 CYS   (  57-)  B      SG  <-> 1132 HOH   ( 640 )  B      O      0.46    2.54  INTRA BF
 563 CYS   (  41-)  B      CB  <-> 1132 HOH   ( 640 )  B      O      0.36    2.44  INTRA BF
 932 ASN   ( 410-)  B      ND2 <-> 1123 NDG   (1681-)  B      O      0.35    2.35  INTRA BF
 357 HIS   ( 388-)  A      N   <->  358 PRO   ( 389-)  A      CD     0.25    2.75  INTRA BL
 982 LEU   ( 460-)  B      N   <-> 1132 HOH   ( 623 )  B      O      0.24    2.46  INTRA BF
 738 MET   ( 216-)  B      SD  <-> 1132 HOH   ( 596 )  B      O      0.23    2.77  INTRA BF
 965 HIS   ( 443-)  B      ND1 <-> 1132 HOH   ( 671 )  B      O      0.23    2.47  INTRA BF
 977 SER   ( 455-)  B      C   <-> 1132 HOH   ( 623 )  B      O      0.21    2.59  INTRA BF
 910 HIS   ( 388-)  B      ND1 <-> 1132 HOH   (  11 )  B      O      0.20    2.50  INTRA BL
 932 ASN   ( 410-)  B      OD1 <-> 1123 NDG   (1681-)  B      C1     0.18    2.62  INTRA BF
 910 HIS   ( 388-)  B      N   <->  911 PRO   ( 389-)  B      CD     0.18    2.82  INTRA BL
1087 LYS   ( 565-)  B      NZ  <-> 1097 CYS   ( 575-)  B      SG     0.18    3.12  INTRA BF
 830 GLU   ( 308-)  B      CD  <->  833 ARG   ( 311-)  B      NH1    0.16    2.94  INTRA BL
 341 GLN   ( 372-)  A      N   <-> 1131 HOH   (  15 )  A      O      0.16    2.54  INTRA BL
 280 ARG   ( 311-)  A      NH2 <-> 1131 HOH   ( 589 )  A      O      0.15    2.55  INTRA BL
 896 ARG   ( 374-)  B      O   <-> 1054 LYS   ( 532-)  B      NZ     0.14    2.56  INTRA BL
 108 TRP   ( 139-)  A      NE1 <->  112 SER   ( 143-)  A      OG     0.14    2.56  INTRA BL
 932 ASN   ( 410-)  B      ND2 <-> 1123 NDG   (1681-)  B      N2     0.14    1.96  INTRA BF
 605 ARG   (  83-)  B      NH2 <->  993 GLY   ( 471-)  B      O      0.13    2.57  INTRA BF
And so on for a total of 102 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

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.

 707 ARG   ( 185-)  B      -6.96
 583 ARG   (  61-)  B      -6.44
 797 TYR   ( 275-)  B      -6.42
  30 ARG   (  61-)  A      -6.34
 709 PHE   ( 187-)  B      -6.29
 156 PHE   ( 187-)  A      -6.09
 184 LYS   ( 215-)  A      -6.08
 154 ARG   ( 185-)  A      -6.00
 244 TYR   ( 275-)  A      -5.87
 896 ARG   ( 374-)  B      -5.83
 343 ARG   ( 374-)  A      -5.82
 574 LEU   (  52-)  B      -5.70
  21 LEU   (  52-)  A      -5.67
 706 ARG   ( 184-)  B      -5.61
 397 ARG   ( 428-)  A      -5.40
 555 VAL   (  33-)  B      -5.40
 950 ARG   ( 428-)  B      -5.38
1095 LYS   ( 573-)  B      -5.30
 153 ARG   ( 184-)  A      -5.30
   2 VAL   (  33-)  A      -5.26
 738 MET   ( 216-)  B      -5.23
 149 ARG   ( 180-)  A      -5.21
 955 ARG   ( 433-)  B      -5.20
1006 GLU   ( 484-)  B      -5.16
 965 HIS   ( 443-)  B      -5.16
 991 ARG   ( 469-)  B      -5.15
 438 ARG   ( 469-)  A      -5.13
 801 ILE   ( 279-)  B      -5.11
 402 ARG   ( 433-)  A      -5.10
 135 LYS   ( 166-)  A      -5.07

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

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 217 LYS   ( 248-)  A   -3.40
 960 ARG   ( 438-)  B   -3.39
 137 LYS   ( 168-)  A   -2.96
 799 ARG   ( 277-)  B   -2.95
 690 LYS   ( 168-)  B   -2.88
  52 ARG   (  83-)  A   -2.81
 708 LYS   ( 186-)  B   -2.69
 155 LYS   ( 186-)  A   -2.68
 918 ARG   ( 396-)  B   -2.62
 692 GLN   ( 170-)  B   -2.60
 334 LEU   ( 365-)  A   -2.52

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 136 GLY   ( 167-)  A     -  139 GLN   ( 170-)  A        -1.95
 152 LEU   ( 183-)  A     -  155 LYS   ( 186-)  A        -1.88
 689 GLY   ( 167-)  B     -  692 GLN   ( 170-)  B        -1.96
 705 LEU   ( 183-)  B     -  708 LYS   ( 186-)  B        -1.84
 886 GLU   ( 364-)  B     -  889 PHE   ( 367-)  B        -1.90

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

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.

1131 HOH   ( 586 )  A      O
1131 HOH   ( 592 )  A      O
1131 HOH   ( 606 )  A      O
1131 HOH   ( 607 )  A      O
1131 HOH   ( 608 )  A      O
1131 HOH   ( 619 )  A      O
1131 HOH   ( 630 )  A      O
1131 HOH   ( 632 )  A      O
1131 HOH   ( 636 )  A      O
1131 HOH   ( 668 )  A      O
1132 HOH   ( 586 )  B      O
1132 HOH   ( 628 )  B      O
1132 HOH   ( 666 )  B      O
1132 HOH   ( 675 )  B      O
Bound group on Asn; dont flip   37 ASN  (  68-) A
Bound to: 1107 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 1110 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 1108 NAG  ( 681-) A
Bound group on Asn; dont flip  590 ASN  (  68-) B
Bound to: 1111 NAG  (1661-) B
Bound group on Asn; dont flip  666 ASN  ( 144-) B
Bound to: 1113 NAG  (1671-) B
Bound group on Asn; dont flip  932 ASN  ( 410-) B
Bound to: 1123 NDG  (1681-) B
Marked this atom as acceptor 1130 FLP  ( 701-) A      F
Metal-coordinating Histidine residue 357 fixed to   1
Metal-coordinating Histidine residue 910 fixed to   1

Error: HIS, ASN, GLN side chain flips

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

 206 ASN   ( 237-)  A
 725 GLN   ( 203-)  B
 763 GLN   ( 241-)  B

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.

  18 ARG   (  49-)  A      NH1
  66 ARG   (  97-)  A      NH2
  89 ARG   ( 120-)  A      NH1
 100 ASN   ( 131-)  A      ND2
 105 TYR   ( 136-)  A      N
 117 TYR   ( 148-)  A      OH
 119 ARG   ( 150-)  A      NH2
 154 ARG   ( 185-)  A      NE
 161 GLN   ( 192-)  A      N
 177 GLN   ( 208-)  A      NE2
 180 LYS   ( 211-)  A      N
 181 THR   ( 212-)  A      N
 196 GLY   ( 227-)  A      N
 204 GLY   ( 235-)  A      N
 206 ASN   ( 237-)  A      N
 217 LYS   ( 248-)  A      N
 236 GLU   ( 267-)  A      N
 262 GLY   ( 293-)  A      N
 266 GLY   ( 297-)  A      N
 317 TYR   ( 348-)  A      OH
 319 GLN   ( 350-)  A      N
 326 LEU   ( 357-)  A      N
 329 LYS   ( 360-)  A      N
 351 ASN   ( 382-)  A      ND2
 357 HIS   ( 388-)  A      N
And so on for a total of 76 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.

 159 ASP   ( 190-)  A      OD1
 172 GLN   ( 203-)  A      OE1
 173 HIS   ( 204-)  A      NE2
 355 HIS   ( 386-)  A      ND1
 493 GLU   ( 524-)  A      OE1
 662 GLU   ( 140-)  B      OE2
 712 ASP   ( 190-)  B      OD1
 726 HIS   ( 204-)  B      ND1
 861 GLU   ( 339-)  B      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.

 385 ASP   ( 416-)  A   H-bonding suggests Asn
 461 GLU   ( 492-)  A   H-bonding suggests Gln; but Alt-Rotamer
 553 ASP   ( 584-)  A   H-bonding suggests Asn
 938 ASP   ( 416-)  B   H-bonding suggests Asn
1046 GLU   ( 524-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
1106 ASP   ( 584-)  B   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 :  -1.812
  2nd generation packing quality :  -2.110
  Ramachandran plot appearance   :  -1.674
  chi-1/chi-2 rotamer normality  :  -2.811
  Backbone conformation          :  -1.128

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.332 (tight)
  Bond angles                    :   0.541 (tight)
  Omega angle restraints         :   0.850
  Side chain planarity           :   0.254 (tight)
  Improper dihedral distribution :   0.461
  B-factor distribution          :   0.360
  Inside/Outside distribution    :   1.101

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 : 2.75


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.7
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.332 (tight)
  Bond angles                    :   0.541 (tight)
  Omega angle restraints         :   0.850
  Side chain planarity           :   0.254 (tight)
  Improper dihedral distribution :   0.461
  B-factor distribution          :   0.360
  Inside/Outside distribution    :   1.101
==============

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.