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 pdb1fok.ent

Checks that need to be done early-on in validation

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: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 2
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 2

Error: Matthews Coefficient (Vm) very high

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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 76830.508
Volume of the Unit Cell V= 548757.000
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.142
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.510 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 2
which would result in the much more normal Vm= 3.571
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

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: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 289 PRO   ( 255-)  A      CG
 289 PRO   ( 255-)  A      CD
 552 HIS   ( 523-)  A      CG
 552 HIS   ( 523-)  A      ND1
 552 HIS   ( 523-)  A      CD2
 552 HIS   ( 523-)  A      CE1
 552 HIS   ( 523-)  A      NE2
 554 LYS   ( 525-)  A      CG
 554 LYS   ( 525-)  A      CD
 554 LYS   ( 525-)  A      CE
 554 LYS   ( 525-)  A      NZ

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.

 290 ASP   ( 256-)  A    High
 418 GLU   ( 389-)  A    High
 566 HIS   ( 537-)  A    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) :130.000

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.

  34 DTHY  ( 934-)  C      C5   C4    1.48    4.3

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.

   7 DGUA  ( 907-)  B      N9   C8   N7  113.24    4.3
  17 DGUA  ( 917-)  B      N9   C8   N7  113.11    4.0
  23 DGUA  ( 923-)  C      N9   C8   N7  113.25    4.3
 136 LYS   (  99-)  A      N    CA   C    93.78   -6.2
 250 GLY   ( 213-)  A      N    CA   C    97.83   -5.1
 289 PRO   ( 255-)  A      N    CA   CB  110.74    7.0
 528 ILE   ( 499-)  A      N    CA   C    93.24   -6.4
 547 LEU   ( 518-)  A      CA   CB   CG  132.16    4.5
 555 GLY   ( 526-)  A      N    CA   C   129.55    5.9
 583 GLY   ( 554-)  A      N    CA   C    99.89   -4.3

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.

 583 GLY   ( 554-)  A    7.03
 136 LYS   (  99-)  A    6.75
 183 ALA   ( 146-)  A    5.86
 528 ILE   ( 499-)  A    5.79
 555 GLY   ( 526-)  A    5.73
 250 GLY   ( 213-)  A    5.65
 251 GLU   ( 214-)  A    5.39
 449 GLN   ( 420-)  A    5.31
 495 VAL   ( 466-)  A    5.15
  82 LEU   (  45-)  A    5.14
 116 ARG   (  79-)  A    4.89
 356 GLN   ( 327-)  A    4.65
 458 MET   ( 429-)  A    4.46
 567 ILE   ( 538-)  A    4.19
  54 PHE   (  17-)  A    4.19
  73 GLU   (  36-)  A    4.14
  57 LEU   (  20-)  A    4.01

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 : 1.818

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 321 TYR   ( 292-)  A      CB   4.49
 321 TYR   ( 292-)  A      OH   4.16

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.

   5 DADE  ( 905-)  B    0.11
 Ramachandran Z-score : -4.026

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 : -4.026

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.

 120 PRO   (  83-)  A    -2.5
 139 ILE   ( 102-)  A    -2.5
 523 THR   ( 494-)  A    -2.5
 529 ASN   ( 500-)  A    -2.5
 489 ILE   ( 460-)  A    -2.4
 451 ARG   ( 422-)  A    -2.4
 502 GLY   ( 473-)  A    -2.4
 587 ILE   ( 558-)  A    -2.4
 206 LEU   ( 169-)  A    -2.3
 252 ILE   ( 215-)  A    -2.3
 204 THR   ( 167-)  A    -2.3
 227 SER   ( 190-)  A    -2.3
 277 VAL   ( 240-)  A    -2.2
 498 LYS   ( 469-)  A    -2.2
  89 GLN   (  52-)  A    -2.2
 160 ILE   ( 123-)  A    -2.2
  51 PRO   (  14-)  A    -2.2
 562 THR   ( 533-)  A    -2.2
 575 LEU   ( 546-)  A    -2.2
 290 ASP   ( 256-)  A    -2.2
 516 ARG   ( 487-)  A    -2.1
 594 LEU   ( 565-)  A    -2.1
 506 LEU   ( 477-)  A    -2.1
 383 THR   ( 354-)  A    -2.1
 196 TYR   ( 159-)  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.

  52 GLY   (  15-)  A  Poor phi/psi
 134 ASN   (  97-)  A  Poor phi/psi
 164 ASP   ( 127-)  A  Poor phi/psi
 223 PHE   ( 186-)  A  Poor phi/psi
 242 ALA   ( 205-)  A  Poor phi/psi
 248 ASP   ( 211-)  A  Poor phi/psi
 257 GLU   ( 220-)  A  Poor phi/psi
 290 ASP   ( 256-)  A  Poor phi/psi
 312 ALA   ( 278-)  A  Poor phi/psi
 326 ALA   ( 297-)  A  Poor phi/psi
 327 THR   ( 298-)  A  Poor phi/psi
 349 ALA   ( 320-)  A  Poor phi/psi
 368 GLU   ( 339-)  A  Poor phi/psi
 490 ASP   ( 461-)  A  Poor phi/psi
 502 GLY   ( 473-)  A  Poor phi/psi
 524 ARG   ( 495-)  A  Poor phi/psi
 530 PRO   ( 501-)  A  Poor phi/psi
 542 THR   ( 513-)  A  Poor phi/psi
 555 GLY   ( 526-)  A  Poor phi/psi
 569 ASN   ( 540-)  A  Poor phi/psi
 583 GLY   ( 554-)  A  Poor phi/psi
 603 ASN   ( 574-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.399

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 : -4.399

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.

 520 GLU   ( 491-)  A    0.33
 493 VAL   ( 464-)  A    0.36
 143 SER   ( 106-)  A    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 DGUA  ( 903-)  B      0
   4 DGUA  ( 904-)  B      0
   5 DADE  ( 905-)  B      0
   6 DTHY  ( 906-)  B      0
   7 DGUA  ( 907-)  B      0
   8 DADE  ( 908-)  B      0
   9 DTHY  ( 909-)  B      0
  10 DADE  ( 910-)  B      0
  11 DADE  ( 911-)  B      0
  12 DCYT  ( 912-)  B      0
  13 DGUA  ( 913-)  B      0
  14 DCYT  ( 914-)  B      0
  15 DTHY  ( 915-)  B      0
  16 DADE  ( 916-)  B      0
  17 DGUA  ( 917-)  B      0
  18 DTHY  ( 918-)  B      0
  19 DCYT  ( 919-)  B      0
  20 DADE  ( 920-)  B      0
  21 DADE  ( 921-)  C      0
  22 DTHY  ( 922-)  C      0
  23 DGUA  ( 923-)  C      0
  24 DADE  ( 924-)  C      0
  25 DCYT  ( 925-)  C      0
  26 DTHY  ( 926-)  C      0
  27 DADE  ( 927-)  C      0
And so on for a total of 212 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 : 1.598

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]

 198 PRO   ( 161-)  A    0.47 HIGH
 289 PRO   ( 255-)  A    0.00 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].

 120 PRO   (  83-)  A    50.5 half-chair C-delta/C-gamma (54 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.

 262 LYS   ( 225-)  A      NZ  <->  266 MET   ( 229-)  A      SD     0.46    2.84  INTRA BL
  32 DTHY  ( 932-)  C      C1' <->  610 HOH   ( 754 )  C      O      0.42    2.38  INTRA
 529 ASN   ( 500-)  A      ND2 <->  531 ASN   ( 502-)  A      CG     0.38    2.72  INTRA
   5 DADE  ( 905-)  B      N7  <->   50 ASN   (  13-)  A      ND2    0.37    2.63  INTRA BL
  16 DADE  ( 916-)  B      N1  <->   26 DTHY  ( 926-)  C      N3     0.36    2.64  INTRA BL
  59 ARG   (  22-)  A      NH1 <->  128 THR   (  91-)  A      CG2    0.35    2.75  INTRA BL
 253 ARG   ( 216-)  A      NH2 <->  294 PHE   ( 260-)  A      CE1    0.29    2.81  INTRA BF
  18 DTHY  ( 918-)  B      N3  <->   24 DADE  ( 924-)  C      N1     0.29    2.71  INTRA BL
   3 DGUA  ( 903-)  B      N3  <->  132 GLN   (  95-)  A      NE2    0.28    2.72  INTRA BL
 489 ILE   ( 460-)  A      CG1 <->  598 ARG   ( 569-)  A      NH2    0.28    2.82  INTRA BF
  59 ARG   (  22-)  A      NH1 <->  128 THR   (  91-)  A      O      0.27    2.43  INTRA BL
  14 DCYT  ( 914-)  B      N3  <->   28 DGUA  ( 928-)  C      N1     0.27    2.73  INTRA BL
  66 ARG   (  29-)  A      NH2 <->   97 ASN   (  60-)  A      O      0.26    2.44  INTRA BF
 565 ASN   ( 536-)  A      CG  <->  603 ASN   ( 574-)  A      ND2    0.26    2.84  INTRA BF
 597 VAL   ( 568-)  A      N   <->  611 HOH   ( 652 )  A      O      0.25    2.45  INTRA BF
 521 ASN   ( 492-)  A      ND2 <->  524 ARG   ( 495-)  A      NH2    0.25    2.60  INTRA
  14 DCYT  ( 914-)  B      N4  <->   28 DGUA  ( 928-)  C      O6     0.24    2.46  INTRA BL
  34 DTHY  ( 934-)  C      C2' <->   35 DCYT  ( 935-)  C      O5'    0.24    2.56  INTRA BL
  66 ARG   (  29-)  A      NH1 <->   71 HIS   (  34-)  A      NE2    0.24    2.76  INTRA BF
  33 DADE  ( 933-)  C      C5' <->  610 HOH   ( 754 )  C      O      0.24    2.56  INTRA
 598 ARG   ( 569-)  A      NH1 <->  611 HOH   ( 651 )  A      O      0.23    2.47  INTRA BF
 195 SER   ( 158-)  A      CB  <->  319 ARG   ( 290-)  A      NH1    0.23    2.87  INTRA
   1 DTHY  ( 901-)  B      C2' <->    2 DCYT  ( 902-)  B      C5     0.23    2.97  INTRA BL
   7 DGUA  ( 907-)  B      N7  <->  116 ARG   (  79-)  A      NE     0.23    2.77  INTRA BL
 554 LYS   ( 525-)  A      O   <->  556 ASN   ( 527-)  A      N      0.23    2.47  INTRA BF
And so on for a total of 193 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.

 132 GLN   (  95-)  A      -6.52
 402 GLN   ( 373-)  A      -6.11
 476 ARG   ( 447-)  A      -6.10
 135 LYS   (  98-)  A      -5.99
 408 ARG   ( 379-)  A      -5.80
 413 GLN   ( 384-)  A      -5.40
 500 TYR   ( 471-)  A      -5.40
  42 ILE   (   5-)  A      -5.33
  49 GLN   (  12-)  A      -5.31
  76 ASN   (  39-)  A      -5.23
  50 ASN   (  13-)  A      -5.19
 247 LYS   ( 210-)  A      -5.14

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.

 500 TYR   ( 471-)  A       502 - GLY    473- ( A)         -4.56

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.

 101 LEU   (  64-)  A   -2.75
 132 GLN   (  95-)  A   -2.65
 324 MET   ( 295-)  A   -2.61
 401 LEU   ( 372-)  A   -2.56

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.

 611 HOH   ( 770 )  A      O     34.76   36.12  -18.82

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.

 611 HOH   ( 653 )  A      O
 611 HOH   ( 677 )  A      O
 611 HOH   ( 718 )  A      O
 611 HOH   ( 737 )  A      O
 611 HOH   ( 747 )  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.

  67 ASN   (  30-)  A
  72 ASN   (  35-)  A
 279 GLN   ( 242-)  A
 449 GLN   ( 420-)  A
 521 ASN   ( 492-)  A
 529 ASN   ( 500-)  A
 560 GLN   ( 531-)  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.

  35 DCYT  ( 935-)  C      N4
  43 ARG   (   6-)  A      N
  47 TRP   (  10-)  A      N
  55 GLU   (  18-)  A      N
  59 ARG   (  22-)  A      NH1
  75 LYS   (  38-)  A      NZ
  88 ILE   (  51-)  A      N
 116 ARG   (  79-)  A      NH1
 122 ASP   (  85-)  A      N
 123 ALA   (  86-)  A      N
 126 GLN   (  89-)  A      N
 135 LYS   (  98-)  A      N
 136 LYS   (  99-)  A      N
 140 ASP   ( 103-)  A      N
 150 TRP   ( 113-)  A      NE1
 184 ILE   ( 147-)  A      N
 185 GLU   ( 148-)  A      N
 208 ASP   ( 171-)  A      N
 214 LYS   ( 177-)  A      NZ
 223 PHE   ( 186-)  A      N
 228 GLY   ( 191-)  A      N
 247 LYS   ( 210-)  A      N
 249 LYS   ( 212-)  A      N
 256 TRP   ( 219-)  A      N
 260 SER   ( 223-)  A      OG
And so on for a total of 51 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.

 211 HIS   ( 174-)  A      ND1
 254 ASN   ( 217-)  A      OD1
 428 HIS   ( 399-)  A      ND1

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.

 611 HOH   ( 683 )  A      O  0.90  K  4
 611 HOH   ( 766 )  A      O  1.08  K  4

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.

 131 ASP   (  94-)  A   H-bonding suggests Asn; but Alt-Rotamer
 248 ASP   ( 211-)  A   H-bonding suggests Asn; but Alt-Rotamer
 261 ASP   ( 224-)  A   H-bonding suggests Asn
 496 ASP   ( 467-)  A   H-bonding suggests Asn; but Alt-Rotamer
 513 GLU   ( 484-)  A   H-bonding suggests Gln; but Alt-Rotamer
 585 GLU   ( 556-)  A   H-bonding suggests Gln; 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 :  -1.038
  2nd generation packing quality :  -2.126
  Ramachandran plot appearance   :  -4.026 (bad)
  chi-1/chi-2 rotamer normality  :  -4.399 (bad)
  Backbone conformation          :   0.575

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.560 (tight)
  Bond angles                    :   0.831
  Omega angle restraints         :   0.291 (tight)
  Side chain planarity           :   0.606 (tight)
  Improper dihedral distribution :   1.117
  B-factor distribution          :   1.435
  Inside/Outside distribution    :   0.994

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :  -2.1
  Backbone conformation          :   1.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.560 (tight)
  Bond angles                    :   0.831
  Omega angle restraints         :   0.291 (tight)
  Side chain planarity           :   0.606 (tight)
  Improper dihedral distribution :   1.117
  B-factor distribution          :   1.435
  Inside/Outside distribution    :   0.994
==============

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.