WHAT IF Check report

This file was created 2013-12-10 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 pdb4kd9.ent

Checks that need to be done early-on in validation

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

Error: Matthews Coefficient (Vm) very high

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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 1381148.5
Volume of the Unit Cell V= 71992768.0
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 13.031
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.600

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: 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: K

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: 0

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 5

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: 8

Note: Ramachandran plot

Chain identifier: 9

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: 1

Note: Ramachandran plot

Chain identifier: 4

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

Warning: B-factors outside the range 0.0 - 100.0

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

   2 LYS   (   3-)  C    High
   3 HIS   (   4-)  C    High
   4 GLY   (   5-)  C    High
   5 LYS   (   6-)  C    High
   7 TYR   (   8-)  C    High
   8 ARG   (   9-)  C    High
   9 ALA   (  10-)  C    High
  10 LEU   (  11-)  C    High
  11 LEU   (  12-)  C    High
  12 GLU   (  13-)  C    High
  13 LYS   (  14-)  C    High
  14 VAL   (  15-)  C    High
  15 ASP   (  16-)  C    High
  16 PRO   (  17-)  C    High
  17 ASN   (  18-)  C    High
  18 LYS   (  19-)  C    High
  19 VAL   (  20-)  C    High
  20 TYR   (  21-)  C    High
  21 THR   (  22-)  C    High
  22 ILE   (  23-)  C    High
  23 ASP   (  24-)  C    High
  24 GLU   (  25-)  C    High
  25 ALA   (  26-)  C    High
  27 ARG   (  28-)  C    High
  28 LEU   (  29-)  C    High
And so on for a total of 1386 lines.

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: 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: K

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: V

Note: B-factor plot

Chain identifier: W

Note: B-factor plot

Chain identifier: X

Note: B-factor plot

Chain identifier: Y

Note: B-factor plot

Chain identifier: Z

Note: B-factor plot

Chain identifier: 0

Note: B-factor plot

Chain identifier: 2

Note: B-factor plot

Chain identifier: 3

Note: B-factor plot

Chain identifier: 5

Note: B-factor plot

Chain identifier: 6

Note: B-factor plot

Chain identifier: 7

Note: B-factor plot

Chain identifier: 8

Note: B-factor plot

Chain identifier: 9

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: 1

Note: B-factor plot

Chain identifier: 4

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.

  53 ARG   (  54-)  C
 466 ARG   ( 239-)  D
 561 ARG   (  58-)  E
1701 ARG   (  41-)  P
1710 ARG   (  50-)  P
1715 ARG   (  55-)  P
1762 ARG   ( 102-)  P
1771 ARG   ( 111-)  P
2014 ARG   (  64-)  R
2038 ARG   (  88-)  R
2296 ARG   ( 129-)  T
2354 ARG   (  50-)  U
2368 ARG   (  64-)  U
3052 ARG   (  32-)  0
3159 ARG   (  55-)  2
3290 ARG   (  55-)  5
3309 ARG   (  18-)  6
3394 ARG   (  49-)  7
3617 ARG   (  52-)  1

Warning: Tyrosine convention problem

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

 289 TYR   (  62-)  D
 331 TYR   ( 104-)  D
 399 TYR   ( 172-)  D
 663 TYR   ( 160-)  E
 767 TYR   (  59-)  F
 805 TYR   (  97-)  F
 927 TYR   (  12-)  G
1169 TYR   (  83-)  H
1574 TYR   (  32-)  O
1770 TYR   ( 110-)  P
1819 TYR   (   9-)  Q
1836 TYR   (  26-)  Q
1971 TYR   (  21-)  R
2037 TYR   (  87-)  R
2044 TYR   (  94-)  R
2199 TYR   (  32-)  T
2328 TYR   (  24-)  U
2349 TYR   (  45-)  U
2351 TYR   (  47-)  U
2380 TYR   (  76-)  U
2568 TYR   (  45-)  W
2593 TYR   (  70-)  W
2703 TYR   (  69-)  X
2748 TYR   (  20-)  Y
2843 TYR   (   9-)  Z
2863 TYR   (  29-)  Z
2933 TYR   (  99-)  Z
3046 TYR   (  26-)  0
3286 TYR   (  51-)  5
3287 TYR   (  52-)  5
3312 TYR   (  21-)  6
3608 TYR   (  43-)  1

Warning: Phenylalanine convention problem

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

 163 PHE   ( 164-)  C
 233 PHE   (   6-)  D
 242 PHE   (  15-)  D
 248 PHE   (  21-)  D
 280 PHE   (  53-)  D
 294 PHE   (  67-)  D
 362 PHE   ( 135-)  D
 518 PHE   (  15-)  E
 570 PHE   (  67-)  E
 587 PHE   (  84-)  E
 616 PHE   ( 113-)  E
 798 PHE   (  90-)  F
 837 PHE   ( 129-)  F
1017 PHE   ( 102-)  G
1040 PHE   ( 125-)  G
1056 PHE   ( 141-)  G
1095 PHE   ( 180-)  G
1328 PHE   (  65-)  K
1711 PHE   (  51-)  P
1751 PHE   (  91-)  P
1839 PHE   (  29-)  Q
1868 PHE   (  58-)  Q
1879 PHE   (  69-)  Q
1914 PHE   ( 104-)  Q
2030 PHE   (  80-)  R
2087 PHE   (  29-)  S
2224 PHE   (  57-)  T
2228 PHE   (  61-)  T
2336 PHE   (  32-)  U
2344 PHE   (  40-)  U
2383 PHE   (  79-)  U
2655 PHE   (  21-)  X
2681 PHE   (  47-)  X
2788 PHE   (  60-)  Y
2882 PHE   (  48-)  Z
2922 PHE   (  88-)  Z
2923 PHE   (  89-)  Z
3065 PHE   (  45-)  0
3505 PHE   (  60-)  E

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.

  55 ASP   (  56-)  C
 105 ASP   ( 106-)  C
 118 ASP   ( 119-)  C
 326 ASP   (  99-)  D
 336 ASP   ( 109-)  D
 398 ASP   ( 171-)  D
 520 ASP   (  17-)  E
 586 ASP   (  83-)  E
 677 ASP   ( 174-)  E
 903 ASP   ( 195-)  F
 905 ASP   ( 197-)  F
 919 ASP   (   4-)  G
1041 ASP   ( 126-)  G
1081 ASP   ( 166-)  G
1325 ASP   (  62-)  K
1382 ASP   ( 119-)  K
1421 ASP   (  17-)  N
1445 ASP   (  41-)  N
1554 ASP   (  12-)  O
1598 ASP   (  56-)  O
1623 ASP   (  81-)  O
1707 ASP   (  47-)  P
2022 ASP   (  72-)  R
2057 ASP   ( 107-)  R
2146 ASP   (  88-)  S
2193 ASP   (  26-)  T
2395 ASP   (  91-)  U
2545 ASP   (  22-)  W
2586 ASP   (  63-)  W
2590 ASP   (  67-)  W
2617 ASP   (  94-)  W
2739 ASP   (  11-)  Y
2879 ASP   (  45-)  Z
2911 ASP   (  77-)  Z
2982 ASP   ( 148-)  Z
2988 ASP   ( 154-)  Z
3035 ASP   (  15-)  0
3076 ASP   (  56-)  0
3252 ASP   (  17-)  5

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.

  24 GLU   (  25-)  C
  31 GLU   (  32-)  C
  39 GLU   (  40-)  C
  42 GLU   (  43-)  C
  98 GLU   (  99-)  C
 151 GLU   ( 152-)  C
 162 GLU   ( 163-)  C
 197 GLU   ( 198-)  C
 250 GLU   (  23-)  D
 310 GLU   (  83-)  D
 328 GLU   ( 101-)  D
 373 GLU   ( 146-)  D
 576 GLU   (  73-)  E
 597 GLU   (  94-)  E
 703 GLU   ( 200-)  E
 743 GLU   (  35-)  F
 835 GLU   ( 127-)  F
 898 GLU   ( 190-)  F
 908 GLU   ( 200-)  F
 928 GLU   (  13-)  G
 929 GLU   (  14-)  G
 933 GLU   (  18-)  G
 950 GLU   (  35-)  G
 960 GLU   (  45-)  G
 974 GLU   (  59-)  G
And so on for a total of 79 lines.

Error: Chain names not unique

The chain names listed below are given for more than one protein/DNA molecule in the structure ('-' represents a chain without chain identifier).

Chain identifier(s): E

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

1028 ARG   ( 113-)  G      CA   C     1.42   -4.8
1029 ILE   ( 114-)  G      N    CA    1.31   -7.8
1030 ARG   ( 115-)  G      N    CA    1.54    4.1
4851 OGUA  (1137-)  A      N9   C4    1.41    4.1
5713 OGUA  (2023-)  A      C5   C6    1.38   -4.0
6676 OADE  ( 101-)  B      N9   C4    1.40    5.0

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

 |  0.999848 -0.000045 -0.000005|
 | -0.000045  1.000304 -0.000008|
 | -0.000005 -0.000008  0.999774|
Proposed new scale matrix

 |  0.003237  0.000000  0.000143|
 |  0.000000  0.001491  0.000000|
 |  0.000000  0.000000  0.002879|
With corresponding cell

    A    = 308.882  B   = 670.895  C    = 347.724
    Alpha=  90.006  Beta=  92.532  Gamma=  90.006

The CRYST1 cell dimensions

    A    = 308.961  B   = 670.662  C    = 347.765
    Alpha=  90.000  Beta=  92.520  Gamma=  90.000

Variance: 38.511
(Under-)estimated Z-score: 4.574

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.

  62 VAL   (  63-)  C      N    CA   C   122.45    4.0
 163 PHE   ( 164-)  C      N    CA   CB  117.46    4.1
 568 GLY   (  65-)  E      N    CA   C   100.66   -4.1
 715 TYR   (   7-)  F      N    CA   C    99.01   -4.4
 716 GLN   (   8-)  F     -C    N    CA  130.08    4.7
 863 LEU   ( 155-)  F      N    CA   C    94.16   -6.1
 864 LEU   ( 156-)  F      N    CA   C    98.46   -4.6
 865 VAL   ( 157-)  F     -C    N    CA  112.59   -5.1
 865 VAL   ( 157-)  F      N    CA   CB  117.33    4.0
 880 TRP   ( 172-)  F      N    CA   C    98.57   -4.5
 882 VAL   ( 174-)  F      N    CA   C    98.05   -4.7
 885 ALA   ( 177-)  F     -C    N    CA  129.09    4.1
 899 ARG   ( 191-)  F      N    CA   C   124.63    4.8
1026 LEU   ( 111-)  G      N    CA   CB  100.65   -5.8
1028 ARG   ( 113-)  G      CA   C    O   127.76    4.1
1029 ILE   ( 114-)  G     -CA  -C    N   107.85   -4.2
1029 ILE   ( 114-)  G     -C    N    CA  113.13   -4.8
1127 MET   (  41-)  H     -C    N    CA  129.98    4.6
1442 HIS   (  38-)  N      CG   ND1  CE1 109.63    4.0
2246 HIS   (  79-)  T      N    CA   C   123.94    4.5
2796 HIS   (  68-)  Y      CG   ND1  CE1 109.64    4.0
2906 ARG   (  72-)  Z     -C    N    CA  128.93    4.0
3298 ILE   (   7-)  6      N    CA   C    98.92   -4.4
3532 LYS   (  87-)  E      CG   CD   CE   98.88   -5.4
3578 ILE   (  13-)  1      C    CA   CB  119.31    4.8
And so on for a total of 1068 lines.

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.

  24 GLU   (  25-)  C
  31 GLU   (  32-)  C
  39 GLU   (  40-)  C
  42 GLU   (  43-)  C
  53 ARG   (  54-)  C
  55 ASP   (  56-)  C
  98 GLU   (  99-)  C
 105 ASP   ( 106-)  C
 118 ASP   ( 119-)  C
 151 GLU   ( 152-)  C
 162 GLU   ( 163-)  C
 197 GLU   ( 198-)  C
 250 GLU   (  23-)  D
 310 GLU   (  83-)  D
 326 ASP   (  99-)  D
 328 GLU   ( 101-)  D
 336 ASP   ( 109-)  D
 373 GLU   ( 146-)  D
 398 ASP   ( 171-)  D
 466 ARG   ( 239-)  D
 520 ASP   (  17-)  E
 561 ARG   (  58-)  E
 576 GLU   (  73-)  E
 586 ASP   (  83-)  E
 597 GLU   (  94-)  E
And so on for a total of 137 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 181 PRO   ( 182-)  C      N      8.2    24.52    -2.48
 899 ARG   ( 191-)  F      CA    -6.7    22.92    33.91
1026 LEU   ( 111-)  G      C      8.5    13.58     0.20
The average deviation= 0.734

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.

 863 LEU   ( 155-)  F    6.62
1026 LEU   ( 111-)  G    6.17
 864 LEU   ( 156-)  F    5.19
 899 ARG   ( 191-)  F    4.99
 880 TRP   ( 172-)  F    4.87
  62 VAL   (  63-)  C    4.79
1914 PHE   ( 104-)  Q    4.73
3584 GLN   (  19-)  1    4.68
 715 TYR   (   7-)  F    4.65
 568 GLY   (  65-)  E    4.63
 882 VAL   ( 174-)  F    4.63
2130 ALA   (  72-)  S    4.62
2197 VAL   (  30-)  T    4.59
 151 GLU   ( 152-)  C    4.56
 862 VAL   ( 154-)  F    4.54
3583 ILE   (  18-)  1    4.39
1988 VAL   (  38-)  R    4.39
3605 ARG   (  40-)  1    4.34
  30 LYS   (  31-)  C    4.27
 120 MET   ( 121-)  C    4.24
 306 VAL   (  79-)  D    4.18
3582 SER   (  17-)  1    4.16
2596 ALA   (  73-)  W    4.15
2246 HIS   (  79-)  T    4.11
2986 ALA   ( 152-)  Z    4.10
 210 ARG   ( 211-)  C    4.09
1011 ARG   (  96-)  G    4.09
2164 ARG   ( 106-)  S    4.08
 222 VAL   ( 223-)  C    4.07
1686 GLY   (  26-)  P    4.06
3390 ALA   (  45-)  7    4.04

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 : -6.089

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.

2105 THR   (  47-)  S    -3.7
1556 THR   (  14-)  O    -3.6
 570 PHE   (  67-)  E    -3.5
 252 THR   (  25-)  D    -3.5
2194 THR   (  27-)  T    -3.5
1718 THR   (  58-)  P    -3.5
 798 PHE   (  90-)  F    -3.5
1576 THR   (  34-)  O    -3.5
2788 PHE   (  60-)  Y    -3.4
2532 TYR   (   9-)  W    -3.4
3599 THR   (  34-)  1    -3.3
3030 THR   (  10-)  0    -3.3
 144 THR   ( 145-)  C    -3.3
 168 THR   ( 169-)  C    -3.2
 554 PHE   (  51-)  E    -3.2
1986 THR   (  36-)  R    -3.2
2763 TYR   (  35-)  Y    -3.1
2760 PRO   (  32-)  Y    -3.1
 138 PRO   ( 139-)  C    -3.1
 718 PRO   (  10-)  F    -3.1
1590 PRO   (  48-)  O    -3.1
 110 PHE   ( 111-)  C    -3.1
3389 PRO   (  44-)  7    -3.1
1690 THR   (  30-)  P    -3.1
 559 PRO   (  56-)  E    -3.1
And so on for a total of 565 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.

  10 LEU   (  11-)  C  Poor phi/psi
  16 PRO   (  17-)  C  Poor phi/psi
  20 TYR   (  21-)  C  Poor phi/psi
  21 THR   (  22-)  C  Poor phi/psi
  23 ASP   (  24-)  C  Poor phi/psi
  29 VAL   (  30-)  C  omega poor
  32 LEU   (  33-)  C  Poor phi/psi
  36 LYS   (  37-)  C  Poor phi/psi
  37 PHE   (  38-)  C  Poor phi/psi
  39 GLU   (  40-)  C  omega poor
  41 VAL   (  42-)  C  Poor phi/psi
  42 GLU   (  43-)  C  Poor phi/psi
  47 LEU   (  48-)  C  Poor phi/psi
  51 PRO   (  52-)  C  Poor phi/psi
  54 SER   (  55-)  C  Poor phi/psi
  58 VAL   (  59-)  C  Poor phi/psi
  59 ARG   (  60-)  C  Poor phi/psi, omega poor
  60 GLY   (  61-)  C  Poor phi/psi
  65 PRO   (  66-)  C  Poor phi/psi
  66 HIS   (  67-)  C  Poor phi/psi
  68 LEU   (  69-)  C  Poor phi/psi
  70 LYS   (  71-)  C  Poor phi/psi
  73 ARG   (  74-)  C  Poor phi/psi
  74 VAL   (  75-)  C  Poor phi/psi
  75 LEU   (  76-)  C  Poor phi/psi
And so on for a total of 762 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -6.267

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.

1149 SER   (  63-)  H    0.35
 974 GLU   (  59-)  G    0.36
2883 ARG   (  49-)  Z    0.38
2276 GLU   ( 109-)  T    0.39

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!

   3 HIS   (   4-)  C      0
  14 VAL   (  15-)  C      0
  15 ASP   (  16-)  C      0
  17 ASN   (  18-)  C      0
  18 LYS   (  19-)  C      0
  19 VAL   (  20-)  C      0
  20 TYR   (  21-)  C      0
  21 THR   (  22-)  C      0
  32 LEU   (  33-)  C      0
  33 ALA   (  34-)  C      0
  34 THR   (  35-)  C      0
  35 ALA   (  36-)  C      0
  36 LYS   (  37-)  C      0
  37 PHE   (  38-)  C      0
  38 ASP   (  39-)  C      0
  40 THR   (  41-)  C      0
  41 VAL   (  42-)  C      0
  42 GLU   (  43-)  C      0
  46 LYS   (  47-)  C      0
  47 LEU   (  48-)  C      0
  49 ILE   (  50-)  C      0
  50 ASP   (  51-)  C      0
  51 PRO   (  52-)  C      0
  52 ARG   (  53-)  C      0
  53 ARG   (  54-)  C      0
And so on for a total of 5017 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!

3383 GLY   (  38-)  7   3.52   14
 627 GLY   ( 124-)  E   3.39   12
2948 GLY   ( 114-)  Z   3.24   50
1726 GLY   (  66-)  P   3.23   12
3574 GLY   (   9-)  1   3.08   53
3146 GLY   (  42-)  2   2.38   18
 450 GLY   ( 223-)  D   2.26   13
1671 GLY   (  11-)  P   2.21   17
1753 GLY   (  93-)  P   2.05   13
 689 GLY   ( 186-)  E   2.02   74
 591 GLY   (  88-)  E   1.91   25
3028 GLY   (   8-)  0   1.90   18
2549 GLY   (  26-)  W   1.87   25
1177 GLY   (  91-)  H   1.86   14
2476 GLY   (  54-)  V   1.79   13
2463 GLY   (  41-)  V   1.76   16
  10 LEU   (  11-)  C   1.72   11
1872 GLY   (  62-)  Q   1.70   15
3542 GLY   (  97-)  E   1.69   39
1092 GLY   ( 177-)  G   1.65   65
 553 GLY   (  50-)  E   1.62   57
 106 GLY   ( 107-)  C   1.59   66
2656 ALA   (  22-)  X   1.59   49
3677 GLY   (  17-)  4   1.55   19
 506 GLY   (   3-)  E   1.54   57
1453 GLY   (  49-)  N   1.50   14

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...

1808 LEU   ( 148-)  P   1.96

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]

1533 PRO   ( 129-)  N    0.46 HIGH

Warning: Unusual PRO puckering phases

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

  51 PRO   (  52-)  C   123.0 half-chair C-beta/C-alpha (126 degrees)
  65 PRO   (  66-)  C   156.2 half-chair C-alpha/N (162 degrees)
 133 PRO   ( 134-)  C   109.2 envelop C-beta (108 degrees)
 138 PRO   ( 139-)  C   156.5 half-chair C-alpha/N (162 degrees)
 140 PRO   ( 141-)  C   105.8 envelop C-beta (108 degrees)
 174 PRO   ( 175-)  C   -60.2 half-chair C-beta/C-alpha (-54 degrees)
 181 PRO   ( 182-)  C   161.8 half-chair C-alpha/N (162 degrees)
 182 PRO   ( 183-)  C   139.7 envelop C-alpha (144 degrees)
 220 PRO   ( 221-)  C  -114.1 envelop C-gamma (-108 degrees)
 226 PRO   ( 227-)  C   113.8 envelop C-beta (108 degrees)
 238 PRO   (  11-)  D  -118.0 half-chair C-delta/C-gamma (-126 degrees)
 263 PRO   (  36-)  D  -164.5 half-chair N/C-delta (-162 degrees)
 303 PRO   (  76-)  D  -121.2 half-chair C-delta/C-gamma (-126 degrees)
 313 PRO   (  86-)  D  -125.6 half-chair C-delta/C-gamma (-126 degrees)
 348 PRO   ( 121-)  D   118.9 half-chair C-beta/C-alpha (126 degrees)
 405 PRO   ( 178-)  D   162.9 half-chair C-alpha/N (162 degrees)
 446 PRO   ( 219-)  D  -125.1 half-chair C-delta/C-gamma (-126 degrees)
 455 PRO   ( 228-)  D  -121.9 half-chair C-delta/C-gamma (-126 degrees)
 492 PRO   ( 265-)  D   126.8 half-chair C-beta/C-alpha (126 degrees)
 535 PRO   (  32-)  E   101.4 envelop C-beta (108 degrees)
 542 PRO   (  39-)  E  -170.2 half-chair N/C-delta (-162 degrees)
 556 PRO   (  53-)  E   100.9 envelop C-beta (108 degrees)
 559 PRO   (  56-)  E    10.3 half-chair N/C-delta (18 degrees)
 565 PRO   (  62-)  E    36.5 envelop C-delta (36 degrees)
 577 PRO   (  74-)  E  -125.4 half-chair C-delta/C-gamma (-126 degrees)
And so on for a total of 84 lines.

Bump checks

Error: Abnormally short interatomic distances

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

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

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

6361 OCYT  (2681-)  A      C5  <-> 6406 OADE  (2725-)  A      N6     1.01    2.09  INTRA BL
5501 OADE  (1802-)  A      C8  <-> 5514 OADE  (1815-)  A      N6     0.87    2.23  INTRA BL
5713 OGUA  (2023-)  A      N1  <-> 5730 OCYT  (2040-)  A      O2     0.85    1.85  INTRA BF
3906 OGUA  ( 226-)  A      N3  <-> 3908 OADE  ( 228-)  A      N6     0.84    2.16  INTRA BF
6361 OCYT  (2681-)  A      C4  <-> 6406 OADE  (2725-)  A      N6     0.78    2.32  INTRA BL
3271 CYS   (  36-)  5      SG  <-> 3272 LYS   (  37-)  5      N      0.73    2.47  INTRA BF
6361 OCYT  (2681-)  A      N4  <-> 6406 OADE  (2725-)  A      N6     0.70    2.15  INTRA BL
1409 VAL   (   5-)  N      O   <-> 1411 LYS   (   7-)  N      NZ     0.70    2.00  INTRA BF
2807 CYS   (  79-)  Y      SG  <-> 2808 GLY   (  80-)  Y      N      0.70    2.50  INTRA BF
3714 OGUA  (  24-)  A      N1  <-> 4232 OCYT  ( 516-)  A      O2     0.68    2.02  INTRA BL
5132 OCYT  (1417-)  A      N3  <-> 5296 OGUA  (1581-)  A      N2     0.65    2.35  INTRA BL
4398 OGUA  ( 682-)  A      N2  <-> 4511 OCYT  ( 795-)  A      N3     0.65    2.35  INTRA BL
3435 ARG   (  42-)  8      NH1 <-> 6031 OGUA  (2351-)  A      N7     0.65    2.35  INTRA BL
1127 MET   (  41-)  H      SD  <-> 1128 ARG   (  42-)  H      N      0.64    2.56  INTRA BF
5946 OADE  (2266-)  A      N6  <-> 5953 OADE  (2273-)  A      N7     0.63    2.37  INTRA BL
4316 OGUA  ( 602-)  A      N2  <-> 4371 OADE  ( 655-)  A      N7     0.63    2.37  INTRA BF
5713 OGUA  (2023-)  A      O6  <-> 5730 OCYT  (2040-)  A      N3     0.63    1.92  INTRA BF
3772 OGUA  (  83-)  A      N2  <-> 3791 OADE  ( 103-)  A      N7     0.62    2.38  INTRA BF
3034 ARG   (  14-)  0      NH2 <-> 5959 OGUA  (2279-)  A      N7     0.62    2.38  INTRA BL
4734 OURA  (1019-)  A      C2  <-> 4735 OADE  (1020-)  A      N7     0.62    2.48  INTRA BL
3485 CYS   (  27-)  9      SG  <-> 3486 GLU   (  28-)  9      N      0.62    2.58  INTRA BF
2511 GLN   (  89-)  V      NE2 <-> 4708 OGUA  ( 993-)  A      N3     0.61    2.39  INTRA BL
6185 OGUA  (2505-)  A      N1  <-> 6290 OCYT  (2610-)  A      N3     0.61    2.39  INTRA BF
2907 GLN   (  73-)  Z      NE2 <-> 6677 OGUA  ( 102-)  B      N3     0.61    2.39  INTRA BL
4722 OCYT  (1007-)  A      N3  <-> 4850 OGUA  (1136-)  A      O6     0.61    1.94  INTRA BL
And so on for a total of 4130 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: 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: K

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

Note: Inside/Outside RMS Z-score plot

Chain identifier: 0

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

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.

 471 ARG   ( 244-)  D      -8.98
3287 TYR   (  52-)  5      -8.81
1681 ARG   (  21-)  P      -8.70
1591 ARG   (  49-)  O      -8.66
 466 ARG   ( 239-)  D      -8.60
3094 ARG   (  74-)  0      -8.32
1815 ARG   (   5-)  Q      -8.19
 782 ARG   (  74-)  F      -8.12
1824 ARG   (  14-)  Q      -8.09
3040 ARG   (  20-)  0      -8.06
3075 ARG   (  55-)  0      -8.06
2263 ARG   (  96-)  T      -8.02
 469 ARG   ( 242-)  D      -8.00
1893 MET   (  83-)  Q      -7.97
1892 ARG   (  82-)  Q      -7.93
1816 ARG   (   6-)  Q      -7.93
3386 ARG   (  41-)  7      -7.77
2235 TYR   (  68-)  T      -7.71
2946 ARG   ( 112-)  Z      -7.69
1678 ARG   (  18-)  P      -7.69
2262 ARG   (  95-)  T      -7.66
3031 ARG   (  11-)  0      -7.66
2055 ARG   ( 105-)  R      -7.65
2081 ARG   (  23-)  S      -7.60
3312 TYR   (  21-)  6      -7.53
And so on for a total of 385 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

   1 PRO   (   2-)  C         3 - HIS      4- ( C)         -5.33
  50 ASP   (  51-)  C        53 - ARG     54- ( C)         -4.47
 225 ASN   ( 226-)  C       227 - HIS    228- ( C)         -5.42
 279 ARG   (  52-)  D       281 - ARG     54- ( D)         -5.58
 338 LEU   ( 111-)  D       340 - VAL    113- ( D)         -5.19
 464 GLU   ( 237-)  D       466 - ARG    239- ( D)         -6.35
 468 PRO   ( 241-)  D       471 - ARG    244- ( D)         -6.38
 484 LEU   ( 257-)  D       490 - ARG    263- ( D)         -5.46
 500 ARG   ( 273-)  D       502 - LYS    275- ( D)         -6.07
 647 ARG   ( 144-)  E       649 - THR    146- ( E)         -5.52
 652 ARG   ( 149-)  E       654 - TYR    151- ( E)         -5.55
 657 LYS   ( 154-)  E       659 - MET    156- ( E)         -5.44
 705 LYS   ( 202-)  E       708 - ALA    205- ( E)         -4.86
 725 ARG   (  17-)  F       727 - GLU     19- ( F)         -4.73
 752 ARG   (  44-)  F       754 - ARG     46- ( F)         -5.43
 775 GLN   (  67-)  F       777 - HIS     69- ( F)         -5.82
 790 ILE   (  82-)  F       793 - GLY     85- ( F)         -4.63
 796 VAL   (  88-)  F       798 - PHE     90- ( F)         -5.61
 913 ARG   ( 205-)  F       916 - GLY    208- ( F)         -4.55
 936 ARG   (  21-)  G       938 - PHE     23- ( G)         -4.94
 943 VAL   (  28-)  G       945 - GLU     30- ( G)         -4.19
1195 PHE   ( 109-)  H      1197 - HIS    111- ( H)         -4.44
1243 TYR   ( 157-)  H      1246 - LYS    160- ( H)         -4.63
1255 VAL   ( 169-)  H      1258 - LYS    172- ( H)         -5.39
1411 LYS   (   7-)  N      1413 - VAL      9- ( N)         -4.60
And so on for a total of 62 lines.

Error: Abnormal average packing environment

The average packing score for the structure is very low.

A molecule is certain to be incorrect if the average packing score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 6693 : -2.259

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: 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: 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

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: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

Note: Quality value plot

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

Chain identifier: V

Note: Quality value plot

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

Chain identifier: W

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: X

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: Y

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: Z

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: 0

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: 2

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: 3

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: 5

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: 6

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: 7

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: 8

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: 9

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: 1

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: 4

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.

3032 ASN   (  12-)  0   -4.05
1449 ASN   (  45-)  N   -3.62
3245 LYS   (  10-)  5   -3.43
2612 ALA   (  89-)  W   -3.39
3348 ARG   (   3-)  7   -3.30
1823 GLN   (  13-)  Q   -3.29
1730 GLN   (  70-)  P   -3.28
2311 GLY   (   7-)  U   -3.28
 652 ARG   ( 149-)  E   -3.27
2309 LYS   (   5-)  U   -3.26
 564 ARG   (  61-)  E   -3.24
2500 LYS   (  78-)  V   -3.22
 286 LYS   (  59-)  D   -3.21
3424 HIS   (  31-)  8   -3.19
3460 LYS   (   2-)  9   -3.16
2732 LYS   (   4-)  Y   -3.14
 482 LYS   ( 255-)  D   -3.13
1609 LYS   (  67-)  O   -3.13
2307 ARG   (   3-)  U   -3.12
1955 LYS   (   5-)  R   -3.11
 879 PRO   ( 171-)  F   -3.10
1724 LYS   (  64-)  P   -3.09
2499 ALA   (  77-)  V   -3.08
3425 LEU   (  32-)  8   -3.08
 798 PHE   (  90-)  F   -3.07
And so on for a total of 148 lines.

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 259 SER   (  32-)  D     -  262 LYS   (  35-)  D        -1.76
 267 THR   (  40-)  D     -  279 ARG   (  52-)  D        -2.12
 293 ASP   (  66-)  D     -  296 ARG   (  69-)  D        -1.50
 461 GLY   ( 234-)  D     -  472 PRO   ( 245-)  D        -2.28
 480 GLN   ( 253-)  D     -  485 LYS   ( 258-)  D        -2.30
 563 ASN   (  60-)  E     -  567 LYS   (  64-)  E        -2.32
 630 ASP   ( 127-)  E     -  634 ALA   ( 131-)  E        -2.19
 640 HIS   ( 137-)  E     -  648 LYS   ( 145-)  E        -2.31
 649 THR   ( 146-)  E     -  652 ARG   ( 149-)  E        -2.19
 688 LYS   ( 185-)  E     -  692 PRO   ( 189-)  E        -1.64
 788 ALA   (  80-)  F     -  793 GLY   (  85-)  F        -1.89
 795 GLY   (  87-)  F     -  799 GLY   (  91-)  F        -2.02
1065 ASP   ( 150-)  G     - 1068 ARG   ( 153-)  G        -1.56
1260 GLY   ( 174-)  H     - 1263 GLY   ( 177-)  H        -1.90
1408 TYR   (   4-)  N     - 1411 LYS   (   7-)  N        -1.83
1569 GLY   (  27-)  O     - 1572 ALA   (  30-)  O        -1.90
1674 LYS   (  14-)  P     - 1678 ARG   (  18-)  P        -2.30
1686 GLY   (  26-)  P     - 1691 ALA   (  31-)  P        -1.94
1697 GLY   (  37-)  P     - 1700 SER   (  40-)  P        -2.34
1710 ARG   (  50-)  P     - 1715 ARG   (  55-)  P        -2.35
1718 THR   (  58-)  P     - 1722 LEU   (  62-)  P        -2.25
1728 GLN   (  68-)  P     - 1737 ARG   (  77-)  P        -2.50
1816 ARG   (   6-)  Q     - 1819 TYR   (   9-)  Q        -2.25
1822 GLN   (  12-)  Q     - 1828 LYS   (  18-)  Q        -2.46
1835 ASP   (  25-)  Q     - 1838 ALA   (  28-)  Q        -1.73
And so on for a total of 53 lines.

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: 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: K

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

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

Note: Second generation quality Z-score plot

Chain identifier: 0

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: 5

Note: Second generation quality Z-score plot

Chain identifier: 6

Note: Second generation quality Z-score plot

Chain identifier: 7

Note: Second generation quality Z-score plot

Chain identifier: 8

Note: Second generation quality Z-score plot

Chain identifier: 9

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: 1

Note: Second generation quality Z-score plot

Chain identifier: 4

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  57 ASN   (  58-)  C
 165 ASN   ( 166-)  C
 425 ASN   ( 198-)  D
 458 HIS   ( 231-)  D
 912 ASN   ( 204-)  F
1038 ASN   ( 123-)  G
1305 ASN   (  42-)  K
1379 ASN   ( 116-)  K
1498 HIS   (  94-)  N
1687 HIS   (  27-)  P
1933 HIS   ( 123-)  Q
2003 HIS   (  53-)  R
2205 ASN   (  38-)  T
2509 HIS   (  87-)  V
2584 ASN   (  61-)  W
2692 HIS   (  58-)  X
2864 ASN   (  30-)  Z
3055 ASN   (  35-)  0
3222 ASN   (  46-)  3
3492 GLN   (  34-)  9
3551 GLN   ( 106-)  E
3581 ASN   (  16-)  1
3584 GLN   (  19-)  1
3621 GLN   (  56-)  1

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.

  11 LEU   (  12-)  C      N
  18 LYS   (  19-)  C      N
  19 VAL   (  20-)  C      N
  37 PHE   (  38-)  C      N
  42 GLU   (  43-)  C      N
  61 THR   (  62-)  C      N
  63 SER   (  64-)  C      N
  66 HIS   (  67-)  C      NE2
  72 VAL   (  73-)  C      N
  73 ARG   (  74-)  C      NE
  74 VAL   (  75-)  C      N
  77 ILE   (  78-)  C      N
  90 GLY   (  91-)  C      N
  98 GLU   (  99-)  C      N
  99 ILE   ( 100-)  C      N
 100 ILE   ( 101-)  C      N
 101 GLN   ( 102-)  C      N
 107 TRP   ( 108-)  C      N
 114 VAL   ( 115-)  C      N
 116 THR   ( 117-)  C      N
 128 GLY   ( 129-)  C      N
 129 ARG   ( 130-)  C      N
 137 LEU   ( 138-)  C      N
 144 THR   ( 145-)  C      N
 146 GLY   ( 147-)  C      N
And so on for a total of 1125 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.

  42 GLU   (  43-)  C      OE1
  44 HIS   (  45-)  C      ND1
  97 GLU   (  98-)  C      OE1
 118 ASP   ( 119-)  C      OD2
 162 GLU   ( 163-)  C      OE2
 188 ASN   ( 189-)  C      OD1
 310 GLU   (  83-)  D      OE2
 312 ASP   (  85-)  D      OD1
 323 HIS   (  96-)  D      ND1
 328 GLU   ( 101-)  D      OE2
 408 GLU   ( 181-)  D      OE1
 425 ASN   ( 198-)  D      OD1
 430 ASN   ( 203-)  D      OD1
 551 GLN   (  48-)  E      OE1
 606 ASP   ( 103-)  E      OD2
 632 HIS   ( 129-)  E      NE2
 739 HIS   (  31-)  F      ND1
 775 GLN   (  67-)  F      OE1
 777 HIS   (  69-)  F      ND1
 828 GLU   ( 120-)  F      OE1
 877 ASN   ( 169-)  F      OD1
 955 ASN   (  40-)  G      OD1
 974 GLU   (  59-)  G      OE2
1041 ASP   ( 126-)  G      OD2
1058 GLU   ( 143-)  G      OE2
And so on for a total of 52 lines.

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.

  24 GLU   (  25-)  C   H-bonding suggests Gln; but Alt-Rotamer
  38 ASP   (  39-)  C   H-bonding suggests Asn
  39 GLU   (  40-)  C   H-bonding suggests Gln
  55 ASP   (  56-)  C   H-bonding suggests Asn
  85 GLU   (  86-)  C   H-bonding suggests Gln; but Alt-Rotamer
  97 GLU   (  98-)  C   H-bonding suggests Gln
 111 ASP   ( 112-)  C   H-bonding suggests Asn
 166 ASP   ( 167-)  C   H-bonding suggests Asn
 257 GLU   (  30-)  D   H-bonding suggests Gln
 336 ASP   ( 109-)  D   H-bonding suggests Asn; but Alt-Rotamer
 373 GLU   ( 146-)  D   H-bonding suggests Gln
 545 ASP   (  42-)  E   H-bonding suggests Asn
 576 GLU   (  73-)  E   H-bonding suggests Gln
 606 ASP   ( 103-)  E   H-bonding suggests Asn
 711 GLU   (   3-)  F   H-bonding suggests Gln
 731 ASP   (  23-)  F   H-bonding suggests Asn; but Alt-Rotamer
 743 GLU   (  35-)  F   H-bonding suggests Gln; but Alt-Rotamer
 804 ASP   (  96-)  F   H-bonding suggests Asn; but Alt-Rotamer
 846 GLU   ( 138-)  F   H-bonding suggests Gln
 860 GLU   ( 152-)  F   H-bonding suggests Gln
 903 ASP   ( 195-)  F   H-bonding suggests Asn
 908 GLU   ( 200-)  F   H-bonding suggests Gln; but Alt-Rotamer
 963 GLU   (  48-)  G   H-bonding suggests Gln
 969 GLU   (  54-)  G   H-bonding suggests Gln; but Alt-Rotamer
1062 ASP   ( 147-)  G   H-bonding suggests Asn
And so on for a total of 94 lines.

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 :  -4.399 (poor)
  2nd generation packing quality :  -5.199 (bad)
  Ramachandran plot appearance   :  -6.089 (bad)
  chi-1/chi-2 rotamer normality  :  -6.267 (bad)
  Backbone conformation          :  -1.454

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.529 (tight)
  Bond angles                    :   0.987
  Omega angle restraints         :   1.220
  Side chain planarity           :   0.246 (tight)
  Improper dihedral distribution :   0.698
  B-factor distribution          :   0.581
  Inside/Outside distribution    :   1.057

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 : 3.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.9
  2nd generation packing quality :  -2.5
  Ramachandran plot appearance   :  -2.9
  chi-1/chi-2 rotamer normality  :  -3.7 (poor)
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.529 (tight)
  Bond angles                    :   0.987
  Omega angle restraints         :   1.220
  Side chain planarity           :   0.246 (tight)
  Improper dihedral distribution :   0.698
  B-factor distribution          :   0.581
  Inside/Outside distribution    :   1.057
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.