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 pdb3t1e.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 : 0.843
CA-only RMS fit for the two chains : 0.509

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

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: E and F

All-atom RMS fit for the two chains : 1.809
CA-only RMS fit for the two chains : 0.738

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: E and F

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 43 21 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 32
Polymer chain multiplicity and SEQRES multiplicity disagree 2 4
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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: 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'.

  11 ILE   ( 133-)  A      CG1
  11 ILE   ( 133-)  A      CG2
  11 ILE   ( 133-)  A      CD1
  14 ILE   ( 136-)  A      CG1
  14 ILE   ( 136-)  A      CG2
  14 ILE   ( 136-)  A      CD1
  19 ILE   ( 141-)  A      CG1
  19 ILE   ( 141-)  A      CG2
  19 ILE   ( 141-)  A      CD1
  21 ASP   ( 143-)  A      CG
  21 ASP   ( 143-)  A      OD1
  21 ASP   ( 143-)  A      OD2
  23 THR   ( 145-)  A      OG1
  23 THR   ( 145-)  A      CG2
  41 ILE   ( 163-)  A      CG1
  41 ILE   ( 163-)  A      CG2
  41 ILE   ( 163-)  A      CD1
  53 ILE   ( 175-)  A      CG1
  53 ILE   ( 175-)  A      CG2
  53 ILE   ( 175-)  A      CD1
  74 ARG   ( 196-)  A      CG
  74 ARG   ( 196-)  A      CD
  74 ARG   ( 196-)  A      NE
  74 ARG   ( 196-)  A      CZ
  74 ARG   ( 196-)  A      NH1
And so on for a total of 508 lines.

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 CYS   ( 123-)  A    High
   2 GLY   ( 124-)  A    High
   3 ALA   ( 125-)  A    High
   4 PRO   ( 126-)  A    High
   6 HIS   ( 128-)  A    High
   7 ASP   ( 129-)  A    High
   8 PRO   ( 130-)  A    High
   9 ASP   ( 131-)  A    High
  10 TYR   ( 132-)  A    High
  11 ILE   ( 133-)  A    High
  12 GLY   ( 134-)  A    High
  13 GLY   ( 135-)  A    High
  14 ILE   ( 136-)  A    High
  15 GLY   ( 137-)  A    High
  16 LYS   ( 138-)  A    High
  17 GLU   ( 139-)  A    High
  18 LEU   ( 140-)  A    High
  19 ILE   ( 141-)  A    High
  20 VAL   ( 142-)  A    High
  21 ASP   ( 143-)  A    High
  22 ASP   ( 144-)  A    High
  23 THR   ( 145-)  A    High
  24 SER   ( 146-)  A    High
  25 ASP   ( 147-)  A    High
  26 VAL   ( 148-)  A    High
And so on for a total of 944 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: 15

Crystal temperature (K) : 77.200

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: E

Note: B-factor plot

Chain identifier: F

Nomenclature related problems

Warning: Tyrosine convention problem

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

  30 TYR   ( 152-)  A
 139 TYR   ( 261-)  A
 176 TYR   ( 298-)  A
 211 TYR   ( 333-)  A
 227 TYR   ( 349-)  A
 236 TYR   ( 358-)  A
 297 TYR   ( 419-)  A
 319 TYR   ( 441-)  A
 351 TYR   ( 473-)  A
 403 TYR   ( 525-)  A
 418 TYR   ( 540-)  A
 455 TYR   ( 132-)  B
 475 TYR   ( 152-)  B
 792 TYR   ( 469-)  B
 936 TYR   (  85-)  F
 963 TYR   ( 112-)  F

Warning: Phenylalanine convention problem

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

  34 PHE   ( 156-)  A
  56 PHE   ( 178-)  A
  70 PHE   ( 192-)  A
  97 PHE   ( 219-)  A
 154 PHE   ( 276-)  A
 169 PHE   ( 291-)  A
 191 PHE   ( 313-)  A
 365 PHE   ( 487-)  A
 383 PHE   ( 505-)  A
 474 PHE   ( 151-)  B
 479 PHE   ( 156-)  B
 515 PHE   ( 192-)  B
 542 PHE   ( 219-)  B
 599 PHE   ( 276-)  B
 636 PHE   ( 313-)  B
 686 PHE   ( 363-)  B
 875 PHE   ( 552-)  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.

 171 ASP   ( 293-)  A
 470 ASP   ( 147-)  B
 893 ASP   (  79-)  E
 930 ASP   (  79-)  F
 933 ASP   (  82-)  F

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.

 133 GLU   ( 255-)  A
 372 GLU   ( 494-)  A
 723 GLU   ( 400-)  B

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.

  76 HIS   ( 198-)  A      CG   ND1  CE1 109.73    4.1
 521 HIS   ( 198-)  B      CG   ND1  CE1 109.63    4.0

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.

 133 GLU   ( 255-)  A
 171 ASP   ( 293-)  A
 372 GLU   ( 494-)  A
 470 ASP   ( 147-)  B
 723 GLU   ( 400-)  B
 893 ASP   (  79-)  E
 930 ASP   (  79-)  F
 933 ASP   (  82-)  F

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.

 677 ALA   ( 354-)  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.

 639 TYR   ( 316-)  B    -3.3
 344 THR   ( 466-)  A    -3.2
 359 HIS   ( 481-)  A    -2.9
 795 PRO   ( 472-)  B    -2.8
 350 PRO   ( 472-)  A    -2.8
 776 PRO   ( 453-)  B    -2.8
 211 TYR   ( 333-)  A    -2.7
 331 PRO   ( 453-)  A    -2.7
 491 THR   ( 168-)  B    -2.6
 584 TYR   ( 261-)  B    -2.4
 490 THR   ( 167-)  B    -2.4
 511 HIS   ( 188-)  B    -2.4
 935 ILE   (  84-)  F    -2.4
 450 VAL   ( 127-)  B    -2.4
 516 SER   ( 193-)  B    -2.4
  46 THR   ( 168-)  A    -2.4
  71 SER   ( 193-)  A    -2.3
 789 THR   ( 466-)  B    -2.3
 899 TYR   (  85-)  E    -2.3
 791 VAL   ( 468-)  B    -2.2
 547 ARG   ( 224-)  B    -2.2
 798 LEU   ( 475-)  B    -2.2
 931 VAL   (  80-)  F    -2.2
 933 ASP   (  82-)  F    -2.2
 510 THR   ( 187-)  B    -2.2
 324 PHE   ( 446-)  A    -2.1
 645 SER   ( 322-)  B    -2.1
 866 SER   ( 543-)  B    -2.1
 104 ILE   ( 226-)  A    -2.1
 642 LEU   ( 319-)  B    -2.0
 320 THR   ( 442-)  A    -2.0
 747 LEU   ( 424-)  B    -2.0
 414 THR   ( 536-)  A    -2.0
 748 LEU   ( 425-)  B    -2.0
 517 GLY   ( 194-)  B    -2.0
 475 TYR   ( 152-)  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.

   4 PRO   ( 126-)  A  Poor phi/psi
  59 SER   ( 181-)  A  Poor phi/psi, omega poor
  73 CYS   ( 195-)  A  Poor phi/psi
  75 ASP   ( 197-)  A  Poor phi/psi
  79 SER   ( 201-)  A  Poor phi/psi
 113 LYS   ( 235-)  A  Poor phi/psi
 160 GLU   ( 282-)  A  Poor phi/psi
 164 ASP   ( 286-)  A  omega poor
 179 VAL   ( 301-)  A  Poor phi/psi
 187 ASN   ( 309-)  A  Poor phi/psi
 200 SER   ( 322-)  A  Poor phi/psi
 211 TYR   ( 333-)  A  Poor phi/psi
 294 GLY   ( 416-)  A  Poor phi/psi
 302 LEU   ( 424-)  A  omega poor
 309 ASN   ( 431-)  A  Poor phi/psi
 310 ASN   ( 432-)  A  Poor phi/psi
 318 PRO   ( 440-)  A  omega poor
 321 PHE   ( 443-)  A  omega poor
 325 THR   ( 447-)  A  omega poor
 330 VAL   ( 452-)  A  PRO omega poor
 332 CYS   ( 454-)  A  omega poor
 340 ASN   ( 462-)  A  Poor phi/psi
 342 CYS   ( 464-)  A  Poor phi/psi
 356 HIS   ( 478-)  A  omega poor
 359 HIS   ( 481-)  A  Poor phi/psi
And so on for a total of 56 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.201

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.

 952 SER   ( 101-)  F    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!

   4 PRO   ( 126-)  A      0
   7 ASP   ( 129-)  A      0
  11 ILE   ( 133-)  A      0
  14 ILE   ( 136-)  A      0
  18 LEU   ( 140-)  A      0
  21 ASP   ( 143-)  A      0
  22 ASP   ( 144-)  A      0
  29 PHE   ( 151-)  A      0
  33 ALA   ( 155-)  A      0
  37 HIS   ( 159-)  A      0
  40 PHE   ( 162-)  A      0
  41 ILE   ( 163-)  A      0
  52 ARG   ( 174-)  A      0
  53 ILE   ( 175-)  A      0
  58 MET   ( 180-)  A      0
  59 SER   ( 181-)  A      0
  60 ALA   ( 182-)  A      0
  61 THR   ( 183-)  A      0
  66 HIS   ( 188-)  A      0
  70 PHE   ( 192-)  A      0
  71 SER   ( 193-)  A      0
  73 CYS   ( 195-)  A      0
  74 ARG   ( 196-)  A      0
  75 ASP   ( 197-)  A      0
  76 HIS   ( 198-)  A      0
And so on for a total of 441 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!

 276 GLY   ( 398-)  A   2.74   11

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].

 199 PRO   ( 321-)  A  -112.7 envelop C-gamma (-108 degrees)
 202 PRO   ( 324-)  A  -146.6 envelop C-delta (-144 degrees)
 350 PRO   ( 472-)  A   -61.4 half-chair C-beta/C-alpha (-54 degrees)
 644 PRO   ( 321-)  B  -114.2 envelop C-gamma (-108 degrees)
 795 PRO   ( 472-)  B   -63.8 envelop C-beta (-72 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.

 221 CYS   ( 343-)  A      SG  <->  228 GLN   ( 350-)  A      NE2    0.72    2.58  INTRA BF
 521 HIS   ( 198-)  B      O   <->  556 ASN   ( 233-)  B      ND2    0.69    2.01  INTRA BF
 521 HIS   ( 198-)  B      NE2 <->  576 VAL   ( 253-)  B      O      0.61    2.09  INTRA BF
 676 MET   ( 353-)  B      O   <->  679 SER   ( 356-)  B      N      0.60    2.10  INTRA BF
 579 THR   ( 256-)  B      N   <->  582 GLU   ( 259-)  B      OE2    0.54    2.16  INTRA BF
  81 GLN   ( 203-)  A      NE2 <->  115 CYS   ( 237-)  A      SG     0.50    2.80  INTRA BF
  77 SER   ( 199-)  A      O   <->  111 ASN   ( 233-)  A      ND2    0.50    2.20  INTRA BF
 896 ASP   (  82-)  E      OD1 <->  897 ARG   (  83-)  E      N      0.49    2.11  INTRA BF
 430 PHE   ( 552-)  A      O   <->  879 ARG   ( 556-)  B      NH2    0.46    2.24  INTRA BF
 508 CYS   ( 185-)  B      SG  <->  569 CYS   ( 246-)  B      CB     0.45    2.05  INTRA BF
 151 ARG   ( 273-)  A      NH2 <->  256 SER   ( 378-)  A      O      0.45    2.25  INTRA BL
 469 SER   ( 146-)  B      O   <->  807 ARG   ( 484-)  B      NH2    0.43    2.27  INTRA BF
 145 THR   ( 267-)  A      OG1 <->  175 ASN   ( 297-)  A      N      0.43    2.27  INTRA BF
 470 ASP   ( 147-)  B      O   <->  473 SER   ( 150-)  B      OG     0.42    1.98  INTRA BF
 555 GLN   ( 232-)  B      OE1 <->  575 LYS   ( 252-)  B      NZ     0.40    2.30  INTRA BF
 633 ARG   ( 310-)  B      NH2 <->  697 SER   ( 374-)  B      O      0.38    2.32  INTRA BF
 933 ASP   (  82-)  F      O   <->  936 TYR   (  85-)  F      N      0.34    2.36  INTRA BF
  85 LEU   ( 207-)  A      N   <->  102 ARG   ( 224-)  A      O      0.33    2.37  INTRA BL
 738 ARG   ( 415-)  B      NE  <->  740 SER   ( 417-)  B      OG     0.33    2.37  INTRA BF
 219 ASP   ( 341-)  A      CB  <->  337 ARG   ( 459-)  A      NE     0.30    2.80  INTRA BF
 583 ASP   ( 260-)  B      O   <->  586 SER   ( 263-)  B      OG     0.30    2.10  INTRA BF
 508 CYS   ( 185-)  B      SG  <->  569 CYS   ( 246-)  B      CA     0.30    2.70  INTRA BF
 231 MET   ( 353-)  A      SD  <->  339 PRO   ( 461-)  A      O      0.30    2.55  INTRA BF
 371 ASP   ( 493-)  A      OD1 <->  372 GLU   ( 494-)  A      N      0.29    2.31  INTRA BF
 600 ASP   ( 277-)  B      OD1 <->  602 GLN   ( 279-)  B      N      0.29    2.41  INTRA BL
And so on for a total of 335 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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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: 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.

 689 LYS   ( 366-)  B   -3.80
 244 LYS   ( 366-)  A   -3.68
 782 ARG   ( 459-)  B   -3.37
 771 ARG   ( 448-)  B   -3.35
 326 ARG   ( 448-)  A   -3.34
 292 GLN   ( 414-)  A   -3.27
 143 ILE   ( 265-)  A   -3.22
 692 GLN   ( 369-)  B   -3.19
 737 GLN   ( 414-)  B   -3.13
  74 ARG   ( 196-)  A   -3.10
 429 LEU   ( 551-)  A   -3.02
 685 ARG   ( 362-)  B   -2.99
 486 ILE   ( 163-)  B   -2.99
 820 ARG   ( 497-)  B   -2.98
 240 ARG   ( 362-)  A   -2.98
 466 ASP   ( 143-)  B   -2.93
 375 ARG   ( 497-)  A   -2.92
 237 LYS   ( 359-)  A   -2.91
 682 LYS   ( 359-)  B   -2.91
 353 LEU   ( 475-)  A   -2.90
  21 ASP   ( 143-)  A   -2.90
 113 LYS   ( 235-)  A   -2.88
 398 ARG   ( 520-)  A   -2.87
 558 LYS   ( 235-)  B   -2.86
 874 LEU   ( 551-)  B   -2.85
 122 LEU   ( 244-)  A   -2.82
 843 ARG   ( 520-)  B   -2.81
 463 LEU   ( 140-)  B   -2.80
  41 ILE   ( 163-)  A   -2.79
 272 VAL   ( 394-)  A   -2.79
 185 ILE   ( 307-)  A   -2.77
 433 PHE   ( 555-)  A   -2.76
  11 ILE   ( 133-)  A   -2.72
 643 LYS   ( 320-)  B   -2.71
 245 ARG   ( 367-)  A   -2.70
 630 ILE   ( 307-)  B   -2.68
 878 PHE   ( 555-)  B   -2.66
 588 ILE   ( 265-)  B   -2.63
 101 LEU   ( 223-)  A   -2.62
 567 LEU   ( 244-)  B   -2.61
 198 LYS   ( 320-)  A   -2.57
 519 ARG   ( 196-)  B   -2.56
 660 LYS   ( 337-)  B   -2.55
 215 LYS   ( 337-)  A   -2.55
 254 LYS   ( 376-)  A   -2.55
 444 LYS   ( 566-)  A   -2.55
 131 VAL   ( 253-)  A   -2.52
 388 ARG   ( 510-)  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.

 252 SER   ( 374-)  A     -  255 VAL   ( 377-)  A        -1.72
 697 SER   ( 374-)  B     -  700 VAL   ( 377-)  B        -1.59

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: 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.

 427 ASN   ( 549-)  A
 525 HIS   ( 202-)  B
 594 HIS   ( 271-)  B
 872 ASN   ( 549-)  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.

   6 HIS   ( 128-)  A      NE2
  16 LYS   ( 138-)  A      N
  27 THR   ( 149-)  A      N
  37 HIS   ( 159-)  A      N
  41 ILE   ( 163-)  A      N
  46 THR   ( 168-)  A      N
  48 SER   ( 170-)  A      N
  55 SER   ( 177-)  A      OG
  61 THR   ( 183-)  A      OG1
  62 HIS   ( 184-)  A      NE2
  64 TYR   ( 186-)  A      OH
  70 PHE   ( 192-)  A      N
  77 SER   ( 199-)  A      N
  98 PHE   ( 220-)  A      N
 116 SER   ( 238-)  A      OG
 129 SER   ( 251-)  A      N
 143 ILE   ( 265-)  A      N
 145 THR   ( 267-)  A      OG1
 147 MET   ( 269-)  A      N
 151 ARG   ( 273-)  A      NH1
 179 VAL   ( 301-)  A      N
 188 ARG   ( 310-)  A      NH1
 203 SER   ( 325-)  A      OG
 210 ARG   ( 332-)  A      NE
 216 ARG   ( 338-)  A      N
And so on for a total of 114 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.

  37 HIS   ( 159-)  A      ND1
  62 HIS   ( 184-)  A      ND1
 162 ASP   ( 284-)  A      OD1
 482 HIS   ( 159-)  B      ND1
 507 HIS   ( 184-)  B      ND1
 511 HIS   ( 188-)  B      ND1
 594 HIS   ( 271-)  B      ND1
 723 GLU   ( 400-)  B      OE2
 829 ASP   ( 506-)  B      OD1
 951 GLU   ( 100-)  F      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.

  57 ASP   ( 179-)  A   H-bonding suggests Asn
 446 ASP   ( 568-)  A   H-bonding suggests Asn
 502 ASP   ( 179-)  B   H-bonding suggests Asn
 600 ASP   ( 277-)  B   H-bonding suggests Asn
 816 ASP   ( 493-)  B   H-bonding suggests Asn
 896 ASP   (  82-)  E   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:

  2nd generation packing quality :  -4.279 (bad)
  Ramachandran plot appearance   :  -2.712
  chi-1/chi-2 rotamer normality  :  -4.201 (bad)
  Backbone conformation          :  -0.571

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.248 (tight)
  Bond angles                    :   0.532 (tight)
  Omega angle restraints         :   1.156
  Side chain planarity           :   0.247 (tight)
  Improper dihedral distribution :   0.529
  B-factor distribution          :   1.066
  Inside/Outside distribution    :   1.091

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 3.30


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -1.8
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.248 (tight)
  Bond angles                    :   0.532 (tight)
  Omega angle restraints         :   1.156
  Side chain planarity           :   0.247 (tight)
  Improper dihedral distribution :   0.529
  B-factor distribution          :   1.066
  Inside/Outside distribution    :   1.091
==============

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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Bond lengths and angles, DNA/RNA
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DSSP
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      Dictionary of protein secondary structure: pattern
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    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      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.