WHAT IF Check report

This file was created 2012-01-12 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 pdb1rcx.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    = 218.300  B   = 219.000  C    = 113.500
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 113.500  B   = 218.300  C    = 219.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 219.000  B   = 218.300  C    = 113.500
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: P 21 21 2

Bravais type of conventional cell is: P

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: 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.

4737 RUB   ( 476-)  L  -
4738 RUB   ( 476-)  B  -
4739 RUB   ( 476-)  E  -
4740 RUB   ( 476-)  H  -
4741 RUB   ( 476-)  K  -
4742 RUB   ( 476-)  O  -
4743 RUB   ( 476-)  R  -
4744 RUB   ( 476-)  V  -

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: L

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

1791 TYR   (  29-)  H
2381 TYR   (  29-)  K
3561 TYR   (  29-)  R

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:

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: L

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

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.

 476 LEU   (   9-)  S      CG   CD2   1.39   -4.1
1066 LEU   (   9-)  C      CG   CD2   1.39   -4.1
1656 LEU   (   9-)  F      CG   CD2   1.39   -4.0
2246 LEU   (   9-)  I      CG   CD2   1.39   -4.1
2836 LEU   (   9-)  M      CG   CD2   1.39   -4.1
3426 LEU   (   9-)  P      CG   CD2   1.39   -4.1
4016 LEU   (   9-)  T      CG   CD2   1.39   -4.1
4606 LEU   (   9-)  W      CG   CD2   1.39   -4.1
 239 CYS   ( 247-)  L      SG  -SG*   2.27    5.9
 829 CYS   ( 247-)  B      SG  -SG*   2.27    5.9
1419 CYS   ( 247-)  E      SG  -SG*   2.26    5.4
2009 CYS   ( 247-)  H      SG  -SG*   2.26    5.4
2599 CYS   ( 247-)  K      SG  -SG*   2.26    5.5
3189 CYS   ( 247-)  O      SG  -SG*   2.26    5.5
3779 CYS   ( 247-)  R      SG  -SG*   2.23    4.6
4369 CYS   ( 247-)  V      SG  -SG*   2.23    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

 |  0.999078 -0.000003 -0.000092|
 | -0.000003  0.999076 -0.000069|
 | -0.000092 -0.000069  1.000496|
Proposed new scale matrix

 |  0.004585  0.000000  0.000000|
 |  0.000000  0.004570  0.000000|
 |  0.000000  0.000000  0.008807|
With corresponding cell

    A    = 218.092  B   = 218.808  C    = 113.551
    Alpha=  90.002  Beta=  90.002  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 218.300  B   = 219.000  C    = 113.500
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 60.959
(Under-)estimated Z-score: 5.754

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.

  16 TYR   (  24-)  L      N    CA   C   122.91    4.2
  18 THR   (  26-)  L      N    CA   CB  103.11   -4.3
  71 ARG   (  79-)  L      CB   CG   CD  105.44   -4.3
  71 ARG   (  79-)  L      CG   CD   NE  119.17    5.1
  74 GLY   (  82-)  L      N    CA   C    99.81   -4.4
 113 VAL   ( 121-)  L      N    CA   CB  102.99   -4.4
 192 THR   ( 200-)  L      N    CA   C    99.42   -4.2
 230 HIS   ( 238-)  L      CG   ND1  CE1 109.70    4.1
 255 PRO   ( 263-)  L      N    CA   C   122.35    4.2
 259 HIS   ( 267-)  L      CG   ND1  CE1 109.61    4.0
 286 HIS   ( 294-)  L      CG   ND1  CE1 109.97    4.4
 302 HIS   ( 310-)  L      CG   ND1  CE1 109.74    4.1
 317 HIS   ( 325-)  L      C    CA   CB  101.56   -4.5
 378 HIS   ( 386-)  L      CG   ND1  CE1 109.64    4.0
 401 HIS   ( 409-)  L      CG   ND1  CE1 109.61    4.0
 500 LEU   (  33-)  S      CA   CB   CG  130.97    4.2
 565 PHE   (  98-)  S      N    CA   C    98.77   -4.4
 572 ASP   ( 105-)  S      N    CA   C    99.43   -4.2
 606 TYR   (  24-)  B      N    CA   C   122.96    4.2
 608 THR   (  26-)  B      N    CA   CB  103.11   -4.3
 661 ARG   (  79-)  B      CB   CG   CD  105.48   -4.3
 661 ARG   (  79-)  B      CG   CD   NE  119.18    5.1
 664 GLY   (  82-)  B      N    CA   C    99.79   -4.4
 703 VAL   ( 121-)  B      N    CA   CB  103.00   -4.4
 782 THR   ( 200-)  B      N    CA   C    99.42   -4.2
And so on for a total of 144 lines.

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.

 606 TYR   (  24-)  B    6.40
1786 TYR   (  24-)  H    6.38
3556 TYR   (  24-)  R    6.38
2376 TYR   (  24-)  K    6.37
  16 TYR   (  24-)  L    6.37
4146 TYR   (  24-)  V    6.37
2966 TYR   (  24-)  O    6.36
1196 TYR   (  24-)  E    6.36
3244 ASP   ( 302-)  O    6.20
 884 ASP   ( 302-)  B    6.18
 294 ASP   ( 302-)  L    6.17
2654 ASP   ( 302-)  K    6.17
2064 ASP   ( 302-)  H    6.17
4424 ASP   ( 302-)  V    6.16
1474 ASP   ( 302-)  E    6.16
3834 ASP   ( 302-)  R    6.15
3972 GLU   ( 440-)  R    5.82
2202 GLU   ( 440-)  H    5.82
1022 GLU   ( 440-)  B    5.82
3382 GLU   ( 440-)  O    5.82
 432 GLU   ( 440-)  L    5.81
1612 GLU   ( 440-)  E    5.81
4562 GLU   ( 440-)  V    5.81
2792 GLU   ( 440-)  K    5.80
3066 VAL   ( 124-)  O    5.67
And so on for a total of 144 lines.

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.727

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.

1915 HIS   ( 153-)  H      CB   5.24
3095 HIS   ( 153-)  O      CB   5.23
2505 HIS   ( 153-)  K      CB   5.23
3685 HIS   ( 153-)  R      CB   5.23
 145 HIS   ( 153-)  L      CB   5.23
 735 HIS   ( 153-)  B      CB   5.22
4275 HIS   ( 153-)  V      CB   5.22
1325 HIS   ( 153-)  E      CB   5.22
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -0.904

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.

4148 THR   (  26-)  V    -2.8
 608 THR   (  26-)  B    -2.8
  18 THR   (  26-)  L    -2.8
3558 THR   (  26-)  R    -2.8
1788 THR   (  26-)  H    -2.8
2378 THR   (  26-)  K    -2.7
2968 THR   (  26-)  O    -2.7
1198 THR   (  26-)  E    -2.7
1541 VAL   ( 369-)  E    -2.6
 951 VAL   ( 369-)  B    -2.6
2721 VAL   ( 369-)  K    -2.6
3311 VAL   ( 369-)  O    -2.6
 361 VAL   ( 369-)  L    -2.6
4491 VAL   ( 369-)  V    -2.6
2131 VAL   ( 369-)  H    -2.6
3901 VAL   ( 369-)  R    -2.6
4606 LEU   (   9-)  W    -2.5
2836 LEU   (   9-)  M    -2.5
2246 LEU   (   9-)  I    -2.5
1656 LEU   (   9-)  F    -2.5
4016 LEU   (   9-)  T    -2.5
3426 LEU   (   9-)  P    -2.5
1066 LEU   (   9-)  C    -2.5
 476 LEU   (   9-)  S    -2.5
3473 HIS   (  56-)  P    -2.4
And so on for a total of 104 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.

   4 GLY   (  12-)  L  Poor phi/psi
  54 SER   (  62-)  L  Poor phi/psi
 115 ASN   ( 123-)  L  Poor phi/psi
 155 ASN   ( 163-)  L  Poor phi/psi
 167 LYS   ( 175-)  L  PRO omega poor
 199 ASN   ( 207-)  L  Poor phi/psi
 289 MET   ( 297-)  L  Poor phi/psi
 323 VAL   ( 331-)  L  Poor phi/psi
 362 SER   ( 370-)  L  Poor phi/psi
 480 GLU   (  13-)  S  Poor phi/psi
 482 LEU   (  15-)  S  Poor phi/psi
 504 LYS   (  37-)  S  Poor phi/psi
 538 LYS   (  71-)  S  Poor phi/psi
 576 GLU   ( 109-)  S  Poor phi/psi
 594 GLY   (  12-)  B  Poor phi/psi
 644 SER   (  62-)  B  Poor phi/psi
 705 ASN   ( 123-)  B  Poor phi/psi
 745 ASN   ( 163-)  B  Poor phi/psi
 757 LYS   ( 175-)  B  PRO omega poor
 789 ASN   ( 207-)  B  Poor phi/psi
 879 MET   ( 297-)  B  Poor phi/psi
 913 VAL   ( 331-)  B  Poor phi/psi
 952 SER   ( 370-)  B  Poor phi/psi
1023 GLY   ( 441-)  B  Poor phi/psi
1070 GLU   (  13-)  C  Poor phi/psi
And so on for a total of 113 lines.

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!

   7 ALA   (  15-)  L      0
   9 VAL   (  17-)  L      0
  15 THR   (  23-)  L      0
  16 TYR   (  24-)  L      0
  17 TYR   (  25-)  L      0
  18 THR   (  26-)  L      0
  38 PRO   (  46-)  L      0
  53 SER   (  61-)  L      0
  54 SER   (  62-)  L      0
  55 THR   (  63-)  L      0
  58 TRP   (  66-)  L      0
  62 TRP   (  70-)  L      0
  66 LEU   (  74-)  L      0
  67 THR   (  75-)  L      0
  77 TYR   (  85-)  L      0
  80 GLU   (  88-)  L      0
  83 ALA   (  91-)  L      0
  86 GLU   (  94-)  L      0
  87 ASN   (  95-)  L      0
  99 LEU   ( 107-)  L      0
 102 GLU   ( 110-)  L      0
 113 VAL   ( 121-)  L      0
 115 ASN   ( 123-)  L      0
 116 VAL   ( 124-)  L      0
 119 PHE   ( 127-)  L      0
And so on for a total of 1795 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 : 1.993

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!

4459 GLY   ( 337-)  V   2.30   13
 919 GLY   ( 337-)  B   2.30   13
3279 GLY   ( 337-)  O   2.30   13
2099 GLY   ( 337-)  H   2.30   13
 329 GLY   ( 337-)  L   2.30   13
3869 GLY   ( 337-)  R   2.30   13
1509 GLY   ( 337-)  E   2.30   13
2689 GLY   ( 337-)  K   2.30   13
1812 PRO   (  50-)  H   1.58   15
1222 PRO   (  50-)  E   1.58   15
4172 PRO   (  50-)  V   1.58   15
2402 PRO   (  50-)  K   1.58   15
  42 PRO   (  50-)  L   1.58   15
3582 PRO   (  50-)  R   1.58   15
 632 PRO   (  50-)  B   1.58   15
2992 PRO   (  50-)  O   1.58   15
3347 GLY   ( 405-)  O   1.51   80
1577 GLY   ( 405-)  E   1.51   80
2757 GLY   ( 405-)  K   1.51   80
4527 GLY   ( 405-)  V   1.51   80
 397 GLY   ( 405-)  L   1.51   80
3937 GLY   ( 405-)  R   1.51   80
2167 GLY   ( 405-)  H   1.51   80
 987 GLY   ( 405-)  B   1.51   80

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].

  36 PRO   (  44-)  L    45.2 half-chair C-delta/C-gamma (54 degrees)
 255 PRO   ( 263-)  L   -49.9 half-chair C-beta/C-alpha (-54 degrees)
 626 PRO   (  44-)  B    45.1 half-chair C-delta/C-gamma (54 degrees)
 845 PRO   ( 263-)  B   -49.9 half-chair C-beta/C-alpha (-54 degrees)
1216 PRO   (  44-)  E    45.1 half-chair C-delta/C-gamma (54 degrees)
1435 PRO   ( 263-)  E   -49.9 half-chair C-beta/C-alpha (-54 degrees)
1806 PRO   (  44-)  H    45.1 half-chair C-delta/C-gamma (54 degrees)
2025 PRO   ( 263-)  H   -49.9 half-chair C-beta/C-alpha (-54 degrees)
2396 PRO   (  44-)  K    45.1 half-chair C-delta/C-gamma (54 degrees)
2615 PRO   ( 263-)  K   -49.8 half-chair C-beta/C-alpha (-54 degrees)
2986 PRO   (  44-)  O    45.1 half-chair C-delta/C-gamma (54 degrees)
3205 PRO   ( 263-)  O   -50.0 half-chair C-beta/C-alpha (-54 degrees)
3576 PRO   (  44-)  R    45.1 half-chair C-delta/C-gamma (54 degrees)
3795 PRO   ( 263-)  R   -49.9 half-chair C-beta/C-alpha (-54 degrees)
4166 PRO   (  44-)  V    45.1 half-chair C-delta/C-gamma (54 degrees)
4385 PRO   ( 263-)  V   -49.9 half-chair C-beta/C-alpha (-54 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.

1885 ASN   ( 123-)  H      ND2  <->  4739 RUB   ( 476-)  E      O4   0.28    2.42  INTRA BF
1295 ASN   ( 123-)  E      ND2  <->  4740 RUB   ( 476-)  H      O4   0.27    2.43  INTRA BF
3065 ASN   ( 123-)  O      ND2  <->  4741 RUB   ( 476-)  K      O4   0.26    2.44  INTRA BF
 115 ASN   ( 123-)  L      ND2  <->  4738 RUB   ( 476-)  B      O4   0.24    2.46  INTRA BF
4148 THR   (  26-)  V      CG2  <->  4151 TYR   (  29-)  V      CB   0.24    2.96  INTRA
1198 THR   (  26-)  E      CG2  <->  1201 TYR   (  29-)  E      CB   0.24    2.96  INTRA
2968 THR   (  26-)  O      CG2  <->  2971 TYR   (  29-)  O      CB   0.24    2.96  INTRA
 608 THR   (  26-)  B      CG2  <->   611 TYR   (  29-)  B      CB   0.24    2.96  INTRA
2378 THR   (  26-)  K      CG2  <->  2381 TYR   (  29-)  K      CB   0.24    2.96  INTRA
3558 THR   (  26-)  R      CG2  <->  3561 TYR   (  29-)  R      CB   0.24    2.96  INTRA
  18 THR   (  26-)  L      CG2  <->    21 TYR   (  29-)  L      CB   0.24    2.96  INTRA
1788 THR   (  26-)  H      CG2  <->  1791 TYR   (  29-)  H      CB   0.24    2.96  INTRA
 705 ASN   ( 123-)  B      ND2  <->  4737 RUB   ( 476-)  L      O4   0.24    2.46  INTRA BF
4245 ASN   ( 123-)  V      ND2  <->  4743 RUB   ( 476-)  R      O4   0.23    2.47  INTRA BF
1636 GLU   ( 464-)  E      OE1  <->  1638 LYS   ( 466-)  E      NZ   0.23    2.47  INTRA BF
4586 GLU   ( 464-)  V      OE1  <->  4588 LYS   ( 466-)  V      NZ   0.23    2.47  INTRA BF
1046 GLU   ( 464-)  B      OE1  <->  1048 LYS   ( 466-)  B      NZ   0.23    2.47  INTRA BF
3996 GLU   ( 464-)  R      OE1  <->  3998 LYS   ( 466-)  R      NZ   0.23    2.47  INTRA BF
3406 GLU   ( 464-)  O      OE1  <->  3408 LYS   ( 466-)  O      NZ   0.23    2.47  INTRA BF
2226 GLU   ( 464-)  H      OE1  <->  2228 LYS   ( 466-)  H      NZ   0.23    2.47  INTRA BF
 456 GLU   ( 464-)  L      OE1  <->   458 LYS   ( 466-)  L      NZ   0.23    2.47  INTRA BF
2816 GLU   ( 464-)  K      OE1  <->  2818 LYS   ( 466-)  K      NZ   0.23    2.47  INTRA BF
4316 ARG   ( 194-)  V      NH1  <->  4603 ILE   (   6-)  W      CD1  0.23    2.87  INTRA
2546 ARG   ( 194-)  K      NH1  <->  2833 ILE   (   6-)  M      CD1  0.23    2.87  INTRA
1366 ARG   ( 194-)  E      NH1  <->  1653 ILE   (   6-)  F      CD1  0.23    2.87  INTRA
And so on for a total of 544 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: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

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.

3663 ARG   ( 131-)  R      -6.21
4253 ARG   ( 131-)  V      -6.18
2483 ARG   ( 131-)  K      -6.11
 713 ARG   ( 131-)  B      -6.08
1303 ARG   ( 131-)  E      -6.08
 123 ARG   ( 131-)  L      -6.08
1893 ARG   ( 131-)  H      -6.07
3073 ARG   ( 131-)  O      -6.07
3091 GLN   ( 149-)  O      -6.02
1911 GLN   ( 149-)  H      -6.01
 141 GLN   ( 149-)  L      -6.01
4271 GLN   ( 149-)  V      -6.01
1321 GLN   ( 149-)  E      -6.01
3681 GLN   ( 149-)  R      -5.98
2501 GLN   ( 149-)  K      -5.97
 731 GLN   ( 149-)  B      -5.97
2791 ARG   ( 439-)  K      -5.71
 431 ARG   ( 439-)  L      -5.71
4561 ARG   ( 439-)  V      -5.71
1021 ARG   ( 439-)  B      -5.71
2201 ARG   ( 439-)  H      -5.71
3971 ARG   ( 439-)  R      -5.71
1611 ARG   ( 439-)  E      -5.71
3381 ARG   ( 439-)  O      -5.71
1186 LYS   (  14-)  E      -5.59
And so on for a total of 81 lines.

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: L

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: S

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: E

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: F

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: H

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: I

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: K

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: M

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: O

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: P

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: R

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: T

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: V

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: W

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.

4421 ALA   ( 299-)  V   -2.85
3241 ALA   ( 299-)  O   -2.83
3831 ALA   ( 299-)  R   -2.83
2651 ALA   ( 299-)  K   -2.82
 291 ALA   ( 299-)  L   -2.81
1471 ALA   ( 299-)  E   -2.81
2061 ALA   ( 299-)  H   -2.81
 881 ALA   ( 299-)  B   -2.81
2347 VAL   ( 110-)  I   -2.63
4707 VAL   ( 110-)  W   -2.63
1167 VAL   ( 110-)  C   -2.63
4117 VAL   ( 110-)  T   -2.63
 577 VAL   ( 110-)  S   -2.63
2937 VAL   ( 110-)  M   -2.63
3527 VAL   ( 110-)  P   -2.63
1757 VAL   ( 110-)  F   -2.63
2457 LEU   ( 105-)  K   -2.60
4227 LEU   ( 105-)  V   -2.59
1867 LEU   ( 105-)  H   -2.59
1277 LEU   ( 105-)  E   -2.59
 687 LEU   ( 105-)  B   -2.59
3047 LEU   ( 105-)  O   -2.58
  97 LEU   ( 105-)  L   -2.57
3637 LEU   ( 105-)  R   -2.56

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: L

Note: Second generation quality Z-score plot

Chain identifier: S

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: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Water, ion, and hydrogenbond related checks

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.

4745 HOH   ( 574 )  L      O      7.71   59.38   14.47
4749 HOH   ( 578 )  E      O    -60.64  105.16   13.53
4751 HOH   ( 634 )  H      O    -57.55  101.70   48.40
4753 HOH   ( 579 )  K      O   -103.51   60.95    7.62
4759 HOH   ( 646 )  V      O    -44.26   -0.75  -18.11

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.

 148 GLN   ( 156-)  L
 176 ASN   ( 184-)  L
 221 GLN   ( 229-)  L
 230 HIS   ( 238-)  L
 233 ASN   ( 241-)  L
 259 HIS   ( 267-)  L
 269 ASN   ( 277-)  L
 274 HIS   ( 282-)  L
 296 GLN   ( 304-)  L
 393 GLN   ( 401-)  L
 412 ASN   ( 420-)  L
 424 ASN   ( 432-)  L
 492 GLN   (  25-)  S
 496 GLN   (  29-)  S
 738 GLN   ( 156-)  B
 766 ASN   ( 184-)  B
 811 GLN   ( 229-)  B
 820 HIS   ( 238-)  B
 823 ASN   ( 241-)  B
 849 HIS   ( 267-)  B
 859 ASN   ( 277-)  B
 864 HIS   ( 282-)  B
 886 GLN   ( 304-)  B
 983 GLN   ( 401-)  B
1002 ASN   ( 420-)  B
And so on for a total of 114 lines.

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.

  55 THR   (  63-)  L      OG1
  57 THR   (  65-)  L      OG1
  59 THR   (  67-)  L      N
  68 ASN   (  76-)  L      N
  75 ARG   (  83-)  L      NE
 117 PHE   ( 125-)  L      N
 126 ARG   ( 134-)  L      NH2
 151 ARG   ( 159-)  L      NH1
 159 ARG   ( 167-)  L      N
 164 CYS   ( 172-)  L      N
 167 LYS   ( 175-)  L      N
 170 LEU   ( 178-)  L      N
 171 GLY   ( 179-)  L      N
 175 LYS   ( 183-)  L      NZ
 189 LEU   ( 197-)  L      N
 193 LYS   ( 201-)  L      NZ
 197 ASN   ( 205-)  L      ND2
 203 PHE   ( 211-)  L      N
 209 ARG   ( 217-)  L      NH1
 287 ARG   ( 295-)  L      N
 287 ARG   ( 295-)  L      NE
 299 HIS   ( 307-)  L      N
 315 GLY   ( 323-)  L      N
 321 GLY   ( 329-)  L      N
 333 ILE   ( 341-)  L      N
And so on for a total of 328 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.

 260 ASP   ( 268-)  L      OD2
 286 HIS   ( 294-)  L      NE2
 319 HIS   ( 327-)  L      ND1
 850 ASP   ( 268-)  B      OD2
 876 HIS   ( 294-)  B      NE2
 909 HIS   ( 327-)  B      ND1
1440 ASP   ( 268-)  E      OD2
1466 HIS   ( 294-)  E      NE2
1499 HIS   ( 327-)  E      ND1
1605 GLU   ( 433-)  E      OE2
1636 GLU   ( 464-)  E      OE2
1702 HIS   (  55-)  F      ND1
2030 ASP   ( 268-)  H      OD2
2056 HIS   ( 294-)  H      NE2
2089 HIS   ( 327-)  H      ND1
2620 ASP   ( 268-)  K      OD2
2646 HIS   ( 294-)  K      NE2
2679 HIS   ( 327-)  K      ND1
3210 ASP   ( 268-)  O      OD2
3236 HIS   ( 294-)  O      NE2
3269 HIS   ( 327-)  O      ND1
3800 ASP   ( 268-)  R      OD2
3826 HIS   ( 294-)  R      NE2
3859 HIS   ( 327-)  R      ND1
3965 GLU   ( 433-)  R      OE2
4390 ASP   ( 268-)  V      OD2
4416 HIS   ( 294-)  V      NE2
4449 HIS   ( 327-)  V      ND1
4555 GLU   ( 433-)  V      OE2

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.

4745 HOH   ( 509 )  L      O  0.96  K  5
4745 HOH   ( 524 )  L      O  1.13  K  4
4745 HOH   ( 636 )  L      O  0.92  K  4
4747 HOH   ( 518 )  B      O  0.96  K  5
4747 HOH   ( 533 )  B      O  1.13  K  4
4747 HOH   ( 641 )  B      O  1.02  K  4
4749 HOH   ( 514 )  E      O  0.94  K  5
4749 HOH   ( 529 )  E      O  1.13  K  4
4749 HOH   ( 642 )  E      O  1.02  K  4
4751 HOH   ( 478 )  H      O  0.93  K  4
4751 HOH   ( 530 )  H      O  1.02  K  5
4751 HOH   ( 545 )  H      O  1.13  K  4
4753 HOH   ( 514 )  K      O  0.97  K  5
4753 HOH   ( 529 )  K      O  1.13  K  4
4753 HOH   ( 604 )  K      O  0.86  K  4 Ion-B
4753 HOH   ( 642 )  K      O  1.00  K  4
4755 HOH   ( 700 )  O      O  0.94  K  4
4755 HOH   (1158 )  O      O  0.98  K  5
4755 HOH   (1177 )  O      O  1.13  K  4
4757 HOH   ( 478 )  R      O  1.06  K  4
4757 HOH   ( 522 )  R      O  0.90  K  5
4757 HOH   ( 537 )  R      O  1.13  K  4
4757 HOH   ( 552 )  R      O  1.07  K  4
4759 HOH   ( 482 )  V      O  0.92  K  4
4759 HOH   ( 531 )  V      O  1.10  K  5
4759 HOH   ( 546 )  V      O  1.13  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.

  86 GLU   (  94-)  L   H-bonding suggests Gln
 152 ASP   ( 160-)  L   H-bonding suggests Asn; but Alt-Rotamer
 294 ASP   ( 302-)  L   H-bonding suggests Asn
 576 GLU   ( 109-)  S   H-bonding suggests Gln; but Alt-Rotamer
 676 GLU   (  94-)  B   H-bonding suggests Gln
 742 ASP   ( 160-)  B   H-bonding suggests Asn; but Alt-Rotamer
 884 ASP   ( 302-)  B   H-bonding suggests Asn
1166 GLU   ( 109-)  C   H-bonding suggests Gln; but Alt-Rotamer
1266 GLU   (  94-)  E   H-bonding suggests Gln
1332 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
1474 ASP   ( 302-)  E   H-bonding suggests Asn
1756 GLU   ( 109-)  F   H-bonding suggests Gln; but Alt-Rotamer
1856 GLU   (  94-)  H   H-bonding suggests Gln
1922 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
2064 ASP   ( 302-)  H   H-bonding suggests Asn
2346 GLU   ( 109-)  I   H-bonding suggests Gln; but Alt-Rotamer
2446 GLU   (  94-)  K   H-bonding suggests Gln
2512 ASP   ( 160-)  K   H-bonding suggests Asn; but Alt-Rotamer
2654 ASP   ( 302-)  K   H-bonding suggests Asn
2936 GLU   ( 109-)  M   H-bonding suggests Gln; but Alt-Rotamer
3036 GLU   (  94-)  O   H-bonding suggests Gln
3102 ASP   ( 160-)  O   H-bonding suggests Asn; but Alt-Rotamer
3244 ASP   ( 302-)  O   H-bonding suggests Asn
3526 GLU   ( 109-)  P   H-bonding suggests Gln; but Alt-Rotamer
3626 GLU   (  94-)  R   H-bonding suggests Gln
3692 ASP   ( 160-)  R   H-bonding suggests Asn; but Alt-Rotamer
3834 ASP   ( 302-)  R   H-bonding suggests Asn
4116 GLU   ( 109-)  T   H-bonding suggests Gln; but Alt-Rotamer
4216 GLU   (  94-)  V   H-bonding suggests Gln
4282 ASP   ( 160-)  V   H-bonding suggests Asn; but Alt-Rotamer
4424 ASP   ( 302-)  V   H-bonding suggests Asn
4706 GLU   ( 109-)  W   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 :  -0.658
  2nd generation packing quality :  -0.063
  Ramachandran plot appearance   :  -0.904
  chi-1/chi-2 rotamer normality  :  -2.002
  Backbone conformation          :  -0.599

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.507 (tight)
  Bond angles                    :   0.818
  Omega angle restraints         :   0.362 (tight)
  Side chain planarity           :   0.579 (tight)
  Improper dihedral distribution :   1.019
  B-factor distribution          :   0.961
  Inside/Outside distribution    :   1.055

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 :   0.2
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :   0.7
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.507 (tight)
  Bond angles                    :   0.818
  Omega angle restraints         :   0.362 (tight)
  Side chain planarity           :   0.579 (tight)
  Improper dihedral distribution :   1.019
  B-factor distribution          :   0.961
  Inside/Outside distribution    :   1.055
==============

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.