WHAT IF Check report

This file was created 2011-12-17 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 pdb1n7d.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) 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.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 79434.578
Volume of the Unit Cell V= 2532731.0
Space group multiplicity: 6
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.314
Vm by authors and this calculated Vm do not agree very well

Warning: Atoms on special positions with too high occupancy

Atoms detected at special positions with too high occupancy. These atoms will upon expansion by applying the symmetry matrices, result in multiple atoms at (nearly) the same position.

Atoms at special positions should have an occupancy that is smaller than 1/N where N is the multiplicity of the symmetry operator. So, an atom on a 2-fold axis should have occupancy less or equal 0.5, for a 3-fold axis this is 0.33, etc. If the occupancy is too high, application of the symmetry matrices will result in the presence of more than one atom at (nearly) the same position. WHAT IF will certainly report this as bumps, but other things will also go wrong. E.g. 3 waters at the same position will make three times more hydrogen bonds, they will be counted three times in packing analysis, etc. So, I suggest you first fix this problem and run WHAT IF again on the fixed PDB file. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

 656 A10   (6003-)  A  -   P1
 656 A10   (6003-)  A  -   O1
 656 A10   (6003-)  A  -   O2

Error: Atoms too close to symmetry axis

The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. The number in the right-hand column is the number of the symmetry matrix that was applied when this problem was detected.

 656 A10   (6003-)  A  -   P1      4
 656 A10   (6003-)  A  -   O1      4
 656 A10   (6003-)  A  -   O2      4

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

 643 MAN   (2035-)  A  -         OK
 644 BMA   (3032-)  A  -         OK
 645 MAN   (3033-)  A  -         OK
 654 KEG   (6001-)  A  -         Atom types
 655 KEG   (6002-)  A  -         Atom types
 656 A10   (6003-)  A  -         Atom types
 657 BMA   (2032-)  A  -         OK
 658 MAN   (2033-)  A  -         OK

Administrative problems that can generate validation failures

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

 295 LEU   ( 346-)  A  -              294 SER   ( 344-)  A  -           3.0
Delete overlapping entity  294 SER  ( 344-) A  -
Delete overlapping entity  460 TRP  ( 515-) A  -

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 294 SER   ( 344-)  A  -
 460 TRP   ( 515-)  A  -

Please also see the previous check
Please see the user course on the WHAT CHECK website if you want to know why this table and the previous one have not been merged.

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 638 NAG   (2030-)  A  -   O4  bound to  639 NAG   (2031-)  A  -   C1
 639 NAG   (2031-)  A  -   O4  bound to  656 BMA   (2032-)  A  -   C1
 640 NAG   (3030-)  A  -   O4  bound to  641 NAG   (3031-)  A  -   C1
 641 NAG   (3031-)  A  -   O4  bound to  643 BMA   (3032-)  A  -   C1

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'.

   1 SER   (  44-)  A      OG
  14 ASN   (  59-)  A      CG
  14 ASN   (  59-)  A      OD1
  14 ASN   (  59-)  A      ND2
  19 GLN   (  64-)  A      CG
  19 GLN   (  64-)  A      CD
  19 GLN   (  64-)  A      OE1
  19 GLN   (  64-)  A      NE2
  26 GLN   (  71-)  A      CG
  26 GLN   (  71-)  A      CD
  26 GLN   (  71-)  A      OE1
  26 GLN   (  71-)  A      NE2
  27 VAL   (  72-)  A      CG1
  27 VAL   (  72-)  A      CG2
  35 GLN   (  81-)  A      CG
  35 GLN   (  81-)  A      CD
  35 GLN   (  81-)  A      OE1
  35 GLN   (  81-)  A      NE2
  43 SER   (  89-)  A      OG
  44 GLN   (  90-)  A      CG
  44 GLN   (  90-)  A      CD
  44 GLN   (  90-)  A      OE1
  44 GLN   (  90-)  A      NE2
  45 ASP   (  91-)  A      CG
  45 ASP   (  91-)  A      OD1
And so on for a total of 250 lines.

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 SER   (  44-)  A    High
   2 VAL   (  45-)  A    High
   3 THR   (  46-)  A    High
   4 CYS   (  47-)  A    High
   5 LYS   (  48-)  A    High
   6 SER   (  49-)  A    High
   7 GLY   (  50-)  A    High
   8 ASP   (  51-)  A    High
   9 PHE   (  52-)  A    High
  10 SER   (  53-)  A    High
  11 CYS   (  54-)  A    High
  12 GLY   (  55-)  A    High
  13 GLY   (  56-)  A    High
  14 ASN   (  59-)  A    High
  15 ARG   (  60-)  A    High
  16 CYS   (  61-)  A    High
  17 ILE   (  62-)  A    High
  18 PRO   (  63-)  A    High
  19 GLN   (  64-)  A    High
  20 PHE   (  65-)  A    High
  21 TRP   (  66-)  A    High
  22 ARG   (  67-)  A    High
  23 CYS   (  68-)  A    High
  24 ASP   (  69-)  A    High
  25 GLY   (  70-)  A    High
And so on for a total of 641 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

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

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

 188 TYR   ( 238-)  A
 328 TYR   ( 379-)  A
 346 TYR   ( 398-)  A
 456 TYR   ( 511-)  A
 602 TYR   ( 658-)  A

Warning: Phenylalanine convention problem

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

   9 PHE   (  52-)  A
  20 PHE   (  65-)  A
 119 PHE   ( 169-)  A
 211 PHE   ( 261-)  A
 273 PHE   ( 323-)  A
 331 PHE   ( 382-)  A
 454 PHE   ( 509-)  A
 532 PHE   ( 588-)  A
 552 PHE   ( 608-)  A
 617 PHE   ( 673-)  A

Warning: Aspartic acid convention problem

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

  28 ASP   (  73-)  A
 156 ASP   ( 206-)  A
 342 ASP   ( 394-)  A
 384 ASP   ( 436-)  A
 539 ASP   ( 595-)  A
 561 ASP   ( 617-)  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.

   9 PHE   (  52-)  A      CA   C     1.61    4.1
  10 SER   (  53-)  A      N    CA    1.54    4.3
  90 ILE   ( 140-)  A      CA   C     1.62    4.6
 130 GLU   ( 180-)  A      N    CA    1.54    4.2
 139 ILE   ( 189-)  A      CA   C     1.64    5.3
 140 HIS   ( 190-)  A      N    CA    1.57    5.7
 197 VAL   ( 247-)  A      CA   CB    1.62    4.5
 293 CYS   ( 343-)  A      CB   SG    1.67   -4.2
 497 ARG   ( 553-)  A      N    CA    1.37   -4.4

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.

   3 THR   (  46-)  A     -C    N    CA  129.84    4.5
   3 THR   (  46-)  A      N    CA   C    87.10   -8.6
   5 LYS   (  48-)  A      N    CA   C    93.34   -6.4
   8 ASP   (  51-)  A      N    CA   CB  103.60   -4.1
   9 PHE   (  52-)  A     -CA  -C    N   126.35    5.1
   9 PHE   (  52-)  A      N    CA   C   131.89    7.4
   9 PHE   (  52-)  A      N    CA   CB  103.59   -4.1
  10 SER   (  53-)  A     -CA  -C    N   126.04    4.9
  10 SER   (  53-)  A      N    CA   C   123.39    4.4
  16 CYS   (  61-)  A      N    CA   C   127.05    5.7
  18 PRO   (  63-)  A      N    CA   C   123.52    4.7
  21 TRP   (  66-)  A      N    CA   C    94.08   -6.1
  23 CYS   (  68-)  A      CA   CB   SG   92.23   -9.6
  24 ASP   (  69-)  A      N    CA   C    98.67   -4.5
  28 ASP   (  73-)  A      N    CA   C    99.64   -4.1
  31 GLY   (  77-)  A      N    CA   C    95.60   -5.8
  32 SER   (  78-)  A      N    CA   C   129.40    6.5
  33 ASP   (  79-)  A     -C    N    CA  130.75    5.0
  33 ASP   (  79-)  A      N    CA   C   126.80    5.6
  34 GLU   (  80-)  A      N    CA   C    93.94   -6.2
  36 GLY   (  82-)  A      N    CA   C    91.99   -7.1
  37 CYS   (  83-)  A      N    CA   C   127.95    6.0
  41 THR   (  87-)  A      N    CA   C   125.84    5.2
  42 CYS   (  88-)  A     -C    N    CA  129.34    4.2
  48 ARG   (  94-)  A      N    CA   C    90.47   -7.4
And so on for a total of 296 lines.

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.

  28 ASP   (  73-)  A
 156 ASP   ( 206-)  A
 342 ASP   ( 394-)  A
 384 ASP   ( 436-)  A
 539 ASP   ( 595-)  A
 561 ASP   ( 617-)  A

Warning: Chirality deviations detected

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

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

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

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 257 VAL   ( 307-)  A      CA    -6.0    24.51    33.23
 257 VAL   ( 307-)  A      C      7.4    10.35     0.15
 290 PRO   ( 340-)  A      N    -14.1   -48.79    -2.48
 462 PRO   ( 518-)  A      N    -14.0   -48.35    -2.48
 584 PRO   ( 640-)  A      N     -7.1   -25.91    -2.48
The average deviation= 1.503

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.

 418 VAL   ( 473-)  A   11.81
 264 GLY   ( 314-)  A   11.53
  84 CYS   ( 134-)  A   11.51
 129 PHE   ( 179-)  A   11.02
 365 SER   ( 417-)  A   10.69
 343 ARG   ( 395-)  A   10.58
 454 PHE   ( 509-)  A    9.90
 151 CYS   ( 201-)  A    9.83
 593 THR   ( 649-)  A    9.50
 179 HIS   ( 229-)  A    9.46
 392 ASP   ( 445-)  A    9.15
 359 LEU   ( 411-)  A    9.08
 104 ASP   ( 154-)  A    8.99
 291 ASP   ( 341-)  A    8.99
 548 ASN   ( 604-)  A    8.92
 249 ASP   ( 299-)  A    8.79
 505 LEU   ( 561-)  A    8.76
 440 GLY   ( 495-)  A    8.73
 604 CYS   ( 660-)  A    8.47
 195 ASP   ( 245-)  A    8.45
 357 VAL   ( 409-)  A    8.31
 138 CYS   ( 188-)  A    8.19
   3 THR   (  46-)  A    8.10
 118 VAL   ( 168-)  A    8.01
 603 LEU   ( 659-)  A    7.97
And so on for a total of 178 lines.

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 : 3.785

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.

 413 TYR   ( 468-)  A      OH   4.62
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -7.120

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 : -7.120

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.

   3 THR   (  46-)  A    -3.7
 594 THR   ( 650-)  A    -3.3
 346 TYR   ( 398-)  A    -3.2
 617 PHE   ( 673-)  A    -3.1
 612 PRO   ( 668-)  A    -3.1
 315 PRO   ( 366-)  A    -3.1
 292 THR   ( 342-)  A    -3.1
  39 PRO   (  85-)  A    -3.0
 462 PRO   ( 518-)  A    -3.0
 110 PRO   ( 160-)  A    -3.0
 395 ILE   ( 448-)  A    -2.9
  18 PRO   (  63-)  A    -2.9
 618 THR   ( 674-)  A    -2.9
 454 PHE   ( 509-)  A    -2.9
  38 PRO   (  84-)  A    -2.8
  41 THR   (  87-)  A    -2.8
 261 LEU   ( 311-)  A    -2.8
 595 LEU   ( 651-)  A    -2.8
 479 VAL   ( 535-)  A    -2.7
 316 HIS   ( 367-)  A    -2.7
 290 PRO   ( 340-)  A    -2.7
 557 LEU   ( 613-)  A    -2.7
  56 VAL   ( 106-)  A    -2.7
 581 LEU   ( 637-)  A    -2.7
 604 CYS   ( 660-)  A    -2.7
And so on for a total of 117 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

   3 THR   (  46-)  A  Poor phi/psi
   4 CYS   (  47-)  A  Poor phi/psi
   9 PHE   (  52-)  A  Poor phi/psi
  11 CYS   (  54-)  A  Poor phi/psi
  16 CYS   (  61-)  A  Poor phi/psi
  18 PRO   (  63-)  A  Poor phi/psi
  19 GLN   (  64-)  A  Poor phi/psi
  20 PHE   (  65-)  A  Poor phi/psi
  23 CYS   (  68-)  A  Poor phi/psi
  26 GLN   (  71-)  A  Poor phi/psi
  33 ASP   (  79-)  A  Poor phi/psi
  34 GLU   (  80-)  A  Poor phi/psi
  35 GLN   (  81-)  A  Poor phi/psi
  38 PRO   (  84-)  A  Poor phi/psi
  42 CYS   (  88-)  A  Poor phi/psi
  44 GLN   (  90-)  A  Poor phi/psi
  45 ASP   (  91-)  A  Poor phi/psi
  46 GLU   (  92-)  A  Poor phi/psi
  50 HIS   (  96-)  A  Poor phi/psi
  51 ASP   (  97-)  A  Poor phi/psi
  56 VAL   ( 106-)  A  Poor phi/psi
  61 ARG   ( 111-)  A  Poor phi/psi
  63 CYS   ( 113-)  A  Poor phi/psi
  64 LEU   ( 114-)  A  Poor phi/psi
  68 ASP   ( 118-)  A  Poor phi/psi
And so on for a total of 153 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -5.939

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 THR   (  46-)  A      0
   4 CYS   (  47-)  A      0
   5 LYS   (  48-)  A      0
   6 SER   (  49-)  A      0
   8 ASP   (  51-)  A      0
   9 PHE   (  52-)  A      0
  10 SER   (  53-)  A      0
  11 CYS   (  54-)  A      0
  12 GLY   (  55-)  A      0
  13 GLY   (  56-)  A      0
  14 ASN   (  59-)  A      0
  15 ARG   (  60-)  A      0
  16 CYS   (  61-)  A      0
  19 GLN   (  64-)  A      0
  20 PHE   (  65-)  A      0
  21 TRP   (  66-)  A      0
  22 ARG   (  67-)  A      0
  23 CYS   (  68-)  A      0
  24 ASP   (  69-)  A      0
  26 GLN   (  71-)  A      0
  27 VAL   (  72-)  A      0
  28 ASP   (  73-)  A      0
  29 CYS   (  74-)  A      0
  30 ASN   (  76-)  A      0
  31 GLY   (  77-)  A      0
And so on for a total of 540 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -3.003

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 : 3.513

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!

 440 GLY   ( 495-)  A   2.85   15
 624 GLY   ( 680-)  A   1.85   15

Warning: Unusual peptide bond conformations

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

  32 SER   (  78-)  A   3.73
  41 THR   (  87-)  A   1.81
 117 TYR   ( 167-)  A   1.76
 257 VAL   ( 307-)  A   2.32
 268 LEU   ( 318-)  A   1.93
 308 GLU   ( 359-)  A   2.55
 354 ARG   ( 406-)  A   1.63
 362 GLU   ( 414-)  A   2.68
 521 ILE   ( 577-)  A   2.27
 578 PHE   ( 634-)  A   3.54
 579 HIS   ( 635-)  A   3.51
 603 LEU   ( 659-)  A   5.13

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]

 167 PRO   ( 217-)  A    0.46 HIGH
 270 PRO   ( 320-)  A    0.46 HIGH
 290 PRO   ( 340-)  A    0.62 HIGH
 351 PRO   ( 403-)  A    0.52 HIGH
 486 PRO   ( 542-)  A    0.47 HIGH
 612 PRO   ( 668-)  A    0.46 HIGH
 615 PRO   ( 671-)  A    0.46 HIGH
 622 PRO   ( 678-)  A    0.46 HIGH

Warning: Unusual PRO puckering phases

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

  38 PRO   (  84-)  A   177.5 envelop N (180 degrees)
  79 PRO   ( 129-)  A   110.9 envelop C-beta (108 degrees)
 100 PRO   ( 150-)  A   115.8 envelop C-beta (108 degrees)
 110 PRO   ( 160-)  A   110.9 envelop C-beta (108 degrees)
 208 PRO   ( 258-)  A   105.7 envelop C-beta (108 degrees)
 315 PRO   ( 366-)  A   109.3 envelop C-beta (108 degrees)
 443 PRO   ( 498-)  A   130.9 half-chair C-beta/C-alpha (126 degrees)
 450 PRO   ( 505-)  A   112.2 envelop C-beta (108 degrees)
 462 PRO   ( 518-)  A   117.6 half-chair C-beta/C-alpha (126 degrees)
 486 PRO   ( 542-)  A   106.2 envelop C-beta (108 degrees)
 531 PRO   ( 587-)  A   156.0 half-chair C-alpha/N (162 degrees)
 608 PRO   ( 664-)  A   109.8 envelop C-beta (108 degrees)
 612 PRO   ( 668-)  A   116.3 envelop C-beta (108 degrees)
 615 PRO   ( 671-)  A   105.6 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 201 ASN   ( 251-)  A      CB  <->  640 NAG   (3030-)  A      C8     1.20    2.00  INTRA BF
 201 ASN   ( 251-)  A      CA  <->  640 NAG   (3030-)  A      C8     1.13    2.07  INTRA BF
 102 CYS   ( 152-)  A      SG  <->  105 GLY   ( 155-)  A      N      1.12    2.18  INTRA BF
 639 NAG   (2031-)  A      O4  <->  656 BMA   (2032-)  A      C1     1.01    1.39  INTRA BF
 530 HIS   ( 586-)  A      CB  <->  546 ILE   ( 602-)  A      CG2    1.00    2.20  INTRA BF
 656 BMA   (2032-)  A      O6  <->  657 MAN   (2033-)  A      C1     0.99    1.41  INTRA BL
  84 CYS   ( 134-)  A      SG  <->  104 ASP   ( 154-)  A      C      0.94    2.46  INTRA BF
 201 ASN   ( 251-)  A      C   <->  640 NAG   (3030-)  A      C8     0.91    2.29  INTRA BF
  83 GLN   ( 133-)  A      O   <->  638 NAG   (2030-)  A      C8     0.84    1.96  INTRA BF
 102 CYS   ( 152-)  A      O   <->  104 ASP   ( 154-)  A      N      0.82    1.88  INTRA BF
 656 BMA   (2032-)  A      C6  <->  657 MAN   (2033-)  A      C1     0.82    2.38  INTRA BL
 463 ALA   ( 519-)  A      CB  <->  483 ILE   ( 539-)  A      CG2    0.81    2.39  INTRA BF
 135 SER   ( 185-)  A      CB  <->  153 ASP   ( 203-)  A      CB     0.81    2.39  INTRA BF
  84 CYS   ( 134-)  A      O   <->   86 SER   ( 136-)  A      N      0.80    1.90  INTRA BF
 529 ALA   ( 585-)  A      CB  <->  546 ILE   ( 602-)  A      CD1    0.80    2.40  INTRA BF
 413 TYR   ( 468-)  A      OH  <->  470 LEU   ( 526-)  A      CD2    0.79    2.01  INTRA BF
  84 CYS   ( 134-)  A      SG  <->  104 ASP   ( 154-)  A      CA     0.79    2.61  INTRA BF
 145 CYS   ( 195-)  A      CA  <->  157 GLU   ( 207-)  A      CB     0.79    2.41  INTRA BF
 375 GLN   ( 427-)  A      NE2 <->  377 MET   ( 429-)  A      SD     0.78    2.52  INTRA BF
 413 TYR   ( 468-)  A      OH  <->  470 LEU   ( 526-)  A      CD1    0.78    2.02  INTRA BF
 639 NAG   (2031-)  A      C4  <->  656 BMA   (2032-)  A      C1     0.76    2.44  INTRA BF
 498 LEU   ( 554-)  A      N   <->  511 ILE   ( 567-)  A      O      0.75    1.95  INTRA BF
  11 CYS   (  54-)  A      SG  <->   12 GLY   (  55-)  A      N      0.74    2.46  INTRA BF
 255 SER   ( 305-)  A      CB  <->  280 ARG   ( 330-)  A      CB     0.74    2.46  INTRA BF
  91 PRO   ( 141-)  A      O   <->   93 LEU   ( 143-)  A      N      0.74    1.96  INTRA BF
And so on for a total of 1121 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.164

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.

 117 TYR   ( 167-)  A      -7.97
 585 ARG   ( 641-)  A      -7.87
 303 TYR   ( 354-)  A      -7.82
 166 ARG   ( 216-)  A      -7.29
 119 PHE   ( 169-)  A      -7.24
 592 ARG   ( 648-)  A      -7.16
 227 MET   ( 277-)  A      -7.12
  40 LYS   (  86-)  A      -6.86
 114 ARG   ( 164-)  A      -6.57
 182 ARG   ( 232-)  A      -6.51
  15 ARG   (  60-)  A      -6.47
 476 TYR   ( 532-)  A      -6.32
 437 ARG   ( 492-)  A      -6.32
 120 GLN   ( 170-)  A      -6.26
 316 HIS   ( 367-)  A      -6.26
 129 PHE   ( 179-)  A      -6.22
 278 GLN   ( 328-)  A      -6.19
  93 LEU   ( 143-)  A      -6.16
 299 LEU   ( 350-)  A      -6.08
   5 LYS   (  48-)  A      -6.05
 116 LEU   ( 166-)  A      -6.04
  50 HIS   (  96-)  A      -6.03
 221 LEU   ( 271-)  A      -6.00
 391 TYR   ( 444-)  A      -5.99
 352 ASN   ( 404-)  A      -5.86
And so on for a total of 52 lines.

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.

  40 LYS   (  86-)  A        42 - CYS     88- ( A)         -5.68
 116 LEU   ( 166-)  A       120 - GLN    170- ( A)         -6.56
 239 ILE   ( 289-)  A       241 - GLU    291- ( A)         -4.98
 278 GLN   ( 328-)  A       280 - ARG    330- ( A)         -5.68
 373 LEU   ( 425-)  A       375 - GLN    427- ( A)         -4.92
 389 SER   ( 442-)  A       391 - TYR    444- ( A)         -4.75
 430 VAL   ( 485-)  A       432 - ARG    487- ( A)         -4.64
 482 ASN   ( 538-)  A       484 - GLN    540- ( A)         -4.47
 580 GLN   ( 636-)  A       583 - GLN    639- ( A)         -4.36
 601 GLN   ( 657-)  A       603 - LEU    659- ( A)         -5.13
 609 GLN   ( 665-)  A       611 - ASN    667- ( A)         -5.02

Error: Abnormal average packing environment

The average packing score for the structure is very low.

A molecule is certain to be incorrect if the average packing score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 641 : -3.030

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.

 397 ARG   ( 450-)  A   -3.85
 616 LYS   ( 672-)  A   -3.83
 349 LEU   ( 401-)  A   -3.79
 183 GLN   ( 233-)  A   -3.75
 144 ARG   ( 194-)  A   -3.75
 334 ARG   ( 385-)  A   -3.69
 186 ARG   ( 236-)  A   -3.56
  26 GLN   (  71-)  A   -3.42
 232 ARG   ( 282-)  A   -3.41
 527 ARG   ( 583-)  A   -3.41
 354 ARG   ( 406-)  A   -3.40
 111 GLN   ( 161-)  A   -3.34
 335 HIS   ( 386-)  A   -3.27
 611 ASN   ( 667-)  A   -3.22
  47 PHE   (  93-)  A   -3.13
 519 LYS   ( 575-)  A   -3.13
 376 ARG   ( 428-)  A   -3.12
 518 ARG   ( 574-)  A   -2.96
 464 LYS   ( 520-)  A   -2.87
 350 ILE   ( 402-)  A   -2.76
 498 LEU   ( 554-)  A   -2.73
  92 GLN   ( 142-)  A   -2.73
 304 LYS   ( 355-)  A   -2.70
 178 ILE   ( 228-)  A   -2.66
 629 ARG   ( 685-)  A   -2.65
  19 GLN   (  64-)  A   -2.64
  48 ARG   (  94-)  A   -2.62
 353 LEU   ( 405-)  A   -2.62
 262 LYS   ( 312-)  A   -2.60
  54 GLN   ( 104-)  A   -2.57
 466 LYS   ( 522-)  A   -2.53
 212 LYS   ( 262-)  A   -2.53
 385 ARG   ( 437-)  A   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

  43 SER   (  89-)  A     -   48 ARG   (  94-)  A        -2.38
  52 GLY   (  98-)  A     -   55 PHE   ( 105-)  A        -1.79
 384 ASP   ( 436-)  A     -  387 HIS   ( 439-)  A        -1.82
 614 SER   ( 670-)  A     -  617 PHE   ( 673-)  A        -2.22
Bound group on Asn; dont flip   85 ASN  ( 135-) A
Bound to:  638 NAG  (2030-) A
Bound group on Asn; dont flip  201 ASN  ( 251-) A
Bound to:  640 NAG  (3030-) A

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

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

 214 HIS   ( 264-)  A
 316 HIS   ( 367-)  A
 352 ASN   ( 404-)  A
 375 GLN   ( 427-)  A
 482 ASN   ( 538-)  A
 506 HIS   ( 562-)  A
 548 ASN   ( 604-)  A
 568 ASN   ( 624-)  A
 583 GLN   ( 639-)  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.

   3 THR   (  46-)  A      N
  11 CYS   (  54-)  A      N
  12 GLY   (  55-)  A      N
  20 PHE   (  65-)  A      N
  21 TRP   (  66-)  A      N
  22 ARG   (  67-)  A      N
  23 CYS   (  68-)  A      N
  25 GLY   (  70-)  A      N
  33 ASP   (  79-)  A      N
  34 GLU   (  80-)  A      N
  35 GLN   (  81-)  A      N
  51 ASP   (  97-)  A      N
  65 ASP   ( 115-)  A      N
  82 PHE   ( 132-)  A      N
  86 SER   ( 136-)  A      N
  96 CYS   ( 146-)  A      N
  99 ASP   ( 149-)  A      N
 102 CYS   ( 152-)  A      N
 107 ASP   ( 157-)  A      N
 108 GLU   ( 158-)  A      N
 109 TRP   ( 159-)  A      N
 113 CYS   ( 163-)  A      N
 118 VAL   ( 168-)  A      N
 131 PHE   ( 181-)  A      N
 140 HIS   ( 190-)  A      N
And so on for a total of 150 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.

  33 ASP   (  79-)  A      OD1
  60 ASP   ( 110-)  A      OD1
  65 ASP   ( 115-)  A      OD1
  69 GLU   ( 119-)  A      OE1
 108 GLU   ( 158-)  A      OE2
 157 GLU   ( 207-)  A      OE2
 168 ASP   ( 218-)  A      OD1
 196 GLU   ( 246-)  A      OE1
 226 ASN   ( 276-)  A      OD1
 230 ASP   ( 280-)  A      OD2
 236 ASP   ( 286-)  A      OD2
 246 GLU   ( 296-)  A      OE1
 283 ASP   ( 333-)  A      OD1
 283 ASP   ( 333-)  A      OD2
 286 GLU   ( 336-)  A      OE1
 449 ASP   ( 504-)  A      OD1
 502 ASP   ( 558-)  A      OD1
 545 ASP   ( 601-)  A      OD2
 588 ASN   ( 644-)  A      OD1
 630 ASP   ( 686-)  A      OD1

Warning: Unusual ion packing

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

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

 645  CA   (1001-)  A   -.-  -.-  Low probability ion. B=124.7
 646  CA   (1002-)  A   -.-  -.-  Low probability ion. B=124.7
 647  CA   (1003-)  A   -.-  -.-  Low probability ion. B=124.7
 648  CA   (1004-)  A   -.-  -.-  Low probability ion. B=124.7
 649  CA   (1005-)  A   -.-  -.-  Low probability ion. B=124.7
 650  CA   (1006-)  A   -.-  -.-  Low probability ion. B=124.7
 651  CA   (1007-)  A   -.-  -.-  Low probability ion. B=124.7
 652  CA   (1008-)  A   -.-  -.-  Low probability ion. B=124.7
Since there are no waters, the water check has been skipped.

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.

  33 ASP   (  79-)  A   H-bonding suggests Asn
  34 GLU   (  80-)  A   H-bonding suggests Gln
  51 ASP   (  97-)  A   H-bonding suggests Asn
  62 ASP   ( 112-)  A   H-bonding suggests Asn
  65 ASP   ( 115-)  A   H-bonding suggests Asn; but Alt-Rotamer
  69 GLU   ( 119-)  A   H-bonding suggests Gln
  99 ASP   ( 149-)  A   H-bonding suggests Asn
 108 GLU   ( 158-)  A   H-bonding suggests Gln
 130 GLU   ( 180-)  A   H-bonding suggests Gln; but Alt-Rotamer
 137 GLU   ( 187-)  A   H-bonding suggests Gln
 156 ASP   ( 206-)  A   H-bonding suggests Asn
 158 GLU   ( 208-)  A   H-bonding suggests Gln
 169 GLU   ( 219-)  A   H-bonding suggests Gln
 189 ASP   ( 239-)  A   H-bonding suggests Asn
 206 GLU   ( 256-)  A   H-bonding suggests Gln; but Alt-Rotamer
 217 GLU   ( 267-)  A   H-bonding suggests Gln; but Alt-Rotamer
 237 GLU   ( 287-)  A   H-bonding suggests Gln; but Alt-Rotamer
 266 GLU   ( 316-)  A   H-bonding suggests Gln
 291 ASP   ( 341-)  A   H-bonding suggests Asn
 362 GLU   ( 414-)  A   H-bonding suggests Gln
 372 ASP   ( 424-)  A   H-bonding suggests Asn; but Alt-Rotamer
 384 ASP   ( 436-)  A   H-bonding suggests Asn; but Alt-Rotamer
 401 ASP   ( 456-)  A   H-bonding suggests Asn
 416 ASP   ( 471-)  A   H-bonding suggests Asn
 426 ASP   ( 481-)  A   H-bonding suggests Asn
 449 ASP   ( 504-)  A   H-bonding suggests Asn
 512 ASP   ( 568-)  A   H-bonding suggests Asn
 539 ASP   ( 595-)  A   H-bonding suggests Asn; but Alt-Rotamer
 545 ASP   ( 601-)  A   H-bonding suggests Asn; but Alt-Rotamer
 574 ASP   ( 630-)  A   H-bonding suggests Asn
 630 ASP   ( 686-)  A   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -6.325 (bad)
  2nd generation packing quality :  -5.879 (bad)
  Ramachandran plot appearance   :  -7.120 (bad)
  chi-1/chi-2 rotamer normality  :  -5.939 (bad)
  Backbone conformation          :  -3.003 (poor)

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.869
  Bond angles                    :   1.755
  Omega angle restraints         :   0.639 (tight)
  Side chain planarity           :   0.414 (tight)
  Improper dihedral distribution :   1.334
  Inside/Outside distribution    :   1.164 (unusual)

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 : 3.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -4.8 (bad)
  2nd generation packing quality :  -3.1 (poor)
  Ramachandran plot appearance   :  -3.9 (poor)
  chi-1/chi-2 rotamer normality  :  -3.4 (poor)
  Backbone conformation          :  -1.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.869
  Bond angles                    :   1.755
  Omega angle restraints         :   0.639 (tight)
  Side chain planarity           :   0.414 (tight)
  Improper dihedral distribution :   1.334
  Inside/Outside distribution    :   1.164 (unusual)
==============

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.