WHAT IF Check report

This file was created 2011-12-28 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 pdb1gku.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  65.198  B   =  67.985  C    = 129.728
    Alpha=  90.000  Beta= 104.010  Gamma=  90.000

Dimensions of a reduced cell

    A    =  65.198  B   =  67.985  C    = 129.728
    Alpha=  90.000  Beta= 104.010  Gamma=  90.000

Dimensions of the conventional cell

    A    =  65.198  B   = 251.749  C    =  67.985
    Alpha=  90.000  Beta=  90.000  Gamma=  90.543

Transformation to conventional cell

 | -1.000000  0.000000  0.000000|
 |  1.000000  0.000000  2.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: C

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 1
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Z, symmetry, and molecular multiplicity disagree
Could it be that Z must be: 2

Error: Matthews Coefficient (Vm) too low

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

The fact that it is lower than 1.5 in this structure might be caused by a miscalculated value of Z on the CRYST1 card.

Molecular weight of all polymer chains: 115571.008
Volume of the Unit Cell V= 557897.250
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z low: Vm= 1.207
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.260 Could it be that Z must be: 2
This number is the multiplication of the spacegroup and NCS symmetry count
Matthews coefficient for observed atoms and corrected Z: Vm= 2.414

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: B

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.

 107 ARG   ( 120-)  B    High
 117 THR   ( 130-)  B    High
 118 GLU   ( 131-)  B    High
 127 ARG   ( 140-)  B    High
 130 LYS   ( 143-)  B    High
 131 ARG   ( 144-)  B    High
 156 HIS   ( 169-)  B    High
 158 ARG   ( 171-)  B    High
 215 LYS   ( 228-)  B    High
 216 LYS   ( 229-)  B    High
 218 LYS   ( 231-)  B    High
 292 THR   ( 305-)  B    High
 293 ALA   ( 306-)  B    High
 294 THR   ( 307-)  B    High
 295 LYS   ( 308-)  B    High
 296 LYS   ( 309-)  B    High
 316 ARG   ( 335-)  B    High
 317 GLY   ( 336-)  B    High
 341 ASP   ( 360-)  B    High
 348 GLN   ( 367-)  B    High
 373 HIS   ( 392-)  B    High
 389 ARG   ( 408-)  B    High
 399 GLU   ( 418-)  B    High
 453 GLU   ( 472-)  B    High
 544 ARG   ( 563-)  B    High
 552 ASN   ( 571-)  B    High
 554 ARG   ( 573-)  B    High
 564 ASP   ( 607-)  B    High
 644 ARG   ( 687-)  B    High
 660 TRP   ( 703-)  B    High
 661 GLU   ( 704-)  B    High
 698 ARG   ( 741-)  B    High
 699 ASP   ( 742-)  B    High
 709 GLU   ( 752-)  B    High
 710 GLU   ( 753-)  B    High
 711 PHE   ( 754-)  B    High
 712 ASP   ( 755-)  B    High
 713 LEU   ( 756-)  B    High
 714 THR   ( 757-)  B    High
 725 ARG   ( 768-)  B    High
 862 GLU   ( 905-)  B    High
 869 GLU   ( 912-)  B    High
 888 TRP   ( 931-)  B    High
 950 TYR   ( 993-)  B    High
 970 TYR   (1013-)  B    High
 972 LYS   (1015-)  B    High
 973 PHE   (1016-)  B    High
 980 ARG   (1023-)  B    High
1010 ILE   (1053-)  B    High
1011 ASP   (1054-)  B    High

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: 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.

 231 ILE   ( 244-)  B      N    CA   C    99.67   -4.1
 260 LYS   ( 273-)  B      N    CA   C    99.29   -4.3
 355 TYR   ( 374-)  B      N    CA   C    97.32   -5.0
 459 GLU   ( 478-)  B      N    CA   C    96.08   -5.4
 527 VAL   ( 546-)  B      N    CA   C    95.50   -5.6
 732 THR   ( 775-)  B      N    CA   C    97.07   -5.0
 914 THR   ( 957-)  B      N    CA   C    98.46   -4.5

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.

 527 VAL   ( 546-)  B    6.02
 355 TYR   ( 374-)  B    5.29
 459 GLU   ( 478-)  B    5.24
 684 ARG   ( 727-)  B    4.97
 732 THR   ( 775-)  B    4.73
 260 LYS   ( 273-)  B    4.63
 342 ILE   ( 361-)  B    4.47
 276 GLU   ( 289-)  B    4.36
 673 ALA   ( 716-)  B    4.32
 914 THR   ( 957-)  B    4.26
 758 LEU   ( 801-)  B    4.16
 158 ARG   ( 171-)  B    4.07

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 : -3.539

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.

 970 TYR   (1013-)  B    -3.6
 950 TYR   ( 993-)  B    -3.5
 973 PHE   (1016-)  B    -2.8
 117 THR   ( 130-)  B    -2.7
 140 LEU   ( 153-)  B    -2.7
 156 HIS   ( 169-)  B    -2.5
 211 THR   ( 224-)  B    -2.5
 711 PHE   ( 754-)  B    -2.5
 541 ILE   ( 560-)  B    -2.5
 787 GLY   ( 830-)  B    -2.4
 792 GLY   ( 835-)  B    -2.4
 125 HIS   ( 138-)  B    -2.4
 534 ILE   ( 553-)  B    -2.4
 663 PHE   ( 706-)  B    -2.3
  23 LEU   (  36-)  B    -2.3
 704 LEU   ( 747-)  B    -2.3
 768 ARG   ( 811-)  B    -2.3
 828 GLY   ( 871-)  B    -2.3
 148 THR   ( 161-)  B    -2.3
 257 ILE   ( 270-)  B    -2.3
 805 ARG   ( 848-)  B    -2.3
 665 ASN   ( 708-)  B    -2.2
 421 PHE   ( 440-)  B    -2.2
1010 ILE   (1053-)  B    -2.2
 802 GLU   ( 845-)  B    -2.2
 872 ARG   ( 915-)  B    -2.2
  42 GLY   (  55-)  B    -2.2
  45 ARG   (  58-)  B    -2.2
 419 ARG   ( 438-)  B    -2.2
 121 ILE   ( 134-)  B    -2.2
 495 PRO   ( 514-)  B    -2.2
  88 ARG   ( 101-)  B    -2.2
 260 LYS   ( 273-)  B    -2.2
 531 THR   ( 550-)  B    -2.1
 320 LEU   ( 339-)  B    -2.1
 706 HIS   ( 749-)  B    -2.1
 453 GLU   ( 472-)  B    -2.1
 708 GLU   ( 751-)  B    -2.1
 589 PRO   ( 632-)  B    -2.1
  43 GLU   (  56-)  B    -2.1
 925 ARG   ( 968-)  B    -2.1
 213 THR   ( 226-)  B    -2.1
 877 GLU   ( 920-)  B    -2.0
 898 PHE   ( 941-)  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.

   3 ALA   (   3-)  B  Poor phi/psi
   8 ALA   (   9-)  B  Poor phi/psi
  14 ALA   (  16-)  B  Poor phi/psi
  43 GLU   (  56-)  B  Poor phi/psi
  58 LYS   (  71-)  B  Poor phi/psi
  88 ARG   ( 101-)  B  Poor phi/psi
 111 GLU   ( 124-)  B  Poor phi/psi
 113 ALA   ( 126-)  B  Poor phi/psi
 117 THR   ( 130-)  B  Poor phi/psi
 127 ARG   ( 140-)  B  Poor phi/psi
 130 LYS   ( 143-)  B  Poor phi/psi
 140 LEU   ( 153-)  B  Poor phi/psi
 159 GLU   ( 172-)  B  Poor phi/psi
 170 ASP   ( 183-)  B  Poor phi/psi
 178 SER   ( 191-)  B  Poor phi/psi
 189 GLY   ( 202-)  B  Poor phi/psi
 197 LYS   ( 210-)  B  Poor phi/psi
 211 THR   ( 224-)  B  Poor phi/psi
 214 ALA   ( 227-)  B  Poor phi/psi
 216 LYS   ( 229-)  B  Poor phi/psi
 248 ASP   ( 261-)  B  Poor phi/psi
 251 ILE   ( 264-)  B  Poor phi/psi
 252 SER   ( 265-)  B  Poor phi/psi
 253 THR   ( 266-)  B  Poor phi/psi
 259 GLU   ( 272-)  B  Poor phi/psi
And so on for a total of 75 lines.

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

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

chi-1/chi-2 correlation Z-score : -3.387

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.

 854 VAL   ( 897-)  B    0.35
  73 SER   (  86-)  B    0.36
 916 SER   ( 959-)  B    0.38

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 ALA   (   3-)  B      0
   5 ALA   (   5-)  B      0
   6 ALA   (   6-)  B      0
   7 ALA   (   8-)  B      0
   8 ALA   (   9-)  B      0
  10 ALA   (  11-)  B      0
  11 ALA   (  12-)  B      0
  12 ALA   (  14-)  B      0
  13 ALA   (  15-)  B      0
  14 ALA   (  16-)  B      0
  18 ALA   (  20-)  B      0
  19 ALA   (  21-)  B      0
  20 SER   (  33-)  B      0
  21 LEU   (  34-)  B      0
  22 CYS   (  35-)  B      0
  40 CYS   (  53-)  B      0
  41 VAL   (  54-)  B      0
  43 GLU   (  56-)  B      0
  57 ARG   (  70-)  B      0
  67 THR   (  80-)  B      0
  85 LYS   (  98-)  B      0
  87 LYS   ( 100-)  B      0
  88 ARG   ( 101-)  B      0
  93 PHE   ( 106-)  B      0
 111 GLU   ( 124-)  B      0
And so on for a total of 375 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 : 1.193

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!

 787 GLY   ( 830-)  B   3.40   21
 386 GLY   ( 405-)  B   2.14   17
 548 GLY   ( 567-)  B   1.74   13
  25 PRO   (  38-)  B   1.74   13

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.

 513 LEU   ( 532-)  B      O   <->  515 GLY   ( 534-)  B      N      0.50    2.20  INTRA BF
 450 TYR   ( 469-)  B      O   <->  452 ILE   ( 471-)  B      N      0.43    2.27  INTRA BF
 942 MET   ( 985-)  B      SD  <->  943 ARG   ( 986-)  B      NH1    0.43    2.87  INTRA BF
  45 ARG   (  58-)  B      NH1 <-> 1013 HOH   (2005 )  B      O      0.41    2.29  INTRA BF
 261 LEU   ( 274-)  B      O   <->  325 ARG   ( 344-)  B      NH2    0.39    2.31  INTRA BL
 332 CYS   ( 351-)  B      N   <->  434 GLU   ( 453-)  B      OE1    0.39    2.31  INTRA BF
 793 ARG   ( 836-)  B      NH2 <->  849 CYS   ( 892-)  B      O      0.37    2.33  INTRA BL
 912 PRO   ( 955-)  B      O   <->  952 ARG   ( 995-)  B      NH1    0.36    2.34  INTRA BL
 250 SER   ( 263-)  B      O   <->  252 SER   ( 265-)  B      N      0.36    2.34  INTRA BF
 398 ARG   ( 417-)  B      NH2 <->  436 ASP   ( 455-)  B      OD2    0.35    2.35  INTRA BF
 221 GLU   ( 234-)  B      OE2 <->  224 ARG   ( 237-)  B      NE     0.35    2.35  INTRA BF
 316 ARG   ( 335-)  B      NH2 <->  319 ASP   ( 338-)  B      N      0.34    2.51  INTRA BF
 459 GLU   ( 478-)  B      N   <->  460 VAL   ( 479-)  B      N      0.33    2.27  INTRA BL
 464 LYS   ( 483-)  B      NZ  <-> 1013 HOH   (2070 )  B      O      0.32    2.38  INTRA BF
 345 LEU   ( 364-)  B      O   <->  378 ARG   ( 397-)  B      NH1    0.32    2.38  INTRA BF
 195 LYS   ( 208-)  B      CG  <->  196 THR   ( 209-)  B      N      0.30    2.70  INTRA BF
 260 LYS   ( 273-)  B      N   <->  261 LEU   ( 274-)  B      N      0.30    2.30  INTRA BF
 270 ARG   ( 283-)  B      N   <-> 1013 HOH   (2036 )  B      O      0.30    2.40  INTRA BL
 802 GLU   ( 845-)  B      OE1 <->  805 ARG   ( 848-)  B      NH1    0.30    2.40  INTRA BL
 300 GLU   ( 313-)  B      O   <->  304 GLU   ( 317-)  B      N      0.29    2.41  INTRA BF
 741 ASN   ( 784-)  B      ND2 <->  916 SER   ( 959-)  B      N      0.29    2.56  INTRA BL
 876 ALA   ( 919-)  B      N   <-> 1013 HOH   (2142 )  B      O      0.28    2.42  INTRA BL
 980 ARG   (1023-)  B      NH1 <->  984 SER   (1027-)  B      CB     0.28    2.82  INTRA BF
 239 ARG   ( 252-)  B      NH2 <->  243 ASP   ( 256-)  B      OD2    0.28    2.42  INTRA BL
 672 ARG   ( 715-)  B      NH1 <-> 1006 GLU   (1049-)  B      OE2    0.27    2.43  INTRA BF
And so on for a total of 347 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: B

Warning: Abnormal packing environment for some residues

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

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

 127 ARG   ( 140-)  B      -8.03
 950 TYR   ( 993-)  B      -6.91
 797 GLU   ( 840-)  B      -6.34
 666 ARG   ( 709-)  B      -6.20
 270 ARG   ( 283-)  B      -6.11
 899 ARG   ( 942-)  B      -6.04
 544 ARG   ( 563-)  B      -5.92
 991 ARG   (1034-)  B      -5.80
 391 GLN   ( 410-)  B      -5.79
 768 ARG   ( 811-)  B      -5.74
 295 LYS   ( 308-)  B      -5.71
 158 ARG   ( 171-)  B      -5.63
 554 ARG   ( 573-)  B      -5.59
 717 LEU   ( 760-)  B      -5.47
 728 LEU   ( 771-)  B      -5.45
 820 GLN   ( 863-)  B      -5.43
 389 ARG   ( 408-)  B      -5.42
 543 ASN   ( 562-)  B      -5.38
 204 ARG   ( 217-)  B      -5.38
 215 LYS   ( 228-)  B      -5.35
 672 ARG   ( 715-)  B      -5.31
 398 ARG   ( 417-)  B      -5.31
 925 ARG   ( 968-)  B      -5.28
 689 ARG   ( 732-)  B      -5.17
 969 ARG   (1012-)  B      -5.09
 142 ASN   ( 155-)  B      -5.09
 524 GLN   ( 543-)  B      -5.08
 225 GLN   ( 238-)  B      -5.01

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.

 968 ARG   (1011-)  B       970 - TYR   1013- ( B)         -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: B

Warning: Low packing Z-score for some residues

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

 808 ARG   ( 851-)  B   -2.55
 158 ARG   ( 171-)  B   -2.53

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: B

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1013 HOH   (2011 )  B      O
1013 HOH   (2012 )  B      O
1013 HOH   (2013 )  B      O
1013 HOH   (2016 )  B      O
1013 HOH   (2020 )  B      O
1013 HOH   (2083 )  B      O
1013 HOH   (2119 )  B      O
1013 HOH   (2120 )  B      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.

  48 GLN   (  61-)  B
 156 HIS   ( 169-)  B
 162 HIS   ( 175-)  B
 186 HIS   ( 199-)  B
 247 ASN   ( 260-)  B
 359 ASN   ( 378-)  B
 480 GLN   ( 499-)  B
 565 ASN   ( 608-)  B
 616 HIS   ( 659-)  B
 706 HIS   ( 749-)  B
 741 ASN   ( 784-)  B
 753 GLN   ( 796-)  B
 833 HIS   ( 876-)  B
 915 GLN   ( 958-)  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.

   8 ALA   (   9-)  B      N
  15 ALA   (  17-)  B      N
  26 GLU   (  39-)  B      N
  88 ARG   ( 101-)  B      N
  95 THR   ( 108-)  B      N
  96 SER   ( 109-)  B      OG
  98 LEU   ( 111-)  B      N
 112 LYS   ( 125-)  B      N
 118 GLU   ( 131-)  B      N
 121 ILE   ( 134-)  B      N
 127 ARG   ( 140-)  B      N
 130 LYS   ( 143-)  B      N
 149 THR   ( 162-)  B      OG1
 157 TYR   ( 170-)  B      N
 158 ARG   ( 171-)  B      N
 204 ARG   ( 217-)  B      NE
 205 GLY   ( 218-)  B      N
 210 SER   ( 223-)  B      N
 211 THR   ( 224-)  B      N
 223 PHE   ( 236-)  B      N
 232 GLY   ( 245-)  B      N
 238 VAL   ( 251-)  B      N
 239 ARG   ( 252-)  B      NE
 254 LEU   ( 267-)  B      N
 259 GLU   ( 272-)  B      N
And so on for a total of 94 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.

 118 GLU   ( 131-)  B      OE1
 170 ASP   ( 183-)  B      OD2
 172 ASP   ( 185-)  B      OD1
 259 GLU   ( 272-)  B      OE1
 453 GLU   ( 472-)  B      OE1
 453 GLU   ( 472-)  B      OE2
 514 ASP   ( 533-)  B      OD1
 599 ASP   ( 642-)  B      OD2
 739 ASP   ( 782-)  B      OD2
 848 GLN   ( 891-)  B      OE1

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.

 164 ASP   ( 177-)  B   H-bonding suggests Asn
 230 ASP   ( 243-)  B   H-bonding suggests Asn; but Alt-Rotamer
 300 GLU   ( 313-)  B   H-bonding suggests Gln; but Alt-Rotamer
 341 ASP   ( 360-)  B   H-bonding suggests Asn; but Alt-Rotamer
 474 ASP   ( 493-)  B   H-bonding suggests Asn
 699 ASP   ( 742-)  B   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.450
  2nd generation packing quality :  -1.257
  Ramachandran plot appearance   :  -3.539 (poor)
  chi-1/chi-2 rotamer normality  :  -3.387 (poor)
  Backbone conformation          :  -0.165

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.315 (tight)
  Bond angles                    :   0.630 (tight)
  Omega angle restraints         :   0.217 (tight)
  Side chain planarity           :   0.200 (tight)
  Improper dihedral distribution :   0.599
  B-factor distribution          :   1.138
  Inside/Outside distribution    :   1.003

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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.7
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.315 (tight)
  Bond angles                    :   0.630 (tight)
  Omega angle restraints         :   0.217 (tight)
  Side chain planarity           :   0.200 (tight)
  Improper dihedral distribution :   0.599
  B-factor distribution          :   1.138
  Inside/Outside distribution    :   1.003
==============

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.