WHAT IF Check report

This file was created 2011-12-18 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 pdb3s40.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  63.608  B   = 130.758  C    =  72.794
    Alpha=  90.000  Beta= 115.040  Gamma=  90.000

Dimensions of a reduced cell

    A    =  63.608  B   =  72.794  C    = 130.758
    Alpha=  90.000  Beta=  90.000  Gamma=  64.960

Dimensions of the conventional cell

    A    =  63.608  B   = 131.920  C    = 130.758
    Alpha=  90.000  Beta=  90.000  Gamma=  90.863

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 | -1.000000  0.000000 -2.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: C

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 4
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 142 LYS   ( 162-)  A      CG
 142 LYS   ( 162-)  A      CD
 142 LYS   ( 162-)  A      CE
 142 LYS   ( 162-)  A      NZ
 143 ILE   ( 163-)  A      CG1
 143 ILE   ( 163-)  A      CG2
 143 ILE   ( 163-)  A      CD1
 442 ARG   ( 171-)  B      CG
 442 ARG   ( 171-)  B      CD
 442 ARG   ( 171-)  B      NE
 442 ARG   ( 171-)  B      CZ
 442 ARG   ( 171-)  B      NH1
 442 ARG   ( 171-)  B      NH2

Warning: B-factors outside the range 0.0 - 100.0

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

   1 LYS   (   3-)  A    High
  17 GLN   (  19-)  A    High
 142 LYS   ( 162-)  A    High
 143 ILE   ( 163-)  A    High
 144 GLY   ( 164-)  A    High
 145 TYR   ( 165-)  A    High
 146 TYR   ( 166-)  A    High
 148 SER   ( 168-)  A    High
 149 THR   ( 169-)  A    High
 150 ILE   ( 170-)  A    High
 151 GLU   ( 177-)  A    High
 207 GLN   ( 233-)  A    High
 211 ASP   ( 237-)  A    High
 223 GLU   ( 249-)  A    High
 224 ASN   ( 250-)  A    High
 239 GLU   ( 265-)  A    High
 240 GLU   ( 266-)  A    High
 248 SER   ( 276-)  A    High
 257 GLU   ( 285-)  A    High
 273 THR   (   2-)  B    High
 274 LYS   (   3-)  B    High
 290 GLN   (  19-)  B    High
 416 VAL   ( 145-)  B    High
 417 SER   ( 146-)  B    High
 418 GLU   ( 147-)  B    High
And so on for a total of 116 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.

 172 MSE   ( 198-)  A    0.59
 265 MSE   ( 293-)  A    0.64
 468 MSE   ( 198-)  B    0.61
 558 MSE   ( 293-)  B    0.68
 750 MSE   ( 198-)  C    0.57
 845 MSE   ( 293-)  C    0.68
1026 MSE   ( 198-)  D    0.43
1109 MSE   ( 293-)  D    0.61

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 1

Crystal temperature (K) :100.000

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 101 ARG   ( 103-)  A
 374 ARG   ( 103-)  B
 666 ARG   ( 103-)  C
 953 ARG   ( 103-)  D

Warning: Tyrosine convention problem

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

 159 TYR   ( 185-)  A
 164 TYR   ( 190-)  A
 178 TYR   ( 204-)  A
 267 TYR   ( 295-)  A
 460 TYR   ( 190-)  B
 474 TYR   ( 204-)  B
 508 TYR   ( 238-)  B
 560 TYR   ( 295-)  B
 742 TYR   ( 190-)  C
 756 TYR   ( 204-)  C
 790 TYR   ( 238-)  C
 847 TYR   ( 295-)  C
1032 TYR   ( 204-)  D
1066 TYR   ( 238-)  D
1111 TYR   ( 295-)  D

Warning: Phenylalanine convention problem

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

  56 PHE   (  58-)  A
 134 PHE   ( 136-)  A
 137 PHE   ( 139-)  A
 329 PHE   (  58-)  B
 407 PHE   ( 136-)  B
 410 PHE   ( 139-)  B
 449 PHE   ( 179-)  B
 699 PHE   ( 136-)  C
 702 PHE   ( 139-)  C
 731 PHE   ( 179-)  C
 908 PHE   (  58-)  D
 986 PHE   ( 136-)  D
 989 PHE   ( 139-)  D
1053 PHE   ( 225-)  D

Warning: Aspartic acid convention problem

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

 193 ASP   ( 219-)  A
 197 ASP   ( 223-)  A
 225 ASP   ( 251-)  A
 247 ASP   ( 273-)  A
 292 ASP   (  21-)  B
 489 ASP   ( 219-)  B
 493 ASP   ( 223-)  B
 584 ASP   (  21-)  C
 707 ASP   ( 153-)  C
 771 ASP   ( 219-)  C
 775 ASP   ( 223-)  C
 871 ASP   (  21-)  D
1020 ASP   ( 192-)  D
1047 ASP   ( 219-)  D
1051 ASP   ( 223-)  D

Warning: Glutamic acid convention problem

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

   5 GLU   (   7-)  A
 177 GLU   ( 203-)  A
 240 GLU   ( 266-)  A
 257 GLU   ( 285-)  A
 278 GLU   (   7-)  B
 318 GLU   (  47-)  B
 347 GLU   (  76-)  B
 384 GLU   ( 113-)  B
 461 GLU   ( 191-)  B
 473 GLU   ( 203-)  B
 515 GLU   ( 245-)  B
 532 GLU   ( 267-)  B
 550 GLU   ( 285-)  B
 570 GLU   (   7-)  C
 610 GLU   (  47-)  C
 639 GLU   (  76-)  C
 648 GLU   (  85-)  C
 743 GLU   ( 191-)  C
 745 GLU   ( 193-)  C
 755 GLU   ( 203-)  C
 801 GLU   ( 249-)  C
 819 GLU   ( 267-)  C
 821 GLU   ( 269-)  C
 827 GLU   ( 275-)  C
 837 GLU   ( 285-)  C
 857 GLU   (   7-)  D
 926 GLU   (  76-)  D
1019 GLU   ( 191-)  D
1031 GLU   ( 203-)  D
1079 GLU   ( 263-)  D
1082 GLU   ( 266-)  D
1083 GLU   ( 267-)  D
1085 GLU   ( 269-)  D
1101 GLU   ( 285-)  D

Geometric checks

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

 |  0.998555 -0.000029  0.000376|
 | -0.000029  0.999119 -0.000035|
 |  0.000376 -0.000035  0.999636|
Proposed new scale matrix

 |  0.015741  0.000000  0.007341|
 |  0.000000  0.007655  0.000000|
 | -0.000006  0.000000  0.015168|
With corresponding cell

    A    =  63.517  B   = 130.638  C    =  72.734
    Alpha=  90.001  Beta= 114.980  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  63.608  B   = 130.758  C    =  72.794
    Alpha=  90.000  Beta= 115.040  Gamma=  90.000

Variance: 31.898
(Under-)estimated Z-score: 4.162

Error: Nomenclature error(s)

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

   5 GLU   (   7-)  A
 101 ARG   ( 103-)  A
 177 GLU   ( 203-)  A
 193 ASP   ( 219-)  A
 197 ASP   ( 223-)  A
 225 ASP   ( 251-)  A
 240 GLU   ( 266-)  A
 247 ASP   ( 273-)  A
 257 GLU   ( 285-)  A
 278 GLU   (   7-)  B
 292 ASP   (  21-)  B
 318 GLU   (  47-)  B
 347 GLU   (  76-)  B
 374 ARG   ( 103-)  B
 384 GLU   ( 113-)  B
 461 GLU   ( 191-)  B
 473 GLU   ( 203-)  B
 489 ASP   ( 219-)  B
 493 ASP   ( 223-)  B
 515 GLU   ( 245-)  B
 532 GLU   ( 267-)  B
 550 GLU   ( 285-)  B
 570 GLU   (   7-)  C
 584 ASP   (  21-)  C
 610 GLU   (  47-)  C
And so on for a total of 53 lines.

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

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

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

1088 THR   ( 272-)  D    -2.8
 824 THR   ( 272-)  C    -2.7
 537 THR   ( 272-)  B    -2.6
 267 TYR   ( 295-)  A    -2.4
1111 TYR   ( 295-)  D    -2.4
 748 LEU   ( 196-)  C    -2.3
 513 LEU   ( 243-)  B    -2.3
1058 THR   ( 230-)  D    -2.3
 560 TYR   ( 295-)  B    -2.3
 179 LEU   ( 205-)  A    -2.3
 807 VAL   ( 255-)  C    -2.2
 166 ASP   ( 192-)  A    -2.2
 441 ILE   ( 170-)  B    -2.2
 149 THR   ( 169-)  A    -2.2
1017 VAL   ( 189-)  D    -2.2
  17 GLN   (  19-)  A    -2.2
 994 LEU   ( 144-)  D    -2.1
 421 ASN   ( 150-)  B    -2.1
 799 SER   ( 247-)  C    -2.1
 520 VAL   ( 255-)  B    -2.1
1071 VAL   ( 255-)  D    -2.1
 415 LEU   ( 144-)  B    -2.1
 795 LEU   ( 243-)  C    -2.1
 998 ILE   ( 163-)  D    -2.1
 451 VAL   ( 181-)  B    -2.1
 465 VAL   ( 195-)  B    -2.1
 454 THR   ( 184-)  B    -2.1
1079 GLU   ( 263-)  D    -2.1
 610 GLU   (  47-)  C    -2.1
 514 PHE   ( 244-)  B    -2.1
 290 GLN   (  19-)  B    -2.0
 579 LYS   (  16-)  C    -2.0
1010 VAL   ( 181-)  D    -2.0
 502 ILE   ( 232-)  B    -2.0
 667 THR   ( 104-)  C    -2.0
 128 LYS   ( 130-)  A    -2.0
 542 SER   ( 277-)  B    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

 119 GLU   ( 121-)  A  Poor phi/psi
 166 ASP   ( 192-)  A  Poor phi/psi
 252 THR   ( 280-)  A  PRO omega poor
 263 PHE   ( 291-)  A  omega poor
 284 VAL   (  13-)  B  omega poor
 392 GLU   ( 121-)  B  Poor phi/psi
 462 ASP   ( 192-)  B  Poor phi/psi
 471 ASN   ( 201-)  B  Poor phi/psi
 484 ASN   ( 214-)  B  Poor phi/psi
 512 LYS   ( 242-)  B  Poor phi/psi
 537 THR   ( 272-)  B  Poor phi/psi
 545 THR   ( 280-)  B  PRO omega poor
 556 PHE   ( 291-)  B  omega poor
 564 VAL   ( 299-)  B  Poor phi/psi
 568 LYS   (   5-)  C  omega poor
 662 ASN   (  99-)  C  Poor phi/psi
 684 GLU   ( 121-)  C  Poor phi/psi
 695 ASN   ( 132-)  C  Poor phi/psi
 739 GLY   ( 187-)  C  Poor phi/psi
 798 ASP   ( 246-)  C  Poor phi/psi
 799 SER   ( 247-)  C  Poor phi/psi
 803 ASP   ( 251-)  C  Poor phi/psi
 832 THR   ( 280-)  C  PRO omega poor
 843 PHE   ( 291-)  C  omega poor
 971 GLU   ( 121-)  D  Poor phi/psi
 982 ASN   ( 132-)  D  Poor phi/psi
1008 PHE   ( 179-)  D  Poor phi/psi
1020 ASP   ( 192-)  D  Poor phi/psi
1042 ASN   ( 214-)  D  Poor phi/psi
1059 GLY   ( 231-)  D  Poor phi/psi
1081 GLU   ( 265-)  D  Poor phi/psi
1096 THR   ( 280-)  D  PRO omega poor
1098 CYS   ( 282-)  D  omega poor
1107 PHE   ( 291-)  D  omega poor
 chi-1/chi-2 correlation Z-score : -2.906

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 665 SER   ( 102-)  C    0.36

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  15 ALA   (  17-)  A      0
  17 GLN   (  19-)  A      0
  37 ASP   (  39-)  A      0
  42 HIS   (  44-)  A      0
  46 GLN   (  48-)  A      0
  59 LYS   (  61-)  A      0
  66 PHE   (  68-)  A      0
  81 PRO   (  83-)  A      0
  92 PRO   (  94-)  A      0
  96 CYS   (  98-)  A      0
 107 GLN   ( 109-)  A      0
 119 GLU   ( 121-)  A      0
 120 HIS   ( 122-)  A      0
 129 ALA   ( 131-)  A      0
 136 ASN   ( 138-)  A      0
 137 PHE   ( 139-)  A      0
 140 ILE   ( 142-)  A      0
 141 GLY   ( 143-)  A      0
 142 LYS   ( 162-)  A      0
 143 ILE   ( 163-)  A      0
 149 THR   ( 169-)  A      0
 150 ILE   ( 170-)  A      0
 151 GLU   ( 177-)  A      0
 152 THR   ( 178-)  A      0
 159 TYR   ( 185-)  A      0
And so on for a total of 452 lines.

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!

1034 GLY   ( 206-)  D   1.89   15
 457 GLY   ( 187-)  B   1.52   80

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]

 303 PRO   (  32-)  B    0.18 LOW

Warning: Unusual PRO puckering phases

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

  30 PRO   (  32-)  A  -113.5 envelop C-gamma (-108 degrees)
 106 PRO   ( 108-)  A   100.1 envelop C-beta (108 degrees)
 269 PRO   ( 297-)  A    43.8 envelop C-delta (36 degrees)
 450 PRO   ( 180-)  B   -63.3 envelop C-beta (-72 degrees)
 833 PRO   ( 281-)  C    51.5 half-chair C-delta/C-gamma (54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 526 HIS   ( 261-)  B      NE2 <-> 1077 HIS   ( 261-)  D      CE1    0.36    2.74  INTRA BF
 981 ALA   ( 131-)  D      N   <->  984 GLN   ( 134-)  D      O      0.36    2.34  INTRA BF
 768 LYS   ( 216-)  C      NZ  <->  797 GLU   ( 245-)  C      CD     0.29    2.81  INTRA BF
1004 THR   ( 169-)  D      C   <-> 1120 HOH   ( 315 )  D      O      0.27    2.53  INTRA BF
 848 ASN   ( 296-)  C      ND2 <->  851 VAL   ( 299-)  C      CG1    0.25    2.85  INTRA BF
  73 PHE   (  75-)  A      CE1 <->   77 ASN   (  79-)  A      ND2    0.24    2.86  INTRA BF
 450 PRO   ( 180-)  B      CG  <->  530 GLU   ( 265-)  B      CG     0.21    2.99  INTRA BF
 218 PHE   ( 244-)  A      N   <-> 1117 HOH   ( 352 )  A      O      0.21    2.49  INTRA BF
 694 ALA   ( 131-)  C      N   <->  697 GLN   ( 134-)  C      O      0.21    2.49  INTRA BF
 508 TYR   ( 238-)  B      CZ  <->  514 PHE   ( 244-)  B      CD1    0.20    3.00  INTRA BF
 235 HIS   ( 261-)  A      NE2 <->  813 HIS   ( 261-)  C      CE1    0.20    2.90  INTRA BF
1070 HIS   ( 254-)  D      CD2 <-> 1071 VAL   ( 255-)  D      N      0.18    2.82  INTRA BF
 403 ASN   ( 132-)  B      ND2 <->  547 CYS   ( 282-)  B      SG     0.18    3.12  INTRA BF
 698 HIS   ( 135-)  C      ND1 <-> 1119 HOH   ( 328 )  C      O      0.17    2.53  INTRA BL
 402 ALA   ( 131-)  B      N   <->  405 GLN   ( 134-)  B      O      0.16    2.54  INTRA BF
 583 GLY   (  20-)  C      C   <-> 1119 HOH   ( 361 )  C      O      0.15    2.65  INTRA BF
 731 PHE   ( 179-)  C      C   <->  745 GLU   ( 193-)  C      OE1    0.15    2.65  INTRA BF
 925 PHE   (  75-)  D      CZ  <->  929 ASN   (  79-)  D      ND2    0.15    2.95  INTRA BF
 156 LYS   ( 182-)  A      NZ  <->  165 GLU   ( 191-)  A      OE2    0.15    2.55  INTRA BF
 997 LYS   ( 162-)  D      NZ  <-> 1120 HOH   ( 313 )  D      O      0.15    2.55  INTRA BF
1060 ILE   ( 232-)  D      CG2 <-> 1061 GLN   ( 233-)  D      N      0.15    2.85  INTRA BF
 353 ALA   (  82-)  B      N   <->  354 PRO   (  83-)  B      CD     0.14    2.86  INTRA BL
 873 HIS   (  23-)  D      ND1 <-> 1120 HOH   ( 374 )  D      O      0.14    2.56  INTRA BF
 996 GLY   ( 161-)  D      O   <-> 1000 TYR   ( 165-)  D      N      0.14    2.56  INTRA BF
 504 ALA   ( 234-)  B      O   <->  508 TYR   ( 238-)  B      N      0.13    2.57  INTRA BF
And so on for a total of 136 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 869 GLN   (  19-)  D      -7.95
 290 GLN   (  19-)  B      -7.87
 582 GLN   (  19-)  C      -7.58
  17 GLN   (  19-)  A      -6.87
 287 LYS   (  16-)  B      -6.24
 579 LYS   (  16-)  C      -6.21
 274 LYS   (   3-)  B      -6.20
 866 LYS   (  16-)  D      -6.17
  14 LYS   (  16-)  A      -6.11
 540 GLU   ( 275-)  B      -6.02
1091 GLU   ( 275-)  D      -6.01
 611 GLN   (  48-)  C      -5.92
  46 GLN   (  48-)  A      -5.83
 319 GLN   (  48-)  B      -5.72
 898 GLN   (  48-)  D      -5.69
 530 GLU   ( 265-)  B      -5.52
 827 GLU   ( 275-)  C      -5.43
1039 PHE   ( 211-)  D      -5.21
 317 LYS   (  46-)  B      -5.20
 896 LYS   (  46-)  D      -5.19
 260 GLN   ( 288-)  A      -5.10
 357 ILE   (  86-)  B      -5.07
 795 LEU   ( 243-)  C      -5.05
 218 PHE   ( 244-)  A      -5.04
 609 LYS   (  46-)  C      -5.04

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.

 609 LYS   (  46-)  C       611 - GLN     48- ( C)         -4.99

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

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: C

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: D

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.

 851 VAL   ( 299-)  C   -2.92
 442 ARG   ( 171-)  B   -2.77
 217 LEU   ( 243-)  A   -2.63

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

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

 406 HIS   ( 135-)  B
 445 ASN   ( 175-)  B
 503 GLN   ( 233-)  B
 586 HIS   (  23-)  C
 604 HIS   (  41-)  C
 813 HIS   ( 261-)  C

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.

 101 ARG   ( 103-)  A      NH1
 133 HIS   ( 135-)  A      N
 164 TYR   ( 190-)  A      OH
 178 TYR   ( 204-)  A      N
 190 LYS   ( 216-)  A      N
 193 ASP   ( 219-)  A      N
 204 THR   ( 230-)  A      N
 224 ASN   ( 250-)  A      N
 247 ASP   ( 273-)  A      N
 409 ASN   ( 138-)  B      N
 421 ASN   ( 150-)  B      N
 423 ILE   ( 152-)  B      N
 435 GLY   ( 164-)  B      N
 442 ARG   ( 171-)  B      N
 460 TYR   ( 190-)  B      OH
 489 ASP   ( 219-)  B      N
 502 ILE   ( 232-)  B      N
 504 ALA   ( 234-)  B      N
 513 LEU   ( 243-)  B      N
 526 HIS   ( 261-)  B      NE2
 531 GLU   ( 266-)  B      N
 539 GLY   ( 274-)  B      N
 541 SER   ( 276-)  B      OG
 696 GLY   ( 133-)  C      N
 701 ASN   ( 138-)  C      N
 711 LYS   ( 157-)  C      N
 718 GLY   ( 164-)  C      N
 756 TYR   ( 204-)  C      N
 763 PHE   ( 211-)  C      N
 782 THR   ( 230-)  C      N
 794 LYS   ( 242-)  C      N
 826 GLY   ( 274-)  C      N
 828 SER   ( 276-)  C      OG
 831 HIS   ( 279-)  C      N
 983 GLY   ( 133-)  D      N
 999 GLY   ( 164-)  D      N
1001 TYR   ( 166-)  D      N
1032 TYR   ( 204-)  D      N
1056 LYS   ( 228-)  D      N
1061 GLN   ( 233-)  D      N
1062 ALA   ( 234-)  D      N
1077 HIS   ( 261-)  D      NE2
1080 THR   ( 264-)  D      N
1090 GLY   ( 274-)  D      N
1094 LEU   ( 278-)  D      N

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 133 HIS   ( 135-)  A      ND1
 175 ASN   ( 201-)  A      OD1
 188 ASN   ( 214-)  A      OD1
 245 ASP   ( 271-)  A      OD1
 262 HIS   ( 290-)  A      ND1
 296 ASN   (  25-)  B      OD1
 447 GLU   ( 177-)  B      OE1
 471 ASN   ( 201-)  B      OD1
 701 ASN   ( 138-)  C      OD1
 745 GLU   ( 193-)  C      OE1
 753 ASN   ( 201-)  C      OD1
 875 ASN   (  25-)  D      OD1
 988 ASN   ( 138-)  D      OD1
1029 ASN   ( 201-)  D      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1117 HOH   ( 342 )  A      O  0.95  K  4

Warning: Possible wrong residue type

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

 160 ASP   ( 186-)  A   H-bonding suggests Asn
 166 ASP   ( 192-)  A   H-bonding suggests Asn
 193 ASP   ( 219-)  A   H-bonding suggests Asn; but Alt-Rotamer
 245 ASP   ( 271-)  A   H-bonding suggests Asn; but Alt-Rotamer
 318 GLU   (  47-)  B   H-bonding suggests Gln
 447 GLU   ( 177-)  B   H-bonding suggests Gln
 456 ASP   ( 186-)  B   H-bonding suggests Asn
 489 ASP   ( 219-)  B   H-bonding suggests Asn; but Alt-Rotamer
 516 ASP   ( 246-)  B   H-bonding suggests Asn
 690 ASP   ( 127-)  C   H-bonding suggests Asn; but Alt-Rotamer
 729 GLU   ( 177-)  C   H-bonding suggests Gln
 745 GLU   ( 193-)  C   H-bonding suggests Gln
 771 ASP   ( 219-)  C   H-bonding suggests Asn; but Alt-Rotamer
 789 ASP   ( 237-)  C   H-bonding suggests Asn; but Alt-Rotamer
 837 GLU   ( 285-)  C   H-bonding suggests Gln
 977 ASP   ( 127-)  D   H-bonding suggests Asn; but Alt-Rotamer
1019 GLU   ( 191-)  D   H-bonding suggests Gln
1047 ASP   ( 219-)  D   H-bonding suggests Asn; but Alt-Rotamer
1065 ASP   ( 237-)  D   H-bonding suggests Asn
1089 ASP   ( 273-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.050
  2nd generation packing quality :  -0.967
  Ramachandran plot appearance   :  -0.559
  chi-1/chi-2 rotamer normality  :  -2.906
  Backbone conformation          :   0.359

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.336 (tight)
  Bond angles                    :   0.573 (tight)
  Omega angle restraints         :   0.993
  Side chain planarity           :   0.364 (tight)
  Improper dihedral distribution :   0.593
  B-factor distribution          :   1.495
  Inside/Outside distribution    :   0.946

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.336 (tight)
  Bond angles                    :   0.573 (tight)
  Omega angle restraints         :   0.993
  Side chain planarity           :   0.364 (tight)
  Improper dihedral distribution :   0.593
  B-factor distribution          :   1.495
  Inside/Outside distribution    :   0.946
==============

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.