WHAT IF Check report

This file was created 2011-12-17 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 pdb2q47.ent

Checks that need to be done early-on in validation

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 : 1.089
CA-only RMS fit for the two chains : 0.788

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 A

All-atom RMS fit for the two chains : 1.064
CA-only RMS fit for the two chains : 0.836

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 A

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 : 1.129
CA-only RMS fit for the two chains : 0.822

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 A

All-atom RMS fit for the two chains : 1.086
CA-only RMS fit for the two chains : 0.837

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 A

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 : 1.204
CA-only RMS fit for the two chains : 0.893

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

Warning: New symmetry found

Independent molecules in the asymmetric unit actually look like symmetry relatives. This fact needs manual checking.

Warning: Problem detected upon counting molecules and matrices

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

Space group as read from CRYST card: P 21 3
Number of matrices in space group: 12
Highest polymer chain multiplicity in structure: 32
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 24
Polymer chain multiplicity and SEQRES multiplicity disagree 32 2
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Error: Matthews Coefficient (Vm) too low

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

The fact that it is lower than 1.5 in this structure might be caused by a miscalculated value of Z on the CRYST1 card.

Molecular weight of all polymer chains: 549467.375
Volume of the Unit Cell V= 1929153.3
Space group multiplicity: 12
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z low: Vm= 0.293
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.580

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.

4835 SO4   ( 203-)  A  1
4836 SO4   ( 204-)  A  1
4837 SO4   ( 203-)  B  1
4838 SO4   ( 204-)  B  1
4841 SO4   ( 203-)  A  2
4842 SO4   ( 204-)  A  2
4843 SO4   ( 203-)  B  2
4844 SO4   ( 204-)  B  2
4847 SO4   ( 203-)  A  3
4848 SO4   ( 204-)  A  3
4849 SO4   ( 203-)  B  3
4850 SO4   ( 204-)  B  3
4853 SO4   ( 203-)  A  4
4854 SO4   ( 204-)  A  4
4855 SO4   ( 203-)  B  4
4856 SO4   ( 204-)  B  4
4859 SO4   ( 203-)  A  5
4860 SO4   ( 204-)  A  5
4861 SO4   ( 203-)  B  5
4862 SO4   ( 204-)  B  5
4865 SO4   ( 203-)  A  6
4866 SO4   ( 204-)  A  6
4867 SO4   ( 203-)  B  6
4868 SO4   ( 204-)  B  6
4871 SO4   ( 203-)  A  7
And so on for a total of 64 lines.

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; Model number 1

Note: Ramachandran plot

Chain identifier: B; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: B; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: B; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: B; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: B; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: B; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: B; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: B; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: B; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: B; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: B; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: B; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: B; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: B; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: B; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: B; Model number 16

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

Warning: Very strange distribution of occupancy values

The distribution of the occupancy values in this file differs very much from distributions commonly observed in well-refined PDB files. This does not need to mean anything, but please look at it. This file should not be used in training sets that need to hold 'good' PDB files.

Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT IF's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal...

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.

   1 HIS   (  52-)  A    0.06
   2 LEU   (  53-)  A    0.06
   3 ILE   (  54-)  A    0.06
   4 PRO   (  55-)  A    0.06
   5 PRO   (  56-)  A    0.06
   6 LEU   (  57-)  A    0.06
   7 ASN   (  58-)  A    0.06
   8 PHE   (  59-)  A    0.06
   9 SER   (  60-)  A    0.06
  10 MSE   (  61-)  A    0.06
  11 VAL   (  62-)  A    0.06
  12 ASP   (  63-)  A    0.06
  13 ASN   (  64-)  A    0.06
  14 GLY   (  65-)  A    0.06
  15 ILE   (  66-)  A    0.06
  16 PHE   (  67-)  A    0.06
  17 ARG   (  68-)  A    0.06
  18 SER   (  69-)  A    0.06
  19 GLY   (  70-)  A    0.06
  20 PHE   (  71-)  A    0.06
  21 PRO   (  72-)  A    0.06
  22 ASP   (  73-)  A    0.06
  23 SER   (  74-)  A    0.06
  24 ALA   (  75-)  A    0.06
  25 ASN   (  76-)  A    0.06
And so on for a total of 4832 lines.

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 137 ARG   ( 188-)  A
 232 ARG   ( 132-)  B
 288 ARG   ( 188-)  B
 439 ARG   ( 188-)  A
 534 ARG   ( 132-)  B
 590 ARG   ( 188-)  B
 741 ARG   ( 188-)  A
 836 ARG   ( 132-)  B
 892 ARG   ( 188-)  B
1043 ARG   ( 188-)  A
1138 ARG   ( 132-)  B
1194 ARG   ( 188-)  B
1345 ARG   ( 188-)  A
1440 ARG   ( 132-)  B
1496 ARG   ( 188-)  B
1647 ARG   ( 188-)  A
1742 ARG   ( 132-)  B
1798 ARG   ( 188-)  B
1949 ARG   ( 188-)  A
2044 ARG   ( 132-)  B
2100 ARG   ( 188-)  B
2251 ARG   ( 188-)  A
2346 ARG   ( 132-)  B
2402 ARG   ( 188-)  B
2553 ARG   ( 188-)  A
2648 ARG   ( 132-)  B
2704 ARG   ( 188-)  B
2855 ARG   ( 188-)  A 1
2950 ARG   ( 132-)  B 1
3006 ARG   ( 188-)  B 1
3157 ARG   ( 188-)  A 1
3252 ARG   ( 132-)  B 1
3308 ARG   ( 188-)  B 1
3459 ARG   ( 188-)  A 1
3554 ARG   ( 132-)  B 1
3610 ARG   ( 188-)  B 1
3761 ARG   ( 188-)  A 1
3856 ARG   ( 132-)  B 1
3912 ARG   ( 188-)  B 1
4063 ARG   ( 188-)  A 1
4158 ARG   ( 132-)  B 1
4214 ARG   ( 188-)  B 1
4365 ARG   ( 188-)  A 1
4460 ARG   ( 132-)  B 1
4516 ARG   ( 188-)  B 1
4667 ARG   ( 188-)  A 1
4762 ARG   ( 132-)  B 1
4818 ARG   ( 188-)  B 1

Warning: Phenylalanine convention problem

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

  52 PHE   ( 103-)  A
1502 PHE   ( 194-)  B
2710 PHE   ( 194-)  B
2930 PHE   ( 112-)  B 1
3374 PHE   ( 103-)  A 1
3525 PHE   ( 103-)  B 1
3534 PHE   ( 112-)  B 1
3632 PHE   (  59-)  A 1
3934 PHE   (  59-)  A 1
4371 PHE   ( 194-)  A 1
4538 PHE   (  59-)  A 1
4661 PHE   ( 182-)  A 1

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.

 148 ASP   ( 199-)  A
 324 ASP   (  73-)  A
 983 ASP   ( 128-)  A
1220 ASP   (  63-)  A
2126 ASP   (  63-)  A
2136 ASP   (  73-)  A
2191 ASP   ( 128-)  A
3042 ASP   (  73-)  A 1
3399 ASP   ( 128-)  A 1
3495 ASP   (  73-)  B 1
3636 ASP   (  63-)  A 1
4003 ASP   ( 128-)  A 1
4305 ASP   ( 128-)  A 1
4542 ASP   (  63-)  A 1
4607 ASP   ( 128-)  A 1

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.

  90 GLU   ( 141-)  A
 241 GLU   ( 141-)  B
 392 GLU   ( 141-)  A
 543 GLU   ( 141-)  B
 651 GLU   (  98-)  A
 694 GLU   ( 141-)  A
 845 GLU   ( 141-)  B
 996 GLU   ( 141-)  A
1147 GLU   ( 141-)  B
1298 GLU   ( 141-)  A
1429 GLU   ( 121-)  B
1449 GLU   ( 141-)  B
1600 GLU   ( 141-)  A
1751 GLU   ( 141-)  B
1902 GLU   ( 141-)  A
2053 GLU   ( 141-)  B
2204 GLU   ( 141-)  A
2355 GLU   ( 141-)  B
2506 GLU   ( 141-)  A
2657 GLU   ( 141-)  B
2808 GLU   ( 141-)  A 1
2959 GLU   ( 141-)  B 1
3110 GLU   ( 141-)  A 1
3261 GLU   ( 141-)  B 1
3412 GLU   ( 141-)  A 1
3520 GLU   (  98-)  B 1
3563 GLU   ( 141-)  B 1
3714 GLU   ( 141-)  A 1
3822 GLU   (  98-)  B 1
3865 GLU   ( 141-)  B 1
3969 GLU   (  94-)  A 1
4016 GLU   ( 141-)  A 1
4167 GLU   ( 141-)  B 1
4318 GLU   ( 141-)  A 1
4469 GLU   ( 141-)  B 1
4577 GLU   (  98-)  A 1
4620 GLU   ( 141-)  A 1
4751 GLU   ( 121-)  B 1
4771 GLU   ( 141-)  B 1

Geometric checks

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.286
Model 2 : 0.292
Model 3 : 0.287
Model 4 : 0.292
Model 5 : 0.285
Model 6 : 0.281
Model 7 : 0.289
Model 8 : 0.281
Model 9 : 0.283
Model 10 : 0.284
Model 11 : 0.289
Model 12 : 0.286
Model 13 : 0.333
Model 14 : 0.323
Model 15 : 0.323
Model 16 : 0.335

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

 |  0.999093 -0.000086  0.000134|
 | -0.000086  0.999237 -0.000141|
 |  0.000134 -0.000141  0.999409|
Proposed new scale matrix

 |  0.008040  0.000000 -0.000001|
 |  0.000000  0.008039  0.000001|
 | -0.000001  0.000001  0.008038|
With corresponding cell

    A    = 124.374  B   = 124.392  C    = 124.413
    Alpha=  90.016  Beta=  89.985  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 124.483  B   = 124.483  C    = 124.483
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 95.108
(Under-)estimated Z-score: 7.187

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.

4570 LEU   (  91-)  A 1    N    CA   C   123.47    4.4

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 0.594
Model 2 : 0.591
Model 3 : 0.593
Model 4 : 0.600
Model 5 : 0.590
Model 6 : 0.589
Model 7 : 0.579
Model 8 : 0.578
Model 9 : 0.591
Model 10 : 0.580
Model 11 : 0.589
Model 12 : 0.597
Model 13 : 0.644
Model 14 : 0.652
Model 15 : 0.666
Model 16 : 0.656

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.

  90 GLU   ( 141-)  A
 137 ARG   ( 188-)  A
 148 ASP   ( 199-)  A
 232 ARG   ( 132-)  B
 241 GLU   ( 141-)  B
 288 ARG   ( 188-)  B
 324 ASP   (  73-)  A
 392 GLU   ( 141-)  A
 439 ARG   ( 188-)  A
 534 ARG   ( 132-)  B
 543 GLU   ( 141-)  B
 590 ARG   ( 188-)  B
 651 GLU   (  98-)  A
 694 GLU   ( 141-)  A
 741 ARG   ( 188-)  A
 836 ARG   ( 132-)  B
 845 GLU   ( 141-)  B
 892 ARG   ( 188-)  B
 983 ASP   ( 128-)  A
 996 GLU   ( 141-)  A
1043 ARG   ( 188-)  A
1138 ARG   ( 132-)  B
1147 GLU   ( 141-)  B
1194 ARG   ( 188-)  B
1220 ASP   (  63-)  A
And so on for a total of 102 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.

3807 LEU   (  83-)  B 1   5.48
3438 LEU   ( 167-)  A 1   5.28
4600 GLU   ( 121-)  A 1   5.10
4570 LEU   (  91-)  A 1   4.94
1784 SER   ( 174-)  B    4.67
3976 LEU   ( 101-)  A 1   4.59
4335 GLY   ( 158-)  A 1   4.53
1608 HIS   ( 149-)  A    4.48
4341 LEU   ( 164-)  A 1   4.46
1676 ILE   (  66-)  B    4.43
 468 ILE   (  66-)  B    4.39
3664 LEU   (  91-)  A 1   4.39
2582 ILE   (  66-)  B    4.37
3488 ILE   (  66-)  B 1   4.36
4334 THR   ( 157-)  A 1   4.33
3543 GLU   ( 121-)  B 1   4.32
3996 GLU   ( 121-)  A 1   4.31
1465 THR   ( 157-)  B    4.31
3586 LEU   ( 164-)  B 1   4.31
3277 THR   ( 157-)  B 1   4.30
1978 ILE   (  66-)  B    4.30
 861 THR   ( 157-)  B    4.28
 976 GLU   ( 121-)  A    4.27
 537 LEU   ( 135-)  B    4.25
 166 ILE   (  66-)  B    4.24
3090 GLU   ( 121-)  A 1   4.23
4239 VAL   (  62-)  A 1   4.20
4068 ARG   ( 193-)  A 1   4.20
4696 ILE   (  66-)  B 1   4.19
1957 GLU   ( 196-)  A    4.14
4041 LYS   ( 166-)  A 1   4.13
3443 LEU   ( 172-)  A 1   4.13
4333 ARG   ( 156-)  A 1   4.08
4794 LEU   ( 164-)  B 1   4.06
4796 LYS   ( 166-)  B 1   4.05
4351 SER   ( 174-)  A 1   4.03
 839 LEU   ( 135-)  B    4.02
1029 SER   ( 174-)  A    4.01
 674 GLU   ( 121-)  A    4.00
3557 LEU   ( 135-)  B 1   4.00

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.716

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -4.815
Model 2 : -4.358
Model 3 : -4.563
Model 4 : -4.563
Model 5 : -4.639
Model 6 : -4.473
Model 7 : -4.406
Model 8 : -4.292
Model 9 : -4.085
Model 10 : -4.650
Model 11 : -4.927
Model 12 : -4.949
Model 13 : -5.249
Model 14 : -5.146
Model 15 : -4.824
Model 16 : -5.520

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.

4572 PRO   (  93-)  A 1   -3.0
3477 PRO   (  55-)  B 1   -3.0
3746 THR   ( 173-)  A 1   -2.9
 257 THR   ( 157-)  B    -2.9
2914 TYR   (  96-)  B 1   -2.9
4685 PRO   (  55-)  B 1   -2.8
3534 PHE   ( 112-)  B 1   -2.8
4740 ARG   ( 110-)  B 1   -2.7
4601 PRO   ( 122-)  A 1   -2.7
3568 VAL   ( 146-)  B 1   -2.7
 325 SER   (  74-)  A    -2.7
2639 PHE   ( 123-)  B    -2.7
3788 ASN   (  64-)  B 1   -2.6
4726 TYR   (  96-)  B 1   -2.6
3795 PHE   (  71-)  B 1   -2.6
3645 PRO   (  72-)  A 1   -2.5
2836 LYS   ( 169-)  A 1   -2.5
3914 SER   ( 190-)  B 1   -2.5
2185 PRO   ( 122-)  A    -2.5
 246 VAL   ( 146-)  B    -2.5
 373 PRO   ( 122-)  A    -2.5
1498 SER   ( 190-)  B    -2.5
4636 THR   ( 157-)  A 1   -2.5
1162 ARG   ( 156-)  B    -2.5
3949 SER   (  74-)  A 1   -2.5
And so on for a total of 229 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.

  11 VAL   (  62-)  A  Poor phi/psi
  12 ASP   (  63-)  A  Poor phi/psi
  13 ASN   (  64-)  A  Poor phi/psi
  30 GLN   (  81-)  A  Poor phi/psi
  31 THR   (  82-)  A  Poor phi/psi
  55 SER   ( 106-)  A  Poor phi/psi
  74 ASN   ( 125-)  A  Poor phi/psi
  93 HIS   ( 144-)  A  PRO omega poor
  99 CYS   ( 150-)  A  Poor phi/psi
 118 LYS   ( 169-)  A  Poor phi/psi
 133 ALA   ( 184-)  A  Poor phi/psi
 134 ALA   ( 185-)  A  Poor phi/psi
 150 SER   ( 201-)  A  Poor phi/psi
 158 ASN   (  58-)  B  Poor phi/psi
 160 SER   (  60-)  B  Poor phi/psi
 169 SER   (  69-)  B  Poor phi/psi
 225 ASN   ( 125-)  B  Poor phi/psi
 244 HIS   ( 144-)  B  PRO omega poor
 246 VAL   ( 146-)  B  Poor phi/psi
 247 LEU   ( 147-)  B  Poor phi/psi
 248 ILE   ( 148-)  B  Poor phi/psi
 250 CYS   ( 150-)  B  Poor phi/psi
 255 HIS   ( 155-)  B  Poor phi/psi
 268 GLN   ( 168-)  B  Poor phi/psi
 269 LYS   ( 169-)  B  Poor phi/psi
And so on for a total of 435 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.090

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -2.708
Model 2 : -2.450
Model 3 : -3.564
Model 4 : -3.128
Model 5 : -2.269
Model 6 : -2.418
Model 7 : -2.275
Model 8 : -2.471
Model 9 : -2.395
Model 10 : -2.461
Model 11 : -2.771
Model 12 : -3.595
Model 13 : -3.503
Model 14 : -4.087
Model 15 : -4.582
Model 16 : -4.765

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.

 274 SER   ( 174-)  B    0.33
2841 SER   ( 174-)  A 1   0.33
4729 SER   (  99-)  B 1   0.35
2292 SER   (  78-)  B    0.36
 221 GLU   ( 121-)  B    0.36
 576 SER   ( 174-)  B    0.36
 727 SER   ( 174-)  A    0.36
 652 SER   (  99-)  A    0.37
 508 SER   ( 106-)  B    0.37
2896 SER   (  78-)  B 1   0.38
4804 SER   ( 174-)  B 1   0.38
 631 SER   (  78-)  A    0.38
1235 SER   (  78-)  A    0.38
2086 SER   ( 174-)  B    0.38
 178 SER   (  78-)  B    0.39
 782 SER   (  78-)  B    0.39
2011 SER   (  99-)  B    0.39
1386 SER   (  78-)  B    0.39
1688 SER   (  78-)  B    0.39
 501 SER   (  99-)  B    0.40
2594 SER   (  78-)  B    0.40

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!

   6 LEU   (  57-)  A      0
   7 ASN   (  58-)  A      0
   8 PHE   (  59-)  A      0
  10 MSE   (  61-)  A      0
  11 VAL   (  62-)  A      0
  13 ASN   (  64-)  A      0
  18 SER   (  69-)  A      0
  20 PHE   (  71-)  A      0
  31 THR   (  82-)  A      0
  34 LEU   (  85-)  A      0
  42 PRO   (  93-)  A      0
  55 SER   ( 106-)  A      0
  56 ASN   ( 107-)  A      0
  63 PHE   ( 114-)  A      0
  68 ASN   ( 119-)  A      0
  71 PRO   ( 122-)  A      0
  72 PHE   ( 123-)  A      0
  74 ASN   ( 125-)  A      0
  82 MSE   ( 133-)  A      0
  93 HIS   ( 144-)  A      0
  98 HIS   ( 149-)  A      0
  99 CYS   ( 150-)  A      0
 100 LYS   ( 151-)  A      0
 101 ARG   ( 152-)  A      0
 103 LYS   ( 154-)  A      0
And so on for a total of 1965 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 : 1.020

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 0.973
Model 2 : 0.946
Model 3 : 0.930
Model 4 : 0.965
Model 5 : 0.942
Model 6 : 0.916
Model 7 : 0.930
Model 8 : 0.947
Model 9 : 0.982
Model 10 : 0.864
Model 11 : 0.925
Model 12 : 0.985
Model 13 : 1.077
Model 14 : 1.141
Model 15 : 1.208
Model 16 : 1.115

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!

2634 GLY   ( 118-)  B   1.93   16
1783 THR   ( 173-)  B   1.86   18
4295 GLY   ( 118-)  A 1  1.82   11
 218 GLY   ( 118-)  B   1.70   13
 520 GLY   ( 118-)  B   1.70   14
1728 GLY   ( 118-)  B   1.64   13
3993 GLY   ( 118-)  A 1  1.62   11
2473 GLY   ( 108-)  A   1.61   25
1664 ILE   (  54-)  B   1.61   13
1275 GLY   ( 118-)  A   1.58   13
2721 ILE   (  54-)  A 1  1.58   20
1513 ILE   (  54-)  A   1.57   18
2367 GLY   ( 153-)  B   1.56   24
2689 THR   ( 173-)  B   1.56   19
1567 GLY   ( 108-)  A   1.54   15
1362 ILE   (  54-)  B   1.53   12
2117 ILE   (  54-)  A   1.53   16
2483 GLY   ( 118-)  A   1.53   13
1966 ILE   (  54-)  B   1.53   12
 305 ILE   (  54-)  A   1.52   18
 607 ILE   (  54-)  A   1.52   18
3983 GLY   ( 108-)  A 1  1.51   34
1815 ILE   (  54-)  A   1.51   23
1060 ILE   (  54-)  B   1.50   12

Warning: Unusual peptide bond conformations

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

4599 LYS   ( 120-)  A 1  1.53

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]

4272 PRO   (  95-)  A 1   0.45 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].

  71 PRO   ( 122-)  A  -113.1 envelop C-gamma (-108 degrees)
 348 PRO   (  97-)  A  -117.7 half-chair C-delta/C-gamma (-126 degrees)
 373 PRO   ( 122-)  A  -116.7 envelop C-gamma (-108 degrees)
 675 PRO   ( 122-)  A  -114.3 envelop C-gamma (-108 degrees)
 826 PRO   ( 122-)  B  -114.2 envelop C-gamma (-108 degrees)
 952 PRO   (  97-)  A  -120.7 half-chair C-delta/C-gamma (-126 degrees)
 977 PRO   ( 122-)  A  -116.0 envelop C-gamma (-108 degrees)
1254 PRO   (  97-)  A  -117.8 half-chair C-delta/C-gamma (-126 degrees)
1430 PRO   ( 122-)  B  -117.6 half-chair C-delta/C-gamma (-126 degrees)
1556 PRO   (  97-)  A  -117.4 half-chair C-delta/C-gamma (-126 degrees)
1833 PRO   (  72-)  A    50.2 half-chair C-delta/C-gamma (54 degrees)
1858 PRO   (  97-)  A  -122.9 half-chair C-delta/C-gamma (-126 degrees)
1883 PRO   ( 122-)  A  -114.0 envelop C-gamma (-108 degrees)
2034 PRO   ( 122-)  B  -112.2 envelop C-gamma (-108 degrees)
2135 PRO   (  72-)  A    42.7 envelop C-delta (36 degrees)
2160 PRO   (  97-)  A  -118.7 half-chair C-delta/C-gamma (-126 degrees)
2185 PRO   ( 122-)  A  -118.5 half-chair C-delta/C-gamma (-126 degrees)
2336 PRO   ( 122-)  B  -113.7 envelop C-gamma (-108 degrees)
2462 PRO   (  97-)  A  -120.7 half-chair C-delta/C-gamma (-126 degrees)
2487 PRO   ( 122-)  A  -116.7 envelop C-gamma (-108 degrees)
2764 PRO   (  97-)  A 1 -127.2 half-chair C-delta/C-gamma (-126 degrees)
2789 PRO   ( 122-)  A 1 -112.7 envelop C-gamma (-108 degrees)
2940 PRO   ( 122-)  B 1 -113.7 envelop C-gamma (-108 degrees)
3066 PRO   (  97-)  A 1 -119.6 half-chair C-delta/C-gamma (-126 degrees)
3091 PRO   ( 122-)  A 1 -112.7 envelop C-gamma (-108 degrees)
3368 PRO   (  97-)  A 1 -114.8 envelop C-gamma (-108 degrees)
3393 PRO   ( 122-)  A 1 -115.7 envelop C-gamma (-108 degrees)
3477 PRO   (  55-)  B 1   42.7 envelop C-delta (36 degrees)
3670 PRO   (  97-)  A 1 -123.7 half-chair C-delta/C-gamma (-126 degrees)
3695 PRO   ( 122-)  A 1 -114.7 envelop C-gamma (-108 degrees)
3972 PRO   (  97-)  A 1 -123.7 half-chair C-delta/C-gamma (-126 degrees)
3997 PRO   ( 122-)  A 1 -117.7 half-chair C-delta/C-gamma (-126 degrees)
4148 PRO   ( 122-)  B 1 -116.5 envelop C-gamma (-108 degrees)
4299 PRO   ( 122-)  A 1 -115.0 envelop C-gamma (-108 degrees)
4450 PRO   ( 122-)  B 1 -117.4 half-chair C-delta/C-gamma (-126 degrees)
4601 PRO   ( 122-)  A 1 -119.1 half-chair C-delta/C-gamma (-126 degrees)
4685 PRO   (  55-)  B 1   41.0 envelop C-delta (36 degrees)

Packing, accessibility and threading

Note: Per-model averages for inside/outside residue distributi ...heck
















Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 16

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: B; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: B; Model number 2

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Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: B; Model number 3

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Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: B; Model number 4

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Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: B; Model number 5

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Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: B; Model number 6

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Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: B; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: B; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: B; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: B; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: B; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: B; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: B; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: B; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: B; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: B; Model number 16

Warning: Low packing Z-score for some residues


Note: Per-model averages for NQA
















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 16

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving


Error: Water molecules without hydrogen bonds


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure







Note: Summary report for depositors of a structure