WHAT IF Check report

This file was created 2012-01-31 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 pdb2v63.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    = 121.377  B   = 177.446  C    = 122.568
    Alpha=  90.000  Beta= 117.650  Gamma=  90.000

Dimensions of a reduced cell

    A    = 121.377  B   = 122.568  C    = 177.446
    Alpha=  90.000  Beta=  90.000  Gamma=  62.350

Dimensions of the conventional cell

    A    = 126.283  B   = 208.718  C    = 177.446
    Alpha=  90.000  Beta=  90.000  Gamma=  90.632

Transformation to conventional cell

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

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.535
CA-only RMS fit for the two chains : 0.492

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.570
CA-only RMS fit for the two chains : 0.501

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.198
CA-only RMS fit for the two chains : 0.066

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.226
CA-only RMS fit for the two chains : 0.059

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.494
CA-only RMS fit for the two chains : 0.486

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and F

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.

4853 CAP   ( 476-)  A  -
4859 CAP   ( 477-)  B  -
4865 CAP   ( 477-)  C  -
4872 CAP   ( 477-)  D  -
4878 CAP   ( 477-)  E  -
4883 CAP   ( 477-)  F  -
4887 CAP   ( 477-)  G  -
4914 CAP   ( 477-)  H  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

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.

 949 TYR   (  25-)  C
 965 ARG   (  41-)  C
3725 MME   (   1-)  I
3865 MME   (   1-)  J
3867 VAL   (   3-)  J
4005 MME   (   1-)  K
4145 MME   (   1-)  L
4285 MME   (   1-)  M
4425 MME   (   1-)  N
4491 TYR   (  67-)  N
4565 MME   (   1-)  O
4705 MME   (   1-)  P

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

3406 GLN   ( 156-)  H    0.50

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :200.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Nomenclature related problems

Warning: Leucine nomenclature problem

The leucine residues listed in the table below have their C-delta-1 and C-delta-2 swapped.

 211 LEU   ( 219-)  A
 677 LEU   ( 219-)  B
1143 LEU   ( 219-)  C
1607 LEU   ( 219-)  D
2071 LEU   ( 219-)  E
2537 LEU   ( 219-)  F
3003 LEU   ( 219-)  G
3469 LEU   ( 219-)  H

Warning: Arginine nomenclature problem

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

 179 ARG   ( 187-)  A
 645 ARG   ( 187-)  B
1111 ARG   ( 187-)  C
1575 ARG   ( 187-)  D
2039 ARG   ( 187-)  E
2505 ARG   ( 187-)  F
2971 ARG   ( 187-)  G
3437 ARG   ( 187-)  H

Warning: Tyrosine convention problem

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

1473 TYR   (  85-)  D
2403 TYR   (  85-)  F
2601 TYR   ( 283-)  F
2887 TYR   ( 103-)  G
3775 TYR   (  51-)  I
3791 TYR   (  67-)  I
3915 TYR   (  51-)  J
3931 TYR   (  67-)  J
4055 TYR   (  51-)  K
4071 TYR   (  67-)  K
4195 TYR   (  51-)  L
4211 TYR   (  67-)  L
4335 TYR   (  51-)  M
4351 TYR   (  67-)  M
4475 TYR   (  51-)  N
4491 TYR   (  67-)  N
4615 TYR   (  51-)  O
4631 TYR   (  67-)  O
4755 TYR   (  51-)  P
4771 TYR   (  67-)  P

Warning: Phenylalanine convention problem

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

 394 PHE   ( 402-)  A
 860 PHE   ( 402-)  B
1326 PHE   ( 402-)  C
1790 PHE   ( 402-)  D
2254 PHE   ( 402-)  E
2321 PHE   ( 469-)  E
2720 PHE   ( 402-)  F
3186 PHE   ( 402-)  G
3652 PHE   ( 402-)  H
3719 PHE   ( 469-)  H
3736 PHE   (  12-)  I
3739 PHE   (  15-)  I
3768 PHE   (  44-)  I
3784 PHE   (  60-)  I
3824 PHE   ( 100-)  I
3845 PHE   ( 121-)  I
3856 PHE   ( 132-)  I
3876 PHE   (  12-)  J
3879 PHE   (  15-)  J
3908 PHE   (  44-)  J
3924 PHE   (  60-)  J
3964 PHE   ( 100-)  J
3985 PHE   ( 121-)  J
3996 PHE   ( 132-)  J
4016 PHE   (  12-)  K
And so on for a total of 66 lines.

Warning: Aspartic acid convention problem

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

3855 ASP   ( 131-)  I
3995 ASP   ( 131-)  J
4135 ASP   ( 131-)  K
4275 ASP   ( 131-)  L
4415 ASP   ( 131-)  M
4555 ASP   ( 131-)  N
4695 ASP   ( 131-)  O
4835 ASP   ( 131-)  P

Warning: Glutamic acid convention problem

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

  80 GLU   (  88-)  A
 452 GLU   ( 460-)  A
 546 GLU   (  88-)  B
 918 GLU   ( 460-)  B
1012 GLU   (  88-)  C
1364 GLU   ( 440-)  C
1384 GLU   ( 460-)  C
1476 GLU   (  88-)  D
1848 GLU   ( 460-)  D
1940 GLU   (  88-)  E
2312 GLU   ( 460-)  E
2406 GLU   (  88-)  F
2778 GLU   ( 460-)  F
2872 GLU   (  88-)  G
3244 GLU   ( 460-)  G
3338 GLU   (  88-)  H
3710 GLU   ( 460-)  H
3770 GLU   (  46-)  I
3779 GLU   (  55-)  I
3910 GLU   (  46-)  J
3919 GLU   (  55-)  J
4050 GLU   (  46-)  K
4059 GLU   (  55-)  K
4190 GLU   (  46-)  L
4199 GLU   (  55-)  L
4330 GLU   (  46-)  M
4339 GLU   (  55-)  M
4470 GLU   (  46-)  N
4479 GLU   (  55-)  N
4610 GLU   (  46-)  O
4619 GLU   (  55-)  O
4750 GLU   (  46-)  P
4759 GLU   (  55-)  P

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 193 KCX   ( 201-)  A      CH     CX
 193 KCX   ( 201-)  A      OX1    OQ1
 193 KCX   ( 201-)  A      OX2    OQ2
 659 KCX   ( 201-)  B      CH     CX
 659 KCX   ( 201-)  B      OX1    OQ1
 659 KCX   ( 201-)  B      OX2    OQ2
1125 KCX   ( 201-)  C      CH     CX
1125 KCX   ( 201-)  C      OX1    OQ1
1125 KCX   ( 201-)  C      OX2    OQ2
1589 KCX   ( 201-)  D      CH     CX
1589 KCX   ( 201-)  D      OX1    OQ1
1589 KCX   ( 201-)  D      OX2    OQ2
2053 KCX   ( 201-)  E      CH     CX
2053 KCX   ( 201-)  E      OX1    OQ1
2053 KCX   ( 201-)  E      OX2    OQ2
2519 KCX   ( 201-)  F      CH     CX
2519 KCX   ( 201-)  F      OX1    OQ1
2519 KCX   ( 201-)  F      OX2    OQ2
2985 KCX   ( 201-)  G      CH     CX
2985 KCX   ( 201-)  G      OX1    OQ1
2985 KCX   ( 201-)  G      OX2    OQ2
3451 KCX   ( 201-)  H      CH     CX
3451 KCX   ( 201-)  H      OX1    OQ1
3451 KCX   ( 201-)  H      OX2    OQ2

Geometric checks

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.388
RMS-deviation in bond distances: 0.009

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

 |  0.997208 -0.000055  0.000154|
 | -0.000055  0.997445  0.000087|
 |  0.000154  0.000087  0.997318|
Proposed new scale matrix

 |  0.008261  0.000000  0.004326|
 |  0.000000  0.005650  0.000000|
 | -0.000001  0.000000  0.009236|
With corresponding cell

    A    = 121.035  B   = 176.978  C    = 122.213
    Alpha=  90.001  Beta= 117.631  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 121.377  B   = 177.446  C    = 122.568
    Alpha=  90.000  Beta= 117.650  Gamma=  90.000

Variance: 1153.776
(Under-)estimated Z-score: 25.034

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.

3022 HIS   ( 238-)  G      CG   ND1  CE1 109.65    4.1
3544 HIS   ( 294-)  H      CG   ND1  CE1 109.62    4.0

Warning: Low bond angle variability

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

RMS Z-score for bond angles: 0.580
RMS-deviation in bond angles: 1.176

Error: Nomenclature error(s)

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

  80 GLU   (  88-)  A
 179 ARG   ( 187-)  A
 452 GLU   ( 460-)  A
 546 GLU   (  88-)  B
 645 ARG   ( 187-)  B
 918 GLU   ( 460-)  B
1012 GLU   (  88-)  C
1111 ARG   ( 187-)  C
1364 GLU   ( 440-)  C
1384 GLU   ( 460-)  C
1476 GLU   (  88-)  D
1575 ARG   ( 187-)  D
1848 GLU   ( 460-)  D
1940 GLU   (  88-)  E
2039 ARG   ( 187-)  E
2312 GLU   ( 460-)  E
2406 GLU   (  88-)  F
2505 ARG   ( 187-)  F
2778 GLU   ( 460-)  F
2872 GLU   (  88-)  G
2971 ARG   ( 187-)  G
3244 GLU   ( 460-)  G
3338 GLU   (  88-)  H
3437 ARG   ( 187-)  H
3710 GLU   ( 460-)  H
3770 GLU   (  46-)  I
3779 GLU   (  55-)  I
3855 ASP   ( 131-)  I
3910 GLU   (  46-)  J
3919 GLU   (  55-)  J
3995 ASP   ( 131-)  J
4050 GLU   (  46-)  K
4059 GLU   (  55-)  K
4135 ASP   ( 131-)  K
4190 GLU   (  46-)  L
4199 GLU   (  55-)  L
4275 ASP   ( 131-)  L
4330 GLU   (  46-)  M
4339 GLU   (  55-)  M
4415 ASP   ( 131-)  M
4470 GLU   (  46-)  N
4479 GLU   (  55-)  N
4555 ASP   ( 131-)  N
4610 GLU   (  46-)  O
4619 GLU   (  55-)  O
4695 ASP   ( 131-)  O
4750 GLU   (  46-)  P
4759 GLU   (  55-)  P
4835 ASP   ( 131-)  P

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.

3086 ASP   ( 302-)  G    4.33
 760 ASP   ( 302-)  B    4.31
2154 ASP   ( 302-)  E    4.15
 294 ASP   ( 302-)  A    4.12

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.

4570 PRO   (   6-)  O    -2.5
4430 PRO   (   6-)  N    -2.4
4716 PHE   (  12-)  P    -2.3
4402 ILE   ( 118-)  M    -2.3
3730 PRO   (   6-)  I    -2.3
3870 PRO   (   6-)  J    -2.3
4822 ILE   ( 118-)  P    -2.3
3489 TYR   ( 239-)  H    -2.3
4262 ILE   ( 118-)  L    -2.3
4682 ILE   ( 118-)  O    -2.3
4403 MET   ( 119-)  M    -2.3
3982 ILE   ( 118-)  J    -2.3
4122 ILE   ( 118-)  K    -2.3
3315 THR   (  65-)  H    -2.3
3842 ILE   ( 118-)  I    -2.3
4542 ILE   ( 118-)  N    -2.3
4823 MET   ( 119-)  P    -2.3
4123 MET   ( 119-)  K    -2.3
2849 THR   (  65-)  G    -2.2
4436 PHE   (  12-)  N    -2.2
3514 ILE   ( 264-)  H    -2.2
4683 MET   ( 119-)  O    -2.2
4290 PRO   (   6-)  M    -2.2
4710 PRO   (   6-)  P    -2.2
4150 PRO   (   6-)  L    -2.2
And so on for a total of 86 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.

  15 THR   (  23-)  A  omega poor
  33 ARG   (  41-)  A  omega poor
  54 SER   (  62-)  A  Poor phi/psi
  55 THR   (  63-)  A  Poor phi/psi
 155 ASN   ( 163-)  A  Poor phi/psi
 167 LYS   ( 175-)  A  PRO omega poor
 191 PHE   ( 199-)  A  omega poor
 199 ASN   ( 207-)  A  Poor phi/psi
 255 PRO   ( 263-)  A  omega poor
 289 MET   ( 297-)  A  Poor phi/psi
 293 ILE   ( 301-)  A  omega poor
 323 ALA   ( 331-)  A  Poor phi/psi
 362 SER   ( 370-)  A  Poor phi/psi
 481 THR   (  23-)  B  omega poor
 499 ARG   (  41-)  B  omega poor
 520 SER   (  62-)  B  Poor phi/psi
 521 THR   (  63-)  B  Poor phi/psi
 621 ASN   ( 163-)  B  Poor phi/psi
 633 LYS   ( 175-)  B  PRO omega poor
 657 PHE   ( 199-)  B  omega poor
 665 ASN   ( 207-)  B  Poor phi/psi
 721 PRO   ( 263-)  B  omega poor
 755 MET   ( 297-)  B  Poor phi/psi
 759 ILE   ( 301-)  B  omega poor
 789 ALA   ( 331-)  B  Poor phi/psi
And so on for a total of 177 lines.

Warning: Unusual rotamers

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

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

 737 SER   ( 279-)  B    0.35
1667 SER   ( 279-)  D    0.35
3529 SER   ( 279-)  H    0.35
1203 SER   ( 279-)  C    0.35
 271 SER   ( 279-)  A    0.36
2131 SER   ( 279-)  E    0.36
2597 SER   ( 279-)  F    0.36
3063 SER   ( 279-)  G    0.36

Warning: Unusual backbone conformations

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

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

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

   7 ALA   (  15-)  A      0
  10 LYS   (  18-)  A      0
  15 THR   (  23-)  A      0
  16 TYR   (  24-)  A      0
  17 TYR   (  25-)  A      0
  18 THR   (  26-)  A      0
  38 PRO   (  46-)  A      0
  53 SER   (  61-)  A      0
  54 SER   (  62-)  A      0
  55 THR   (  63-)  A      0
  58 TRP   (  66-)  A      0
  62 TRP   (  70-)  A      0
  66 LEU   (  74-)  A      0
  77 TYR   (  85-)  A      0
  78 ASP   (  86-)  A      0
  83 PRO   (  91-)  A      0
  86 ASP   (  94-)  A      0
  87 ASN   (  95-)  A      0
  88 GLN   (  96-)  A      0
  96 HYP   ( 104-)  A      0
 102 GLU   ( 110-)  A      0
 113 VAL   ( 121-)  A      0
 115 ASN   ( 123-)  A      0
 116 VAL   ( 124-)  A      0
 119 PHE   ( 127-)  A      0
And so on for a total of 1804 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

2655 GLY   ( 337-)  F   2.44   14
 795 GLY   ( 337-)  B   2.43   15
2189 GLY   ( 337-)  E   2.42   14
1261 GLY   ( 337-)  C   2.42   13
3121 GLY   ( 337-)  G   2.41   17
 329 GLY   ( 337-)  A   2.40   15
3587 GLY   ( 337-)  H   2.38   15
1725 GLY   ( 337-)  D   2.36   16
3189 GLY   ( 405-)  G   1.60   80
1793 GLY   ( 405-)  D   1.58   80
2723 GLY   ( 405-)  F   1.56   80
 863 GLY   ( 405-)  B   1.55   80
 397 GLY   ( 405-)  A   1.54   80
1329 GLY   ( 405-)  C   1.53   80
3655 GLY   ( 405-)  H   1.51   80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

3764 PRO   (  40-)  I    0.13 LOW
3904 PRO   (  40-)  J    0.13 LOW
4044 PRO   (  40-)  K    0.19 LOW
4184 PRO   (  40-)  L    0.12 LOW
4324 PRO   (  40-)  M    0.14 LOW
4464 PRO   (  40-)  N    0.14 LOW
4604 PRO   (  40-)  O    0.12 LOW
4744 PRO   (  40-)  P    0.17 LOW

Warning: Unusual PRO puckering phases

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

3513 PRO   ( 263-)  H   -64.2 envelop C-beta (-72 degrees)
3730 PRO   (   6-)  I   -63.1 envelop C-beta (-72 degrees)
3850 PRO   ( 126-)  I  -113.7 envelop C-gamma (-108 degrees)
3870 PRO   (   6-)  J   -64.1 envelop C-beta (-72 degrees)
3990 PRO   ( 126-)  J  -118.2 half-chair C-delta/C-gamma (-126 degrees)
4130 PRO   ( 126-)  K  -115.7 envelop C-gamma (-108 degrees)
4150 PRO   (   6-)  L   -64.4 envelop C-beta (-72 degrees)
4270 PRO   ( 126-)  L  -115.1 envelop C-gamma (-108 degrees)
4290 PRO   (   6-)  M   -65.7 envelop C-beta (-72 degrees)
4410 PRO   ( 126-)  M  -114.0 envelop C-gamma (-108 degrees)
4430 PRO   (   6-)  N   -56.4 half-chair C-beta/C-alpha (-54 degrees)
4570 PRO   (   6-)  O   -64.8 envelop C-beta (-72 degrees)
4690 PRO   ( 126-)  O  -114.5 envelop C-gamma (-108 degrees)
4710 PRO   (   6-)  P   -63.7 envelop C-beta (-72 degrees)
4830 PRO   ( 126-)  P  -112.0 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.

3699 CYS   ( 449-)  H      SG   <->  3709 CYS   ( 459-)  H      SG   0.84    2.61  INTRA
 441 CYS   ( 449-)  A      SG   <->   451 CYS   ( 459-)  A      SG   0.79    2.66  INTRA
2301 CYS   ( 449-)  E      SG   <->  2311 CYS   ( 459-)  E      SG   0.75    2.70  INTRA
3233 CYS   ( 449-)  G      SG   <->  3243 CYS   ( 459-)  G      SG   0.74    2.71  INTRA
 907 CYS   ( 449-)  B      SG   <->   917 CYS   ( 459-)  B      SG   0.74    2.71  INTRA
1373 CYS   ( 449-)  C      SG   <->  1383 CYS   ( 459-)  C      SG   0.74    2.71  INTRA
2767 CYS   ( 449-)  F      SG   <->  2777 CYS   ( 459-)  F      SG   0.73    2.72  INTRA
1837 CYS   ( 449-)  D      SG   <->  1847 CYS   ( 459-)  D      SG   0.70    2.75  INTRA
1555 ARG   ( 167-)  D      NE   <->  4918 HOH   (2116 )  D      O    0.42    2.28  INTRA
1546 GLU   ( 158-)  D      OE2  <->  1713 HIS   ( 325-)  D      NE2  0.36    2.34  INTRA
3548 HIS   ( 298-)  H      ND1  <->  3552 ASP   ( 302-)  H      OD2  0.34    2.36  INTRA
3408 GLU   ( 158-)  H      OE2  <->  3575 HIS   ( 325-)  H      NE2  0.33    2.37  INTRA
 150 GLU   ( 158-)  A      OE2  <->   317 HIS   ( 325-)  A      NE2  0.33    2.37  INTRA
 616 GLU   ( 158-)  B      OE2  <->   783 HIS   ( 325-)  B      NE2  0.33    2.37  INTRA
2010 GLU   ( 158-)  E      OE2  <->  2177 HIS   ( 325-)  E      NE2  0.32    2.38  INTRA
2942 GLU   ( 158-)  G      OE2  <->  3109 HIS   ( 325-)  G      NE2  0.32    2.38  INTRA
2476 GLU   ( 158-)  F      OE2  <->  2643 HIS   ( 325-)  F      NE2  0.31    2.39  INTRA
1082 GLU   ( 158-)  C      OE2  <->  1249 HIS   ( 325-)  C      NE2  0.29    2.41  INTRA
4366 GLY   (  82-)  M      N    <->  4908 EDO   (1142-)  M      C1   0.28    2.82  INTRA BL
3051 HIS   ( 267-)  G      CD2  <->  3061 ASN   ( 277-)  G      ND2  0.27    2.83  INTRA BL
1655 HIS   ( 267-)  D      CD2  <->  1665 ASN   ( 277-)  D      ND2  0.27    2.83  INTRA BL
 259 HIS   ( 267-)  A      CD2  <->   269 ASN   ( 277-)  A      ND2  0.25    2.85  INTRA BL
2877 GLU   (  93-)  G      O    <->  4921 HOH   (2058 )  G      O    0.25    2.15  INTRA
 391 CYS   ( 399-)  A      SG   <->  4915 HOH   (2164 )  A      O    0.25    2.75  INTRA
4226 GLY   (  82-)  L      N    <->  4906 EDO   (1142-)  L      C1   0.25    2.85  INTRA
And so on for a total of 336 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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: G

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: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

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.

4788 ARG   (  84-)  P      -7.41
4228 ARG   (  84-)  L      -7.36
4368 ARG   (  84-)  M      -7.34
3808 ARG   (  84-)  I      -6.92
4088 ARG   (  84-)  K      -6.86
4648 ARG   (  84-)  O      -6.76
4508 ARG   (  84-)  N      -6.76
3948 ARG   (  84-)  J      -6.62
1363 ARG   ( 439-)  C      -6.31
3689 ARG   ( 439-)  H      -5.70
3223 ARG   ( 439-)  G      -5.69
 897 ARG   ( 439-)  B      -5.67
2757 ARG   ( 439-)  F      -5.65
 431 ARG   ( 439-)  A      -5.64
 443 TRP   ( 451-)  A      -5.61
3701 TRP   ( 451-)  H      -5.61
3235 TRP   ( 451-)  G      -5.61
1402 LYS   (  14-)  D      -5.60
3264 LYS   (  14-)  H      -5.60
2798 LYS   (  14-)  G      -5.59
2769 TRP   ( 451-)  F      -5.59
2303 TRP   ( 451-)  E      -5.59
2291 ARG   ( 439-)  E      -5.58
1839 TRP   ( 451-)  D      -5.58
4641 LYS   (  77-)  O      -5.57
And so on for a total of 96 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: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

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: G

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: J

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: 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: 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: N

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

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.

3083 ALA   ( 299-)  G   -2.79
1687 ALA   ( 299-)  D   -2.79
2617 ALA   ( 299-)  F   -2.79
2151 ALA   ( 299-)  E   -2.77
3549 ALA   ( 299-)  H   -2.77
4680 VAL   ( 116-)  O   -2.76
4260 VAL   ( 116-)  L   -2.76
4820 VAL   ( 116-)  P   -2.75
2755 LEU   ( 437-)  F   -2.75
2289 LEU   ( 437-)  E   -2.75
 757 ALA   ( 299-)  B   -2.75
 291 ALA   ( 299-)  A   -2.75
1223 ALA   ( 299-)  C   -2.74
 429 LEU   ( 437-)  A   -2.72
3221 LEU   ( 437-)  G   -2.71
 895 LEU   ( 437-)  B   -2.70
1825 LEU   ( 437-)  D   -2.70
3687 LEU   ( 437-)  H   -2.68
2891 LEU   ( 107-)  G   -2.58
2425 LEU   ( 107-)  F   -2.58
1361 LEU   ( 437-)  C   -2.57
1495 LEU   ( 107-)  D   -2.57
1031 LEU   ( 107-)  C   -2.57
 565 LEU   ( 107-)  B   -2.56
  99 LEU   ( 107-)  A   -2.56
1959 LEU   ( 107-)  E   -2.55
3357 LEU   ( 107-)  H   -2.53

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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: G

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: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Water, ion, and hydrogenbond related checks

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.

4915 HOH   (2233 )  A      O
4917 HOH   (2001 )  C      O
4919 HOH   (2040 )  E      O
4919 HOH   (2249 )  E      O
4920 HOH   (2185 )  F      O
4922 HOH   (2225 )  H      O
4923 HOH   (2051 )  I      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-)  A
 221 GLN   ( 229-)  A
 230 HIS   ( 238-)  A
 233 ASN   ( 241-)  A
 259 HIS   ( 267-)  A
 269 ASN   ( 277-)  A
 296 GLN   ( 304-)  A
 319 HIS   ( 327-)  A
 378 HIS   ( 386-)  A
 412 ASN   ( 420-)  A
 424 ASN   ( 432-)  A
 611 HIS   ( 153-)  B
 614 GLN   ( 156-)  B
 687 GLN   ( 229-)  B
 696 HIS   ( 238-)  B
 699 ASN   ( 241-)  B
 725 HIS   ( 267-)  B
 735 ASN   ( 277-)  B
 762 GLN   ( 304-)  B
 785 HIS   ( 327-)  B
 878 ASN   ( 420-)  B
 890 ASN   ( 432-)  B
1080 GLN   ( 156-)  C
1153 GLN   ( 229-)  C
1162 HIS   ( 238-)  C
And so on for a total of 128 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.

  57 THR   (  65-)  A      OG1
  59 THR   (  67-)  A      N
  88 GLN   (  96-)  A      N
 165 THR   ( 173-)  A      N
 167 LYS   ( 175-)  A      N
 167 LYS   ( 175-)  A      NZ
 170 LEU   ( 178-)  A      N
 171 GLY   ( 179-)  A      N
 203 PHE   ( 211-)  A      N
 231 TYR   ( 239-)  A      OH
 238 THR   ( 246-)  A      N
 287 ARG   ( 295-)  A      NE
 287 ARG   ( 295-)  A      NH1
 295 ARG   ( 303-)  A      NE
 299 HIS   ( 307-)  A      N
 324 VAL   ( 332-)  A      N
 371 SER   ( 379-)  A      N
 373 GLY   ( 381-)  A      N
 393 GLN   ( 401-)  A      NE2
 396 GLY   ( 404-)  A      N
 405 ASN   ( 413-)  A      ND2
 446 GLU   ( 454-)  A      N
 510 GLU   (  52-)  B      N
 523 THR   (  65-)  B      OG1
 525 THR   (  67-)  B      N
And so on for a total of 239 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.

 145 HIS   ( 153-)  A      NE2
 260 ASP   ( 268-)  A      OD1
 284 HIS   ( 292-)  A      NE2
 726 ASP   ( 268-)  B      OD1
 726 ASP   ( 268-)  B      OD2
 750 HIS   ( 292-)  B      NE2
 844 HIS   ( 386-)  B      NE2
1077 HIS   ( 153-)  C      NE2
1192 ASP   ( 268-)  C      OD1
1216 HIS   ( 292-)  C      NE2
1656 ASP   ( 268-)  D      OD1
1680 HIS   ( 292-)  D      NE2
1924 ASP   (  72-)  E      OD1
2120 ASP   ( 268-)  E      OD1
2120 ASP   ( 268-)  E      OD2
2144 HIS   ( 292-)  E      NE2
2586 ASP   ( 268-)  F      OD1
2586 ASP   ( 268-)  F      OD2
2610 HIS   ( 292-)  F      NE2
3052 ASP   ( 268-)  G      OD1
3052 ASP   ( 268-)  G      OD2
3076 HIS   ( 292-)  G      NE2
3170 HIS   ( 386-)  G      NE2
3518 ASP   ( 268-)  H      OD1
3636 HIS   ( 386-)  H      NE2
3651 GLN   ( 401-)  H      OE1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

4915 HOH   (2086 )  A      O  1.11  K  4 Ion-B NCS 7/7
4915 HOH   (2130 )  A      O  0.85  K  5 NCS 7/7
4915 HOH   (2180 )  A      O  0.88  K  4 NCS 7/7
4915 HOH   (2241 )  A      O  1.10  K  4 Ion-B NCS 3/3
4916 HOH   (2064 )  B      O  0.96  K  4 Ion-B NCS 7/7
4916 HOH   (2163 )  B      O  0.87  K  4 NCS 7/7
4917 HOH   (2035 )  C      O  0.89  K  5 NCS 6/6
4917 HOH   (2125 )  C      O  1.02  K  4 NCS 7/7
4918 HOH   (2122 )  D      O  1.02  K  4 NCS 7/7
4918 HOH   (2129 )  D      O  0.89  K  4 Ion-B NCS 6/6
4919 HOH   (2190 )  E      O  1.04  K  4 Ion-B NCS 3/3
4919 HOH   (2216 )  E      O  1.02  K  4 Ion-B NCS 5/5
4920 HOH   (2158 )  F      O  0.85  K  4 NCS 7/7
4920 HOH   (2161 )  F      O  0.92  K  4 NCS 7/7
4921 HOH   (2066 )  G      O  0.88  K  4 Ion-B NCS 7/7
4921 HOH   (2154 )  G      O  1.11  K  4 NCS 6/6
4921 HOH   (2224 )  G      O  1.05  K  4 Ion-B NCS 3/3
4922 HOH   (2122 )  H      O  1.10  K  4 NCS 7/7
4923 HOH   (2027 )  I      O  0.94  K  4 NCS 7/7
4924 HOH   (2070 )  J      O  0.95  K  4 ION-B NCS 5/5
4925 HOH   (2035 )  K      O  0.95  K  4 NCS 7/7
4926 HOH   (2034 )  L      O  0.91  K  4 NCS 6/6
4928 HOH   (2021 )  N      O  0.95  K  4 NCS 7/7
4930 HOH   (2005 )  P      O  0.93  K  7 ION-B
4930 HOH   (2028 )  P      O  0.96  K  4 NCS 7/7

Warning: Possible wrong residue type

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

  44 GLU   (  52-)  A   H-bonding suggests Gln; Ligand-contact
 260 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 294 ASP   ( 302-)  A   H-bonding suggests Asn
 618 ASP   ( 160-)  B   H-bonding suggests Asn; but Alt-Rotamer
 726 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 760 ASP   ( 302-)  B   H-bonding suggests Asn
1192 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1226 ASP   ( 302-)  C   H-bonding suggests Asn
1397 ASP   ( 473-)  C   H-bonding suggests Asn; Ligand-contact
1656 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
1690 ASP   ( 302-)  D   H-bonding suggests Asn
2120 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
2370 GLU   (  52-)  F   H-bonding suggests Gln; Ligand-contact
2478 ASP   ( 160-)  F   H-bonding suggests Asn; but Alt-Rotamer
2586 ASP   ( 268-)  F   H-bonding suggests Asn; but Alt-Rotamer
2620 ASP   ( 302-)  F   H-bonding suggests Asn
2836 GLU   (  52-)  G   H-bonding suggests Gln; Ligand-contact
3052 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
3086 ASP   ( 302-)  G   H-bonding suggests Asn
3257 ASP   ( 473-)  G   H-bonding suggests Asn; Ligand-contact
3302 GLU   (  52-)  H   H-bonding suggests Gln; Ligand-contact
3518 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
3552 ASP   ( 302-)  H   H-bonding suggests Asn; Ligand-contact
3779 GLU   (  55-)  I   H-bonding suggests Gln; Ligand-contact
3919 GLU   (  55-)  J   H-bonding suggests Gln; Ligand-contact
4059 GLU   (  55-)  K   H-bonding suggests Gln; Ligand-contact
4199 GLU   (  55-)  L   H-bonding suggests Gln; Ligand-contact
4339 GLU   (  55-)  M   H-bonding suggests Gln; Ligand-contact
4479 GLU   (  55-)  N   H-bonding suggests Gln; Ligand-contact
4619 GLU   (  55-)  O   H-bonding suggests Gln; Ligand-contact
4759 GLU   (  55-)  P   H-bonding suggests Gln; Ligand-contact

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 :  -0.645
  2nd generation packing quality :  -0.178
  Ramachandran plot appearance   :  -0.211
  chi-1/chi-2 rotamer normality  :  -0.673
  Backbone conformation          :  -0.473

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.388 (tight)
  Bond angles                    :   0.580 (tight)
  Omega angle restraints         :   1.019
  Side chain planarity           :   0.387 (tight)
  Improper dihedral distribution :   0.583
  B-factor distribution          :   0.392
  Inside/Outside distribution    :   1.050

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.388 (tight)
  Bond angles                    :   0.580 (tight)
  Omega angle restraints         :   1.019
  Side chain planarity           :   0.387 (tight)
  Improper dihedral distribution :   0.583
  B-factor distribution          :   0.392
  Inside/Outside distribution    :   1.050
==============

WHAT IF
    G.Vriend,
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    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.