WHAT IF Check report

This file was created 2012-01-30 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 pdb3i55.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 2 2 21
Number of matrices in space group: 8
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 3D multiplicity

Warning: Matthews Coefficient (Vm) 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.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 1359891.4
Volume of the Unit Cell V= 36374772.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 6.687
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.070 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

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.

6980 MYL   (2924-)  0  -
6981 MYL   ( 177-)  4  -
6982 2OP   (  77-)  4  -

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

6981 MYL   ( 177-)  4  -

Non-validating, descriptive output paragraph

Warning: Ions bound to the wrong chain

The ions listed in the table have a chain identifier that is the same as one of the protein, nucleic acid, or sugar chains. However, the ion seems bound to protein, nucleic acid, or sugar, with another chain identifier.

Obviously, this is not wrong, but it is confusing for users of this PDB file.

6772  NA   (8515-)  0  -

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

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: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

1520 OURA  (1561-)  0      P
1520 OURA  (1561-)  0      OP1
1520 OURA  (1561-)  0      OP2
6654 5AA   (  76-)  4      O3'
6654 5AA   (  76-)  4      O5'
6654 5AA   (  76-)  4      C5'
6654 5AA   (  76-)  4      C4'
6654 5AA   (  76-)  4      O4'
6654 5AA   (  76-)  4      C1'
6654 5AA   (  76-)  4      N9
6654 5AA   (  76-)  4      C4
6654 5AA   (  76-)  4      N3
6654 5AA   (  76-)  4      C2
6654 5AA   (  76-)  4      N1
6654 5AA   (  76-)  4      C6
6654 5AA   (  76-)  4      N6
6654 5AA   (  76-)  4      C5
6654 5AA   (  76-)  4      N7
6654 5AA   (  76-)  4      C8
6654 5AA   (  76-)  4      C9
6654 5AA   (  76-)  4      C10
6654 5AA   (  76-)  4      C2'
6654 5AA   (  76-)  4      O2'
6655 PSU   (2621-)  0      C3'
6655 PSU   (2621-)  0      O5'
6655 PSU   (2621-)  0      C5'
6655 PSU   (2621-)  0      N1
6655 PSU   (2621-)  0      C2
6655 PSU   (2621-)  0      N3
6655 PSU   (2621-)  0      C4
6655 PSU   (2621-)  0      C5
6655 PSU   (2621-)  0      C6
6655 PSU   (2621-)  0      O2
6655 PSU   (2621-)  0      O4
6655 PSU   (2621-)  0      C1'
6655 PSU   (2621-)  0      C2'
6655 PSU   (2621-)  0      O2'
6655 PSU   (2621-)  0      C4'
6655 PSU   (2621-)  0      O4'
6656 5AA   (  76-)  4      C3'
6656 5AA   (  76-)  4      O3'

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.

  78 OCYT  (  87-)  0    High
  79 OGUA  (  88-)  0    High
  80 OGUA  (  89-)  0    High
  87 OADE  (  96-)  0    High
 117 OADE  ( 128-)  0    High
 118 OADE  ( 129-)  0    High
 127 OURA  ( 138-)  0    High
 128 OCYT  ( 139-)  0    High
 189 OCYT  ( 200-)  0    High
 243 OCYT  ( 254-)  0    High
 244 OADE  ( 255-)  0    High
 245 OCYT  ( 256-)  0    High
 260 OCYT  ( 271-)  0    High
 261 OADE  ( 272-)  0    High
 262 OGUA  ( 273-)  0    High
 266 OURA  ( 277-)  0    High
 267 OADE  ( 278-)  0    High
 268 OCYT  ( 279-)  0    High
 269 OCYT  ( 280-)  0    High
 270 OURA  ( 281-)  0    High
 271 OCYT  ( 282-)  0    High
 272 OURA  ( 283-)  0    High
 273 OCYT  ( 284-)  0    High
 274 OADE  ( 285-)  0    High
 275 OURA  ( 286-)  0    High
And so on for a total of 1071 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

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: 1

Note: B-factor plot

Chain identifier: 2

Note: B-factor plot

Chain identifier: 3

Nomenclature related problems

Warning: Tyrosine convention problem

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

2777 TYR   (  23-)  A
3083 TYR   (  92-)  B
3190 TYR   ( 199-)  B
3374 TYR   (  46-)  C
3379 TYR   (  51-)  C
4053 TYR   (  22-)  H
4160 TYR   ( 140-)  H
4688 TYR   (   5-)  M
4897 TYR   (  20-)  N
4959 TYR   (  82-)  N
5114 TYR   (  51-)  O
5925 TYR   (  41-)  W
6271 TYR   (  42-)  Z
6322 TYR   (  93-)  Z
6383 TYR   (  48-)  1

Warning: Phenylalanine convention problem

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

2872 PHE   ( 118-)  A
2923 PHE   ( 169-)  A
2955 PHE   ( 201-)  A
3017 PHE   (  26-)  B
3096 PHE   ( 105-)  B
3185 PHE   ( 194-)  B
3275 PHE   ( 284-)  B
3389 PHE   (  61-)  C
3459 PHE   ( 131-)  C
3575 PHE   (  10-)  D
3621 PHE   (  61-)  D
3664 PHE   ( 104-)  D
3779 PHE   (  65-)  E
3787 PHE   (  73-)  E
3962 PHE   (  76-)  F
4140 PHE   ( 120-)  H
4173 PHE   ( 153-)  H
4220 PHE   (  91-)  I
4340 PHE   (  79-)  J
4589 PHE   (  51-)  L
4843 PHE   ( 160-)  M
4993 PHE   ( 116-)  N
5309 PHE   ( 131-)  P
5475 PHE   (  59-)  R
5520 PHE   ( 104-)  R
5586 PHE   (  20-)  S
6154 PHE   ( 128-)  Y
6194 PHE   ( 168-)  Y
6208 PHE   ( 182-)  Y
6267 PHE   (  38-)  Z
6317 PHE   (  88-)  Z
6527 PHE   (  90-)  3

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.

2780 ASP   (  26-)  A
2886 ASP   ( 132-)  A
3373 ASP   (  45-)  C
3425 ASP   (  97-)  C
3495 ASP   ( 167-)  C
3539 ASP   ( 211-)  C
3550 ASP   ( 222-)  C
3659 ASP   (  99-)  D
3685 ASP   ( 145-)  D
4134 ASP   ( 114-)  H
4274 ASP   (  13-)  J
5050 ASP   ( 173-)  N
5058 ASP   ( 181-)  N
5190 ASP   (  12-)  P
5193 ASP   (  15-)  P
5299 ASP   ( 121-)  P
5625 ASP   (  59-)  S
5637 ASP   (  71-)  S
5639 ASP   (  73-)  S
5701 ASP   (  54-)  T
5962 ASP   (  78-)  W
6059 ASP   (  27-)  X
6078 ASP   (  46-)  X
6083 ASP   (  51-)  X
6382 ASP   (  47-)  1
6436 ASP   (  48-)  2

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.

2782 GLU   (  28-)  A
2800 GLU   (  46-)  A
2813 GLU   (  59-)  A
2826 GLU   (  72-)  A
2841 GLU   (  87-)  A
2898 GLU   ( 144-)  A
3054 GLU   (  63-)  B
3178 GLU   ( 187-)  B
3565 GLU   ( 237-)  C
3570 GLU   ( 242-)  C
3620 GLU   (  60-)  D
3718 GLU   (   4-)  E
3815 GLU   ( 101-)  E
3853 GLU   ( 139-)  E
3899 GLU   (  13-)  F
3964 GLU   (  78-)  F
4019 GLU   (  25-)  G
4193 GLU   ( 173-)  H
4264 GLU   ( 135-)  I
4303 GLU   (  42-)  J
4945 GLU   (  68-)  N
4949 GLU   (  72-)  N
4976 GLU   (  99-)  N
5097 GLU   (  34-)  O
5242 GLU   (  64-)  P
5270 GLU   (  92-)  P
5352 GLU   (  31-)  Q
5560 GLU   ( 144-)  R
5627 GLU   (  61-)  S
5762 GLU   ( 115-)  T
6039 GLU   (   7-)  X
6120 GLU   (  88-)  X
6191 GLU   ( 165-)  Y
6210 GLU   ( 184-)  Y
6220 GLU   ( 194-)  Y
6384 GLU   (  49-)  1
6453 GLU   (  16-)  3

Warning: Phosphate group convention problem

The nucleic acid residues listed in the table below have the OP1 and OP2 atom names exchanged.

1520 OURA  (1561-)  0
6654 5AA   (  76-)  4

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): 0, 4

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  1.001033  0.000045  0.000002|
 |  0.000045  1.001019 -0.000001|
 |  0.000002 -0.000001  1.000895|
Proposed new scale matrix

 |  0.004727  0.000000  0.000000|
 |  0.000000  0.003334  0.000000|
 |  0.000000  0.000000  0.001739|
With corresponding cell

    A    = 211.546  B   = 299.976  C    = 574.897
    Alpha=  90.005  Beta=  90.005  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 211.327  B   = 299.670  C    = 574.383
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1559.302
(Under-)estimated Z-score: 29.103

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.

  12 OGUA  (  21-)  0      N9   C8   N7  113.11    4.0
  15 OGUA  (  24-)  0      N9   C8   N7  113.17    4.1
  19 OGUA  (  28-)  0      N9   C8   N7  113.16    4.1
  23 OGUA  (  32-)  0      N9   C8   N7  113.13    4.1
  24 OGUA  (  33-)  0      N9   C8   N7  113.19    4.2
  29 OGUA  (  38-)  0      N9   C8   N7  113.10    4.0
  32 OGUA  (  41-)  0      N9   C8   N7  113.17    4.1
  35 OGUA  (  44-)  0      N9   C8   N7  113.14    4.1
  38 OGUA  (  47-)  0      N9   C8   N7  113.40    4.6
  41 OGUA  (  50-)  0      N9   C8   N7  113.13    4.1
  45 OGUA  (  54-)  0      N9   C8   N7  113.25    4.3
  47 OGUA  (  56-)  0      N9   C8   N7  113.20    4.2
  52 OGUA  (  61-)  0      N9   C8   N7  113.13    4.1
  57 OGUA  (  66-)  0      N9   C8   N7  113.26    4.3
  62 OGUA  (  71-)  0      N9   C8   N7  113.21    4.2
  65 OGUA  (  74-)  0      N9   C8   N7  113.16    4.1
  67 OGUA  (  76-)  0      N9   C8   N7  113.13    4.1
  69 OGUA  (  78-)  0      N9   C8   N7  113.21    4.2
  70 OGUA  (  79-)  0      N9   C8   N7  113.11    4.0
  72 OGUA  (  81-)  0      N9   C8   N7  113.14    4.1
  80 OGUA  (  89-)  0      N9   C8   N7  113.11    4.0
  88 OGUA  (  97-)  0      N9   C8   N7  113.23    4.3
 107 OGUA  ( 116-)  0      N9   C8   N7  113.13    4.1
 129 OGUA  ( 140-)  0      N9   C8   N7  113.31    4.4
 136 OGUA  ( 147-)  0      N9   C8   N7  113.30    4.4
And so on for a total of 438 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.

2780 ASP   (  26-)  A
2782 GLU   (  28-)  A
2800 GLU   (  46-)  A
2813 GLU   (  59-)  A
2826 GLU   (  72-)  A
2841 GLU   (  87-)  A
2886 ASP   ( 132-)  A
2898 GLU   ( 144-)  A
3054 GLU   (  63-)  B
3178 GLU   ( 187-)  B
3373 ASP   (  45-)  C
3425 ASP   (  97-)  C
3495 ASP   ( 167-)  C
3539 ASP   ( 211-)  C
3550 ASP   ( 222-)  C
3565 GLU   ( 237-)  C
3570 GLU   ( 242-)  C
3620 GLU   (  60-)  D
3659 ASP   (  99-)  D
3685 ASP   ( 145-)  D
3718 GLU   (   4-)  E
3815 GLU   ( 101-)  E
3853 GLU   ( 139-)  E
3899 GLU   (  13-)  F
3964 GLU   (  78-)  F
And so on for a total of 63 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.

4891 ARG   (  14-)  N    6.71
5953 ARG   (  69-)  W    6.45
5040 PHE   ( 163-)  N    5.09
5046 PRO   ( 169-)  N    4.83
5047 GLU   ( 170-)  N    4.77
3166 LEU   ( 175-)  B    4.68
5845 GLU   (  26-)  V    4.61
3945 ILE   (  59-)  F    4.55
6141 ARG   ( 115-)  Y    4.54
2952 ASP   ( 198-)  A    4.46
5663 LEU   (  16-)  T    4.46
6035 GLU   ( 151-)  W    4.44
3946 VAL   (  60-)  F    4.40
5163 GLN   ( 100-)  O    4.36
4336 PRO   (  75-)  J    4.26
3533 ARG   ( 205-)  C    4.21
3213 LYS   ( 222-)  B    4.21
5835 ARG   (  16-)  V    4.11
6054 ASN   (  22-)  X    4.10
3966 GLN   (  80-)  F    4.10
2920 ASP   ( 166-)  A    4.07
5952 THR   (  68-)  W    4.05
4353 GLN   (  92-)  J    4.04
5557 VAL   ( 141-)  R    4.02

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 : -4.533

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.

3621 PHE   (  61-)  D    -3.2
3677 PRO   ( 137-)  D    -3.1
5339 PRO   (  18-)  Q    -3.0
3385 PRO   (  57-)  C    -3.0
3609 PRO   (  49-)  D    -2.9
3374 TYR   (  46-)  C    -2.9
6340 THR   (   5-)  1    -2.8
3419 PRO   (  91-)  C    -2.8
3089 THR   (  98-)  B    -2.7
3459 PHE   ( 131-)  C    -2.7
5429 THR   (  13-)  R    -2.7
5736 ARG   (  89-)  T    -2.6
4468 PRO   (  62-)  K    -2.6
5396 ILE   (  75-)  Q    -2.6
4405 THR   ( 144-)  J    -2.5
3355 ARG   (  27-)  C    -2.5
5369 PRO   (  48-)  Q    -2.5
5686 ASN   (  39-)  T    -2.4
4326 ASN   (  65-)  J    -2.4
3295 PRO   ( 304-)  B    -2.4
3846 THR   ( 132-)  E    -2.4
3709 THR   ( 169-)  D    -2.4
3040 THR   (  49-)  B    -2.4
3562 VAL   ( 234-)  C    -2.4
5936 VAL   (  52-)  W    -2.4
And so on for a total of 134 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.

2764 GLY   (  10-)  A  Poor phi/psi
2769 THR   (  15-)  A  Poor phi/psi
2773 PRO   (  19-)  A  Poor phi/psi
2788 ASP   (  34-)  A  Poor phi/psi
2790 ASP   (  36-)  A  Poor phi/psi
2791 VAL   (  37-)  A  Poor phi/psi
2806 SER   (  52-)  A  Poor phi/psi
2869 GLY   ( 115-)  A  Poor phi/psi
2883 LEU   ( 129-)  A  Poor phi/psi
2924 VAL   ( 170-)  A  Poor phi/psi
2927 GLY   ( 173-)  A  Poor phi/psi
2940 TRP   ( 186-)  A  PRO omega poor
2941 PRO   ( 187-)  A  Poor phi/psi
2960 ARG   ( 206-)  A  Poor phi/psi
2962 HIS   ( 208-)  A  Poor phi/psi
2986 ARG   ( 232-)  A  Poor phi/psi
2993 GLN   (   2-)  B  Poor phi/psi
2996 ARG   (   5-)  B  Poor phi/psi
3005 GLY   (  14-)  B  PRO omega poor
3024 ASP   (  33-)  B  Poor phi/psi
3092 TRP   ( 101-)  B  Poor phi/psi
3093 THR   ( 102-)  B  Poor phi/psi
3103 THR   ( 112-)  B  Poor phi/psi
3175 ASP   ( 184-)  B  Poor phi/psi
3176 GLY   ( 185-)  B  Poor phi/psi
And so on for a total of 200 lines.

Warning: Unusual rotamers

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

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

3781 SER   (  67-)  E    0.35
3441 SER   ( 113-)  C    0.35
4734 SER   (  51-)  M    0.37
4789 SER   ( 106-)  M    0.37
3774 SER   (  60-)  E    0.38
4285 SER   (  24-)  J    0.38
5501 SER   (  85-)  R    0.39
5071 SER   (   8-)  O    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!

   3 OURA  (  12-)  0      0
   4 OGUA  (  13-)  0      0
   5 OCYT  (  14-)  0      0
   6 OCYT  (  15-)  0      0
   7 OADE  (  16-)  0      0
   8 OGUA  (  17-)  0      0
   9 OCYT  (  18-)  0      0
  10 OURA  (  19-)  0      0
  11 OGUA  (  20-)  0      0
  12 OGUA  (  21-)  0      0
  13 OURA  (  22-)  0      0
  14 OGUA  (  23-)  0      0
  15 OGUA  (  24-)  0      0
  16 OADE  (  25-)  0      0
  17 OURA  (  26-)  0      0
  18 OURA  (  27-)  0      0
  19 OGUA  (  28-)  0      0
  20 OCYT  (  29-)  0      0
  21 OURA  (  30-)  0      0
  22 OCYT  (  31-)  0      0
  23 OGUA  (  32-)  0      0
  24 OGUA  (  33-)  0      0
  25 OCYT  (  34-)  0      0
  26 OURA  (  35-)  0      0
  27 OCYT  (  36-)  0      0
And so on for a total of 4467 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 : 1.026

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!

5773 GLY   (  10-)  U   2.16   65
3626 GLY   (  66-)  D   2.13   15
2827 GLY   (  73-)  A   1.75   26
3957 GLY   (  71-)  F   1.72   80
5317 ARG   ( 139-)  P   1.67   80
6182 GLY   ( 156-)  Y   1.66   80
4670 GLY   ( 137-)  L   1.57   66
6020 GLY   ( 136-)  W   1.55   12
4718 GLY   (  35-)  M   1.55   20
4260 GLY   ( 131-)  I   1.51   80

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...

3314 LEU   ( 323-)  B   1.62
3965 GLN   (  79-)  F   1.58
4765 ARG   (  82-)  M   1.59
6109 PHE   (  77-)  X   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]

3295 PRO   ( 304-)  B    0.46 HIGH
4369 PRO   ( 108-)  J    0.45 HIGH
4489 PRO   (  83-)  K    0.45 HIGH
6257 PRO   ( 231-)  Y    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].

2895 PRO   ( 141-)  A  -115.0 envelop C-gamma (-108 degrees)
3308 PRO   ( 317-)  B    49.9 half-chair C-delta/C-gamma (54 degrees)
3677 PRO   ( 137-)  D   101.4 envelop C-beta (108 degrees)
4592 PRO   (  54-)  L  -125.6 half-chair C-delta/C-gamma (-126 degrees)
5369 PRO   (  48-)  Q    52.4 half-chair C-delta/C-gamma (54 degrees)
6341 PRO   (   6-)  1  -112.6 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

6981 MYL   ( 177-)  4      CAB <-> 6982 HOH   (7215 )  0      O      1.42    1.38  INTRA BL
6981 MYL   ( 177-)  4      OAU <-> 7013 HOH   (6229 )  4      O      1.10    1.30  INTRA BL
6981 MYL   ( 177-)  4      CAV <-> 6982 HOH   (4863 )  0      O      1.08    1.62  INTRA BF
6657 DADE  ( 176-)  4      O3' <-> 6981 MYL   ( 177-)  4      CBC    0.93    0.97  INTRA BL
6981 MYL   ( 177-)  4      CAA <-> 6982 HOH   (4863 )  0      O      0.84    1.86  INTRA BF
6981 MYL   ( 177-)  4      CBA <-> 7013 HOH   (6229 )  4      O      0.81    1.99  INTRA BL
6658 OCYT  ( 175-)  4      O3' <-> 6981 MYL   ( 177-)  4      CAG    0.72    1.68  INTRA BL
6981 MYL   ( 177-)  4      CAA <-> 6982 HOH   (6854 )  0      O      0.72    1.98  INTRA BL
6981 MYL   ( 177-)  4      CAF <-> 7013 HOH   (6229 )  4      O      0.71    2.09  INTRA BL
6981 MYL   ( 177-)  4      CAN <-> 6982 HOH   (4863 )  0      O      0.67    2.03  INTRA BF
6657 DADE  ( 176-)  4      P   <-> 6981 MYL   ( 177-)  4      CAM    0.64    2.76  INTRA BL
2430 OMG   (2588-)  0      N1  <-> 6653 OCYT  (  75-)  4      N3     0.61    2.39  INTRA BL
6657 DADE  ( 176-)  4      O3' <-> 6981 MYL   ( 177-)  4      CBG    0.61    1.79  INTRA BL
2460 OGUA  (2618-)  0      N3  <-> 6656 5AA   (  76-)  4      C2     0.57    2.53  INTRA BL
2430 OMG   (2588-)  0      O6  <-> 6653 OCYT  (  75-)  4      N4     0.55    2.15  INTRA BL
6657 DADE  ( 176-)  4      P   <-> 6981 MYL   ( 177-)  4      CAG    0.53    1.97  INTRA BL
6981 MYL   ( 177-)  4      CAD <-> 6982 HOH   (7343 )  0      O      0.52    2.28  INTRA BF
6981 MYL   ( 177-)  4      CBG <-> 7013 HOH   (6229 )  4      O      0.52    2.28  INTRA BL
2460 OGUA  (2618-)  0      N2  <-> 6656 5AA   (  76-)  4      N3     0.51    2.49  INTRA BL
2479 OADE  (2637-)  0      C5' <-> 6658 OCYT  ( 175-)  4      OP2    0.51    2.29  INTRA BL
1794 OURA  (1835-)  0      C5  <-> 1799 OADE  (1840-)  0      N7     0.50    2.60  INTRA BL
6653 OCYT  (  75-)  4      C2' <-> 7013 HOH   (6378 )  4      O      0.50    2.30  INTRA BF
5690 ASN   (  43-)  T      ND2 <-> 5755 ARG   ( 108-)  T      CZ     0.49    2.61  INTRA BF
2479 OADE  (2637-)  0      N6  <-> 6657 DADE  ( 176-)  4      C2'    0.48    2.62  INTRA BL
2462 OURA  (2620-)  0      C4' <-> 6981 MYL   ( 177-)  4      CAE    0.48    2.72  INTRA BL
And so on for a total of 4628 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

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: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

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.

2989 ARG   ( 235-)  A      -8.99
6463 ARG   (  26-)  3      -8.22
6411 ARG   (  20-)  2      -8.11
3710 TYR   ( 170-)  D      -8.04
2986 ARG   ( 232-)  A      -8.00
3083 TYR   (  92-)  B      -7.88
6006 ARG   ( 122-)  W      -7.82
3026 GLN   (  35-)  B      -7.68
4546 ARG   (   8-)  L      -7.67
2887 ARG   ( 133-)  A      -7.60
4560 ARG   (  22-)  L      -7.54
4559 ARG   (  21-)  L      -7.54
6524 ARG   (  87-)  3      -7.46
2998 ARG   (   7-)  B      -7.44
6195 ARG   ( 169-)  Y      -7.43
4751 ARG   (  68-)  M      -7.40
5258 ARG   (  80-)  P      -7.39
4565 ARG   (  27-)  L      -7.36
3226 ARG   ( 235-)  B      -7.31
6270 ARG   (  41-)  Z      -7.25
4137 ARG   ( 117-)  H      -7.22
4882 ARG   (   5-)  N      -7.16
3327 GLN   ( 336-)  B      -7.12
6517 ARG   (  80-)  3      -7.09
4648 ARG   ( 115-)  L      -7.06
And so on for a total of 249 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.

2959 GLY   ( 205-)  A      2962 - HIS    208- ( A)         -5.71
2985 LYS   ( 231-)  A      2991 - GLY    237- ( A)         -5.89
3007 ARG   (  16-)  B      3009 - ARG     18- ( B)         -4.79
3108 GLU   ( 117-)  B      3110 - HIS    119- ( B)         -4.69
3147 LYS   ( 156-)  B      3149 - LYS    158- ( B)         -5.05
3309 ASN   ( 318-)  B      3311 - GLN    320- ( B)         -5.01
3391 SER   (  63-)  C      3393 - ARG     65- ( C)         -5.09
3553 PRO   ( 225-)  C      3555 - GLY    227- ( C)         -4.63
4122 ARG   (  91-)  H      4124 - PHE     93- ( H)         -4.22
4581 HIS   (  43-)  L      4584 - LEU     46- ( L)         -4.95
4586 LYS   (  48-)  L      4591 - ARG     53- ( L)         -5.50
5030 GLN   ( 153-)  N      5032 - GLU    155- ( N)         -4.60
5257 SER   (  79-)  P      5259 - LYS     81- ( P)         -5.59
5323 SER   (   2-)  Q      5325 - ASN      4- ( Q)         -4.79
5340 ARG   (  19-)  Q      5342 - ARG     21- ( Q)         -4.97
5546 MET   ( 130-)  R      5548 - ARG    132- ( R)         -4.67
6333 ARG   ( 104-)  Z      6335 - SER    106- ( Z)         -5.10
6430 TRP   (  42-)  2      6432 - ARG     44- ( 2)         -5.06
6450 HIS   (  13-)  3      6452 - ASN     15- ( 3)         -4.77
6491 LYS   (  54-)  3      6493 - PRO     56- ( 3)         -5.07
6495 GLY   (  58-)  3      6497 - LYS     60- ( 3)         -4.71
6516 LEU   (  79-)  3      6518 - GLU     81- ( 3)         -6.10

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 6659 : -1.624

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

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: 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: 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

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.

4448 ASN   (  42-)  K   -3.93
6347 ASN   (  12-)  1   -3.92
5235 ASN   (  57-)  P   -3.84
3229 ASN   ( 238-)  B   -3.60
6431 ARG   (  43-)  2   -3.57
3372 GLN   (  44-)  C   -3.46
2960 ARG   ( 206-)  A   -3.43
4039 MET   (   8-)  H   -3.40
5376 ARG   (  55-)  Q   -3.32
2942 ASN   ( 188-)  A   -3.30
6497 LYS   (  60-)  3   -3.30
2996 ARG   (   5-)  B   -3.30
5259 LYS   (  81-)  P   -3.29
4579 HIS   (  41-)  L   -3.27
6491 LYS   (  54-)  3   -3.27
2997 PRO   (   6-)  B   -3.27
3410 GLN   (  82-)  C   -3.26
6234 LYS   ( 208-)  Y   -3.26
2965 LYS   ( 211-)  A   -3.24
3826 ALA   ( 112-)  E   -3.22
4808 ARG   ( 125-)  M   -3.21
6516 LEU   (  79-)  3   -3.21
4557 LYS   (  19-)  L   -3.21
4549 ARG   (  11-)  L   -3.19
6488 LYS   (  51-)  3   -3.18
And so on for a total of 170 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.

2762 ARG   (   8-)  A     - 2765 ARG   (  11-)  A        -1.79
2768 SER   (  14-)  A     - 2772 ALA   (  18-)  A        -2.09
2933 MET   ( 179-)  A     - 2936 ARG   ( 182-)  A        -1.84
2937 GLY   ( 183-)  A     - 2942 ASN   ( 188-)  A        -2.48
2956 GLY   ( 202-)  A     - 2962 HIS   ( 208-)  A        -2.35
2963 PRO   ( 209-)  A     - 2968 SER   ( 214-)  A        -2.37
2984 SER   ( 230-)  A     - 2988 GLY   ( 234-)  A        -2.36
2991 GLY   ( 237-)  A     - 2994 PRO   (   3-)  B        -1.67
2995 SER   (   4-)  B     - 2998 ARG   (   7-)  B        -2.55
3001 SER   (  10-)  B     - 3006 PRO   (  15-)  B        -2.10
3211 VAL   ( 220-)  B     - 3215 LYS   ( 224-)  B        -1.93
3218 HIS   ( 227-)  B     - 3222 GLY   ( 231-)  B        -2.25
3226 ARG   ( 235-)  B     - 3229 ASN   ( 238-)  B        -2.44
3230 LEU   ( 239-)  B     - 3237 ARG   ( 246-)  B        -2.54
3323 ASN   ( 332-)  B     - 3328 GLY   ( 337-)  B        -2.14
3369 ASN   (  41-)  C     - 3372 GLN   (  44-)  C        -2.31
3373 ASP   (  45-)  C     - 3376 SER   (  48-)  C        -1.67
3389 PHE   (  61-)  C     - 3392 GLY   (  64-)  C        -1.80
3393 ARG   (  65-)  C     - 3398 VAL   (  70-)  C        -2.25
3416 SER   (  88-)  C     - 3419 PRO   (  91-)  C        -2.21
3422 THR   (  94-)  C     - 3426 ARG   (  98-)  C        -2.27
3502 ILE   ( 174-)  C     - 3506 GLN   ( 178-)  C        -2.30
3609 PRO   (  49-)  D     - 3612 THR   (  52-)  D        -1.72
4121 LEU   (  90-)  H     - 4124 PHE   (  93-)  H        -1.58
4134 ASP   ( 114-)  H     - 4140 PHE   ( 120-)  H        -2.11
And so on for a total of 59 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: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

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: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

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

6982 HOH   (3635 )  0      O
6982 HOH   (4354 )  0      O
6982 HOH   (4355 )  0      O
6982 HOH   (4453 )  0      O
6982 HOH   (4499 )  0      O
6982 HOH   (5346 )  0      O
6982 HOH   (5624 )  0      O
6982 HOH   (6317 )  0      O
6982 HOH   (7036 )  0      O
6982 HOH   (7820 )  0      O
6982 HOH   (8464 )  0      O
6982 HOH   (9016 )  0      O
6983 HOH   ( 830 )  A      O
6984 HOH   (4327 )  B      O
6985 HOH   (2669 )  C      O
6985 HOH   (5165 )  C      O
6988 HOH   (5966 )  F      O
6990 HOH   (6268 )  H      O
6990 HOH   (7229 )  H      O
6992 HOH   (6256 )  J      O
6995 HOH   (7208 )  M      O
6997 HOH   (6252 )  O      O
6999 HOH   (3342 )  Q      O
7006 HOH   (7847 )  X      O
7007 HOH   (4892 )  Y      O
Marked this atom as acceptor 6823  CL  (8803-) 0     CL
Marked this atom as acceptor 6824  CL  (8805-) 0     CL
Marked this atom as acceptor 6825  CL  (8811-) Q     CL
Marked this atom as acceptor 6826  CL  (8812-) K     CL
Marked this atom as acceptor 6827  CL  (8813-) 0     CL
Marked this atom as acceptor 6828  CL  (8814-) L     CL
Marked this atom as acceptor 6829  CL  (8815-) 0     CL
Marked this atom as acceptor 6830  CL  (8816-) 0     CL
Marked this atom as acceptor 6831  CL  (8817-) Y     CL
Marked this atom as acceptor 6832  CL  (8822-) 0     CL
Marked this atom as acceptor 6928  CL  (8809-) A     CL
Marked this atom as acceptor 6933  CL  (8819-) B     CL
Marked this atom as acceptor 6941  CL  (8801-) J     CL
Marked this atom as acceptor 6942  CL  (8802-) J     CL
Marked this atom as acceptor 6943  CL  (8821-) J     CL
Marked this atom as acceptor 6945  CL  (8810-) L     CL
Marked this atom as acceptor 6948  CL  (8818-) M     CL
Marked this atom as acceptor 6949  CL  (8807-) N     CL
Marked this atom as acceptor 6951  CL  (8808-) O     CL
Marked this atom as acceptor 6956  CL  (8806-) R     CL
Marked this atom as acceptor 6963  CL  (8820-) Y     CL
Marked this atom as acceptor 6970  CL  (8804-) 3     CL
ERROR. Strange cone in HB2INI
Affected atom  617 1MA  ( 628-) 0      P
ERROR. Strange cone in HB2INI
Affected atom 2429 OMU  (2587-) 0      P
ERROR. Strange cone in HB2INI
Affected atom 2430 OMG  (2588-) 0      P
ERROR. Strange cone in HB2INI
Affected atom 2461 UR3  (2619-) 0      P
ERROR. Strange cone in HB2INI
Affected atom 2463 PSU  (2621-) 0      P
Strange metal coordination for HIS 2962
Metal-coordinating Histidine residue5103 fixed to   1
Metal-coordinating Histidine residue5573 fixed to   1
Strange metal coordination for HIS 6159
Expected ambiguity-2 in FILL1HARR 0 364 13268
Expected ambiguity-2 in FILL1HARR 0 364 13268
Expected ambiguity-2 in FILL1HARR 0 364 13268
Expected ambiguity-2 in FILL1HARR 0 364 13268
Expected ambiguity-2 in FILL1HARR 0 364 13268
ERROR. No convergence in HB2STD
Old,New value: 11084.325 11084.339
ERROR. No convergence in HB2STD
Old,New value: 11049.707 11049.732

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.

2759 GLN   (   5-)  A
2879 ASN   ( 125-)  A
2953 HIS   ( 199-)  A
3097 HIS   ( 106-)  B
3229 ASN   ( 238-)  B
3251 HIS   ( 260-)  B
3323 ASN   ( 332-)  B
3491 HIS   ( 163-)  C
3833 HIS   ( 119-)  E
3857 GLN   ( 143-)  E
4090 GLN   (  59-)  H
4286 GLN   (  25-)  J
4328 ASN   (  67-)  J
4368 ASN   ( 107-)  J
4416 GLN   (  10-)  K
4525 GLN   ( 119-)  K
4556 HIS   (  18-)  L
4697 ASN   (  14-)  M
4707 GLN   (  24-)  M
4760 HIS   (  77-)  M
4769 GLN   (  86-)  M
4853 ASN   ( 170-)  M
4898 HIS   (  21-)  N
4984 ASN   ( 107-)  N
5134 GLN   (  71-)  O
And so on for a total of 62 lines.

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  29 OGUA  (  38-)  0      N2
  38 OGUA  (  47-)  0      N2
  69 OGUA  (  78-)  0      N2
  89 OADE  (  98-)  0      N6
 103 OGUA  ( 112-)  0      O2'
 159 OURA  ( 170-)  0      N3
 171 OGUA  ( 182-)  0      N2
 182 OADE  ( 193-)  0      N6
 248 OGUA  ( 259-)  0      N2
 383 OGUA  ( 394-)  0      N1
 383 OGUA  ( 394-)  0      N2
 471 OGUA  ( 482-)  0      O2'
 490 OGUA  ( 501-)  0      N2
 501 OGUA  ( 512-)  0      N1
 543 OGUA  ( 554-)  0      N2
 548 OURA  ( 559-)  0      N3
 560 OCYT  ( 571-)  0      N4
 576 OADE  ( 587-)  0      N6
 599 OGUA  ( 610-)  0      N2
 613 OURA  ( 624-)  0      N3
 614 OURA  ( 625-)  0      N3
 629 OGUA  ( 640-)  0      N2
 646 OGUA  ( 657-)  0      O2'
 696 OCYT  ( 707-)  0      N4
 725 OADE  ( 737-)  0      N6
And so on for a total of 454 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.

2790 ASP   (  36-)  A      OD1
2801 HIS   (  47-)  A      ND1
2802 ASP   (  48-)  A      OD1
2861 ASN   ( 107-)  A      OD1
3057 GLU   (  66-)  B      OE1
3247 GLN   ( 256-)  B      OE1
3493 ASP   ( 165-)  C      OD2
3545 GLU   ( 217-)  C      OE2
3627 ASP   (  67-)  D      OD1
3659 ASP   (  99-)  D      OD2
3673 ASN   ( 133-)  D      OD1
3711 ASP   ( 171-)  D      OD2
3878 ASP   ( 164-)  E      OD2
3944 GLU   (  58-)  F      OE1
3944 GLU   (  58-)  F      OE2
4428 ASP   (  22-)  K      OD1
4450 HIS   (  44-)  K      ND1
4556 HIS   (  18-)  L      ND1
4608 ASP   (  70-)  L      OD1
4840 ASP   ( 157-)  M      OD2
4932 ASP   (  55-)  N      OD2
5041 ASP   ( 164-)  N      OD1
5044 ASP   ( 167-)  N      OD2
5273 GLU   (  95-)  P      OE2
5823 HIS   (   4-)  V      ND1
6003 HIS   ( 119-)  W      ND1
6290 HIS   (  61-)  Z      NE2
6437 GLU   (  49-)  2      OE1
6457 HIS   (  20-)  3      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

6675  MG   (8001-)  0     0.48   0.95 Is perhaps NA *1
6676  MG   (8002-)  0     0.42   0.84 Scores about as good as NA *1
6677  MG   (8003-)  0   -.-  -.-  Part of ionic cluster
6677  MG   (8003-)  0     0.52   1.03 Is perhaps NA *1
6678  MG   (8004-)  0     0.63   1.02 Scores about as good as CA
6679  MG   (8005-)  0     0.44   0.88 Is perhaps NA *1
6680  MG   (8006-)  0     0.38   0.75 Scores about as good as NA *1
6681  MG   (8007-)  0   -.-  -.-  Part of ionic cluster
6681  MG   (8007-)  0     0.51   1.02 Is perhaps NA *1
6682  MG   (8008-)  0     0.39   0.79 Scores about as good as NA *1
6683  MG   (8009-)  0   -.-  -.-  Part of ionic cluster
6683  MG   (8009-)  0     0.40   0.80 Scores about as good as NA *1
6684  MG   (8010-)  0     0.36   0.72 Scores about as good as NA *1
6685  MG   (8011-)  0     0.52   1.04 Is perhaps NA *1
6686  MG   (8012-)  0     0.46   0.92 Is perhaps NA *1
6687  MG   (8013-)  0     0.36   1.75 Scores about as good as  K *1 and *2
6688  MG   (8014-)  0     0.44   0.88 Is perhaps NA *1
6689  MG   (8015-)  0     0.46   0.92 Is perhaps NA *1
6690  MG   (8016-)  0     0.44   0.88 Is perhaps NA *1
6691  MG   (8017-)  0     0.31   1.07 Is perhaps  K (Few ligands (4) ) *1 and *2
6692  MG   (8018-)  0   -.-  -.-  Part of ionic cluster
6692  MG   (8018-)  0     0.44   0.88 Is perhaps NA *1
6693  MG   (8019-)  0     0.40   0.80 Scores about as good as NA *1
6694  MG   (8020-)  0     0.34   1.49 Is perhaps  K *1 and *2
6695  MG   (8021-)  0     0.46   0.93 Is perhaps NA *1
And so on for a total of 200 lines.

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

6982 HOH   (5522 )  0      O  0.82  K  5 *1 and *2 Ion-B
6982 HOH   (8748 )  0      O  0.84  K  4 *1 and *2 ION-B
6994 HOH   ( 353 )  L      O  1.16  K  5 *1 and *2
6994 HOH   (7471 )  L      O  0.87  K  5 *1 and *2 Ion-B
6996 HOH   (2957 )  N      O  0.82  K  4 *1 and *2 Ion-B H2O-B
6997 HOH   (1937 )  O      O  0.98  K  5 *1 and *2
7002 HOH   (7276 )  T      O  1.11  K  4 *1 and *2

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.

2832 ASP   (  78-)  A   H-bonding suggests Asn
2852 GLU   (  98-)  A   H-bonding suggests Gln; but Alt-Rotamer
2855 GLU   ( 101-)  A   H-bonding suggests Gln; but Alt-Rotamer
2868 ASP   ( 114-)  A   H-bonding suggests Asn
2920 ASP   ( 166-)  A   H-bonding suggests Asn
3024 ASP   (  33-)  B   H-bonding suggests Asn
3048 GLU   (  57-)  B   H-bonding suggests Gln
3080 ASP   (  89-)  B   H-bonding suggests Asn
3101 ASP   ( 110-)  B   H-bonding suggests Asn
3167 ASP   ( 176-)  B   H-bonding suggests Asn
3175 ASP   ( 184-)  B   H-bonding suggests Asn
3262 ASP   ( 271-)  B   H-bonding suggests Asn; but Alt-Rotamer
3272 ASP   ( 281-)  B   H-bonding suggests Asn
3296 ASP   ( 305-)  B   H-bonding suggests Asn
3335 ASP   (   7-)  C   H-bonding suggests Asn; but Alt-Rotamer
3432 ASP   ( 104-)  C   H-bonding suggests Asn
3454 ASP   ( 126-)  C   H-bonding suggests Asn
3460 ASP   ( 132-)  C   H-bonding suggests Asn; but Alt-Rotamer
3539 ASP   ( 211-)  C   H-bonding suggests Asn
3580 GLU   (  15-)  D   H-bonding suggests Gln; but Alt-Rotamer
3599 ASP   (  39-)  D   H-bonding suggests Asn
3627 ASP   (  67-)  D   H-bonding suggests Asn
3711 ASP   ( 171-)  D   H-bonding suggests Asn
3726 ASP   (  12-)  E   H-bonding suggests Asn; but Alt-Rotamer
3751 ASP   (  37-)  E   H-bonding suggests Asn
And so on for a total of 80 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 :  -2.810
  2nd generation packing quality :  -4.215 (bad)
  Ramachandran plot appearance   :  -4.533 (bad)
  chi-1/chi-2 rotamer normality  :  -2.835
  Backbone conformation          :  -0.004

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.412 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   0.186 (tight)
  Side chain planarity           :   0.202 (tight)
  Improper dihedral distribution :   0.580
  B-factor distribution          :   0.372
  Inside/Outside distribution    :   0.989

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 : 3.11


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.6
  2nd generation packing quality :  -1.9
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.412 (tight)
  Bond angles                    :   0.644 (tight)
  Omega angle restraints         :   0.186 (tight)
  Side chain planarity           :   0.202 (tight)
  Improper dihedral distribution :   0.580
  B-factor distribution          :   0.372
  Inside/Outside distribution    :   0.989
==============

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.