WHAT IF Check report

This file was created 2011-12-16 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 pdb1ing.ent

Checks that need to be done early-on in validation

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.

 796 BMA   ( 476-)  A  -
 797 BMA   ( 480-)  A  -
 798 MAN   ( 481-)  A  -
 799 MAN   ( 482-)  A  -
 800 MAN   ( 483-)  A  -
 802 ST5   ( 471-)  A  -
 803 BMA   ( 476-)  B  -
 804 MAN   ( 481-)  B  -
 805 MAN   ( 482-)  B  -
 807 ST5   ( 471-)  B  -
 808 MAN   ( 483-)  B  -
 809 BMA   ( 480-)  B  -
 810 FUL   ( 477-)  A  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 762 THR   ( 455-)  B  -   OG1  781 NAG   ( 478-)  A  -   C6
 763 GLY   ( 456-)  B  -   O    800 MAN   ( 483-)  A  -   O3

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.

 777 NAG   ( 472-)  A  -   O4  bound to  778 NAG   ( 473-)  A  -   C1
 779 NAG   ( 474-)  A  -   O4  bound to  780 NAG   ( 475-)  A  -   C1
 780 NAG   ( 475-)  A  -   O4  bound to  796 BMA   ( 476-)  A  -   C1
 781 NAG   ( 478-)  A  -   O4  bound to  782 NAG   ( 479-)  A  -   C1
 782 NAG   ( 479-)  A  -   O4  bound to  797 BMA   ( 480-)  A  -   C1
 783 NAG   ( 484-)  A  -   O4  bound to  784 NAG   ( 485-)  A  -   C1
 785 NAG   ( 472-)  B  -   O4  bound to  786 NAG   ( 473-)  B  -   C1
 787 NAG   ( 474-)  B  -   O4  bound to  788 NAG   ( 475-)  B  -   C1
 788 NAG   ( 475-)  B  -   O4  bound to  803 BMA   ( 476-)  B  -   C1
 790 NAG   ( 478-)  B  -   O4  bound to  791 NAG   ( 479-)  B  -   C1
 791 NAG   ( 479-)  B  -   O4  bound to  809 BMA   ( 480-)  B  -   C1
 792 NAG   ( 484-)  B  -   O4  bound to  793 NAG   ( 485-)  B  -   C1

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

Note: Ramachandran plot

Chain identifier: B

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Error: Weights outside the 0.0 -- 1.0 range

The atoms listed in the table below have their weight/occupancy outside the 0.0-1.0 range. This problem is not hampering proper WHAT IF functioning, but it is indicative of problems with the X-ray refinement.

 812 HOH   ( 539 )  B      O   1.56
 811 HOH   ( 524 )  A      O   1.56
 812 HOH   ( 564 )  B      O   1.43
 811 HOH   ( 550 )  A      O   1.43
 811 HOH   ( 538 )  A      O   1.43
 812 HOH   ( 553 )  B      O   1.43
 812 HOH   ( 501 )  B      O   1.36
 811 HOH   ( 493 )  A      O   1.36
 812 HOH   ( 548 )  B      O   1.34
 811 HOH   ( 533 )  A      O   1.34
 812 HOH   ( 586 )  B      O   1.33
 811 HOH   ( 574 )  A      O   1.33
 811 HOH   ( 587 )  A      O   1.29
 811 HOH   ( 604 )  A      O   1.29
 811 HOH   ( 502 )  A      O   1.29
 812 HOH   ( 599 )  B      O   1.29
 811 HOH   ( 578 )  A      O   1.28
 812 HOH   ( 590 )  B      O   1.28
 812 HOH   ( 528 )  B      O   1.28
 811 HOH   ( 513 )  A      O   1.28
 812 HOH   ( 512 )  B      O   1.27
 811 HOH   ( 503 )  A      O   1.27
 812 HOH   ( 542 )  B      O   1.27
 811 HOH   ( 527 )  A      O   1.27
 812 HOH   ( 544 )  B      O   1.26
And so on for a total of 132 lines.

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.

 777 NAG   ( 472-)  A    0.80
 778 NAG   ( 473-)  A    0.73
 779 NAG   ( 474-)  A    0.85
 780 NAG   ( 475-)  A    0.69
 781 NAG   ( 478-)  A    1.03
 782 NAG   ( 479-)  A    0.78
 783 NAG   ( 484-)  A    0.77
 784 NAG   ( 485-)  A    0.84
 785 NAG   ( 472-)  B    0.80
 786 NAG   ( 473-)  B    0.73
 787 NAG   ( 474-)  B    0.85
 788 NAG   ( 475-)  B    0.69
 789 FUC   ( 477-)  B    0.89
 790 NAG   ( 478-)  B    1.03
 791 NAG   ( 479-)  B    0.78
 792 NAG   ( 484-)  B    0.77
 793 NAG   ( 485-)  B    0.84

Warning: What type of B-factor?

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

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

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

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

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

Percentage of buried atoms with B less than 5 : 20.73

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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.

 364 VAL   ( 445-)  A      CA   CB    1.62    4.3
 752 VAL   ( 445-)  B      CA   CB    1.62    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.

  44 ASP   ( 125-)  A      N    CA   C    97.49   -4.9
 143 ARG   ( 224-)  A      CG   CD   NE  117.43    4.1
 145 GLN   ( 226-)  A      N    CA   C   123.69    4.5
 209 ILE   ( 290-)  A      N    CA   C    97.68   -4.8
 211 ARG   ( 292-)  A      CB   CG   CD  105.08   -4.5
 243 ASP   ( 324-)  A      N    CA   C    98.44   -4.6
 265 THR   ( 346-)  A      N    CA   C    97.10   -5.0
 432 ASP   ( 125-)  B      N    CA   C    97.49   -4.9
 531 ARG   ( 224-)  B      CG   CD   NE  117.43    4.1
 533 GLN   ( 226-)  B      N    CA   C   123.69    4.5
 597 ILE   ( 290-)  B      N    CA   C    97.68   -4.8
 599 ARG   ( 292-)  B      CB   CG   CD  105.08   -4.5
 631 ASP   ( 324-)  B      N    CA   C    98.44   -4.6
 653 THR   ( 346-)  B      N    CA   C    97.10   -5.0

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.

 322 ARG   ( 403-)  A    5.37
 710 ARG   ( 403-)  B    5.37
  93 VAL   ( 174-)  A    5.09
 481 VAL   ( 174-)  B    5.09
 209 ILE   ( 290-)  A    4.88
 597 ILE   ( 290-)  B    4.88
 145 GLN   ( 226-)  A    4.84
 533 GLN   ( 226-)  B    4.84
 265 THR   ( 346-)  A    4.72
 653 THR   ( 346-)  B    4.72
  44 ASP   ( 125-)  A    4.67
 432 ASP   ( 125-)  B    4.67
  62 LYS   ( 143-)  A    4.66
 450 LYS   ( 143-)  B    4.66
 198 SER   ( 279-)  A    4.35
 586 SER   ( 279-)  B    4.35
 243 ASP   ( 324-)  A    4.34
 631 ASP   ( 324-)  B    4.34
 113 ILE   ( 194-)  A    4.26
 501 ILE   ( 194-)  B    4.26
  99 SER   ( 180-)  A    4.12
 487 SER   ( 180-)  B    4.12
 219 ARG   ( 300-)  A    4.12
 607 ARG   ( 300-)  B    4.12
 349 ARG   ( 430-)  A    4.11
 737 ARG   ( 430-)  B    4.11
 312 ASN   ( 393-)  A    4.06
 700 ASN   ( 393-)  B    4.06

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 : 1.843

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 : -5.023

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.

 532 THR   ( 225-)  B    -2.9
 144 THR   ( 225-)  A    -2.9
 204 PRO   ( 285-)  A    -2.8
 592 PRO   ( 285-)  B    -2.8
  57 THR   ( 138-)  A    -2.8
 445 THR   ( 138-)  B    -2.8
 522 ILE   ( 215-)  B    -2.7
 134 ILE   ( 215-)  A    -2.7
 283 ARG   ( 364-)  A    -2.7
 671 ARG   ( 364-)  B    -2.7
 311 ILE   ( 392-)  A    -2.7
 699 ILE   ( 392-)  B    -2.7
 427 PRO   ( 120-)  B    -2.5
  39 PRO   ( 120-)  A    -2.5
 756 THR   ( 449-)  B    -2.5
 368 THR   ( 449-)  A    -2.5
 337 ILE   ( 418-)  A    -2.4
 725 ILE   ( 418-)  B    -2.4
 256 CYS   ( 337-)  A    -2.4
 644 CYS   ( 337-)  B    -2.4
 622 SER   ( 315-)  B    -2.4
 234 SER   ( 315-)  A    -2.4
  45 PRO   ( 126-)  A    -2.4
 433 PRO   ( 126-)  B    -2.4
 502 THR   ( 195-)  B    -2.3
And so on for a total of 64 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.

   6 TRP   (  87-)  A  Poor phi/psi
   7 SER   (  88-)  A  Poor phi/psi
  21 LYS   ( 102-)  A  Poor phi/psi
  40 TYR   ( 121-)  A  Poor phi/psi
  66 ASP   ( 147-)  A  Poor phi/psi
  94 CYS   ( 175-)  A  Poor phi/psi
 100 SER   ( 181-)  A  Poor phi/psi
 106 LYS   ( 187-)  A  Poor phi/psi
 127 ASP   ( 208-)  A  Poor phi/psi
 128 GLY   ( 209-)  A  Poor phi/psi
 144 THR   ( 225-)  A  Poor phi/psi
 146 GLU   ( 227-)  A  Poor phi/psi
 153 ASN   ( 234-)  A  Poor phi/psi
 164 SER   ( 245-)  A  Poor phi/psi
 178 GLU   ( 259-)  A  Poor phi/psi
 183 HIS   ( 264-)  A  Poor phi/psi
 188 ALA   ( 269-)  A  Poor phi/psi
 189 GLY   ( 270-)  A  Poor phi/psi
 193 HIS   ( 274-)  A  Poor phi/psi
 196 GLU   ( 277-)  A  Poor phi/psi
 203 TYR   ( 284-)  A  Poor phi/psi, PRO omega poor
 210 CYS   ( 291-)  A  Poor phi/psi
 214 TRP   ( 295-)  A  Poor phi/psi
 229 TYR   ( 310-)  A  Poor phi/psi
 234 SER   ( 315-)  A  Poor phi/psi
And so on for a total of 92 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 : -4.079

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 TYR   (  84-)  A      0
   4 ARG   (  85-)  A      0
   5 ASN   (  86-)  A      0
   6 TRP   (  87-)  A      0
   7 SER   (  88-)  A      0
  14 THR   (  95-)  A      0
  17 ALA   (  98-)  A      0
  19 PHE   ( 100-)  A      0
  20 SER   ( 101-)  A      0
  21 LYS   ( 102-)  A      0
  22 ASP   ( 103-)  A      0
  24 SER   ( 105-)  A      0
  32 ASP   ( 113-)  A      0
  37 ARG   ( 118-)  A      0
  38 GLU   ( 119-)  A      0
  39 PRO   ( 120-)  A      0
  46 VAL   ( 127-)  A      0
  47 LYS   ( 128-)  A      0
  55 GLN   ( 136-)  A      0
  61 ASN   ( 142-)  A      0
  63 HIS   ( 144-)  A      0
  65 ASN   ( 146-)  A      0
  66 ASP   ( 147-)  A      0
  67 THR   ( 148-)  A      0
  68 VAL   ( 149-)  A      0
And so on for a total of 459 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 : 1.030

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!

 551 GLY   ( 244-)  B   2.69   22
 163 GLY   ( 244-)  A   2.69   22

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]

   9 PRO   (  90-)  A    0.46 HIGH
  18 PRO   (  99-)  A    0.51 HIGH
  39 PRO   ( 120-)  A    0.49 HIGH
  45 PRO   ( 126-)  A    0.48 HIGH
  73 PRO   ( 154-)  A    0.48 HIGH
  85 PRO   ( 166-)  A    0.49 HIGH
 186 PRO   ( 267-)  A    0.49 HIGH
 201 PRO   ( 282-)  A    0.46 HIGH
 204 PRO   ( 285-)  A    0.50 HIGH
 220 PRO   ( 301-)  A    0.48 HIGH
 245 PRO   ( 326-)  A    0.50 HIGH
 305 PRO   ( 386-)  A    0.46 HIGH
 378 PRO   ( 459-)  A    0.46 HIGH
 387 PRO   ( 468-)  A    0.50 HIGH
 397 PRO   (  90-)  B    0.46 HIGH
 406 PRO   (  99-)  B    0.51 HIGH
 427 PRO   ( 120-)  B    0.49 HIGH
 433 PRO   ( 126-)  B    0.48 HIGH
 461 PRO   ( 154-)  B    0.48 HIGH
 473 PRO   ( 166-)  B    0.49 HIGH
 574 PRO   ( 267-)  B    0.49 HIGH
 589 PRO   ( 282-)  B    0.46 HIGH
 592 PRO   ( 285-)  B    0.50 HIGH
 608 PRO   ( 301-)  B    0.48 HIGH
 633 PRO   ( 326-)  B    0.50 HIGH
 693 PRO   ( 386-)  B    0.46 HIGH
 766 PRO   ( 459-)  B    0.46 HIGH
 775 PRO   ( 468-)  B    0.50 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].

 220 PRO   ( 301-)  A    99.4 envelop C-beta (108 degrees)
 608 PRO   ( 301-)  B    99.4 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 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 477 GLY   ( 170-)  B      CA   <->   812 HOH   ( 486 )  B      O    2.01    0.79  INTRA
 701 ARG   ( 394-)  B      CA   <->   812 HOH   ( 489 )  B      O    1.74    1.06  INTRA BL
 701 ARG   ( 394-)  B      N    <->   812 HOH   ( 489 )  B      O    1.49    1.21  INTRA BL
 701 ARG   ( 394-)  B      C    <->   812 HOH   ( 489 )  B      O    1.23    1.57  INTRA BL
 477 GLY   ( 170-)  B      C    <->   812 HOH   ( 486 )  B      O    1.21    1.59  INTRA
 763 GLY   ( 456-)  B      O    <->   800 MAN   ( 483-)  A      O3   1.06    1.34  INTRA
 790 NAG   ( 478-)  B      O6   <->   808 MAN   ( 483-)  B      C1   0.97    1.43  INTRA B3
 779 NAG   ( 474-)  A      O6   <->   810 FUL   ( 477-)  A      C1   0.96    1.44  INTRA B3
 791 NAG   ( 479-)  B      O4   <->   809 BMA   ( 480-)  B      C1   0.95    1.45  INTRA B3
 701 ARG   ( 394-)  B      CB   <->   812 HOH   ( 489 )  B      O    0.85    1.95  INTRA BL
 779 NAG   ( 474-)  A      C6   <->   810 FUL   ( 477-)  A      C1   0.80    2.40  INTRA
 763 GLY   ( 456-)  B      C    <->   800 MAN   ( 483-)  A      O3   0.78    2.02  INTRA
 762 THR   ( 455-)  B      CG2  <->   781 NAG   ( 478-)  A      C1   0.75    2.45  INTRA BL
 790 NAG   ( 478-)  B      C6   <->   808 MAN   ( 483-)  B      C1   0.72    2.48  INTRA
 791 NAG   ( 479-)  B      C4   <->   809 BMA   ( 480-)  B      C1   0.68    2.52  INTRA
 409 LYS   ( 102-)  B      CE   <->   812 HOH   ( 488 )  B      O    0.66    2.14  INTRA BL
 762 THR   ( 455-)  B      CG2  <->   781 NAG   ( 478-)  A      C5   0.66    2.54  INTRA
 477 GLY   ( 170-)  B      N    <->   812 HOH   ( 486 )  B      O    0.61    2.09  INTRA
 700 ASN   ( 393-)  B      C    <->   812 HOH   ( 489 )  B      O    0.56    2.24  INTRA BL
 701 ARG   ( 394-)  B      O    <->   812 HOH   ( 489 )  B      O    0.46    1.94  INTRA BL
 763 GLY   ( 456-)  B      C    <->   800 MAN   ( 483-)  A      C3   0.39    2.81  INTRA
  55 GLN   ( 136-)  A      CD   <->    75 ARG   ( 156-)  A      NH1  0.37    2.73  INTRA BL
 443 GLN   ( 136-)  B      CD   <->   463 ARG   ( 156-)  B      NH1  0.37    2.73  INTRA BL
 595 ARG   ( 288-)  B      NH1  <->   690 TRP   ( 383-)  B      CZ2  0.36    2.74  INTRA BL
 207 ARG   ( 288-)  A      NH1  <->   302 TRP   ( 383-)  A      CZ2  0.36    2.74  INTRA BL
And so on for a total of 296 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Warning: Abnormal packing environment for some residues

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

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

 168 ARG   ( 249-)  A      -7.07
 556 ARG   ( 249-)  B      -7.07
 203 TYR   ( 284-)  A      -6.90
 591 TYR   ( 284-)  B      -6.86
 372 TYR   ( 453-)  A      -6.81
 202 ARG   ( 283-)  A      -6.52
 590 ARG   ( 283-)  B      -6.52
 334 LYS   ( 415-)  A      -5.95
 722 LYS   ( 415-)  B      -5.86
 742 ARG   ( 435-)  B      -5.49
 354 ARG   ( 435-)  A      -5.49
 760 TYR   ( 453-)  B      -5.13
 645 ARG   ( 338-)  B      -5.07
 257 ARG   ( 338-)  A      -5.07

Warning: Abnormal packing environment for sequential residues

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

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

 371 THR   ( 452-)  A       374 - THR    455- ( A)         -5.15

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: Quality value plot

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

Chain identifier: B

Warning: Low packing Z-score for some residues

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

  65 ASN   ( 146-)  A   -2.86
 453 ASN   ( 146-)  B   -2.86
   5 ASN   (  86-)  A   -2.51
 393 ASN   (  86-)  B   -2.51

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

Note: Second generation quality Z-score plot

Chain identifier: B

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

 811 HOH   ( 584 )  A      O

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.

 811 HOH   ( 489 )  A      O     33.24  -32.35  -33.57
 811 HOH   ( 492 )  A      O     45.72    0.11   -1.82
 811 HOH   ( 502 )  A      O     33.96  -16.31   -2.84
 811 HOH   ( 535 )  A      O     31.36  -22.81  -45.59
 811 HOH   ( 552 )  A      O     55.21   -1.74   -0.55
 811 HOH   ( 602 )  A      O     42.76    0.84   -5.40
 812 HOH   ( 496 )  B      O     55.99  -11.59  -35.43
 812 HOH   ( 498 )  B      O     33.24   33.29  -32.63
 812 HOH   ( 504 )  B      O     56.58   20.92    4.72
 812 HOH   ( 517 )  B      O     39.97   40.04   -1.34
 812 HOH   ( 523 )  B      O     23.33   33.03    1.09
 812 HOH   ( 550 )  B      O     31.36   45.31  -23.09
 812 HOH   ( 576 )  B      O     50.42  -15.57  -43.36
 812 HOH   ( 582 )  B      O     58.50  -16.44  -34.50
 812 HOH   ( 596 )  B      O     64.83  -27.96  -18.77
 812 HOH   ( 609 )  B      O     56.18    0.79  -37.51
 812 HOH   ( 613 )  B      O     52.72  -16.76  -42.41

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.

 811 HOH   ( 487 )  A      O
 811 HOH   ( 491 )  A      O
 811 HOH   ( 519 )  A      O
 811 HOH   ( 533 )  A      O
 811 HOH   ( 554 )  A      O
 811 HOH   ( 560 )  A      O
 811 HOH   ( 570 )  A      O
 811 HOH   ( 584 )  A      O
 811 HOH   ( 597 )  A      O
 811 HOH   ( 598 )  A      O
 811 HOH   ( 599 )  A      O
 811 HOH   ( 600 )  A      O
 811 HOH   ( 602 )  A      O
 812 HOH   ( 486 )  B      O
 812 HOH   ( 534 )  B      O
 812 HOH   ( 548 )  B      O
 812 HOH   ( 566 )  B      O
 812 HOH   ( 572 )  B      O
 812 HOH   ( 596 )  B      O
 812 HOH   ( 611 )  B      O
 812 HOH   ( 612 )  B      O
Bound group on Asn; dont flip    5 ASN  (  86-) A
Bound to:  777 NAG  ( 472-) A
Bound group on Asn; dont flip   65 ASN  ( 146-) A
Bound to:  779 NAG  ( 474-) A
Bound group on Asn; dont flip  119 ASN  ( 200-) A
Bound to:  781 NAG  ( 478-) A
Bound group on Asn; dont flip  153 ASN  ( 234-) A
Bound to:  783 NAG  ( 484-) A
Bound group on Asn; dont flip  393 ASN  (  86-) B
Bound to:  785 NAG  ( 472-) B
Bound group on Asn; dont flip  453 ASN  ( 146-) B
Bound to:  787 NAG  ( 474-) B
Bound group on Asn; dont flip  507 ASN  ( 200-) B
Bound to:  790 NAG  ( 478-) B
Bound group on Asn; dont flip  541 ASN  ( 234-) B
Bound to:  792 NAG  ( 484-) B

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.

  80 ASN   ( 161-)  A
 110 HIS   ( 191-)  A
 145 GLN   ( 226-)  A
 247 ASN   ( 328-)  A
 384 ASN   ( 465-)  A
 468 ASN   ( 161-)  B
 498 HIS   ( 191-)  B
 533 GLN   ( 226-)  B
 635 ASN   ( 328-)  B
 772 ASN   ( 465-)  B

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   6 TRP   (  87-)  A      N
  10 GLN   (  91-)  A      NE2
  21 LYS   ( 102-)  A      NZ
  23 ASN   ( 104-)  A      N
  23 ASN   ( 104-)  A      ND2
  32 ASP   ( 113-)  A      N
  41 VAL   ( 122-)  A      N
  56 GLY   ( 137-)  A      N
  57 THR   ( 138-)  A      N
  58 THR   ( 139-)  A      N
  58 THR   ( 139-)  A      OG1
  60 ASP   ( 141-)  A      N
  61 ASN   ( 142-)  A      ND2
  63 HIS   ( 144-)  A      N
  68 VAL   ( 149-)  A      N
  72 ILE   ( 153-)  A      N
  74 HIS   ( 155-)  A      N
  75 ARG   ( 156-)  A      NE
  94 CYS   ( 175-)  A      N
  98 SER   ( 179-)  A      N
 101 SER   ( 182-)  A      N
 105 GLY   ( 186-)  A      N
 106 LYS   ( 187-)  A      N
 108 TRP   ( 189-)  A      NE1
 118 LYS   ( 199-)  A      N
And so on for a total of 149 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.

  55 GLN   ( 136-)  A      OE1
  61 ASN   ( 142-)  A      OD1
  63 HIS   ( 144-)  A      ND1
  92 GLN   ( 173-)  A      OE1
 103 HIS   ( 184-)  A      ND1
 104 ASP   ( 185-)  A      OD2
 153 ASN   ( 234-)  A      OD1
 196 GLU   ( 277-)  A      OE2
 213 ASN   ( 294-)  A      OD1
 338 ASN   ( 419-)  A      OD1
 443 GLN   ( 136-)  B      OE1
 449 ASN   ( 142-)  B      OD1
 451 HIS   ( 144-)  B      ND1
 480 GLN   ( 173-)  B      OE1
 491 HIS   ( 184-)  B      ND1
 492 ASP   ( 185-)  B      OD2
 541 ASN   ( 234-)  B      OD1
 584 GLU   ( 277-)  B      OE2
 601 ASN   ( 294-)  B      OD1
 631 ASP   ( 324-)  B      OD2
 726 ASN   ( 419-)  B      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+.

 801  CA   ( 470-)  A     3.65   1.60 Should be MG
 806  CA   ( 470-)  B     3.65   1.60 Should be MG

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.

 811 HOH   ( 552 )  A      O  0.89  K  6
 811 HOH   ( 606 )  A      O  0.89  K  6 NCS 1/1

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.

 104 ASP   ( 185-)  A   H-bonding suggests Asn
 116 ASP   ( 197-)  A   H-bonding suggests Asn; Ligand-contact
 146 GLU   ( 227-)  A   H-bonding suggests Gln
 162 ASP   ( 243-)  A   H-bonding suggests Asn
 227 GLU   ( 308-)  A   H-bonding suggests Gln
 492 ASP   ( 185-)  B   H-bonding suggests Asn
 534 GLU   ( 227-)  B   H-bonding suggests Gln
 550 ASP   ( 243-)  B   H-bonding suggests Asn
 615 GLU   ( 308-)  B   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 :  -1.038
  2nd generation packing quality :  -2.074
  Ramachandran plot appearance   :  -5.023 (bad)
  chi-1/chi-2 rotamer normality  :  -4.079 (bad)
  Backbone conformation          :  -1.286

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.529 (tight)
  Bond angles                    :   0.927
  Omega angle restraints         :   0.187 (tight)
  Side chain planarity           :   0.714
  Improper dihedral distribution :   1.258
  Inside/Outside distribution    :   1.048

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -2.6
  chi-1/chi-2 rotamer normality  :  -2.2
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.529 (tight)
  Bond angles                    :   0.927
  Omega angle restraints         :   0.187 (tight)
  Side chain planarity           :   0.714
  Improper dihedral distribution :   1.258
  Inside/Outside distribution    :   1.048
==============

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.