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 pdb1ive.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.

 794 BMA   ( 480-)  A  -
 795 MAN   ( 482-)  B  -
 796 MAN   ( 483-)  A  -
 797 BMA   ( 476-)  B  -
 798 BMA   ( 480-)  B  -
 799 MAN   ( 484-)  B  -
 800 MAN   ( 485-)  B  -
 801 MAN   ( 486-)  B  -
 802 NDG   ( 488-)  B  -
 805 ST3   ( 471-)  B  -
 806 BMA   ( 476-)  A  -
 807 FUL   ( 477-)  A  -
 808 MAN   ( 481-)  B  -
 809 NDG   ( 485-)  A  -
 810 ST3   ( 471-)  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.

  91 ARG   ( 172-)  A  -   NH1  470 LEU   ( 163-)  B  -   O
 794 BMA   ( 480-)  A  -   O3   808 MAN   ( 481-)  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  806 BMA   ( 476-)  A  -   C1
 781 NAG   ( 478-)  A  -   O4  bound to  782 NAG   ( 479-)  A  -   C1
 782 NAG   ( 479-)  A  -   O4  bound to  794 BMA   ( 480-)  A  -   C1
 783 NAG   ( 484-)  A  -   O4  bound to  809 NDG   ( 485-)  A  -   C1
 784 NAG   ( 472-)  B  -   O4  bound to  785 NAG   ( 473-)  B  -   C1
 786 NAG   ( 474-)  B  -   O4  bound to  787 NAG   ( 475-)  B  -   C1
 787 NAG   ( 475-)  B  -   O4  bound to  797 BMA   ( 476-)  B  -   C1
 789 NAG   ( 478-)  B  -   O4  bound to  790 NAG   ( 479-)  B  -   C1
 790 NAG   ( 479-)  B  -   O4  bound to  798 BMA   ( 480-)  B  -   C1
 791 NAG   ( 487-)  B  -   O4  bound to  802 NDG   ( 488-)  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

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 : 12.07

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.

  41 VAL   ( 122-)  A      CA   CB    1.62    4.4
 121 THR   ( 202-)  A      CA   CB    1.61    4.2
 150 VAL   ( 231-)  A      CA   CB    1.62    4.7
 161 THR   ( 242-)  A      CA   CB    1.62    4.5
 241 VAL   ( 322-)  A      CA   CB    1.64    5.4
 346 ILE   ( 427-)  A      CA   CB    1.62    4.6
 429 VAL   ( 122-)  B      CA   CB    1.62    4.4
 509 THR   ( 202-)  B      CA   CB    1.61    4.2
 538 VAL   ( 231-)  B      CA   CB    1.62    4.7
 549 THR   ( 242-)  B      CA   CB    1.62    4.5
 629 VAL   ( 322-)  B      CA   CB    1.64    5.4
 734 ILE   ( 427-)  B      CA   CB    1.62    4.6

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

 |  0.999056 -0.000166 -0.000091|
 | -0.000166  0.995960 -0.000002|
 | -0.000091 -0.000002  0.995956|
Proposed new scale matrix

 |  0.008213  0.000001  0.000000|
 |  0.000001  0.007127  0.000000|
 |  0.000000  0.000000  0.007097|
With corresponding cell

    A    = 121.762  B   = 140.316  C    = 140.911
    Alpha=  90.002  Beta=  90.002  Gamma=  90.019

The CRYST1 cell dimensions

    A    = 121.880  B   = 140.880  C    = 141.490
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 240.202
(Under-)estimated Z-score: 11.422

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.

 193 HIS   ( 274-)  A      CG   ND1  CE1 109.62    4.0
 246 ARG   ( 327-)  A      CG   CD   NE  117.86    4.3
 581 HIS   ( 274-)  B      CG   ND1  CE1 109.62    4.0
 634 ARG   ( 327-)  B      CG   CD   NE  117.86    4.3
 777 NAG   ( 472-)  A      N2   C2   C1  101.73   -4.1
 784 NAG   ( 472-)  B      N2   C2   C1  101.73   -4.1

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.

  13 ILE   (  94-)  A      C      6.1     8.00     0.03
  36 THR   ( 117-)  A      C     -8.0   -11.72     0.30
  41 VAL   ( 122-)  A      C     -8.5   -11.50     0.15
  57 THR   ( 138-)  A      C     -9.2   -13.49     0.30
 106 LYS   ( 187-)  A      C      6.9    10.51     0.11
 111 VAL   ( 192-)  A      C     -7.5   -10.16     0.15
 129 ARG   ( 210-)  A      C     -6.6    -9.97     0.13
 140 ASN   ( 221-)  A      C      7.4    11.84     0.27
 161 THR   ( 242-)  A      C     -7.3   -10.63     0.30
 176 ILE   ( 257-)  A      C     -6.4    -8.42     0.03
 184 ILE   ( 265-)  A      C     -8.2   -10.73     0.03
 202 ARG   ( 283-)  A      C      6.7    10.39     0.13
 213 ASN   ( 294-)  A      C     -6.0    -9.19     0.27
 276 GLY   ( 357-)  A      C      7.7    10.26     0.06
 320 ASP   ( 401-)  A      C      7.1    10.94    -0.01
 328 ILE   ( 409-)  A      C     -7.4    -9.64     0.03
 349 ARG   ( 430-)  A      C      9.3    14.34     0.13
 401 ILE   (  94-)  B      C      6.1     8.00     0.03
 424 THR   ( 117-)  B      C     -8.0   -11.72     0.30
 429 VAL   ( 122-)  B      C     -8.5   -11.50     0.15
 445 THR   ( 138-)  B      C     -9.2   -13.49     0.30
 494 LYS   ( 187-)  B      C      6.9    10.51     0.11
 499 VAL   ( 192-)  B      C     -7.5   -10.16     0.15
 517 ARG   ( 210-)  B      C     -6.6    -9.97     0.13
 528 ASN   ( 221-)  B      C      7.4    11.84     0.27
 549 THR   ( 242-)  B      C     -7.3   -10.63     0.30
 564 ILE   ( 257-)  B      C     -6.4    -8.42     0.03
 572 ILE   ( 265-)  B      C     -8.2   -10.73     0.03
 590 ARG   ( 283-)  B      C      6.7    10.39     0.13
 601 ASN   ( 294-)  B      C     -6.0    -9.19     0.27
 664 GLY   ( 357-)  B      C      7.7    10.26     0.06
 708 ASP   ( 401-)  B      C      7.1    10.94    -0.01
 716 ILE   ( 409-)  B      C     -7.4    -9.64     0.03
 737 ARG   ( 430-)  B      C      9.3    14.34     0.13
The average deviation= 2.229

Warning: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.0 worries us a bit. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.143

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.

 312 ASN   ( 393-)  A    4.47
 700 ASN   ( 393-)  B    4.47
 196 GLU   ( 277-)  A    4.41
 584 GLU   ( 277-)  B    4.41
  24 SER   ( 105-)  A    4.11
 412 SER   ( 105-)  B    4.11
 362 ILE   ( 443-)  A    4.10
 750 ILE   ( 443-)  B    4.10

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.

 384 ASN   ( 465-)  A    8.12
 772 ASN   ( 465-)  B    8.09
 338 ASN   ( 419-)  A    7.09
 726 ASN   ( 419-)  B    7.07
 213 ASN   ( 294-)  A    6.22
 601 ASN   ( 294-)  B    6.22
 453 ASN   ( 146-)  B    6.13
  65 ASN   ( 146-)  A    6.13
 600 ASP   ( 293-)  B    4.54
 212 ASP   ( 293-)  A    4.54
 665 ASN   ( 358-)  B    4.40
 277 ASN   ( 358-)  A    4.39
 274 ASP   ( 355-)  A    4.24
 662 ASP   ( 355-)  B    4.24
 253 ASN   ( 334-)  A    4.07
 641 ASN   ( 334-)  B    4.07
 468 ASN   ( 161-)  B    4.06
  80 ASN   ( 161-)  A    4.06

Error: Connections to aromatic rings out of plane

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

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

 591 TYR   ( 284-)  B      CB   7.23
 203 TYR   ( 284-)  A      CB   7.23
   3 TYR   (  84-)  A      CB   6.41
 391 TYR   (  84-)  B      CB   6.41
 271 TRP   ( 352-)  A      CB   5.32
 659 TRP   ( 352-)  B      CB   5.32
 203 TYR   ( 284-)  A      OH   5.24
 591 TYR   ( 284-)  B      OH   5.24
 730 TYR   ( 423-)  B      OH   5.09
 342 TYR   ( 423-)  A      OH   5.09
 302 TRP   ( 383-)  A      CB   5.00
 690 TRP   ( 383-)  B      CB   5.00
 760 TYR   ( 453-)  B      OH   4.84
 372 TYR   ( 453-)  A      OH   4.84
 214 TRP   ( 295-)  A      CB   4.77
 602 TRP   ( 295-)  B      CB   4.77
 498 HIS   ( 191-)  B      CB   4.62
 110 HIS   ( 191-)  A      CB   4.62
 428 TYR   ( 121-)  B      CB   4.47
  40 TYR   ( 121-)  A      CB   4.47
 623 TYR   ( 316-)  B      OH   4.39
 235 TYR   ( 316-)  A      OH   4.39
  63 HIS   ( 144-)  A      CB   4.34
 451 HIS   ( 144-)  B      CB   4.34
  69 HIS   ( 150-)  A      CB   4.31
 457 HIS   ( 150-)  B      CB   4.31
 491 HIS   ( 184-)  B      CB   4.19
 103 HIS   ( 184-)  A      CB   4.19
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.002

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.002

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.

 203 TYR   ( 284-)  A    -3.5
 591 TYR   ( 284-)  B    -3.5
 589 PRO   ( 282-)  B    -2.7
 201 PRO   ( 282-)  A    -2.7
 634 ARG   ( 327-)  B    -2.7
 246 ARG   ( 327-)  A    -2.7
  13 ILE   (  94-)  A    -2.6
 401 ILE   (  94-)  B    -2.6
 134 ILE   ( 215-)  A    -2.6
 522 ILE   ( 215-)  B    -2.6
 350 LYS   ( 431-)  A    -2.6
 738 LYS   ( 431-)  B    -2.6
 532 THR   ( 225-)  B    -2.6
 144 THR   ( 225-)  A    -2.6
 464 THR   ( 157-)  B    -2.5
  76 THR   ( 157-)  A    -2.5
 455 THR   ( 148-)  B    -2.5
  67 THR   ( 148-)  A    -2.5
 121 THR   ( 202-)  A    -2.5
 509 THR   ( 202-)  B    -2.5
 290 ARG   ( 371-)  A    -2.4
 678 ARG   ( 371-)  B    -2.4
 762 THR   ( 455-)  B    -2.4
 374 THR   ( 455-)  A    -2.4
 603 LYS   ( 296-)  B    -2.4
And so on for a total of 80 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.

   9 PRO   (  90-)  A  omega poor
  13 ILE   (  94-)  A  omega poor
  21 LYS   ( 102-)  A  Poor phi/psi
  23 ASN   ( 104-)  A  Poor phi/psi
  32 ASP   ( 113-)  A  omega poor
  36 THR   ( 117-)  A  omega poor
  37 ARG   ( 118-)  A  Poor phi/psi
  39 PRO   ( 120-)  A  omega poor
  43 CYS   ( 124-)  A  omega poor
  46 VAL   ( 127-)  A  Poor phi/psi
  60 ASP   ( 141-)  A  omega poor
  66 ASP   ( 147-)  A  Poor phi/psi
  67 THR   ( 148-)  A  omega poor
  94 CYS   ( 175-)  A  Poor phi/psi
  96 ALA   ( 177-)  A  omega poor
 100 SER   ( 181-)  A  Poor phi/psi
 105 GLY   ( 186-)  A  omega poor
 113 ILE   ( 194-)  A  omega poor
 127 ASP   ( 208-)  A  Poor phi/psi
 129 ARG   ( 210-)  A  omega poor
 139 GLN   ( 220-)  A  Poor phi/psi
 140 ASN   ( 221-)  A  omega poor
 141 ILE   ( 222-)  A  Poor phi/psi
 144 THR   ( 225-)  A  omega poor
 146 GLU   ( 227-)  A  Poor phi/psi
And so on for a total of 130 lines.

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

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

chi-1/chi-2 correlation Z-score : -5.289

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
  19 PHE   ( 100-)  A      0
  20 SER   ( 101-)  A      0
  22 ASP   ( 103-)  A      0
  34 TRP   ( 115-)  A      0
  37 ARG   ( 118-)  A      0
  38 GLU   ( 119-)  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
  68 VAL   ( 149-)  A      0
  69 HIS   ( 150-)  A      0
  71 ARG   ( 152-)  A      0
  72 ILE   ( 153-)  A      0
  75 ARG   ( 156-)  A      0
  82 LEU   ( 163-)  A      0
And so on for a total of 465 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 10.394

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!

 655 GLY   ( 348-)  B   1.56   40
 267 GLY   ( 348-)  A   1.56   40

Warning: Unusual peptide bond conformations

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

 140 ASN   ( 221-)  A   1.83
 528 ASN   ( 221-)  B   1.83

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].

  45 PRO   ( 126-)  A  -127.0 half-chair C-delta/C-gamma (-126 degrees)
 433 PRO   ( 126-)  B  -127.0 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

 779 NAG   ( 474-)  A      O6   <->   807 FUL   ( 477-)  A      C1   0.99    1.41  INTRA B3
 780 NAG   ( 475-)  A      O4   <->   806 BMA   ( 476-)  A      C1   0.97    1.43  INTRA B3
 783 NAG   ( 484-)  A      O4   <->   809 NDG   ( 485-)  A      C1   0.95    1.45  INTRA B3
 794 BMA   ( 480-)  A      O3   <->   808 MAN   ( 481-)  B      C1   0.83    1.57  INTRA B3
 779 NAG   ( 474-)  A      C6   <->   807 FUL   ( 477-)  A      C1   0.79    2.41  INTRA
 780 NAG   ( 475-)  A      C4   <->   806 BMA   ( 476-)  A      C1   0.75    2.45  INTRA
 762 THR   ( 455-)  B      CG2  <->   782 NAG   ( 479-)  A      C8   0.74    2.46  INTRA
 783 NAG   ( 484-)  A      C4   <->   809 NDG   ( 485-)  A      C1   0.62    2.58  INTRA
 794 BMA   ( 480-)  A      C3   <->   808 MAN   ( 481-)  B      C1   0.57    2.63  INTRA
 595 ARG   ( 288-)  B      NH1  <->   690 TRP   ( 383-)  B      CZ2  0.55    2.55  INTRA BL
 207 ARG   ( 288-)  A      NH1  <->   302 TRP   ( 383-)  A      CZ2  0.55    2.55  INTRA BL
 762 THR   ( 455-)  B      CB   <->   781 NAG   ( 478-)  A      O5   0.46    2.34  INTRA
 762 THR   ( 455-)  B      OG1  <->   782 NAG   ( 479-)  A      C8   0.43    2.37  INTRA
 742 ARG   ( 435-)  B      NH1  <->   771 ILE   ( 464-)  B      O    0.37    2.33  INTRA
 354 ARG   ( 435-)  A      NH1  <->   383 ILE   ( 464-)  A      O    0.37    2.33  INTRA
 783 NAG   ( 484-)  A      C4   <->   809 NDG   ( 485-)  A      O    0.37    2.43  INTRA
 799 MAN   ( 484-)  B      O3   <->   800 MAN   ( 485-)  B      C1   0.33    2.47  INTRA
 795 MAN   ( 482-)  B      C1   <->   808 MAN   ( 481-)  B      O3   0.33    2.47  INTRA
 762 THR   ( 455-)  B      CB   <->   781 NAG   ( 478-)  A      C5   0.32    2.88  INTRA
 744 TRP   ( 437-)  B      N    <->   776 ILE   ( 469-)  B      CG2  0.32    2.78  INTRA BL
 356 TRP   ( 437-)  A      N    <->   388 ILE   ( 469-)  A      CG2  0.32    2.78  INTRA BL
  55 GLN   ( 136-)  A      CD   <->    75 ARG   ( 156-)  A      NH1  0.29    2.81  INTRA BL
 443 GLN   ( 136-)  B      CD   <->   463 ARG   ( 156-)  B      NH1  0.29    2.81  INTRA BL
 127 ASP   ( 208-)  A      O    <->   129 ARG   ( 210-)  A      NH2  0.28    2.42  INTRA
 515 ASP   ( 208-)  B      O    <->   517 ARG   ( 210-)  B      NH2  0.28    2.42  INTRA
And so on for a total of 199 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      -7.50
 556 ARG   ( 249-)  B      -7.50
 372 TYR   ( 453-)  A      -7.05
 590 ARG   ( 283-)  B      -6.48
 202 ARG   ( 283-)  A      -6.44
 591 TYR   ( 284-)  B      -6.44
 203 TYR   ( 284-)  A      -6.44
 334 LYS   ( 415-)  A      -6.19
 645 ARG   ( 338-)  B      -6.13
 257 ARG   ( 338-)  A      -6.13
 354 ARG   ( 435-)  A      -5.99
 742 ARG   ( 435-)  B      -5.99
 760 TYR   ( 453-)  B      -5.95
 722 LYS   ( 415-)  B      -5.87
 654 GLN   ( 347-)  B      -5.69
 266 GLN   ( 347-)  A      -5.69
 580 GLN   ( 273-)  B      -5.51
 192 GLN   ( 273-)  A      -5.51
 459 ARG   ( 152-)  B      -5.40
  71 ARG   ( 152-)  A      -5.40
 400 GLN   (  93-)  B      -5.33
  12 GLN   (  93-)  A      -5.33
 385 PHE   ( 466-)  A      -5.07
 710 ARG   ( 403-)  B      -5.06
 322 ARG   ( 403-)  A      -5.06

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)         -5.28

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   -2.67
 453 ASN   ( 146-)  B   -2.67
 734 ILE   ( 427-)  B   -2.56
 346 ILE   ( 427-)  A   -2.56

Warning: Abnormal packing Z-score for sequential residues

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

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

  64 SER   ( 145-)  A     -   67 THR   ( 148-)  A        -1.85
 452 SER   ( 145-)  B     -  455 THR   ( 148-)  B        -1.85

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: 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
  80 ASN   ( 161-)  A
 145 GLN   ( 226-)  A
 193 HIS   ( 274-)  A
 338 ASN   ( 419-)  A
 411 ASN   ( 104-)  B
 438 GLN   ( 131-)  B
 449 ASN   ( 142-)  B
 462 HIS   ( 155-)  B
 468 ASN   ( 161-)  B
 533 GLN   ( 226-)  B
 581 HIS   ( 274-)  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.

   2 GLU   (  83-)  A      N
  21 LYS   ( 102-)  A      NZ
  23 ASN   ( 104-)  A      N
  23 ASN   ( 104-)  A      ND2
  25 ILE   ( 106-)  A      N
  32 ASP   ( 113-)  A      N
  37 ARG   ( 118-)  A      NH1
  41 VAL   ( 122-)  A      N
  43 CYS   ( 124-)  A      N
  56 GLY   ( 137-)  A      N
  57 THR   ( 138-)  A      N
  68 VAL   ( 149-)  A      N
  71 ARG   ( 152-)  A      NE
  72 ILE   ( 153-)  A      N
  74 HIS   ( 155-)  A      N
  75 ARG   ( 156-)  A      NE
  80 ASN   ( 161-)  A      ND2
  86 PHE   ( 167-)  A      N
  98 SER   ( 179-)  A      N
 101 SER   ( 182-)  A      N
 118 LYS   ( 199-)  A      N
 119 ASN   ( 200-)  A      N
 129 ARG   ( 210-)  A      N
 135 GLY   ( 216-)  A      N
 142 LEU   ( 223-)  A      N
And so on for a total of 117 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.

  70 ASP   ( 151-)  A      OD2
 103 HIS   ( 184-)  A      ND1
 183 HIS   ( 264-)  A      ND1
 223 ASP   ( 304-)  A      OD1
 243 ASP   ( 324-)  A      OD2
 491 HIS   ( 184-)  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+.

 803  CA   ( 470-)  A     1.41   0.80 Scores about as good as MG
 804  CA   ( 470-)  B     1.41   0.80 Scores about as good as MG
Since there are no waters, the water check has been skipped.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  44 ASP   ( 125-)  A   H-bonding suggests Asn; but Alt-Rotamer
  70 ASP   ( 151-)  A   H-bonding suggests Asn
 104 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 116 ASP   ( 197-)  A   H-bonding suggests Asn
 146 GLU   ( 227-)  A   H-bonding suggests Gln
 162 ASP   ( 243-)  A   H-bonding suggests Asn; but Alt-Rotamer
 227 GLU   ( 308-)  A   H-bonding suggests Gln
 248 ASP   ( 329-)  A   H-bonding suggests Asn
 262 GLU   ( 343-)  A   H-bonding suggests Gln; but Alt-Rotamer
 432 ASP   ( 125-)  B   H-bonding suggests Asn; but Alt-Rotamer
 458 ASP   ( 151-)  B   H-bonding suggests Asn
 492 ASP   ( 185-)  B   H-bonding suggests Asn; but Alt-Rotamer
 534 GLU   ( 227-)  B   H-bonding suggests Gln
 550 ASP   ( 243-)  B   H-bonding suggests Asn; but Alt-Rotamer
 615 GLU   ( 308-)  B   H-bonding suggests Gln
 636 ASP   ( 329-)  B   H-bonding suggests Asn
 650 GLU   ( 343-)  B   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.570
  2nd generation packing quality :  -2.296
  Ramachandran plot appearance   :  -4.002 (bad)
  chi-1/chi-2 rotamer normality  :  -5.289 (bad)
  Backbone conformation          :  -1.523

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.690
  Bond angles                    :   0.796
  Omega angle restraints         :   1.890 (loose)
  Side chain planarity           :   1.954
  Improper dihedral distribution :   2.143 (loose)
  Inside/Outside distribution    :   1.057

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 :  -0.9
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -1.8
  chi-1/chi-2 rotamer normality  :  -3.3 (poor)
  Backbone conformation          :  -1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.690
  Bond angles                    :   0.796
  Omega angle restraints         :   1.890 (loose)
  Side chain planarity           :   1.954
  Improper dihedral distribution :   2.143 (loose)
  Inside/Outside distribution    :   1.057
==============

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.