WHAT IF Check report

This file was created 2012-01-31 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 pdb2pi5.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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

Warning: 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 DCYT  (   5-)  T    High
   2 DTHY  (   6-)  T    High
   3 DADE  (   7-)  T    High
   4 DTHY  (   8-)  T    High
  31 DCYT  ( 113-)  P    High
  32 DTHY  ( 114-)  P    High
  33 ILE   (   6-)  A    High
  34 ALA   (   7-)  A    High
  35 LYS   (   8-)  A    High
  36 ASN   (   9-)  A    High
  37 ASP   (  10-)  A    High
  38 PHE   (  11-)  A    High
  42 GLU   (  15-)  A    High
  53 ASP   (  26-)  A    High
  57 GLU   (  30-)  A    High
  58 ARG   (  31-)  A    High
  61 ARG   (  34-)  A    High
  74 GLY   (  47-)  A    High
  75 GLU   (  48-)  A    High
  76 ALA   (  49-)  A    High
  77 ARG   (  50-)  A    High
  78 PHE   (  51-)  A    High
  79 ARG   (  52-)  A    High
  80 LYS   (  53-)  A    High
  81 MET   (  54-)  A    High
And so on for a total of 184 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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

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

 328 TYR   ( 317-)  A

Warning: Phenylalanine convention problem

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

 762 PHE   ( 751-)  A

Warning: Aspartic acid convention problem

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

  37 ASP   (  10-)  A
 141 ASP   ( 130-)  A
 167 ASP   ( 156-)  A
 377 ASP   ( 366-)  A
 517 ASP   ( 506-)  A

Warning: Glutamic acid convention problem

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

  57 GLU   (  30-)  A
  72 GLU   (  45-)  A
 210 GLU   ( 199-)  A
 256 GLU   ( 245-)  A
 488 GLU   ( 477-)  A
 495 GLU   ( 484-)  A
 564 GLU   ( 553-)  A
 618 GLU   ( 607-)  A
 694 GLU   ( 683-)  A

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.

   2 DTHY  (   6-)  T      C3'  C4'  C5' 108.70   -4.0
   6 DGUA  (  10-)  T      C2'  C1'  N9  107.32   -4.3
   8 DGUA  (  12-)  T      N9   C8   N7  113.23    4.3
  13 DGUA  (  17-)  T      N9   C8   N7  113.53    4.9
  17 DTHY  (  21-)  T      C2'  C1'  N1  120.82    4.1
  20 DADE  ( 102-)  P      C2'  C1'  N9  120.85    4.2
  21 DADE  ( 103-)  P      C3'  C4'  C5' 107.05   -5.1
  24 DCYT  ( 106-)  P      O4'  C1'  N1  111.77    5.0
  25 DGUA  ( 107-)  P      N9   C8   N7  113.22    4.2
 161 ARG   ( 150-)  A      N    CA   C    99.71   -4.1
 535 HIS   ( 524-)  A      CG   ND1  CE1 109.70    4.1
 795 HIS   ( 784-)  A      CG   ND1  CE1 109.67    4.1
 801 HIS   ( 790-)  A      CG   ND1  CE1 109.87    4.3
 822 HIS   ( 811-)  A      CG   ND1  CE1 109.71    4.1
 865 HIS   ( 854-)  A      CG   ND1  CE1 109.61    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.

  37 ASP   (  10-)  A
  57 GLU   (  30-)  A
  72 GLU   (  45-)  A
 141 ASP   ( 130-)  A
 167 ASP   ( 156-)  A
 210 GLU   ( 199-)  A
 256 GLU   ( 245-)  A
 377 ASP   ( 366-)  A
 488 GLU   ( 477-)  A
 495 GLU   ( 484-)  A
 517 ASP   ( 506-)  A
 564 GLU   ( 553-)  A
 618 GLU   ( 607-)  A
 694 GLU   ( 683-)  A

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 336 ASN   ( 325-)  A    5.05
 231 LEU   ( 220-)  A    5.04
 351 VAL   ( 340-)  A    5.04
  46 ILE   (  19-)  A    4.86
 161 ARG   ( 150-)  A    4.34
 476 ALA   ( 465-)  A    4.33
 172 HIS   ( 161-)  A    4.31
 117 LEU   ( 106-)  A    4.05
 225 VAL   ( 214-)  A    4.03

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

   6 DGUA  (  10-)  T    0.11
 Ramachandran Z-score : -4.773

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.773

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.

 827 THR   ( 816-)  A    -3.2
  55 TYR   (  28-)  A    -2.9
 259 PRO   ( 248-)  A    -2.8
 756 THR   ( 745-)  A    -2.6
 616 ILE   ( 605-)  A    -2.5
 463 ILE   ( 452-)  A    -2.5
  36 ASN   (   9-)  A    -2.5
 302 ARG   ( 291-)  A    -2.4
  85 ILE   (  74-)  A    -2.4
 224 GLY   ( 213-)  A    -2.4
 581 ILE   ( 570-)  A    -2.4
 658 ARG   ( 647-)  A    -2.4
 757 ARG   ( 746-)  A    -2.3
 487 PRO   ( 476-)  A    -2.3
 749 GLU   ( 738-)  A    -2.3
 873 PRO   ( 862-)  A    -2.3
 863 GLN   ( 852-)  A    -2.2
 725 LYS   ( 714-)  A    -2.2
 864 LEU   ( 853-)  A    -2.2
 456 THR   ( 445-)  A    -2.2
 383 GLU   ( 372-)  A    -2.2
 741 PRO   ( 730-)  A    -2.2
 256 GLU   ( 245-)  A    -2.2
 145 VAL   ( 134-)  A    -2.2
 635 GLY   ( 624-)  A    -2.1
 841 GLU   ( 830-)  A    -2.1
 518 SER   ( 507-)  A    -2.1
 187 HIS   ( 176-)  A    -2.1
  75 GLU   (  48-)  A    -2.1
 606 VAL   ( 595-)  A    -2.1
 430 ASN   ( 419-)  A    -2.1
 180 GLN   ( 169-)  A    -2.1
 869 LEU   ( 858-)  A    -2.1
 640 VAL   ( 629-)  A    -2.1
 303 ARG   ( 292-)  A    -2.1
 829 PRO   ( 818-)  A    -2.1
 681 PRO   ( 670-)  A    -2.1
 323 TYR   ( 312-)  A    -2.0
 210 GLU   ( 199-)  A    -2.0
  89 LEU   (  78-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  36 ASN   (   9-)  A  Poor phi/psi
  55 TYR   (  28-)  A  Poor phi/psi
 162 PHE   ( 151-)  A  Poor phi/psi
 179 GLU   ( 168-)  A  Poor phi/psi
 180 GLN   ( 169-)  A  Poor phi/psi
 185 VAL   ( 174-)  A  Poor phi/psi
 187 HIS   ( 176-)  A  Poor phi/psi
 188 VAL   ( 177-)  A  Poor phi/psi
 189 TYR   ( 178-)  A  Poor phi/psi
 190 LYS   ( 179-)  A  Poor phi/psi
 210 GLU   ( 199-)  A  Poor phi/psi
 224 GLY   ( 213-)  A  Poor phi/psi
 236 GLY   ( 225-)  A  Poor phi/psi
 244 ASN   ( 233-)  A  Poor phi/psi
 250 GLN   ( 239-)  A  Poor phi/psi
 259 PRO   ( 248-)  A  Poor phi/psi
 281 PRO   ( 270-)  A  Poor phi/psi
 305 LEU   ( 294-)  A  Poor phi/psi
 323 TYR   ( 312-)  A  Poor phi/psi
 361 GLU   ( 350-)  A  Poor phi/psi
 362 ASP   ( 351-)  A  Poor phi/psi
 375 PRO   ( 364-)  A  Poor phi/psi
 376 GLU   ( 365-)  A  Poor phi/psi
 383 GLU   ( 372-)  A  Poor phi/psi
 384 ALA   ( 373-)  A  Poor phi/psi
And so on for a total of 55 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 : -4.267

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.

 644 SER   ( 633-)  A    0.37
 558 SER   ( 547-)  A    0.38
 408 SER   ( 397-)  A    0.39
 800 SER   ( 789-)  A    0.40

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 DADE  (   7-)  T      0
   4 DTHY  (   8-)  T      0
   5 DADE  (   9-)  T      0
   6 DGUA  (  10-)  T      0
   7 DTHY  (  11-)  T      0
   8 DGUA  (  12-)  T      0
   9 DADE  (  13-)  T      0
  10 DGUA  (  14-)  T      0
  11 DTHY  (  15-)  T      0
  12 DCYT  (  16-)  T      0
  13 DGUA  (  17-)  T      0
  14 DTHY  (  18-)  T      0
  15 DADE  (  19-)  T      0
  16 DTHY  (  20-)  T      0
  17 DTHY  (  21-)  T      0
  18 DADE  (  22-)  T      0
  19 DTHY  ( 101-)  P      0
  20 DADE  ( 102-)  P      0
  21 DADE  ( 103-)  P      0
  22 DTHY  ( 104-)  P      0
  23 DADE  ( 105-)  P      0
  24 DCYT  ( 106-)  P      0
  25 DGUA  ( 107-)  P      0
  26 DADE  ( 108-)  P      0
  27 DCYT  ( 109-)  P      0
And so on for a total of 329 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.023

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!

 435 GLY   ( 424-)  A   1.76   80
 508 LEU   ( 497-)  A   1.59   25

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 178 GLU   ( 167-)  A   1.64

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]

 259 PRO   ( 248-)  A    0.46 HIGH
 277 PRO   ( 266-)  A    0.45 HIGH
 445 PRO   ( 434-)  A    0.46 HIGH
 462 PRO   ( 451-)  A    0.46 HIGH
 745 PRO   ( 734-)  A    0.46 HIGH

Warning: Unusual PRO puckering phases

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

 285 PRO   ( 274-)  A    99.6 envelop C-beta (108 degrees)
 741 PRO   ( 730-)  A   102.1 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.

 865 HIS   ( 854-)  A      NE2 <->  867 SER   ( 856-)  A      C      0.60    2.50  INTRA BF
 840 ARG   ( 829-)  A      NH1 <->  889 SER   ( 878-)  A      O      0.51    2.19  INTRA BF
 865 HIS   ( 854-)  A      CG  <->  866 GLU   ( 855-)  A      N      0.40    2.60  INTRA BF
 161 ARG   ( 150-)  A      O   <->  163 GLY   ( 152-)  A      N      0.36    2.34  INTRA BL
 235 THR   ( 224-)  A      O   <->  237 MET   ( 226-)  A      N      0.29    2.41  INTRA BL
 548 ASP   ( 537-)  A      OD1 <->  824 SER   ( 813-)  A      OG     0.29    2.11  INTRA BF
 534 HIS   ( 523-)  A      C   <->  535 HIS   ( 524-)  A      ND1    0.28    2.72  INTRA BF
 630 GLN   ( 619-)  A      NE2 <->  677 MET   ( 666-)  A      O      0.28    2.42  INTRA BF
 289 TRP   ( 278-)  A      N   <->  332 ASN   ( 321-)  A      ND2    0.27    2.58  INTRA BL
 436 ARG   ( 425-)  A      NH1 <->  795 HIS   ( 784-)  A      CG     0.27    2.83  INTRA BL
 865 HIS   ( 854-)  A      NE2 <->  867 SER   ( 856-)  A      N      0.26    2.74  INTRA BF
  33 ILE   (   6-)  A      CG2 <->   35 LYS   (   8-)  A      NZ     0.26    2.84  INTRA BF
 381 ASN   ( 370-)  A      ND2 <->  386 THR   ( 375-)  A      OG1    0.26    2.44  INTRA BF
 474 HIS   ( 463-)  A      CE1 <->  478 CYS   ( 467-)  A      SG     0.25    3.15  INTRA BL
 484 VAL   ( 473-)  A      CG2 <->  485 PRO   ( 474-)  A      CD     0.25    2.95  INTRA BL
 522 PHE   ( 511-)  A      O   <->  525 PHE   ( 514-)  A      N      0.24    2.46  INTRA BL
 381 ASN   ( 370-)  A      N   <->  382 PRO   ( 371-)  A      CD     0.24    2.76  INTRA BF
 865 HIS   ( 854-)  A      CD2 <->  869 LEU   ( 858-)  A      N      0.23    2.87  INTRA BF
 463 ILE   ( 452-)  A      CG2 <->  464 GLY   ( 453-)  A      N      0.22    2.78  INTRA BF
 353 THR   ( 342-)  A      O   <->  406 ARG   ( 395-)  A      NH2    0.22    2.48  INTRA BF
 266 ALA   ( 255-)  A      O   <->  354 LYS   ( 343-)  A      NZ     0.22    2.48  INTRA BL
 741 PRO   ( 730-)  A      CD  <->  797 GLN   ( 786-)  A      NE2    0.21    2.89  INTRA BL
 210 GLU   ( 199-)  A      OE1 <->  313 LYS   ( 302-)  A      NZ     0.21    2.49  INTRA BF
  49 ASN   (  22-)  A      C   <->   51 LEU   (  24-)  A      N      0.21    2.69  INTRA BF
 836 PHE   ( 825-)  A      CE1 <->  840 ARG   ( 829-)  A      NH2    0.20    2.90  INTRA BL
And so on for a total of 276 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 107 ARG   (  96-)  A      -8.32
 373 MET   ( 362-)  A      -7.46
 323 TYR   ( 312-)  A      -7.34
 109 LYS   (  98-)  A      -6.93
 189 TYR   ( 178-)  A      -6.63
 268 ARG   ( 257-)  A      -6.36
 725 LYS   ( 714-)  A      -6.34
 309 ARG   ( 298-)  A      -6.19
 871 LYS   ( 860-)  A      -6.00
 757 ARG   ( 746-)  A      -5.90
 357 HIS   ( 346-)  A      -5.90
 178 GLU   ( 167-)  A      -5.48
 106 LYS   (  95-)  A      -5.39
 621 LYS   ( 610-)  A      -5.20
 311 HIS   ( 300-)  A      -5.18
 534 HIS   ( 523-)  A      -5.14
 248 VAL   ( 237-)  A      -5.12
 863 GLN   ( 852-)  A      -5.04
 459 LYS   ( 448-)  A      -5.03
 356 LYS   ( 345-)  A      -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.

 189 TYR   ( 178-)  A       191 - LYS    180- ( A)         -5.14

Note: Quality value plot

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

Chain identifier: A

Warning: Low packing Z-score for some residues

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

 108 GLY   (  97-)  A   -2.96
 109 LYS   (  98-)  A   -2.77
 514 ALA   ( 503-)  A   -2.58

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.

 106 LYS   (  95-)  A     -  109 LYS   (  98-)  A        -2.28

Note: Second generation quality Z-score plot

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

Chain identifier: A

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

  49 ASN   (  22-)  A
 182 ASN   ( 171-)  A
 300 ASN   ( 289-)  A
 311 HIS   ( 300-)  A
 332 ASN   ( 321-)  A
 335 GLN   ( 324-)  A
 421 ASN   ( 410-)  A
 422 HIS   ( 411-)  A
 474 HIS   ( 463-)  A
 496 ASN   ( 485-)  A
 599 ASN   ( 588-)  A
 659 GLN   ( 648-)  A
 737 HIS   ( 726-)  A
 748 GLN   ( 737-)  A
 755 GLN   ( 744-)  A
 785 GLN   ( 774-)  A
 792 ASN   ( 781-)  A
 859 GLN   ( 848-)  A
 880 ASN   ( 869-)  A

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  26 DADE  ( 108-)  P      N6
  41 ILE   (  14-)  A      N
  48 PHE   (  21-)  A      N
  54 HIS   (  27-)  A      N
  59 LEU   (  32-)  A      N
  61 ARG   (  34-)  A      NH2
  63 GLN   (  36-)  A      NE2
  85 ILE   (  74-)  A      N
 106 LYS   (  95-)  A      N
 113 ALA   ( 102-)  A      N
 123 GLU   ( 112-)  A      N
 131 LYS   ( 120-)  A      NZ
 143 THR   ( 132-)  A      OG1
 158 ASP   ( 147-)  A      N
 165 ILE   ( 154-)  A      N
 166 ARG   ( 155-)  A      NH1
 177 VAL   ( 166-)  A      N
 182 ASN   ( 171-)  A      N
 183 LYS   ( 172-)  A      N
 188 VAL   ( 177-)  A      N
 189 TYR   ( 178-)  A      N
 196 VAL   ( 185-)  A      N
 197 VAL   ( 186-)  A      N
 211 ALA   ( 200-)  A      N
 212 TRP   ( 201-)  A      N
And so on for a total of 122 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.

 222 HIS   ( 211-)  A      ND1
 253 GLU   ( 242-)  A      OE1
 399 ASP   ( 388-)  A      OD1
 660 GLN   ( 649-)  A      OE1
 683 GLN   ( 672-)  A      OE1
 742 ASP   ( 731-)  A      OD2

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.

  98 ASP   (  87-)  A   H-bonding suggests Asn
 158 ASP   ( 147-)  A   H-bonding suggests Asn; but Alt-Rotamer
 210 GLU   ( 199-)  A   H-bonding suggests Gln
 253 GLU   ( 242-)  A   H-bonding suggests Gln; but Alt-Rotamer
 263 GLU   ( 252-)  A   H-bonding suggests Gln
 369 GLU   ( 358-)  A   H-bonding suggests Gln
 377 ASP   ( 366-)  A   H-bonding suggests Asn; but Alt-Rotamer
 414 GLU   ( 403-)  A   H-bonding suggests Gln; but Alt-Rotamer
 515 GLU   ( 504-)  A   H-bonding suggests Gln; but Alt-Rotamer
 564 GLU   ( 553-)  A   H-bonding suggests Gln
 596 ASP   ( 585-)  A   H-bonding suggests Asn
 611 GLU   ( 600-)  A   H-bonding suggests Gln
 671 ASP   ( 660-)  A   H-bonding suggests Asn
 723 ASP   ( 712-)  A   H-bonding suggests Asn
 798 ASP   ( 787-)  A   H-bonding suggests Asn
 855 ASP   ( 844-)  A   H-bonding suggests Asn
 858 ASP   ( 847-)  A   H-bonding suggests Asn
 885 ASP   ( 874-)  A   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.802
  2nd generation packing quality :  -2.595
  Ramachandran plot appearance   :  -4.773 (bad)
  chi-1/chi-2 rotamer normality  :  -4.267 (bad)
  Backbone conformation          :  -0.764

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.460 (tight)
  Bond angles                    :   0.689
  Omega angle restraints         :   0.186 (tight)
  Side chain planarity           :   0.261 (tight)
  Improper dihedral distribution :   0.660
  B-factor distribution          :   0.358
  Inside/Outside distribution    :   1.017

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 : 2.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -2.2
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.460 (tight)
  Bond angles                    :   0.689
  Omega angle restraints         :   0.186 (tight)
  Side chain planarity           :   0.261 (tight)
  Improper dihedral distribution :   0.660
  B-factor distribution          :   0.358
  Inside/Outside distribution    :   1.017
==============

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.