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 pdb1rco.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    = 220.600  B   = 221.700  C    = 115.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 115.300  B   = 220.600  C    = 221.700
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 221.700  B   = 220.600  C    = 115.300
    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 XDP   ( 476-)  L  -
4738 XDP   ( 476-)  B  -
4739 XDP   ( 476-)  E  -
4740 XDP   ( 476-)  H  -
4741 XDP   ( 476-)  K  -
4742 XDP   ( 476-)  O  -
4743 XDP   ( 476-)  R  -
4744 XDP   ( 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: 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) :279.000

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: 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

 |  1.002911 -0.000004 -0.000007|
 | -0.000004  1.002910 -0.000015|
 | -0.000007 -0.000015  1.003083|
Proposed new scale matrix

 |  0.004520  0.000000  0.000000|
 |  0.000000  0.004498  0.000000|
 |  0.000000  0.000000  0.008646|
With corresponding cell

    A    = 221.247  B   = 222.325  C    = 115.656
    Alpha=  90.002  Beta=  90.002  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 220.600  B   = 221.700  C    = 115.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1413.281
(Under-)estimated Z-score: 27.706

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.

  17 TYR   (  25-)  L      N    CA   C    99.94   -4.0
  28 ILE   (  36-)  L      N    CA   C    99.19   -4.3
  67 THR   (  75-)  L      C    CA   CB   99.86   -5.4
  71 ARG   (  79-)  L      CB   CG   CD  104.97   -4.6
 145 HIS   ( 153-)  L      CG   ND1  CE1 109.70    4.1
 191 PHE   ( 199-)  L      C    CA   CB  101.60   -4.5
 192 THR   ( 200-)  L      N    CA   C    99.96   -4.0
 230 HIS   ( 238-)  L      CG   ND1  CE1 109.95    4.3
 255 PRO   ( 263-)  L      N    CA   C   123.28    4.6
 259 HIS   ( 267-)  L      CG   ND1  CE1 110.00    4.4
 274 HIS   ( 282-)  L      CG   ND1  CE1 109.74    4.1
 290 HIS   ( 298-)  L      CG   ND1  CE1 109.60    4.0
 299 HIS   ( 307-)  L      CG   ND1  CE1 109.70    4.1
 302 HIS   ( 310-)  L      CG   ND1  CE1 109.67    4.1
 317 HIS   ( 325-)  L      C    CA   CB   99.99   -5.3
 317 HIS   ( 325-)  L      CG   ND1  CE1 109.62    4.0
 401 HIS   ( 409-)  L      CG   ND1  CE1 109.61    4.0
 522 HIS   (  55-)  S      CG   ND1  CE1 109.75    4.1
 565 PHE   (  98-)  S      N    CA   C    97.85   -4.8
 572 ASP   ( 105-)  S      N    CA   C    98.99   -4.4
 607 TYR   (  25-)  B      N    CA   C    99.95   -4.0
 618 ILE   (  36-)  B      N    CA   C    99.20   -4.3
 657 THR   (  75-)  B      C    CA   CB   99.90   -5.4
 661 ARG   (  79-)  B      CB   CG   CD  104.98   -4.6
 735 HIS   ( 153-)  B      CG   ND1  CE1 109.65    4.1
And so on for a total of 164 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.

3834 ASP   ( 302-)  R    6.78
3244 ASP   ( 302-)  O    6.76
2064 ASP   ( 302-)  H    6.76
 294 ASP   ( 302-)  L    6.75
4424 ASP   ( 302-)  V    6.75
2654 ASP   ( 302-)  K    6.75
 884 ASP   ( 302-)  B    6.75
1474 ASP   ( 302-)  E    6.74
 706 VAL   ( 124-)  B    5.62
1886 VAL   ( 124-)  H    5.61
3066 VAL   ( 124-)  O    5.61
3656 VAL   ( 124-)  R    5.60
4246 VAL   ( 124-)  V    5.59
 116 VAL   ( 124-)  L    5.59
2476 VAL   ( 124-)  K    5.59
1296 VAL   ( 124-)  E    5.59
4391 TYR   ( 269-)  V    5.47
 851 TYR   ( 269-)  B    5.47
2621 TYR   ( 269-)  K    5.46
 261 TYR   ( 269-)  L    5.46
1441 TYR   ( 269-)  E    5.46
3211 TYR   ( 269-)  O    5.45
2031 TYR   ( 269-)  H    5.44
3801 TYR   ( 269-)  R    5.44
3882 ARG   ( 350-)  R    5.34
And so on for a total of 143 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 : 1.715

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.

2968 THR   (  26-)  O    -2.7
2378 THR   (  26-)  K    -2.7
1788 THR   (  26-)  H    -2.7
  18 THR   (  26-)  L    -2.7
 608 THR   (  26-)  B    -2.7
1198 THR   (  26-)  E    -2.7
3558 THR   (  26-)  R    -2.7
4148 THR   (  26-)  V    -2.7
3901 VAL   ( 369-)  R    -2.6
2721 VAL   ( 369-)  K    -2.6
3311 VAL   ( 369-)  O    -2.6
 951 VAL   ( 369-)  B    -2.6
2131 VAL   ( 369-)  H    -2.6
1541 VAL   ( 369-)  E    -2.6
4491 VAL   ( 369-)  V    -2.6
 361 VAL   ( 369-)  L    -2.6
1066 LEU   (   9-)  C    -2.5
1656 LEU   (   9-)  F    -2.5
2836 LEU   (   9-)  M    -2.5
2246 LEU   (   9-)  I    -2.5
3426 LEU   (   9-)  P    -2.5
4016 LEU   (   9-)  T    -2.5
 476 LEU   (   9-)  S    -2.5
4606 LEU   (   9-)  W    -2.5
3582 PRO   (  50-)  R    -2.5
And so on for a total of 120 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.

   2 SER   (  10-)  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
 545 THR   (  78-)  S  Poor phi/psi
 592 SER   (  10-)  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
1070 GLU   (  13-)  C  Poor phi/psi
1072 LEU   (  15-)  C  Poor phi/psi
And so on for a total of 112 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
  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
  68 ASN   (  76-)  L      0
  77 TYR   (  85-)  L      0
  80 GLU   (  88-)  L      0
  83 ALA   (  91-)  L      0
  86 GLU   (  94-)  L      0
  99 LEU   ( 107-)  L      0
 102 GLU   ( 110-)  L      0
 112 ILE   ( 120-)  L      0
 113 VAL   ( 121-)  L      0
 115 ASN   ( 123-)  L      0
 119 PHE   ( 127-)  L      0
 123 ARG   ( 131-)  L      0
 124 ALA   ( 132-)  L      0
And so on for a total of 1756 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 : 1.936

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!

 919 GLY   ( 337-)  B   2.25   16
2689 GLY   ( 337-)  K   2.25   16
3869 GLY   ( 337-)  R   2.25   16
2099 GLY   ( 337-)  H   2.25   16
3279 GLY   ( 337-)  O   2.25   16
4459 GLY   ( 337-)  V   2.25   16
 329 GLY   ( 337-)  L   2.25   16
1509 GLY   ( 337-)  E   2.25   16
2402 PRO   (  50-)  K   1.72   17
  42 PRO   (  50-)  L   1.72   17
 632 PRO   (  50-)  B   1.72   17
2992 PRO   (  50-)  O   1.72   17
3582 PRO   (  50-)  R   1.72   17
4172 PRO   (  50-)  V   1.72   17
1222 PRO   (  50-)  E   1.68   18
1812 PRO   (  50-)  H   1.68   18

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]

 380 PRO   ( 388-)  L    0.46 HIGH
 970 PRO   ( 388-)  B    0.46 HIGH
1560 PRO   ( 388-)  E    0.46 HIGH
2150 PRO   ( 388-)  H    0.46 HIGH
2740 PRO   ( 388-)  K    0.46 HIGH
3330 PRO   ( 388-)  O    0.46 HIGH
3920 PRO   ( 388-)  R    0.46 HIGH
4510 PRO   ( 388-)  V    0.46 HIGH

Warning: Unusual PRO puckering phases

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

  36 PRO   (  44-)  L    48.7 half-chair C-delta/C-gamma (54 degrees)
  96 PRO   ( 104-)  L  -123.0 half-chair C-delta/C-gamma (-126 degrees)
 462 PRO   ( 470-)  L  -115.5 envelop C-gamma (-108 degrees)
 526 PRO   (  59-)  S  -137.4 envelop C-delta (-144 degrees)
 547 PRO   (  80-)  S  -115.5 envelop C-gamma (-108 degrees)
 626 PRO   (  44-)  B    48.7 half-chair C-delta/C-gamma (54 degrees)
 686 PRO   ( 104-)  B  -123.0 half-chair C-delta/C-gamma (-126 degrees)
1052 PRO   ( 470-)  B  -115.4 envelop C-gamma (-108 degrees)
1116 PRO   (  59-)  C  -137.3 envelop C-delta (-144 degrees)
1137 PRO   (  80-)  C  -115.5 envelop C-gamma (-108 degrees)
1216 PRO   (  44-)  E    48.8 half-chair C-delta/C-gamma (54 degrees)
1276 PRO   ( 104-)  E  -123.0 half-chair C-delta/C-gamma (-126 degrees)
1642 PRO   ( 470-)  E  -115.5 envelop C-gamma (-108 degrees)
1706 PRO   (  59-)  F  -137.3 envelop C-delta (-144 degrees)
1727 PRO   (  80-)  F  -115.6 envelop C-gamma (-108 degrees)
1806 PRO   (  44-)  H    48.8 half-chair C-delta/C-gamma (54 degrees)
1866 PRO   ( 104-)  H  -123.0 half-chair C-delta/C-gamma (-126 degrees)
2232 PRO   ( 470-)  H  -115.5 envelop C-gamma (-108 degrees)
2296 PRO   (  59-)  I  -137.4 envelop C-delta (-144 degrees)
2317 PRO   (  80-)  I  -115.5 envelop C-gamma (-108 degrees)
2396 PRO   (  44-)  K    48.7 half-chair C-delta/C-gamma (54 degrees)
2456 PRO   ( 104-)  K  -123.0 half-chair C-delta/C-gamma (-126 degrees)
2822 PRO   ( 470-)  K  -115.5 envelop C-gamma (-108 degrees)
2886 PRO   (  59-)  M  -137.2 envelop C-delta (-144 degrees)
2907 PRO   (  80-)  M  -115.5 envelop C-gamma (-108 degrees)
2986 PRO   (  44-)  O    48.8 half-chair C-delta/C-gamma (54 degrees)
3046 PRO   ( 104-)  O  -123.0 half-chair C-delta/C-gamma (-126 degrees)
3412 PRO   ( 470-)  O  -115.5 envelop C-gamma (-108 degrees)
3476 PRO   (  59-)  P  -137.4 envelop C-delta (-144 degrees)
3497 PRO   (  80-)  P  -115.5 envelop C-gamma (-108 degrees)
3576 PRO   (  44-)  R    48.8 half-chair C-delta/C-gamma (54 degrees)
3636 PRO   ( 104-)  R  -123.0 half-chair C-delta/C-gamma (-126 degrees)
4002 PRO   ( 470-)  R  -115.5 envelop C-gamma (-108 degrees)
4066 PRO   (  59-)  T  -137.3 envelop C-delta (-144 degrees)
4087 PRO   (  80-)  T  -115.6 envelop C-gamma (-108 degrees)
4166 PRO   (  44-)  V    48.7 half-chair C-delta/C-gamma (54 degrees)
4226 PRO   ( 104-)  V  -123.0 half-chair C-delta/C-gamma (-126 degrees)
4592 PRO   ( 470-)  V  -115.5 envelop C-gamma (-108 degrees)
4656 PRO   (  59-)  W  -137.4 envelop C-delta (-144 degrees)
4677 PRO   (  80-)  W  -115.6 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

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

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

  75 ARG   (  83-)  L      NH1  <->  4745 HOH   ( 588 )  L      O    0.49    2.21  INTRA
3025 ARG   (  83-)  O      NH1  <->  4755 HOH   (1338 )  O      O    0.49    2.21  INTRA
2435 ARG   (  83-)  K      NH1  <->  4753 HOH   (1100 )  K      O    0.49    2.21  INTRA
3615 ARG   (  83-)  R      NH1  <->  4757 HOH   ( 601 )  R      O    0.49    2.21  INTRA
 665 ARG   (  83-)  B      NH1  <->  4747 HOH   ( 592 )  B      O    0.49    2.21  INTRA
1255 ARG   (  83-)  E      NH1  <->  4749 HOH   ( 596 )  E      O    0.49    2.21  INTRA
1845 ARG   (  83-)  H      NH1  <->  4751 HOH   ( 603 )  H      O    0.49    2.21  INTRA
4205 ARG   (  83-)  V      NH1  <->  4759 HOH   ( 611 )  V      O    0.49    2.21  INTRA
 592 SER   (  10-)  B      O    <->  1723 GLY   (  76-)  F      N    0.34    2.36  INTRA BF
1133 GLY   (  76-)  C      N    <->  1182 SER   (  10-)  E      O    0.31    2.39  INTRA BF
3493 GLY   (  76-)  P      N    <->  3542 SER   (  10-)  R      O    0.29    2.41  INTRA BF
2952 SER   (  10-)  O      OG   <->  4083 GLY   (  76-)  T      N    0.27    2.43  INTRA BF
 592 SER   (  10-)  B      OG   <->  1723 GLY   (  76-)  F      N    0.27    2.43  INTRA BF
 543 GLY   (  76-)  S      N    <->  4132 SER   (  10-)  V      OG   0.25    2.45  INTRA BF
3660 LYS   ( 128-)  R      NZ   <->  4455 GLY   ( 333-)  V      O    0.24    2.46  INTRA
 783 LYS   ( 201-)  B      NZ   <->   876 HIS   ( 294-)  B      NE2  0.24    2.76  INTRA BL
3143 LYS   ( 201-)  O      NZ   <->  3236 HIS   ( 294-)  O      NE2  0.24    2.76  INTRA BL
2553 LYS   ( 201-)  K      NZ   <->  2646 HIS   ( 294-)  K      NE2  0.24    2.76  INTRA BL
1373 LYS   ( 201-)  E      NZ   <->  1466 HIS   ( 294-)  E      NE2  0.24    2.76  INTRA BL
 193 LYS   ( 201-)  L      NZ   <->   286 HIS   ( 294-)  L      NE2  0.24    2.76  INTRA BL
1963 LYS   ( 201-)  H      NZ   <->  2056 HIS   ( 294-)  H      NE2  0.24    2.76  INTRA BL
4323 LYS   ( 201-)  V      NZ   <->  4416 HIS   ( 294-)  V      NE2  0.23    2.77  INTRA BL
3733 LYS   ( 201-)  R      NZ   <->  3826 HIS   ( 294-)  R      NE2  0.23    2.77  INTRA BL
4759 HOH   ( 486 )  V      O    <->  4759 HOH   ( 651 )  V      O    0.23    1.97  INTRA
1724 CYS   (  77-)  F      SG   <->  1729 GLN   (  82-)  F      OE1  0.23    2.62  INTRA BF
And so on for a total of 512 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      -6.37
4253 ARG   ( 131-)  V      -6.34
 123 ARG   ( 131-)  L      -6.34
 713 ARG   ( 131-)  B      -6.33
2483 ARG   ( 131-)  K      -6.32
1893 ARG   ( 131-)  H      -6.31
1303 ARG   ( 131-)  E      -6.31
3073 ARG   ( 131-)  O      -6.30
 731 GLN   ( 149-)  B      -6.06
1321 GLN   ( 149-)  E      -6.06
1911 GLN   ( 149-)  H      -6.06
3681 GLN   ( 149-)  R      -6.06
 141 GLN   ( 149-)  L      -6.06
3091 GLN   ( 149-)  O      -6.05
2501 GLN   ( 149-)  K      -6.05
4271 GLN   ( 149-)  V      -6.05
2201 ARG   ( 439-)  H      -5.78
1021 ARG   ( 439-)  B      -5.78
3971 ARG   ( 439-)  R      -5.78
2791 ARG   ( 439-)  K      -5.78
3381 ARG   ( 439-)  O      -5.78
1611 ARG   ( 439-)  E      -5.78
4561 ARG   ( 439-)  V      -5.78
 431 ARG   ( 439-)  L      -5.78
1776 LYS   (  14-)  H      -5.62
And so on for a total of 82 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   -2.83
 881 ALA   ( 299-)  B   -2.81
3831 ALA   ( 299-)  R   -2.79
3241 ALA   ( 299-)  O   -2.79
 291 ALA   ( 299-)  L   -2.79
1471 ALA   ( 299-)  E   -2.77
2061 ALA   ( 299-)  H   -2.76
2651 ALA   ( 299-)  K   -2.76
1167 VAL   ( 110-)  C   -2.65
 577 VAL   ( 110-)  S   -2.65
2347 VAL   ( 110-)  I   -2.65
2937 VAL   ( 110-)  M   -2.65
1757 VAL   ( 110-)  F   -2.65
3527 VAL   ( 110-)  P   -2.65
4707 VAL   ( 110-)  W   -2.65
4117 VAL   ( 110-)  T   -2.65

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.

4749 HOH   ( 602 )  E      O    -50.01  100.13   12.45
4755 HOH   (1347 )  O      O   -106.82   39.84   46.88

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

4747 HOH   ( 555 )  B      O
4751 HOH   ( 566 )  H      O
4753 HOH   (1049 )  K      O
4757 HOH   ( 564 )  R      O
4759 HOH   ( 573 )  V      O

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
 155 ASN   ( 163-)  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
 378 HIS   ( 386-)  L
 412 ASN   ( 420-)  L
 424 ASN   ( 432-)  L
 492 GLN   (  25-)  S
 496 GLN   (  29-)  S
 515 HIS   (  48-)  S
 524 ASN   (  57-)  S
 738 GLN   ( 156-)  B
 745 ASN   ( 163-)  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
And so on for a total of 131 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.

  43 GLU   (  51-)  L      N
  57 THR   (  65-)  L      OG1
  59 THR   (  67-)  L      N
  75 ARG   (  83-)  L      NE
  88 GLN   (  96-)  L      N
 151 ARG   ( 159-)  L      NH1
 159 ARG   ( 167-)  L      N
 165 THR   ( 173-)  L      N
 167 LYS   ( 175-)  L      N
 167 LYS   ( 175-)  L      NZ
 170 LEU   ( 178-)  L      N
 171 GLY   ( 179-)  L      N
 199 ASN   ( 207-)  L      ND2
 203 PHE   ( 211-)  L      N
 209 ARG   ( 217-)  L      NH1
 231 TYR   ( 239-)  L      OH
 238 THR   ( 246-)  L      N
 287 ARG   ( 295-)  L      NE
 288 ALA   ( 296-)  L      N
 295 ARG   ( 303-)  L      NE
 315 GLY   ( 323-)  L      N
 326 LYS   ( 334-)  L      NZ
 333 ILE   ( 341-)  L      N
 361 VAL   ( 369-)  L      N
 371 SER   ( 379-)  L      N
And so on for a total of 279 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.

 196 GLU   ( 204-)  L      OE1
 260 ASP   ( 268-)  L      OD1
 260 ASP   ( 268-)  L      OD2
 319 HIS   ( 327-)  L      ND1
 393 GLN   ( 401-)  L      OE1
 786 GLU   ( 204-)  B      OE1
 850 ASP   ( 268-)  B      OD1
 909 HIS   ( 327-)  B      ND1
 983 GLN   ( 401-)  B      OE1
1440 ASP   ( 268-)  E      OD1
1440 ASP   ( 268-)  E      OD2
1499 HIS   ( 327-)  E      ND1
1573 GLN   ( 401-)  E      OE1
1966 GLU   ( 204-)  H      OE1
2030 ASP   ( 268-)  H      OD1
2030 ASP   ( 268-)  H      OD2
2089 HIS   ( 327-)  H      ND1
2163 GLN   ( 401-)  H      OE1
2556 GLU   ( 204-)  K      OE1
2620 ASP   ( 268-)  K      OD1
2679 HIS   ( 327-)  K      ND1
2753 GLN   ( 401-)  K      OE1
3146 GLU   ( 204-)  O      OE1
3210 ASP   ( 268-)  O      OD1
3210 ASP   ( 268-)  O      OD2
3269 HIS   ( 327-)  O      ND1
3343 GLN   ( 401-)  O      OE1
3736 GLU   ( 204-)  R      OE1
3800 ASP   ( 268-)  R      OD1
3800 ASP   ( 268-)  R      OD2
3824 HIS   ( 292-)  R      NE2
3933 GLN   ( 401-)  R      OE1
4275 HIS   ( 153-)  V      ND1
4326 GLU   ( 204-)  V      OE1
4390 ASP   ( 268-)  V      OD1
4449 HIS   ( 327-)  V      ND1
4523 GLN   ( 401-)  V      OE1

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   ( 498 )  L      O  0.89  K  4
4745 HOH   ( 510 )  L      O  1.13  K  4
4745 HOH   ( 582 )  L      O  1.14  K  4
4745 HOH   ( 607 )  L      O  0.91  K  4
4745 HOH   ( 664 )  L      O  1.10 NA  5 *2 (or CA) Ion-B
4746 HOH   ( 162 )  S      O  0.89 NA  4 *2 ION-B
4747 HOH   ( 505 )  B      O  0.89  K  4
4747 HOH   ( 516 )  B      O  1.12  K  4
4747 HOH   ( 586 )  B      O  1.14  K  4
4747 HOH   ( 611 )  B      O  0.93  K  4
4747 HOH   ( 667 )  B      O  1.06 NA  5 *2 Ion-B
4748 HOH   ( 920 )  C      O  0.88 NA  4 *2 ION-B
4749 HOH   ( 506 )  E      O  0.89  K  4
4749 HOH   ( 590 )  E      O  1.15  K  4
4749 HOH   ( 615 )  E      O  0.92  K  4
4749 HOH   ( 670 )  E      O  1.02 NA  5 *2 Ion-B
4750 HOH   ( 127 )  F      O  0.89 NA  4 *2 ION-B
4751 HOH   ( 479 )  H      O  1.07 NA  5 *2 Ion-B
4751 HOH   ( 512 )  H      O  0.89  K  4
4751 HOH   ( 524 )  H      O  1.13  K  4
4751 HOH   ( 597 )  H      O  1.14  K  4
4751 HOH   ( 622 )  H      O  0.94  K  4
4752 HOH   (1396 )  I      O  0.91 NA  4 *2 ION-B
4753 HOH   ( 979 )  K      O  0.89  K  4
4753 HOH   (1093 )  K      O  1.15  K  4
4753 HOH   (1125 )  K      O  0.91  K  4
4753 HOH   (1492 )  K      O  1.10 NA  5 *2 (or CA) Ion-B
4754 HOH   ( 682 )  M      O  0.93 NA  4 *2 ION-B
4755 HOH   ( 778 )  O      O  1.10 NA  5 *2 (or CA) Ion-B
4755 HOH   (1217 )  O      O  0.89  K  4
4755 HOH   (1232 )  O      O  1.14  K  4
4755 HOH   (1331 )  O      O  1.14  K  4
4755 HOH   (1363 )  O      O  0.90  K  4
4757 HOH   ( 479 )  R      O  1.00 NA  5 *2 Ion-B
4757 HOH   ( 511 )  R      O  0.89  K  4
4757 HOH   ( 522 )  R      O  1.14  K  4
4757 HOH   ( 595 )  R      O  1.14  K  4
4757 HOH   ( 620 )  R      O  0.92  K  4
4758 HOH   (1158 )  T      O  0.92 NA  4 *2 ION-B
4759 HOH   ( 486 )  V      O  0.96 CA  5 (or NA *2) Ion-B
4759 HOH   ( 520 )  V      O  0.89  K  4
4759 HOH   ( 532 )  V      O  1.08  K  4
4759 HOH   ( 605 )  V      O  1.14  K  4
4759 HOH   ( 630 )  V      O  1.00  K  4
4760 HOH   ( 444 )  W      O  0.84 NA  4 *2 ION-B

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.

 152 ASP   ( 160-)  L   H-bonding suggests Asn; but Alt-Rotamer
 260 ASP   ( 268-)  L   H-bonding suggests Asn; but Alt-Rotamer
 576 GLU   ( 109-)  S   H-bonding suggests Gln; but Alt-Rotamer
 742 ASP   ( 160-)  B   H-bonding suggests Asn; but Alt-Rotamer
 850 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
1166 GLU   ( 109-)  C   H-bonding suggests Gln; but Alt-Rotamer
1332 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
1440 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
1756 GLU   ( 109-)  F   H-bonding suggests Gln; but Alt-Rotamer
1922 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
2030 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
2346 GLU   ( 109-)  I   H-bonding suggests Gln; but Alt-Rotamer
2512 ASP   ( 160-)  K   H-bonding suggests Asn; but Alt-Rotamer
2620 ASP   ( 268-)  K   H-bonding suggests Asn; but Alt-Rotamer
2936 GLU   ( 109-)  M   H-bonding suggests Gln; but Alt-Rotamer
3102 ASP   ( 160-)  O   H-bonding suggests Asn; but Alt-Rotamer
3210 ASP   ( 268-)  O   H-bonding suggests Asn; but Alt-Rotamer
3526 GLU   ( 109-)  P   H-bonding suggests Gln; but Alt-Rotamer
3692 ASP   ( 160-)  R   H-bonding suggests Asn; but Alt-Rotamer
3800 ASP   ( 268-)  R   H-bonding suggests Asn; but Alt-Rotamer
4116 GLU   ( 109-)  T   H-bonding suggests Gln; but Alt-Rotamer
4282 ASP   ( 160-)  V   H-bonding suggests Asn; but Alt-Rotamer
4390 ASP   ( 268-)  V   H-bonding suggests Asn; but Alt-Rotamer
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 :  -1.087
  2nd generation packing quality :  -0.657
  Ramachandran plot appearance   :  -1.434
  chi-1/chi-2 rotamer normality  :  -2.175
  Backbone conformation          :  -0.698

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.618 (tight)
  Bond angles                    :   0.869
  Omega angle restraints         :   0.352 (tight)
  Side chain planarity           :   0.611 (tight)
  Improper dihedral distribution :   1.081
  B-factor distribution          :   0.485
  Inside/Outside distribution    :   1.052

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.618 (tight)
  Bond angles                    :   0.869
  Omega angle restraints         :   0.352 (tight)
  Side chain planarity           :   0.611 (tight)
  Improper dihedral distribution :   1.081
  B-factor distribution          :   0.485
  Inside/Outside distribution    :   1.052
==============

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.