WHAT IF Check report

This file was created 2014-03-06 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 pdb1us0.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    =  49.280  B   =  66.590  C    =  47.260
    Alpha=  90.000  Beta=  92.400  Gamma=  90.000

Dimensions of a reduced cell

    A    =  47.260  B   =  49.280  C    =  66.590
    Alpha=  90.000  Beta=  90.000  Gamma=  92.400

Dimensions of the conventional cell

    A    =  47.260  B   =  66.590  C    =  49.280
    Alpha=  90.000  Beta=  92.400  Gamma=  90.000

Transformation to conventional cell

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

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 315 CIT   ( 400-)  A  -
 316 CIT   ( 450-)  A  -
 317 LDT   ( 320-)  A  -
 318 NDP   ( 318-)  A  -

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 120 LYS   ( 119-)  A  -   CE
 120 LYS   ( 119-)  A  -   NZ
 127 GLU   ( 126-)  A  -   CD
 127 GLU   ( 126-)  A  -   OE1
 127 GLU   ( 126-)  A  -   OE2
 222 LYS   ( 221-)  A  -   CD
 222 LYS   ( 221-)  A  -   CE
 222 LYS   ( 221-)  A  -   NZ
 280 GLU   ( 279-)  A  -   CD
 280 GLU   ( 279-)  A  -   OE1
 280 GLU   ( 279-)  A  -   OE2

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'.

 313 HIS   ( 312-)  A      ND1
 313 HIS   ( 312-)  A      CD2
 313 HIS   ( 312-)  A      CE1
 313 HIS   ( 312-)  A      NE2

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 314 GLU   ( 313-)  A

Warning: Strange distribution of occupancy values

The distribution of the occupancy values in this file differs significantly from distributions commonly observed in well-refined PDB files. This does not need to mean anything, but please look at it. This file is not very suitable for use in training sets that need to hold 'good' PDB files.

Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT IF's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal...

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

   1 MET   (   0-)  A    0.80
  27 GLN   (  26-)  A    0.70
  61 GLU   (  60-)  A    0.67
  64 ARG   (  63-)  A    0.67
  65 GLU   (  64-)  A    0.67
  71 GLU   (  70-)  A    0.37
  72 GLU   (  71-)  A    0.71
 127 GLU   ( 126-)  A    0.30
 147 GLU   ( 146-)  A    0.54
 179 LYS   ( 178-)  A    0.65
 195 LYS   ( 194-)  A    0.70
 230 GLU   ( 229-)  A    0.53
 235 LYS   ( 234-)  A    0.60
 240 LYS   ( 239-)  A    0.50
 268 GLU   ( 267-)  A    0.41
 278 ASP   ( 277-)  A    0.62
 280 GLU   ( 279-)  A    0.60
 283 SER   ( 282-)  A    0.80
 308 LYS   ( 307-)  A    0.56
 313 HIS   ( 312-)  A    0.85

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

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 : 67.86

Note: B-factor plot

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

Chain identifier: A

Nomenclature related problems

Warning: Phenylalanine convention problem

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

 277 PHE   ( 276-)  A

Warning: Glutamic acid convention problem

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

  71 GLU   (  70-)  A
 121 GLU   ( 120-)  A
 127 GLU   ( 126-)  A
 194 GLU   ( 193-)  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.

  60 GLN   (  59-)  A      CD   OE1   1.14   -4.6
 140 ASP   ( 139-)  A      CG   OD2   1.13   -6.5
 151 GLU   ( 150-)  A      CD   OE2   1.13   -6.1
 164 HIS   ( 163-)  A      CG   CD2   1.31   -4.5
 168 GLU   ( 167-)  A      CD   OE1   1.10   -7.9
 168 GLU   ( 167-)  A      CD   OE2   1.37    6.1
 201 GLN   ( 200-)  A      CD   OE1   1.34    5.3
 224 GLU   ( 223-)  A      CD   OE1   1.55   16.0
 224 GLU   ( 223-)  A      CD   OE2   1.53   14.9
 273 ASN   ( 272-)  A      CA   CB    1.45   -4.0

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.

   1 MET   (   0-)  A      CG   SD   CE  110.06    4.2
  42 HIS   (  41-)  A      NE2  CD2  CG  110.58    4.1
  42 HIS   (  41-)  A      CB   CG   CD2 135.58    5.0
  60 GLN   (  59-)  A      CG   CD   OE1 131.33    5.3
  60 GLN   (  59-)  A      NE2  CD   OE1 115.67   -6.9
  61 GLU   (  60-)  A      CB   CG   CD  119.70    4.2
  64 ARG   (  63-)  A      CD   NE   CZ  133.09    6.3
  84 HIS   (  83-)  A      CG   ND1  CE1 109.73    4.1
  84 HIS   (  83-)  A      CB   CG   CD2 135.43    4.9
  85 GLU   (  84-)  A      N    CA   C    98.30   -4.6
  85 GLU   (  84-)  A      CA   C    O   110.65   -6.0
 103 ASP   ( 102-)  A      CA   CB   CG  118.36    5.8
 106 ASP   ( 105-)  A      CA   CB   CG  107.52   -5.1
 116 PHE   ( 115-)  A      CA   CB   CG  118.24    4.4
 120 LYS   ( 119-)  A      CB   CG   CD  120.79    4.1
 135 ASP   ( 134-)  A      CA   CB   CG  120.78    8.2
 135 ASP   ( 134-)  A      CB   CG   OD2 107.49   -4.7
 137 ASN   ( 136-)  A      CA   CB   CG  108.14   -4.5
 140 ASP   ( 139-)  A      CA   CB   CG  118.85    6.3
 164 HIS   ( 163-)  A      NE2  CD2  CG  113.45    6.9
 164 HIS   ( 163-)  A      CB   CG   CD2 137.76    6.7
 169 MET   ( 168-)  A      CA   CB   CG  126.70    6.3
 224 GLU   ( 223-)  A     -O   -C    N   114.81   -5.1
 224 GLU   ( 223-)  A      CG   CD   OE2  93.72  -10.7
 224 GLU   ( 223-)  A      OE2  CD   OE1 144.51    9.0
 225 ASP   ( 224-)  A     -CA  -C    N   124.29    4.0
 225 ASP   ( 224-)  A     -C    N    CA  129.52    4.3
 257 ASN   ( 256-)  A      CA   CB   CG  108.56   -4.0
 273 ASN   ( 272-)  A      N    CA   CB  102.19   -4.9
 277 PHE   ( 276-)  A      CA   CB   CG  119.93    6.1
 277 PHE   ( 276-)  A      CB   CG   CD2 128.60    4.6
 285 ASP   ( 284-)  A      CA   CB   CG  116.99    4.4
 294 ARG   ( 293-)  A      N    CA   CB  117.42    4.1
 294 ARG   ( 293-)  A      CA   CB   CG  101.88   -6.1
 295 ASN   ( 294-)  A      CA   CB   CG  108.04   -4.6
 295 ASN   ( 294-)  A      ND2  CG   OD1 117.28   -5.3

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  71 GLU   (  70-)  A
 121 GLU   ( 120-)  A
 127 GLU   ( 126-)  A
 194 GLU   ( 193-)  A

Error: Tau angle problems

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

  85 GLU   (  84-)  A    4.48

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.

 151 GLU   ( 150-)  A    5.06
 164 HIS   ( 163-)  A    4.82
  60 GLN   (  59-)  A    4.70

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 215 SER   ( 214-)  A    -2.4
 188 HIS   ( 187-)  A    -2.2
 191 LEU   ( 190-)  A    -2.1
 211 SER   ( 210-)  A    -2.1
  68 VAL   (  67-)  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.

  22 LYS   (  21-)  A  Poor phi/psi
  50 GLN   (  49-)  A  Poor phi/psi
  66 GLN   (  65-)  A  Poor phi/psi
  85 GLU   (  84-)  A  omega poor
 101 LYS   ( 100-)  A  Poor phi/psi
 109 LEU   ( 108-)  A  omega poor
 133 PRO   ( 132-)  A  omega poor
 161 ASN   ( 160-)  A  Poor phi/psi
 182 VAL   ( 181-)  A  omega poor
 193 GLN   ( 192-)  A  Poor phi/psi
 257 ASN   ( 256-)  A  Poor phi/psi
 258 LEU   ( 257-)  A  omega poor
 263 LYS   ( 262-)  A  omega poor
 264 SER   ( 263-)  A  omega poor
 297 ARG   ( 296-)  A  omega poor
 311 PRO   ( 310-)  A  omega poor
 chi-1/chi-2 correlation Z-score : 0.615

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.

  98 SER   (  97-)  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 SER   (   2-)  A      0
   8 ASN   (   7-)  A      0
  15 ILE   (  14-)  A      0
  20 THR   (  19-)  A      0
  21 TRP   (  20-)  A      0
  22 LYS   (  21-)  A      0
  23 SER   (  22-)  A      0
  27 GLN   (  26-)  A      0
  28 VAL   (  27-)  A      0
  38 VAL   (  37-)  A      0
  42 HIS   (  41-)  A      0
  45 CYS   (  44-)  A      0
  47 HIS   (  46-)  A      0
  49 TYR   (  48-)  A      0
  51 ASN   (  50-)  A      0
  65 GLU   (  64-)  A      0
  66 GLN   (  65-)  A      0
  67 VAL   (  66-)  A      0
  73 LEU   (  72-)  A      0
  83 TYR   (  82-)  A      0
  84 HIS   (  83-)  A      0
  85 GLU   (  84-)  A      0
  89 VAL   (  88-)  A      0
 101 LYS   ( 100-)  A      0
 104 TYR   ( 103-)  A      0
And so on for a total of 118 lines.

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]

 219 PRO   ( 218-)  A    0.11 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].

 216 PRO   ( 215-)  A  -112.6 envelop C-gamma (-108 degrees)
 223 PRO   ( 222-)  A  -126.3 half-chair C-delta/C-gamma (-126 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.

 314 CIT   ( 400-)  A      O5  <->  318 HOH   (2603 )  A      O      2.11    0.29  INTRA BL
 315 CIT   ( 450-)  A      O1  <->  318 HOH   (2609 )  A      O      1.91    0.49  INTRA
 315 CIT   ( 450-)  A      C1  <->  318 HOH   (2609 )  A      O      1.76    1.04  INTRA
 314 CIT   ( 400-)  A      C6  <->  318 HOH   (2603 )  A      O      1.62    1.18  INTRA BL
 314 CIT   ( 400-)  A      O1  <->  318 HOH   (2600 )  A      O      1.28    1.12  INTRA BL
 314 CIT   ( 400-)  A      C1  <->  318 HOH   (2600 )  A      O      1.17    1.63  INTRA BL
 314 CIT   ( 400-)  A      C3  <->  318 HOH   (2602 )  A      O      1.09    1.71  INTRA
 314 CIT   ( 400-)  A      O7  <->  318 HOH   (2602 )  A      O      0.95    1.45  INTRA
 314 CIT   ( 400-)  A      C2  <->  318 HOH   (2600 )  A      O      0.91    1.89  INTRA BL
 314 CIT   ( 400-)  A      C2  <->  318 HOH   (2602 )  A      O      0.91    1.89  INTRA
 314 CIT   ( 400-)  A      C3  <->  318 HOH   (2600 )  A      O      0.87    1.93  INTRA BL
 314 CIT   ( 400-)  A      C5  <->  318 HOH   (2602 )  A      O      0.82    1.98  INTRA
 314 CIT   ( 400-)  A      O7  <->  318 HOH   (2600 )  A      O      0.81    1.59  INTRA BL
 314 CIT   ( 400-)  A      C4  <->  318 HOH   (2602 )  A      O      0.73    2.07  INTRA
 315 CIT   ( 450-)  A      O2  <->  318 HOH   (2609 )  A      O      0.58    1.82  INTRA
 314 CIT   ( 400-)  A      C3  <->  318 HOH   (2603 )  A      O      0.50    2.30  INTRA BL
 315 CIT   ( 450-)  A      C2  <->  318 HOH   (2609 )  A      O      0.40    2.40  INTRA
 314 CIT   ( 400-)  A      C6  <->  318 HOH   (2600 )  A      O      0.31    2.49  INTRA BL
 300 ALA   ( 299-)  A      C   <->  316 LDT   ( 320-)  A      F14    0.21    2.99  INTRA
 195 LYS   ( 194-)  A      NZ  <->  318 HOH   (2390 )  A      O      0.21    2.49  INTRA
 314 CIT   ( 400-)  A      O6  <->  318 HOH   (2603 )  A      O      0.20    2.20  INTRA BL
 195 LYS   ( 194-)  A      NZ  <->  318 HOH   (2392 )  A      O      0.14    2.56  INTRA
 300 ALA   ( 299-)  A      CA  <->  316 LDT   ( 320-)  A      F14    0.14    3.06  INTRA
 307 HIS   ( 306-)  A      ND1 <->  309 ASP   ( 308-)  A      N      0.12    2.88  INTRA BL
 137 ASN   ( 136-)  A    A ND2 <->  318 HOH   (2319 )  A      O      0.12    2.58  INTRA
 186 GLU   ( 185-)  A      OE2 <->  298 VAL   ( 297-)  A    A N      0.11    2.59  INTRA BL
 121 GLU   ( 120-)  A    A OE1 <->  318 HOH   (2291 )  A      O      0.11    2.29  INTRA
  80 TRP   (  79-)  A      CG  <->   81 CYS   (  80-)  A      N      0.09    2.91  INTRA BL
 211 SER   ( 210-)  A      N   <->  212 PRO   ( 211-)  A      CD     0.08    2.92  INTRA BL
 203 LYS   ( 202-)  A    A NZ  <->  318 HOH   (2412 )  A      O      0.07    2.63  INTRA BL
  99 ASP   (  98-)  A    A OD2 <->  315 CIT   ( 450-)  A      O5     0.05    2.35  INTRA
 111 HIS   ( 110-)  A      NE2 <->  316 LDT   ( 320-)  A      O33    0.04    2.66  INTRA
 314 CIT   ( 400-)  A      O4  <->  318 HOH   (2602 )  A      O      0.04    2.36  INTRA
  44 ASP   (  43-)  A      OD2 <->   78 LYS   (  77-)  A      NZ     0.04    2.66  INTRA BL
 241 HIS   ( 240-)  A      NE2 <->  285 ASP   ( 284-)  A      OD2    0.03    2.67  INTRA BL
  47 HIS   (  46-)  A      ND1 <->  318 HOH   (2139 )  A      O      0.03    2.67  INTRA BL
  61 GLU   (  60-)  A      OE2 <->   64 ARG   (  63-)  A      NH2    0.02    2.68  INTRA
 103 ASP   ( 102-)  A    A O   <->  318 HOH   (2275 )  A      O      0.02    2.38  INTRA
  47 HIS   (  46-)  A      ND1 <->  318 HOH   (2255 )  A      O      0.01    2.69  INTRA BL
 210 TYR   ( 209-)  A      CD1 <->  317 NDP   ( 318-)  A      C5N    0.01    3.19  INTRA
 169 MET   ( 168-)  A    A SD  <->  318 HOH   (2127 )  A      O      0.01    2.99  INTRA

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.

 312 PHE   ( 311-)  A      -5.75
 127 GLU   ( 126-)  A      -5.56
 294 ARG   ( 293-)  A      -5.52
 241 HIS   ( 240-)  A      -5.40

Note: Quality value plot

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

Chain identifier: A

Note: 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.

 318 HOH   (2020 )  A      O      0.81  -18.36   13.13
 318 HOH   (2023 )  A      O      3.54   19.08   34.63
 318 HOH   (2036 )  A      O     -2.09  -10.79    5.86
 318 HOH   (2038 )  A      O     -4.95  -10.96    5.95
 318 HOH   (2073 )  A      O     -2.01   -8.17    5.62
 318 HOH   (2239 )  A      O      3.03  -19.77   14.80
 318 HOH   (2241 )  A      O     20.22  -12.73   11.14
 318 HOH   (2388 )  A      O     19.07  -16.04   24.49
 318 HOH   (2518 )  A      O     13.57  -13.37   14.40
 318 HOH   (2521 )  A      O     20.20  -12.62   12.12

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.

 201 GLN   ( 200-)  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.

  20 THR   (  19-)  A      N
  21 TRP   (  20-)  A      N
  42 HIS   (  41-)  A      N
  49 TYR   (  48-)  A      OH
  53 ASN   (  52-)  A      N
 111 HIS   ( 110-)  A      NE2
 112 TRP   ( 111-)  A      NE1
 121 GLU   ( 120-)  A      N
 161 ASN   ( 160-)  A      ND2
 182 VAL   ( 181-)  A      N
 211 SER   ( 210-)  A      N
 211 SER   ( 210-)  A      OG
 213 LEU   ( 212-)  A      N
 215 SER   ( 214-)  A      N
 220 TRP   ( 219-)  A      N
 263 LYS   ( 262-)  A      N
 264 SER   ( 263-)  A      N
 265 VAL   ( 264-)  A      N
 312 PHE   ( 311-)  A      N

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.

  99 ASP   (  98-)  A    A OD2
 184 GLN   ( 183-)  A      OE1
 273 ASN   ( 272-)  A      OD1

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.

 318 HOH   (2279 )  A      O  0.97  K  4
 318 HOH   (2331 )  A      O  0.96  K  6 Ion-B
 318 HOH   (2335 )  A      O  0.90  K  6
 318 HOH   (2384 )  A      O  1.00 CA  4 (or NA) Ion-B
 318 HOH   (2512 )  A      O  1.12  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.

  85 GLU   (  84-)  A   H-bonding suggests Gln

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 :  -0.387
  2nd generation packing quality :   1.306
  Ramachandran plot appearance   :   0.562
  chi-1/chi-2 rotamer normality  :   0.615
  Backbone conformation          :  -0.026

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.736
  Bond angles                    :   1.146
  Omega angle restraints         :   1.097
  Side chain planarity           :   1.468
  Improper dihedral distribution :   0.979
  Inside/Outside distribution    :   0.986

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 : 0.66


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.736
  Bond angles                    :   1.146
  Omega angle restraints         :   1.097
  Side chain planarity           :   1.468
  Improper dihedral distribution :   0.979
  Inside/Outside distribution    :   0.986
==============

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.