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 pdb1ivg.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  -
 798 BMA   ( 480-)  B  -
 799 MAN   ( 481-)  B  -
 800 MAN   ( 482-)  B  -
 801 MAN   ( 483-)  B  -
 802 BMA   ( 476-)  B  -
 803 MAN   ( 487-)  B  -
 804 MAN   ( 488-)  B  -
 806 MAN   ( 489-)  B  -
 807 BMA   ( 486-)  B  -
 808 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.

 119 ASN   ( 200-)  A  -   ND2  783 NAG   ( 478-)  B  -   C1

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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   ( 484-)  A  -   O4  bound to  782 NAG   ( 485-)  A  -   C1
 783 NAG   ( 478-)  B  -   O4  bound to  784 NAG   ( 479-)  B  -   C1
 784 NAG   ( 479-)  B  -   O4  bound to  798 BMA   ( 480-)  B  -   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  802 BMA   ( 476-)  B  -   C1
 790 NAG   ( 484-)  B  -   O4  bound to  791 NAG   ( 485-)  B  -   C1
 791 NAG   ( 485-)  B  -   O4  bound to  807 BMA   ( 486-)  B  -   C1
 792 NAG   ( 490-)  B  -   O4  bound to  793 NAG   ( 491-)  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.

 809 HOH   ( 571 )  A      O   1.18
 809 HOH   ( 541 )  A      O   1.18
 809 HOH   ( 587 )  A      O   1.17
 809 HOH   ( 546 )  A      O   1.17
 809 HOH   ( 525 )  A      O   1.17
 809 HOH   ( 535 )  A      O   1.17
 809 HOH   ( 562 )  A      O   1.16
 809 HOH   ( 542 )  A      O   1.14
 809 HOH   ( 488 )  A      O   1.13
 809 HOH   ( 539 )  A      O   1.12
 809 HOH   ( 551 )  A      O   1.11
 809 HOH   ( 586 )  A      O   1.11
 809 HOH   ( 523 )  A      O   1.11
 809 HOH   ( 603 )  A      O   1.11
 810 HOH   ( 512 )  B      O   1.10
 809 HOH   ( 521 )  A      O   1.10
 809 HOH   ( 604 )  A      O   1.09
 809 HOH   ( 591 )  A      O   1.08
 809 HOH   ( 557 )  A      O   1.08
 809 HOH   ( 589 )  A      O   1.07
 809 HOH   ( 561 )  A      O   1.07
 809 HOH   ( 522 )  A      O   1.06
 809 HOH   ( 598 )  A      O   1.06
 809 HOH   ( 500 )  A      O   1.06
 809 HOH   ( 585 )  A      O   1.06
 809 HOH   ( 548 )  A      O   1.05
 809 HOH   ( 534 )  A      O   1.05
 809 HOH   ( 576 )  A      O   1.05
 809 HOH   ( 575 )  A      O   1.05
 809 HOH   ( 540 )  A      O   1.04
 809 HOH   ( 547 )  A      O   1.04
 809 HOH   ( 503 )  A      O   1.04
 809 HOH   ( 553 )  A      O   1.04
 809 HOH   ( 596 )  A      O   1.04
 809 HOH   ( 496 )  A      O   1.03
 809 HOH   ( 526 )  A      O   1.03
 810 HOH   ( 518 )  B      O   1.03
 809 HOH   ( 532 )  A      O   1.03
 809 HOH   ( 533 )  A      O   1.03
 810 HOH   ( 501 )  B      O   1.03
 809 HOH   ( 583 )  A      O   1.02
 809 HOH   ( 498 )  A      O   1.02
 809 HOH   ( 514 )  A      O   1.02
 809 HOH   ( 538 )  A      O   1.02
 809 HOH   ( 563 )  A      O   1.02
 809 HOH   ( 567 )  A      O   1.02
 809 HOH   ( 510 )  A      O   1.01
 809 HOH   ( 505 )  A      O   1.01
 809 HOH   ( 509 )  A      O   1.01

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.

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: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.519
RMS-deviation in bond distances: 0.013

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999329 -0.000092  0.000027|
 | -0.000092  0.997556  0.000000|
 |  0.000027  0.000000  0.997556|
Proposed new scale matrix

 |  0.008273  0.000000  0.000000|
 |  0.000000  0.007102  0.000000|
 |  0.000000  0.000000  0.007051|
With corresponding cell

    A    = 120.882  B   = 140.798  C    = 141.819
    Alpha=  90.002  Beta=  90.002  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 120.970  B   = 141.140  C    = 142.160
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 96.354
(Under-)estimated Z-score: 7.234

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.

  74 HIS   ( 155-)  A      CG   ND1  CE1 109.84    4.2
 110 HIS   ( 191-)  A      CG   ND1  CE1 109.61    4.0
 145 GLN   ( 226-)  A      N    CA   C   124.50    4.8
 183 HIS   ( 264-)  A      CG   ND1  CE1 109.68    4.1
 207 ARG   ( 288-)  A      CG   CD   NE  118.14    4.5
 363 VAL   ( 444-)  A      C    CA   CB  101.95   -4.3
 386 MET   ( 467-)  A      N    CA   C   127.63    5.9
 387 PRO   ( 468-)  A      N    CA   C   124.38    5.0
 387 PRO   ( 468-)  A      CD   N    CA  103.96   -5.7
 388 ILE   ( 469-)  A      N    CA   C   124.21    4.6
 462 HIS   ( 155-)  B      CG   ND1  CE1 109.84    4.2
 498 HIS   ( 191-)  B      CG   ND1  CE1 109.61    4.0
 533 GLN   ( 226-)  B      N    CA   C   124.50    4.8
 571 HIS   ( 264-)  B      CG   ND1  CE1 109.68    4.1
 595 ARG   ( 288-)  B      CG   CD   NE  118.14    4.5
 751 VAL   ( 444-)  B      C    CA   CB  101.95   -4.3
 774 MET   ( 467-)  B      N    CA   C   127.63    5.9
 775 PRO   ( 468-)  B      N    CA   C   124.38    5.0
 775 PRO   ( 468-)  B      CD   N    CA  103.96   -5.7
 776 ILE   ( 469-)  B      N    CA   C   124.21    4.6
 781 NAG   ( 484-)  A      N2   C2   C1  101.93   -4.0
 782 NAG   ( 485-)  A      N2   C2   C1  100.39   -4.3
 783 NAG   ( 478-)  B      C6   C5   C4  137.86    5.0
 790 NAG   ( 484-)  B      C6   C5   C4  137.86    5.0
 792 NAG   ( 490-)  B      N2   C2   C1  101.93   -4.0
 793 NAG   ( 491-)  B      N2   C2   C1  100.39   -4.3

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.

 386 MET   ( 467-)  A      CA    -8.3    19.16    34.17
 387 PRO   ( 468-)  A      N      9.2    27.65    -2.48
 774 MET   ( 467-)  B      CA    -8.3    19.16    34.17
 775 PRO   ( 468-)  B      N      9.2    27.65    -2.48
The average deviation= 1.347

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.

 145 GLN   ( 226-)  A    5.16
 533 GLN   ( 226-)  B    5.16
 199 CYS   ( 280-)  A    4.98
 587 CYS   ( 280-)  B    4.98
 388 ILE   ( 469-)  A    4.91
 776 ILE   ( 469-)  B    4.91
 386 MET   ( 467-)  A    4.81
 774 MET   ( 467-)  B    4.81
 387 PRO   ( 468-)  A    4.52
 775 PRO   ( 468-)  B    4.52
  25 ILE   ( 106-)  A    4.21
 413 ILE   ( 106-)  B    4.21
 257 ARG   ( 338-)  A    4.11
 645 ARG   ( 338-)  B    4.11
  93 VAL   ( 174-)  A    4.10
 481 VAL   ( 174-)  B    4.10
 349 ARG   ( 430-)  A    4.04
 737 ARG   ( 430-)  B    4.04

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 : 1.734

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 119 ASN   ( 200-)  A    4.38
 507 ASN   ( 200-)  B    4.38

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.182

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.

 775 PRO   ( 468-)  B    -3.1
 387 PRO   ( 468-)  A    -3.1
 532 THR   ( 225-)  B    -3.1
 144 THR   ( 225-)  A    -3.1
 378 PRO   ( 459-)  A    -2.8
 766 PRO   ( 459-)  B    -2.8
 502 THR   ( 195-)  B    -2.8
 114 THR   ( 195-)  A    -2.8
 566 GLU   ( 259-)  B    -2.6
 178 GLU   ( 259-)  A    -2.6
  57 THR   ( 138-)  A    -2.6
 445 THR   ( 138-)  B    -2.6
 774 MET   ( 467-)  B    -2.5
 386 MET   ( 467-)  A    -2.5
 522 ILE   ( 215-)  B    -2.5
 134 ILE   ( 215-)  A    -2.5
  39 PRO   ( 120-)  A    -2.4
 427 PRO   ( 120-)  B    -2.4
 425 ARG   ( 118-)  B    -2.4
  37 ARG   ( 118-)  A    -2.4
 771 ILE   ( 464-)  B    -2.3
 383 ILE   ( 464-)  A    -2.3
 727 ARG   ( 420-)  B    -2.3
 339 ARG   ( 420-)  A    -2.3
 738 LYS   ( 431-)  B    -2.3
And so on for a total of 60 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.

  23 ASN   ( 104-)  A  Poor phi/psi
  52 ALA   ( 133-)  A  Poor phi/psi
  66 ASP   ( 147-)  A  Poor phi/psi
  94 CYS   ( 175-)  A  Poor phi/psi
 139 GLN   ( 220-)  A  Poor phi/psi
 146 GLU   ( 227-)  A  Poor phi/psi
 196 GLU   ( 277-)  A  Poor phi/psi
 203 TYR   ( 284-)  A  PRO omega poor
 214 TRP   ( 295-)  A  Poor phi/psi
 227 GLU   ( 308-)  A  Poor phi/psi
 229 TYR   ( 310-)  A  Poor phi/psi
 234 SER   ( 315-)  A  Poor phi/psi
 240 LEU   ( 321-)  A  Poor phi/psi
 241 VAL   ( 322-)  A  Poor phi/psi
 244 THR   ( 325-)  A  PRO omega poor
 253 ASN   ( 334-)  A  Poor phi/psi
 256 CYS   ( 337-)  A  Poor phi/psi
 266 GLN   ( 347-)  A  Poor phi/psi
 306 ASN   ( 387-)  A  Poor phi/psi
 323 SER   ( 404-)  A  Poor phi/psi
 350 LYS   ( 431-)  A  Poor phi/psi
 386 MET   ( 467-)  A  Poor phi/psi
 411 ASN   ( 104-)  B  Poor phi/psi
 440 ALA   ( 133-)  B  Poor phi/psi
 454 ASP   ( 147-)  B  Poor phi/psi
 482 CYS   ( 175-)  B  Poor phi/psi
 527 GLN   ( 220-)  B  Poor phi/psi
 534 GLU   ( 227-)  B  Poor phi/psi
 584 GLU   ( 277-)  B  Poor phi/psi
 591 TYR   ( 284-)  B  PRO omega poor
 602 TRP   ( 295-)  B  Poor phi/psi
 615 GLU   ( 308-)  B  Poor phi/psi
 617 TYR   ( 310-)  B  Poor phi/psi
 622 SER   ( 315-)  B  Poor phi/psi
 628 LEU   ( 321-)  B  Poor phi/psi
 629 VAL   ( 322-)  B  Poor phi/psi
 632 THR   ( 325-)  B  PRO omega poor
 641 ASN   ( 334-)  B  Poor phi/psi
 644 CYS   ( 337-)  B  Poor phi/psi
 654 GLN   ( 347-)  B  Poor phi/psi
 694 ASN   ( 387-)  B  Poor phi/psi
 711 SER   ( 404-)  B  Poor phi/psi
 738 LYS   ( 431-)  B  Poor phi/psi
 774 MET   ( 467-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.060

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 : -4.060

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!

   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
  16 PHE   (  97-)  A      0
  19 PHE   ( 100-)  A      0
  20 SER   ( 101-)  A      0
  22 ASP   ( 103-)  A      0
  32 ASP   ( 113-)  A      0
  34 TRP   ( 115-)  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
  51 PHE   ( 132-)  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
  71 ARG   ( 152-)  A      0
And so on for a total of 443 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 : 1.801

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]

 387 PRO   ( 468-)  A    0.48 HIGH
 775 PRO   ( 468-)  B    0.48 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].

 201 PRO   ( 282-)  A  -115.3 envelop C-gamma (-108 degrees)
 387 PRO   ( 468-)  A   169.7 half-chair C-alpha/N (162 degrees)
 589 PRO   ( 282-)  B  -115.3 envelop C-gamma (-108 degrees)
 775 PRO   ( 468-)  B   169.7 half-chair C-alpha/N (162 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.

 701 ARG   ( 394-)  B      CB   <->   799 MAN   ( 481-)  B      C2   2.55    0.65  INTRA
 411 ASN   ( 104-)  B      CG   <->   810 HOH   ( 501 )  B      O    2.17    0.63  INTRA
 436 CYS   ( 129-)  B      SG   <->   810 HOH   ( 518 )  B      O    2.01    0.99  INTRA
 685 LYS   ( 378-)  B      CB   <->   810 HOH   ( 511 )  B      O    1.65    1.15  INTRA
 411 ASN   ( 104-)  B      ND2  <->   810 HOH   ( 501 )  B      O    1.53    1.17  INTRA
 761 GLY   ( 454-)  B      CA   <->   810 HOH   ( 512 )  B      O    1.47    1.33  INTRA BL
 702 GLN   ( 395-)  B      CG   <->   800 MAN   ( 482-)  B      C4   1.46    1.74  INTRA
 700 ASN   ( 393-)  B      C    <->   800 MAN   ( 482-)  B      O2   1.46    1.34  INTRA BF
 701 ARG   ( 394-)  B      CB   <->   799 MAN   ( 481-)  B      C3   1.45    1.75  INTRA
 411 ASN   ( 104-)  B      CB   <->   810 HOH   ( 501 )  B      O    1.43    1.37  INTRA
 698 GLN   ( 391-)  B      OE1  <->   799 MAN   ( 481-)  B      C5   1.43    1.37  INTRA
 701 ARG   ( 394-)  B      N    <->   800 MAN   ( 482-)  B      C1   1.38    0.82  INTRA B2
 436 CYS   ( 129-)  B      CB   <->   810 HOH   ( 518 )  B      O    1.33    1.47  INTRA
 701 ARG   ( 394-)  B      CA   <->   799 MAN   ( 481-)  B      C2   1.32    1.88  INTRA
 685 LYS   ( 378-)  B      CA   <->   810 HOH   ( 511 )  B      O    1.31    1.49  INTRA BL
 700 ASN   ( 393-)  B      CA   <->   800 MAN   ( 482-)  B      O2   1.24    1.56  INTRA BF
 431 CYS   ( 124-)  B      SG   <->   810 HOH   ( 518 )  B      O    1.23    1.77  INTRA
 701 ARG   ( 394-)  B      CG   <->   799 MAN   ( 481-)  B      C2   1.20    2.00  INTRA
 760 TYR   ( 453-)  B      CD1  <->   783 NAG   ( 478-)  B      C8   1.16    2.04  INTRA
 701 ARG   ( 394-)  B      CA   <->   800 MAN   ( 482-)  B      O5   1.15    1.65  INTRA
 701 ARG   ( 394-)  B      C    <->   800 MAN   ( 482-)  B      O5   1.05    1.75  INTRA
 700 ASN   ( 393-)  B      CB   <->   800 MAN   ( 482-)  B      O2   1.02    1.78  INTRA BF
 698 GLN   ( 391-)  B      CD   <->   799 MAN   ( 481-)  B      C5   1.01    2.19  INTRA
 761 GLY   ( 454-)  B      N    <->   810 HOH   ( 512 )  B      O    1.00    1.70  INTRA BL
 701 ARG   ( 394-)  B      CB   <->   799 MAN   ( 481-)  B      C1   1.00    2.20  INTRA
And so on for a total of 308 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.

 386 MET   ( 467-)  A      -7.07
 774 MET   ( 467-)  B      -6.98
 372 TYR   ( 453-)  A      -6.81
 168 ARG   ( 249-)  A      -6.68
 556 ARG   ( 249-)  B      -6.68
 590 ARG   ( 283-)  B      -6.67
 202 ARG   ( 283-)  A      -6.67
 266 GLN   ( 347-)  A      -6.58
 654 GLN   ( 347-)  B      -6.58
 591 TYR   ( 284-)  B      -6.14
 203 TYR   ( 284-)  A      -6.14
 334 LYS   ( 415-)  A      -6.07
 722 LYS   ( 415-)  B      -6.07
 645 ARG   ( 338-)  B      -5.86
 257 ARG   ( 338-)  A      -5.86
 760 TYR   ( 453-)  B      -5.86
 354 ARG   ( 435-)  A      -5.67
 742 ARG   ( 435-)  B      -5.67
 385 PHE   ( 466-)  A      -5.58
 350 LYS   ( 431-)  A      -5.29
 738 LYS   ( 431-)  B      -5.29
  12 GLN   (  93-)  A      -5.20
 400 GLN   (  93-)  B      -5.20
 459 ARG   ( 152-)  B      -5.13
  71 ARG   ( 152-)  A      -5.13

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.

 349 ARG   ( 430-)  A       351 - GLN    432- ( A)         -4.51
 371 THR   ( 452-)  A       374 - THR    455- ( A)         -5.22
 737 ARG   ( 430-)  B       739 - GLN    432- ( B)         -4.51

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.

 453 ASN   ( 146-)  B   -2.86
 328 ILE   ( 409-)  A   -2.51
 716 ILE   ( 409-)  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.

 809 HOH   ( 487 )  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.

 809 HOH   ( 489 )  A      O     32.55  -31.71  -43.95
 809 HOH   ( 492 )  A      O     42.33    0.34   -1.73
 809 HOH   ( 505 )  A      O     32.80  -15.31   -3.89

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.

 809 HOH   ( 487 )  A      O
 809 HOH   ( 539 )  A      O
 809 HOH   ( 540 )  A      O
 809 HOH   ( 545 )  A      O
 809 HOH   ( 569 )  A      O
 809 HOH   ( 579 )  A      O
 809 HOH   ( 585 )  A      O
 809 HOH   ( 590 )  A      O
 809 HOH   ( 603 )  A      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:  783 NAG  ( 478-) B
Bound group on Asn; dont flip  153 ASN  ( 234-) A
Bound to:  781 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  ( 484-) B
Bound group on Asn; dont flip  541 ASN  ( 234-) B
Bound to:  792 NAG  ( 490-) B
Bound group on Gln; dont flip  698 GLN  ( 391-) B
Bound to:  799 MAN  ( 481-) 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.

  23 ASN   ( 104-)  A
  50 GLN   ( 131-)  A
  61 ASN   ( 142-)  A
  74 HIS   ( 155-)  A
  87 HIS   ( 168-)  A
  92 GLN   ( 173-)  A
 253 ASN   ( 334-)  A
 314 GLN   ( 395-)  A
 338 ASN   ( 419-)  A
 411 ASN   ( 104-)  B
 438 GLN   ( 131-)  B
 449 ASN   ( 142-)  B
 457 HIS   ( 150-)  B
 480 GLN   ( 173-)  B
 641 ASN   ( 334-)  B
 702 GLN   ( 395-)  B
 726 ASN   ( 419-)  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.

   3 TYR   (  84-)  A      N
  21 LYS   ( 102-)  A      NZ
  43 CYS   ( 124-)  A      N
  56 GLY   ( 137-)  A      N
  57 THR   ( 138-)  A      N
  61 ASN   ( 142-)  A      ND2
  68 VAL   ( 149-)  A      N
  72 ILE   ( 153-)  A      N
  74 HIS   ( 155-)  A      N
  76 THR   ( 157-)  A      N
  94 CYS   ( 175-)  A      N
  98 SER   ( 179-)  A      N
 101 SER   ( 182-)  A      N
 105 GLY   ( 186-)  A      N
 120 ALA   ( 201-)  A      N
 121 THR   ( 202-)  A      OG1
 142 LEU   ( 223-)  A      N
 145 GLN   ( 226-)  A      NE2
 147 SER   ( 228-)  A      N
 154 GLY   ( 235-)  A      N
 167 GLY   ( 248-)  A      N
 188 ALA   ( 269-)  A      N
 198 SER   ( 279-)  A      N
 200 TYR   ( 281-)  A      OH
 213 ASN   ( 294-)  A      N
And so on for a total of 115 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.

 103 HIS   ( 184-)  A      ND1
 193 HIS   ( 274-)  A      ND1
 310 GLN   ( 391-)  A      OE1
 462 HIS   ( 155-)  B      ND1
 491 HIS   ( 184-)  B      ND1
 581 HIS   ( 274-)  B      ND1
 631 ASP   ( 324-)  B      OD2

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+.

 797  CA   ( 470-)  A     1.72   0.92 Is perhaps MG

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.

  32 ASP   ( 113-)  A   H-bonding suggests Asn
  44 ASP   ( 125-)  A   H-bonding suggests Asn; but Alt-Rotamer
 162 ASP   ( 243-)  A   H-bonding suggests Asn
 294 GLU   ( 375-)  A   H-bonding suggests Gln
 432 ASP   ( 125-)  B   H-bonding suggests Asn; but Alt-Rotamer
 550 ASP   ( 243-)  B   H-bonding suggests Asn
 682 GLU   ( 375-)  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 :  -1.336
  2nd generation packing quality :  -2.166
  Ramachandran plot appearance   :  -3.182 (poor)
  chi-1/chi-2 rotamer normality  :  -4.060 (bad)
  Backbone conformation          :  -1.049

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.519 (tight)
  Bond angles                    :   0.864
  Omega angle restraints         :   0.327 (tight)
  Side chain planarity           :   0.685
  Improper dihedral distribution :   1.158
  B-factor distribution          :   1.117
  Inside/Outside distribution    :   1.068

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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -3.3 (poor)
  chi-1/chi-2 rotamer normality  :  -3.1 (poor)
  Backbone conformation          :  -1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.519 (tight)
  Bond angles                    :   0.864
  Omega angle restraints         :   0.327 (tight)
  Side chain planarity           :   0.685
  Improper dihedral distribution :   1.158
  B-factor distribution          :   1.117
  Inside/Outside distribution    :   1.068
==============

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.