WHAT IF Check report

This file was created 2011-12-29 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 pdb1kit.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: 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 30.51

Note: B-factor plot

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

Chain identifier: A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 349 SER   ( 373-)  A      C    O     1.15   -4.2

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.

  50 ARG   (  74-)  A      CB   CG   CD  105.31   -4.4
  51 ALA   (  75-)  A      N    CA   C    98.63   -4.5
 109 VAL   ( 133-)  A      C    CA   CB  100.85   -4.9
 190 GLN   ( 214-)  A      N    CA   C   123.34    4.3
 191 GLY   ( 215-)  A      N    CA   C   125.06    4.3
 233 THR   ( 257-)  A      N    CA   C    99.96   -4.0
 238 THR   ( 262-)  A      C    CA   CB  100.35   -5.1
 255 THR   ( 279-)  A      N    CA   C   123.10    4.2
 370 ASN   ( 394-)  A      N    CA   C    99.04   -4.3
 388 ASP   ( 412-)  A      N    CA   CB  103.48   -4.1
 451 ASN   ( 475-)  A      C    CA   CB  101.20   -4.7
 452 ILE   ( 476-)  A      N    CA   C    99.99   -4.0
 477 HIS   ( 501-)  A      CG   ND1  CE1 109.64    4.0
 516 GLY   ( 540-)  A     -C    N    CA  128.33    4.5
 529 THR   ( 553-)  A      C    CA   CB  101.49   -4.5
 561 ILE   ( 585-)  A      N    CA   C    98.71   -4.5
 599 VAL   ( 623-)  A      C    CA   CB  102.39   -4.1
 609 THR   ( 633-)  A      C    CA   CB  102.04   -4.2
 613 ASP   ( 637-)  A      N    CA   C   128.94    6.3

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

 625 PRO   ( 649-)  A      N     -8.1   -28.93    -2.48
The average deviation= 1.662

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.

 613 ASP   ( 637-)  A    5.98
 371 GLN   ( 395-)  A    5.12
 750 GLN   ( 774-)  A    4.82
 161 ALA   ( 185-)  A    4.74
 190 GLN   ( 214-)  A    4.70
  51 ALA   (  75-)  A    4.61
 201 ILE   ( 225-)  A    4.51
  96 LEU   ( 120-)  A    4.49
 561 ILE   ( 585-)  A    4.42
 726 ASN   ( 750-)  A    4.30
 451 ASN   ( 475-)  A    4.28
 288 PRO   ( 312-)  A    4.16
 140 SER   ( 164-)  A    4.13
 191 GLY   ( 215-)  A    4.12
 753 THR   ( 777-)  A    4.08
 255 THR   ( 279-)  A    4.06
 328 VAL   ( 352-)  A    4.01
 233 THR   ( 257-)  A    4.00

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.689

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 474 GLN   ( 498-)  A    7.01
 427 ASN   ( 451-)  A    6.05
 359 ASN   ( 383-)  A    5.96
 351 ASN   ( 375-)  A    5.43
 541 ASN   ( 565-)  A    5.06
 615 ASN   ( 639-)  A    4.86
 490 GLN   ( 514-)  A    4.84
 249 ASP   ( 273-)  A    4.83
 533 GLN   ( 557-)  A    4.58
 535 ASN   ( 559-)  A    4.15

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.109

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.

 744 PRO   ( 768-)  A    -2.9
 625 PRO   ( 649-)  A    -2.8
 662 THR   ( 686-)  A    -2.8
 426 LEU   ( 450-)  A    -2.8
 514 LEU   ( 538-)  A    -2.7
 201 ILE   ( 225-)  A    -2.7
 682 PRO   ( 706-)  A    -2.6
 587 ILE   ( 611-)  A    -2.6
 742 ARG   ( 766-)  A    -2.5
 429 THR   ( 453-)  A    -2.5
 657 VAL   ( 681-)  A    -2.5
 246 ILE   ( 270-)  A    -2.5
 590 THR   ( 614-)  A    -2.5
 196 ARG   ( 220-)  A    -2.5
 153 ILE   ( 177-)  A    -2.5
 684 GLY   ( 708-)  A    -2.5
 661 ILE   ( 685-)  A    -2.4
 205 VAL   ( 229-)  A    -2.4
 198 PRO   ( 222-)  A    -2.4
 699 GLU   ( 723-)  A    -2.4
 237 ILE   ( 261-)  A    -2.3
 162 SER   ( 186-)  A    -2.3
 379 ARG   ( 403-)  A    -2.3
  32 VAL   (  56-)  A    -2.3
 481 GLU   ( 505-)  A    -2.3
And so on for a total of 54 lines.

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.

  11 THR   (  35-)  A  Poor phi/psi
  27 ASN   (  51-)  A  Poor phi/psi
  28 ASN   (  52-)  A  Poor phi/psi
  41 ALA   (  65-)  A  Poor phi/psi
  80 SER   ( 104-)  A  Poor phi/psi
  91 GLY   ( 115-)  A  Poor phi/psi
  92 THR   ( 116-)  A  Poor phi/psi
 105 GLY   ( 129-)  A  Poor phi/psi
 143 SER   ( 167-)  A  Poor phi/psi
 149 ASP   ( 173-)  A  Poor phi/psi
 156 ASN   ( 180-)  A  Poor phi/psi
 162 SER   ( 186-)  A  Poor phi/psi
 166 MET   ( 190-)  A  Poor phi/psi
 190 GLN   ( 214-)  A  Poor phi/psi
 197 GLY   ( 221-)  A  PRO omega poor
 201 ILE   ( 225-)  A  Poor phi/psi
 245 GLY   ( 269-)  A  Poor phi/psi
 262 ASP   ( 286-)  A  Poor phi/psi
 278 ASN   ( 302-)  A  Poor phi/psi
 292 ALA   ( 316-)  A  Poor phi/psi
 352 SER   ( 376-)  A  Poor phi/psi
 426 LEU   ( 450-)  A  Poor phi/psi
 436 GLY   ( 460-)  A  Poor phi/psi
 475 GLN   ( 499-)  A  Poor phi/psi
 586 SER   ( 610-)  A  Poor phi/psi
 594 SER   ( 618-)  A  Poor phi/psi
 619 ASN   ( 643-)  A  Poor phi/psi
 624 SER   ( 648-)  A  Poor phi/psi
 643 ALA   ( 667-)  A  Poor phi/psi
 645 ASN   ( 669-)  A  Poor phi/psi
 651 ASN   ( 675-)  A  Poor phi/psi
 677 ASN   ( 701-)  A  Poor phi/psi
 684 GLY   ( 708-)  A  Poor phi/psi
 699 GLU   ( 723-)  A  Poor phi/psi
 705 GLY   ( 729-)  A  Poor phi/psi
 715 ALA   ( 739-)  A  Poor phi/psi
 733 THR   ( 757-)  A  Poor phi/psi
 736 SER   ( 760-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.289

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 : -5.289

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.

  66 SER   (  90-)  A    0.36
 599 VAL   ( 623-)  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 PHE   (  27-)  A      0
   4 ASP   (  28-)  A      0
   8 THR   (  32-)  A      0
  11 THR   (  35-)  A      0
  19 GLN   (  43-)  A      0
  21 TRP   (  45-)  A      0
  23 GLN   (  47-)  A      0
  25 ASN   (  49-)  A      0
  26 THR   (  50-)  A      0
  27 ASN   (  51-)  A      0
  28 ASN   (  52-)  A      0
  36 ALA   (  60-)  A      0
  40 PRO   (  64-)  A      0
  45 GLN   (  69-)  A      0
  47 ILE   (  71-)  A      0
  51 ALA   (  75-)  A      0
  70 TRP   (  94-)  A      0
  75 GLU   (  99-)  A      0
  76 MET   ( 100-)  A      0
  80 SER   ( 104-)  A      0
  83 MET   ( 107-)  A      0
  86 ASN   ( 110-)  A      0
  87 TYR   ( 111-)  A      0
  92 THR   ( 116-)  A      0
  93 GLN   ( 117-)  A      0
And so on for a total of 371 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 : 2.957

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!

 224 GLY   ( 248-)  A   3.08   12
   9 GLY   (  33-)  A   1.52   54

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]

 678 PRO   ( 702-)  A    0.14 LOW

Warning: Unusual PRO puckering phases

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

  16 PRO   (  40-)  A   124.2 half-chair C-beta/C-alpha (126 degrees)
  97 PRO   ( 121-)  A   -54.9 half-chair C-beta/C-alpha (-54 degrees)
 159 PRO   ( 183-)  A    30.2 envelop C-delta (36 degrees)
 202 PRO   ( 226-)  A   -64.1 envelop C-beta (-72 degrees)
 269 PRO   ( 293-)  A    51.5 half-chair C-delta/C-gamma (54 degrees)
 275 PRO   ( 299-)  A   101.6 envelop C-beta (108 degrees)
 303 PRO   ( 327-)  A    42.2 envelop C-delta (36 degrees)
 579 PRO   ( 603-)  A  -119.9 half-chair C-delta/C-gamma (-126 degrees)
 593 PRO   ( 617-)  A   131.2 half-chair C-beta/C-alpha (126 degrees)
 625 PRO   ( 649-)  A    99.6 envelop C-beta (108 degrees)
 682 PRO   ( 706-)  A    27.0 half-chair N/C-delta (18 degrees)
 706 PRO   ( 730-)  A   -26.9 half-chair C-alpha/N (-18 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.

 602 GLN   ( 626-)  A      NE2 <->  663 ARG   ( 687-)  A      NH2    0.60    2.25  INTRA BL
 602 GLN   ( 626-)  A      NE2 <->  671 HIS   ( 695-)  A      NE2    0.55    2.45  INTRA BL
 158 GLN   ( 182-)  A      NE2 <->  761 HOH   (1519 )  A      O      0.45    2.25  INTRA
 462 ASP   ( 486-)  A      N   <->  761 HOH   ( 852 )  A      O      0.44    2.26  INTRA BL
 408 SER   ( 432-)  A      N   <->  761 HOH   ( 897 )  A      O      0.44    2.26  INTRA BL
 380 LYS   ( 404-)  A      NZ  <->  449 GLU   ( 473-)  A      OE1    0.43    2.27  INTRA BL
 253 ASN   ( 277-)  A      N   <->  761 HOH   (1131 )  A      O      0.42    2.28  INTRA BL
 657 VAL   ( 681-)  A      N   <->  761 HOH   ( 976 )  A      O      0.42    2.28  INTRA BL
   9 GLY   (  33-)  A      N   <->   14 ASP   (  38-)  A      OD2    0.42    2.28  INTRA BF
  23 GLN   (  47-)  A      NE2 <->  761 HOH   (1494 )  A      O      0.41    2.29  INTRA BF
 684 GLY   ( 708-)  A      N   <->  761 HOH   (1192 )  A      O      0.41    2.29  INTRA BF
 396 ASN   ( 420-)  A      ND2 <->  761 HOH   ( 868 )  A      O      0.41    2.29  INTRA
 448 GLN   ( 472-)  A      NE2 <->  761 HOH   (1438 )  A      O      0.41    2.29  INTRA BF
 332 SER   ( 356-)  A      O   <->  516 GLY   ( 540-)  A      N      0.40    2.30  INTRA BF
 164 GLN   ( 188-)  A      NE2 <->  761 HOH   (1010 )  A      O      0.40    2.30  INTRA BL
  71 ARG   (  95-)  A      NH1 <->  761 HOH   (1069 )  A      O      0.40    2.30  INTRA BL
 183 ARG   ( 207-)  A      NH2 <->  761 HOH   (1467 )  A      O      0.39    2.31  INTRA BF
 526 HIS   ( 550-)  A      ND1 <->  761 HOH   ( 928 )  A      O      0.38    2.32  INTRA BL
 327 GLN   ( 351-)  A      OE1 <->  570 TRP   ( 594-)  A      N      0.37    2.33  INTRA BL
 113 GLY   ( 137-)  A      N   <->  761 HOH   (1007 )  A      O      0.37    2.33  INTRA
  90 ASN   ( 114-)  A      O   <->   92 THR   ( 116-)  A      N      0.36    2.34  INTRA
 688 ARG   ( 712-)  A      N   <->  761 HOH   ( 982 )  A      O      0.36    2.34  INTRA BL
 543 ARG   ( 567-)  A      NE  <->  564 ASP   ( 588-)  A      OD1    0.35    2.35  INTRA BL
 377 GLY   ( 401-)  A      N   <->  449 GLU   ( 473-)  A      O      0.34    2.36  INTRA
 114 GLN   ( 138-)  A      NE2 <->  761 HOH   (1064 )  A      O      0.32    2.38  INTRA
And so on for a total of 440 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.

 756 GLN   ( 780-)  A      -7.18
 242 ARG   ( 266-)  A      -6.50
 475 GLN   ( 499-)  A      -6.14
 319 GLN   ( 343-)  A      -5.71
 614 PHE   ( 638-)  A      -5.68
 114 GLN   ( 138-)  A      -5.68
 389 GLU   ( 413-)  A      -5.54
 602 GLN   ( 626-)  A      -5.51
  27 ASN   (  51-)  A      -5.43
 742 ARG   ( 766-)  A      -5.38
 735 ASN   ( 759-)  A      -5.25
 632 LYS   ( 656-)  A      -5.13
 540 GLN   ( 564-)  A      -5.09
 141 ASN   ( 165-)  A      -5.07

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 293 GLN   ( 317-)  A       295 - GLY    319- ( A)         -4.47

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.

 158 GLN   ( 182-)  A   -2.57
 514 LEU   ( 538-)  A   -2.53

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.

 293 GLN   ( 317-)  A     -  297 ARG   ( 321-)  A        -1.88

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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 761 HOH   ( 886 )  A      O      9.63   62.69   98.94
 761 HOH   ( 988 )  A      O     47.58   62.43   73.57
 761 HOH   ( 990 )  A      O     42.47   62.23   71.27
 761 HOH   (1011 )  A      O     24.29   35.71   46.30
 761 HOH   (1013 )  A      O     47.60   67.50   36.17
 761 HOH   (1014 )  A      O     49.23   66.72   33.04
 761 HOH   (1018 )  A      O     53.27   60.83   27.84
 761 HOH   (1038 )  A      O      5.98   49.21   57.66
 761 HOH   (1054 )  A      O     34.45   60.25  113.01
 761 HOH   (1062 )  A      O     40.41   67.46  130.34
 761 HOH   (1097 )  A      O     31.40   22.28  125.07
 761 HOH   (1113 )  A      O     30.88   24.35  137.92
 761 HOH   (1118 )  A      O     14.96   55.56   59.51
 761 HOH   (1199 )  A      O     44.55   63.70   59.35
 761 HOH   (1200 )  A      O     44.86   60.69   60.36
 761 HOH   (1210 )  A      O     51.87   55.87   43.83
 761 HOH   (1233 )  A      O     38.83   24.35  130.44
 761 HOH   (1248 )  A      O     13.02   50.80   61.74
 761 HOH   (1356 )  A      O     13.51   60.25  102.66
 761 HOH   (1359 )  A      O      2.96   45.06   95.15
 761 HOH   (1372 )  A      O     19.08   63.90   73.50
 761 HOH   (1373 )  A      O     19.31   75.62   83.06
 761 HOH   (1444 )  A      O     40.82   28.36   47.46
 761 HOH   (1465 )  A      O     37.06   59.37  112.52
 761 HOH   (1471 )  A      O     14.70   59.99   59.05
 761 HOH   (1496 )  A      O     45.39   68.63   33.14
 761 HOH   (1511 )  A      O     20.72   70.58   97.22
 761 HOH   (1512 )  A      O     12.47   63.65  102.26
 761 HOH   (1513 )  A      O     10.50   61.48  101.16
 761 HOH   (1528 )  A      O     12.30   52.98   61.57
 761 HOH   (1532 )  A      O     19.53   64.39   59.75
 761 HOH   (1539 )  A      O     58.76   52.96   35.59
 761 HOH   (1544 )  A      O     60.06   50.64   53.01
 761 HOH   (1545 )  A      O     56.45   49.93   53.15

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.

 761 HOH   (1012 )  A      O
 761 HOH   (1085 )  A      O
 761 HOH   (1255 )  A      O
 761 HOH   (1324 )  A      O
 761 HOH   (1476 )  A      O
 761 HOH   (1488 )  A      O
 761 HOH   (1508 )  A      O

Error: HIS, ASN, GLN side chain flips

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

  23 GLN   (  47-)  A
  27 ASN   (  51-)  A
  93 GLN   ( 117-)  A
 156 ASN   ( 180-)  A
 293 GLN   ( 317-)  A
 304 ASN   ( 328-)  A
 357 GLN   ( 381-)  A
 417 HIS   ( 441-)  A
 427 ASN   ( 451-)  A
 450 ASN   ( 474-)  A
 451 ASN   ( 475-)  A
 453 GLN   ( 477-)  A
 466 HIS   ( 490-)  A
 540 GLN   ( 564-)  A
 644 ASN   ( 668-)  A
 686 ASN   ( 710-)  A
 726 ASN   ( 750-)  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.

   6 ASN   (  30-)  A      N
  15 SER   (  39-)  A      N
  21 TRP   (  45-)  A      NE1
  33 LEU   (  57-)  A      N
  47 ILE   (  71-)  A      N
  50 ARG   (  74-)  A      N
  57 LEU   (  81-)  A      N
  64 GLN   (  88-)  A      NE2
  88 TYR   ( 112-)  A      N
  92 THR   ( 116-)  A      N
  94 ARG   ( 118-)  A      NH1
 111 PHE   ( 135-)  A      N
 126 ALA   ( 150-)  A      N
 127 THR   ( 151-)  A      N
 143 SER   ( 167-)  A      N
 169 TRP   ( 193-)  A      NE1
 173 SER   ( 197-)  A      N
 175 ASN   ( 199-)  A      N
 176 THR   ( 200-)  A      OG1
 182 TYR   ( 206-)  A      OH
 191 GLY   ( 215-)  A      N
 200 ARG   ( 224-)  A      NH2
 206 ALA   ( 230-)  A      N
 234 ASN   ( 258-)  A      ND2
 255 THR   ( 279-)  A      OG1
And so on for a total of 72 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.

  62 HIS   (  86-)  A      NE2
 155 ASP   ( 179-)  A      OD1
 171 ASN   ( 195-)  A      OD1
 175 ASN   ( 199-)  A      OD1
 234 ASN   ( 258-)  A      OD1
 235 ASP   ( 259-)  A      OD1
 342 GLU   ( 366-)  A      OE1
 370 ASN   ( 394-)  A      OD1
 373 GLN   ( 397-)  A      OE1
 628 GLN   ( 652-)  A      OE1
 633 ASP   ( 657-)  A      OD2

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 759  CA   ( 802-)  A     0.91   1.14 Scores about as good as NA
 760  CA   ( 803-)  A     0.66   0.89 Scores about as good as NA

Warning: Unusual water packing

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

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

 761 HOH   ( 940 )  A      O  1.01 CA  5 *1
 761 HOH   ( 991 )  A      O  1.15  K  6 Ion-B
 761 HOH   (1164 )  A      O  0.94 NA  5
 761 HOH   (1168 )  A      O  1.08  K  4 ION-B H2O-B
 761 HOH   (1306 )  A      O  1.03  K  5

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  14 ASP   (  38-)  A   H-bonding suggests Asn; but Alt-Rotamer
 184 ASP   ( 208-)  A   H-bonding suggests Asn
 249 ASP   ( 273-)  A   H-bonding suggests Asn; but Alt-Rotamer
 262 ASP   ( 286-)  A   H-bonding suggests Asn
 323 ASP   ( 347-)  A   H-bonding suggests Asn
 355 ASP   ( 379-)  A   H-bonding suggests Asn; but Alt-Rotamer
 376 ASP   ( 400-)  A   H-bonding suggests Asn
 483 ASP   ( 507-)  A   H-bonding suggests Asn; but Alt-Rotamer
 552 ASP   ( 576-)  A   H-bonding suggests Asn; but Alt-Rotamer
 633 ASP   ( 657-)  A   H-bonding suggests Asn; but Alt-Rotamer
 698 ASP   ( 722-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.156
  2nd generation packing quality :  -1.837
  Ramachandran plot appearance   :  -3.109 (poor)
  chi-1/chi-2 rotamer normality  :  -5.289 (bad)
  Backbone conformation          :  -0.781

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.715
  Bond angles                    :   0.844
  Omega angle restraints         :   0.538 (tight)
  Side chain planarity           :   1.752
  Improper dihedral distribution :   1.364
  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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -3.3 (poor)
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.715
  Bond angles                    :   0.844
  Omega angle restraints         :   0.538 (tight)
  Side chain planarity           :   1.752
  Improper dihedral distribution :   1.364
  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.