WHAT IF Check report

This file was created 2012-01-04 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 pdb1m8q.ent

Checks that need to be done early-on in validation

Warning: Class of space group could be incorrect

The space group symbol indicates a different class than the unit cell given on the CRYST1 card of the PDB file.

Possible cause: The unit cell may have pseudo-symmetry, or one of the cell dimensions or the space group might be given incorrectly.

Crystal class of the cell: CUBIC

Crystal class of the space group: TRICLINIC

Space group name: P 1

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 7.227
CA-only RMS fit for the two chains : 7.221

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and G

All-atom RMS fit for the two chains : 12.531
CA-only RMS fit for the two chains : 12.558

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and G

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and P

All-atom RMS fit for the two chains : 9.815
CA-only RMS fit for the two chains : 9.823

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and P

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: 1066131.0
Volume of the Unit Cell V= 27008100.0
Space group multiplicity: 1
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 25.333
Vm by authors and this calculated Vm do not agree very well

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.

 212 GLN   ( 215-)  A  -
 405 VAL   ( 408-)  A  -
 406 GLY   ( 409-)  A  -
 408 GLU   ( 411-)  A  -
 498 GLU   ( 501-)  A  -
 534 GLU   ( 537-)  A  -
 535 GLU   ( 538-)  A  -
 540 PRO   ( 543-)  A  -
 626 GLU   ( 629-)  A  -
 629 GLY   ( 632-)  A  -
 630 GLY   ( 633-)  A  -
 634 LYS   ( 637-)  A  -
 639 LYS   ( 642-)  A  -
 644 GLN   ( 647-)  A  -
 729 ILE   ( 732-)  A  -
 733 GLN   ( 736-)  A  -
 758 GLY   ( 761-)  A  -
 768 LEU   ( 771-)  A  -
 816 ASN   ( 819-)  A  -
 933 SER   ( 111-)  B  -
 959 TRP   ( 137-)  B  -
 987 LYS   (   4-)  C  -
1026 ASN   (  43-)  C  -
1344 GLN   ( 215-)  D  -
1537 VAL   ( 408-)  D  -
And so on for a total of 119 lines.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

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: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: 7

Note: Ramachandran plot

Chain identifier: 8

Note: Ramachandran plot

Chain identifier: 9

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: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

Chain identifier: 5

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

  16 MLY   (  19-)  A
  27 MLY   (  30-)  A
  32 MLY   (  35-)  A
  46 MLY   (  49-)  A
  52 MLY   (  55-)  A
  56 MLY   (  59-)  A
  60 MLY   (  63-)  A
  81 MLY   (  84-)  A
  84 MLY   (  87-)  A
 104 MLY   ( 107-)  A
 127 MLY   ( 130-)  A
 135 MLY   ( 138-)  A
 187 MLY   ( 190-)  A
 233 MLY   ( 236-)  A
 245 MLY   ( 248-)  A
 269 MLY   ( 272-)  A
 292 MLY   ( 295-)  A
 293 MLY   ( 296-)  A
 344 MLY   ( 348-)  A
 349 MLY   ( 353-)  A
 363 MLY   ( 367-)  A
 365 MLY   ( 369-)  A
 381 MLY   ( 385-)  A
 411 MLY   ( 415-)  A
 427 MLY   ( 431-)  A
And so on for a total of 179 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 not mentioned in PDB file. This most likely means that the temperature record is absent.
Room temperature assumed

Warning: Low M-factor

The B-factor flatness, the M-factor, is very low. This is very worrisome. I suggest you consult the WHAT CHECK website and/or a seasoned crystallographer.

The M-factor = 0.000

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: A

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: B

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: C

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: D

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: E

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: F

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: G

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: H

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: I

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: P

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Q

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: R

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 7

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 8

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 9

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: V

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: W

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: X

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Y

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: Z

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 0

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 1

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 2

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 3

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 4

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 5

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.

 985 ARG   (  19-)  C
1001 ARG   (  35-)  C
1058 ARG   (  92-)  C
1074 ARG   ( 108-)  C
2100 ARG   (  19-)  F
2116 ARG   (  35-)  F
2173 ARG   (  92-)  F
2189 ARG   ( 108-)  F
3218 ARG   (  19-)  I
3234 ARG   (  35-)  I
3291 ARG   (  92-)  I
3307 ARG   ( 108-)  I
4335 ARG   (  19-)  R
4351 ARG   (  35-)  R
4408 ARG   (  92-)  R
4424 ARG   ( 108-)  R

Warning: Tyrosine convention problem

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

 956 TYR   ( 150-)  B
1105 TYR   ( 139-)  C
2071 TYR   ( 150-)  E
2220 TYR   ( 139-)  F
3189 TYR   ( 150-)  H
3338 TYR   ( 139-)  I
4306 TYR   ( 150-)  Q
4455 TYR   ( 139-)  R

Warning: Phenylalanine convention problem

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

 840 PHE   (  31-)  B
 889 PHE   (  80-)  B
 909 PHE   ( 101-)  B
 924 PHE   ( 116-)  B
 948 PHE   ( 140-)  B
 980 PHE   (  14-)  C
 983 PHE   (  17-)  C
1031 PHE   (  65-)  C
1053 PHE   (  87-)  C
1060 PHE   (  94-)  C
1955 PHE   (  31-)  E
2004 PHE   (  80-)  E
2025 PHE   ( 101-)  E
2039 PHE   ( 116-)  E
2062 PHE   ( 140-)  E
2095 PHE   (  14-)  F
2098 PHE   (  17-)  F
2146 PHE   (  65-)  F
2168 PHE   (  87-)  F
2175 PHE   (  94-)  F
3072 PHE   (  31-)  H
3121 PHE   (  80-)  H
3142 PHE   ( 101-)  H
3157 PHE   ( 116-)  H
3181 PHE   ( 140-)  H
3213 PHE   (  14-)  I
3216 PHE   (  17-)  I
3264 PHE   (  65-)  I
3286 PHE   (  87-)  I
3293 PHE   (  94-)  I
4189 PHE   (  31-)  Q
4238 PHE   (  80-)  Q
4259 PHE   ( 101-)  Q
4274 PHE   ( 116-)  Q
4297 PHE   ( 140-)  Q
4330 PHE   (  14-)  R
4333 PHE   (  17-)  R
4381 PHE   (  65-)  R
4403 PHE   (  87-)  R
4410 PHE   (  94-)  R

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.

 829 ASP   (  20-)  B
 835 ASP   (  26-)  B
 854 ASP   (  45-)  B
 855 ASP   (  46-)  B
 903 ASP   (  95-)  B
 955 ASP   ( 149-)  B
 968 ASP   ( 162-)  B
 974 ASP   (   8-)  C
 998 ASP   (  32-)  C
1052 ASP   (  86-)  C
1061 ASP   (  95-)  C
1944 ASP   (  20-)  E
1950 ASP   (  26-)  E
1969 ASP   (  45-)  E
1970 ASP   (  46-)  E
2019 ASP   (  95-)  E
2070 ASP   ( 149-)  E
2083 ASP   ( 162-)  E
2089 ASP   (   8-)  F
2113 ASP   (  32-)  F
2167 ASP   (  86-)  F
2176 ASP   (  95-)  F
3061 ASP   (  20-)  H
3067 ASP   (  26-)  H
3086 ASP   (  45-)  H
3087 ASP   (  46-)  H
3136 ASP   (  95-)  H
3188 ASP   ( 149-)  H
3201 ASP   ( 162-)  H
3207 ASP   (   8-)  I
3231 ASP   (  32-)  I
3285 ASP   (  86-)  I
3294 ASP   (  95-)  I
4178 ASP   (  20-)  Q
4184 ASP   (  26-)  Q
4203 ASP   (  45-)  Q
4204 ASP   (  46-)  Q
4253 ASP   (  95-)  Q
4305 ASP   ( 149-)  Q
4318 ASP   ( 162-)  Q
4324 ASP   (   8-)  R
4348 ASP   (  32-)  R
4402 ASP   (  86-)  R
4411 ASP   (  95-)  R

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.

 832 GLU   (  23-)  B
 834 GLU   (  25-)  B
 838 GLU   (  29-)  B
 858 GLU   (  49-)  B
 879 GLU   (  70-)  B
 895 GLU   (  86-)  B
 978 GLU   (  12-)  C
1033 GLU   (  67-)  C
1051 GLU   (  85-)  C
1055 GLU   (  89-)  C
1072 GLU   ( 106-)  C
1082 GLU   ( 116-)  C
1086 GLU   ( 120-)  C
1087 GLU   ( 121-)  C
1097 GLU   ( 131-)  C
1947 GLU   (  23-)  E
1949 GLU   (  25-)  E
1953 GLU   (  29-)  E
1973 GLU   (  49-)  E
1994 GLU   (  70-)  E
2010 GLU   (  86-)  E
2093 GLU   (  12-)  F
2148 GLU   (  67-)  F
2166 GLU   (  85-)  F
2170 GLU   (  89-)  F
And so on for a total of 60 lines.

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.

   1 ASP   (   4-)  A      CG   OD1   1.33    4.3
  20 GLU   (  23-)  A      CD   OE1   1.33    4.4
  23 GLU   (  26-)  A      CD   OE1   1.33    4.1
  65 GLU   (  68-)  A      CD   OE2   1.33    4.2
  72 ASP   (  75-)  A      CG   OD1   1.34    4.8
  83 ASP   (  86-)  A      CG   OD1   1.34    4.6
  95 HIS   (  98-)  A      CB   CG    1.44   -4.3
 105 GLU   ( 108-)  A      CD   OE1   1.34    4.7
 199 SER   ( 202-)  A      CB   OG    1.52    5.0
 199 SER   ( 202-)  A      N   -C     1.24   -4.2
 214 THR   ( 217-)  A      CA   CB    1.61    4.0
 215 LEU   ( 218-)  A      CB   CG    1.69    7.8
 216 GLU   ( 219-)  A      N   -C     1.21   -5.8
 238 ASP   ( 241-)  A      CG   OD1   1.34    4.7
 285 PHE   ( 288-)  A      CA   C     1.44   -4.1
 303 THR   ( 306-)  A      CB   OG1   1.36   -4.4
 324 ASP   ( 327-)  A      CG   OD1   1.33    4.4
 327 GLU   ( 330-)  A      CD   OE1   1.33    4.1
 342 ASP   ( 346-)  A      CG   OD2   1.33    4.5
 343 GLU   ( 347-)  A      CD   OE1   1.33    4.3
 372 GLU   ( 376-)  A      CD   OE1   1.33    4.2
 377 GLU   ( 381-)  A      CD   OE1   1.34    4.8
 407 GLU   ( 411-)  A      CD   OE1   1.34    5.0
 430 TYR   ( 434-)  A      CA   CB    1.44   -4.5
 472 GLU   ( 476-)  A      CD   OE1   1.35    5.2
And so on for a total of 285 lines.

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

 |  1.001878  0.000016 -0.000014|
 |  0.000016  1.001798  0.000003|
 | -0.000014  0.000003  1.001532|
Proposed new scale matrix

 |  0.003327  0.000000  0.000000|
 |  0.000000  0.003327  0.000000|
 |  0.000000  0.000000  0.003328|
With corresponding cell

    A    = 300.594  B   = 300.570  C    = 300.490
    Alpha=  90.003  Beta=  90.003  Gamma=  90.003

The CRYST1 cell dimensions

    A    = 300.000  B   = 300.000  C    = 300.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 926.735
(Under-)estimated Z-score: 22.436

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.

  19 LYS   (  22-)  A      C    CA   CB  118.51    4.4
  35 VAL   (  38-)  A      N    CA   CB  102.71   -4.6
  44 PHE   (  47-)  A      C    CA   CB  100.98   -4.8
  68 THR   (  71-)  A      N    CA   CB  117.39    4.1
  72 ASP   (  75-)  A      N    CA   CB  122.97    7.3
  72 ASP   (  75-)  A      C    CA   CB  117.75    4.0
  79 PRO   (  82-)  A      N    CA   CB  109.38    5.8
  85 ILE   (  88-)  A      CB   CG1  CD1 101.59   -5.8
  95 HIS   (  98-)  A      C    CA   CB   87.34  -12.0
  95 HIS   (  98-)  A      CD2  CG   ND1 110.46    4.4
 101 TYR   ( 104-)  A      C    CA   CB  117.97    4.1
 115 TYR   ( 118-)  A      C    CA   CB  101.53   -4.5
 125 PRO   ( 128-)  A      N    CA   CB  108.16    4.7
 134 PRO   ( 137-)  A     -CA  -C    N   108.46   -5.6
 138 LEU   ( 141-)  A      C    CA   CB   97.93   -6.4
 150 PRO   ( 153-)  A      N    CA   CB  107.44    4.0
 158 ASN   ( 161-)  A      CA   CB   CG  107.59   -5.0
 158 ASN   ( 161-)  A      ND2  CG   OD1 127.41    4.8
 162 PHE   ( 165-)  A      N    CA   CB  100.31   -6.0
 162 PHE   ( 165-)  A      CA   CB   CG  108.75   -5.1
 169 ASN   ( 172-)  A      N    CA   CB  118.19    4.5
 170 GLN   ( 173-)  A      N    CA   CB  102.93   -4.5
 177 GLU   ( 180-)  A      N    CA   CB  118.52    4.7
 189 VAL   ( 192-)  A      CA   CB   CG1 102.03   -5.0
 193 PHE   ( 196-)  A      CA   CB   CG  108.20   -5.6
And so on for a total of 2712 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.

 829 ASP   (  20-)  B
 832 GLU   (  23-)  B
 834 GLU   (  25-)  B
 835 ASP   (  26-)  B
 838 GLU   (  29-)  B
 854 ASP   (  45-)  B
 855 ASP   (  46-)  B
 858 GLU   (  49-)  B
 879 GLU   (  70-)  B
 895 GLU   (  86-)  B
 903 ASP   (  95-)  B
 955 ASP   ( 149-)  B
 968 ASP   ( 162-)  B
 974 ASP   (   8-)  C
 978 GLU   (  12-)  C
 985 ARG   (  19-)  C
 998 ASP   (  32-)  C
1001 ARG   (  35-)  C
1033 GLU   (  67-)  C
1051 GLU   (  85-)  C
1052 ASP   (  86-)  C
1055 GLU   (  89-)  C
1058 ARG   (  92-)  C
1061 ASP   (  95-)  C
1072 GLU   ( 106-)  C
And so on for a total of 120 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.

  72 ASP   (  75-)  A      CA   -12.3     9.24    33.73
  95 HIS   (  98-)  A      CA     8.3    49.40    34.11
  95 HIS   (  98-)  A      C      8.6    13.03     0.15
 134 PRO   ( 137-)  A      N      6.1    17.48    -2.48
 261 ASP   ( 264-)  A      CA     7.8    49.30    33.73
 337 LEU   ( 341-)  A      CA    -8.5    21.14    34.19
 443 GLN   ( 447-)  A      CA   -12.3    10.22    33.96
 476 ILE   ( 480-)  A      CB     6.5    40.78    32.31
 617 THR   ( 625-)  A      CB     6.5    48.67    34.09
 620 GLY   ( 628-)  A      C     -6.2    -8.14     0.06
 637 THR   ( 648-)  A      CB   -13.7     3.46    34.09
 638 VAL   ( 649-)  A      C      7.9    10.99     0.15
 638 VAL   ( 649-)  A      CB   -35.1   -78.98   -32.96
 687 ASN   ( 698-)  A      C     -6.0    -9.22     0.27
 743 THR   ( 756-)  A      CA     6.6    44.80    33.84
 816 MET   ( 832-)  A      CA    -7.6    20.55    34.17
 824 PRO   ( 840-)  A      N     -6.2   -22.82    -2.48
 830 GLU   (  21-)  B      C      6.6     9.47    -0.03
 831 THR   (  22-)  B      C      7.5    11.50     0.30
 833 ILE   (  24-)  B      C      6.4     8.36     0.03
 854 ASP   (  45-)  B      C      6.3     9.62    -0.01
 861 ALA   (  52-)  B      C      6.2     9.58     0.08
 870 ASN   (  61-)  B      C      6.6    10.71     0.27
 872 GLU   (  63-)  B      C      7.1    10.24    -0.03
 876 MET   (  67-)  B      C      6.2     9.34     0.17
And so on for a total of 210 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.

8836 ARG   ( 335-)  3    7.43
5527 ARG   ( 335-)  9    7.41
9208 ARG   ( 335-)  4    7.41
7361 ARG   ( 335-)  Z    7.41
8465 ARG   ( 335-)  2    7.40
6256 ARG   ( 335-)  W    7.39
8096 ARG   ( 335-)  1    7.39
4798 ARG   ( 335-)  7    7.38
6990 ARG   ( 335-)  Y    7.37
6622 ARG   ( 335-)  X    7.36
9445 PHE   ( 200-)  5    6.90
4117 ALA   ( 784-)  P    6.65
1883 ALA   ( 784-)  D    6.61
3001 ALA   ( 784-)  G    6.57
 769 ALA   ( 784-)  A    6.57
9392 ARG   ( 147-)  5    6.54
3563 GLU   ( 219-)  P    6.28
2445 GLU   ( 219-)  G    6.27
9196 SER   ( 323-)  4    6.26
 216 GLU   ( 219-)  A    6.22
1331 GLU   ( 219-)  D    6.20
8126 ALA   ( 365-)  1    6.10
8866 ALA   ( 365-)  3    6.10
7391 ALA   ( 365-)  Z    6.09
7020 ALA   ( 365-)  Y    6.09
And so on for a total of 286 lines.

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.717

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 956 TYR   ( 150-)  B   15.57
2071 TYR   ( 150-)  E   15.55
3189 TYR   ( 150-)  H   15.05
4306 TYR   ( 150-)  Q   14.81
4334 ASP   (  18-)  R    9.74
3217 ASP   (  18-)  I    9.71
 984 ASP   (  18-)  C    9.71
2099 ASP   (  18-)  F    9.69
2031 ASP   ( 107-)  E    8.30
4265 ASP   ( 107-)  Q    8.19
 915 ASP   ( 107-)  B    8.17
3148 ASP   ( 107-)  H    8.10
4405 GLU   (  89-)  R    7.04
1055 GLU   (  89-)  C    6.90
3288 GLU   (  89-)  I    6.88
2170 GLU   (  89-)  F    6.83
4317 GLU   ( 161-)  Q    5.81
2187 GLU   ( 106-)  F    5.72
4422 GLU   ( 106-)  R    5.70
 967 GLU   ( 161-)  B    5.69
2082 GLU   ( 161-)  E    5.63
3200 GLU   ( 161-)  H    5.63
3324 GLU   ( 125-)  I    5.61
1072 GLU   ( 106-)  C    5.59
3305 GLU   ( 106-)  I    5.54
And so on for a total of 74 lines.

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 615 PHE   ( 623-)  A      CB   7.04
1728 PHE   ( 623-)  D      CB   7.01
3963 PHE   ( 623-)  P      CB   6.98
2846 PHE   ( 623-)  G      CB   6.98
9616 HIS   ( 371-)  5      CB   5.62
5923 HIS   ( 371-)  V      CB   5.62
4834 HIS   ( 371-)  7      CB   5.60
7761 HIS   ( 371-)  0      CB   5.60
7397 HIS   ( 371-)  Z      CB   5.60
7026 HIS   ( 371-)  Y      CB   5.59
6292 HIS   ( 371-)  W      CB   5.59
9244 HIS   ( 371-)  4      CB   5.58
5196 HIS   ( 371-)  8      CB   5.58
8501 HIS   ( 371-)  2      CB   5.58
8132 HIS   ( 371-)  1      CB   5.57
5561 HIS   ( 371-)  9      CB   5.57
8872 HIS   ( 371-)  3      CB   5.57
6658 HIS   ( 371-)  X      CB   5.56
6096 HIS   ( 173-)  W      CB   4.18
8675 HIS   ( 173-)  3      CB   4.18
4638 HIS   ( 173-)  7      CB   4.18
6465 HIS   ( 173-)  X      CB   4.18
7200 HIS   ( 173-)  Z      CB   4.17
6832 HIS   ( 173-)  Y      CB   4.17
5367 HIS   ( 173-)  9      CB   4.17
8305 HIS   ( 173-)  2      CB   4.17
9046 HIS   ( 173-)  4      CB   4.16
5731 HIS   ( 173-)  V      CB   4.16
7935 HIS   ( 173-)  1      CB   4.16
7569 HIS   ( 173-)  0      CB   4.16
9418 HIS   ( 173-)  5      CB   4.16
5003 HIS   ( 173-)  8      CB   4.16
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.361

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 : -4.361

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.

4298 PRO   ( 141-)  Q    -2.9
3182 PRO   ( 141-)  H    -2.9
 949 PRO   ( 141-)  B    -2.9
2063 PRO   ( 141-)  E    -2.9
3046 PRO   ( 830-)  G    -2.9
 814 PRO   ( 830-)  A    -2.9
1929 PRO   ( 830-)  D    -2.9
4163 PRO   ( 830-)  P    -2.9
4120 ILE   ( 787-)  P    -2.9
1241 TYR   ( 129-)  D    -2.8
3474 TYR   ( 129-)  P    -2.8
 126 TYR   ( 129-)  A    -2.8
2356 TYR   ( 129-)  G    -2.8
8611 PRO   ( 109-)  3    -2.8
9354 PRO   ( 109-)  5    -2.8
6401 PRO   ( 109-)  X    -2.8
5303 PRO   ( 109-)  9    -2.8
5669 PRO   ( 109-)  V    -2.8
7871 PRO   ( 109-)  1    -2.8
8241 PRO   ( 109-)  2    -2.8
4941 PRO   ( 109-)  8    -2.8
7136 PRO   ( 109-)  Z    -2.8
6032 PRO   ( 109-)  W    -2.8
4574 PRO   ( 109-)  7    -2.8
7506 PRO   ( 109-)  0    -2.8
And so on for a total of 548 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.

   8 GLY   (  11-)  A  Poor phi/psi
  18 GLU   (  21-)  A  Poor phi/psi
  55 GLY   (  58-)  A  Poor phi/psi
  70 LYS   (  73-)  A  Poor phi/psi
 110 TRP   ( 113-)  A  Poor phi/psi
 126 TYR   ( 129-)  A  Poor phi/psi
 167 ARG   ( 170-)  A  Poor phi/psi
 196 ILE   ( 199-)  A  Poor phi/psi
 198 ALA   ( 201-)  A  Poor phi/psi
 199 SER   ( 202-)  A  Poor phi/psi
 201 GLU   ( 204-)  A  Poor phi/psi
 208 SER   ( 211-)  A  Poor phi/psi
 210 LYS   ( 213-)  A  Poor phi/psi
 216 GLU   ( 219-)  A  Poor phi/psi
 291 ASN   ( 294-)  A  Poor phi/psi
 301 LEU   ( 304-)  A  Poor phi/psi
 367 ARG   ( 371-)  A  Poor phi/psi
 407 GLU   ( 411-)  A  Poor phi/psi
 502 GLY   ( 507-)  A  Poor phi/psi
 552 GLY   ( 560-)  A  Poor phi/psi
 564 LYS   ( 572-)  A  Poor phi/psi
 569 ALA   ( 577-)  A  omega poor
 638 VAL   ( 649-)  A  omega poor
 639 SER   ( 650-)  A  Poor phi/psi
 655 SER   ( 666-)  A  Poor phi/psi
And so on for a total of 326 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 : -4.622

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.

2562 SER   ( 336-)  G    0.33
 156 SER   ( 159-)  A    0.36
1271 SER   ( 159-)  D    0.36
2386 SER   ( 159-)  G    0.36
3503 SER   ( 159-)  P    0.36
 333 SER   ( 336-)  A    0.37
1448 SER   ( 336-)  D    0.37
 416 SER   ( 420-)  A    0.37
1530 SER   ( 420-)  D    0.37
2646 SER   ( 420-)  G    0.37
3762 SER   ( 420-)  P    0.37
4746 SER   ( 281-)  7    0.40
5111 SER   ( 281-)  8    0.40
5475 SER   ( 281-)  9    0.40
5837 SER   ( 281-)  V    0.40
6203 SER   ( 281-)  W    0.40
6570 SER   ( 281-)  X    0.40
6938 SER   ( 281-)  Y    0.40
7307 SER   ( 281-)  Z    0.40
7675 SER   ( 281-)  0    0.40
8042 SER   ( 281-)  1    0.40
8413 SER   ( 281-)  2    0.40
8783 SER   ( 281-)  3    0.40
9154 SER   ( 281-)  4    0.40
9526 SER   ( 281-)  5    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!

   4 MET   (   7-)  A      0
   7 PHE   (  10-)  A      0
  14 LEU   (  17-)  A      0
  15 ARG   (  18-)  A      0
  16 MLY   (  19-)  A      0
  27 MLY   (  30-)  A      0
  28 PRO   (  31-)  A      0
  32 MLY   (  35-)  A      0
  33 SER   (  36-)  A      0
  34 SER   (  37-)  A      0
  42 GLN   (  45-)  A      0
  43 SER   (  46-)  A      0
  44 PHE   (  47-)  A      0
  46 MLY   (  49-)  A      0
  52 MLY   (  55-)  A      0
  53 GLU   (  56-)  A      0
  56 MLY   (  59-)  A      0
  60 MLY   (  63-)  A      0
  62 GLU   (  65-)  A      0
  65 GLU   (  68-)  A      0
  72 ASP   (  75-)  A      0
  73 GLN   (  76-)  A      0
  81 MLY   (  84-)  A      0
  83 ASP   (  86-)  A      0
  84 MLY   (  87-)  A      0
And so on for a total of 3744 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!

2294 GLY   (  67-)  G   2.50   80
3412 GLY   (  67-)  P   2.50   80
1179 GLY   (  67-)  D   2.50   80
  64 GLY   (  67-)  A   2.49   80
2755 PRO   ( 529-)  G   2.29   11
3870 PRO   ( 529-)  P   2.29   11
1639 PRO   ( 529-)  D   2.29   11
 524 PRO   ( 529-)  A   2.29   11
3624 PRO   ( 280-)  P   2.20   10
2506 PRO   ( 280-)  G   2.20   10
1392 PRO   ( 280-)  D   2.20   10
 277 PRO   ( 280-)  A   2.20   10
2633 GLY   ( 407-)  G   2.03   16
 403 GLY   ( 407-)  A   2.03   16
3750 GLY   ( 407-)  P   2.03   16
7173 GLY   ( 146-)  Z   1.59   80
6438 GLY   ( 146-)  X   1.59   80
9391 GLY   ( 146-)  5   1.59   80
8278 GLY   ( 146-)  2   1.58   80
9019 GLY   ( 146-)  4   1.58   80
8648 GLY   ( 146-)  3   1.58   80
6069 GLY   ( 146-)  W   1.58   80
5340 GLY   ( 146-)  9   1.58   80
7908 GLY   ( 146-)  1   1.58   80
4611 GLY   ( 146-)  7   1.58   80
6805 GLY   ( 146-)  Y   1.58   80

Warning: Unusual PRO puckering amplitudes

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

  12 PRO   (  15-)  A    0.04 LOW
  28 PRO   (  31-)  A    0.09 LOW
  40 PRO   (  43-)  A    0.10 LOW
  79 PRO   (  82-)  A    0.15 LOW
  80 PRO   (  83-)  A    0.13 LOW
  97 PRO   ( 100-)  A    0.20 LOW
 125 PRO   ( 128-)  A    0.07 LOW
 130 PRO   ( 133-)  A    0.15 LOW
 134 PRO   ( 137-)  A    0.17 LOW
 149 PRO   ( 152-)  A    0.20 LOW
 224 PRO   ( 227-)  A    0.04 LOW
 277 PRO   ( 280-)  A    0.12 LOW
 294 PRO   ( 297-)  A    0.08 LOW
 306 PRO   ( 309-)  A    0.20 LOW
 320 PRO   ( 323-)  A    0.14 LOW
 373 PRO   ( 377-)  A    0.08 LOW
 400 PRO   ( 404-)  A    0.15 LOW
 450 PRO   ( 454-)  A    0.02 LOW
 524 PRO   ( 529-)  A    0.13 LOW
 538 PRO   ( 543-)  A    0.06 LOW
 560 PRO   ( 568-)  A    0.02 LOW
 562 PRO   ( 570-)  A    0.07 LOW
 594 PRO   ( 602-)  A    0.03 LOW
 658 PRO   ( 669-)  A    0.13 LOW
 666 PRO   ( 677-)  A    0.02 LOW
And so on for a total of 213 lines.

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].

 150 PRO   ( 153-)  A   171.5 envelop N (180 degrees)
 814 PRO   ( 830-)  A   156.3 half-chair C-alpha/N (162 degrees)
 949 PRO   ( 141-)  B  -160.0 half-chair N/C-delta (-162 degrees)
1007 PRO   (  41-)  C   -10.3 half-chair C-alpha/N (-18 degrees)
1265 PRO   ( 153-)  D   171.4 envelop N (180 degrees)
1929 PRO   ( 830-)  D   156.5 half-chair C-alpha/N (162 degrees)
2063 PRO   ( 141-)  E  -160.3 half-chair N/C-delta (-162 degrees)
2122 PRO   (  41-)  F   -10.7 half-chair C-alpha/N (-18 degrees)
2380 PRO   ( 153-)  G   171.6 envelop N (180 degrees)
3046 PRO   ( 830-)  G   156.8 half-chair C-alpha/N (162 degrees)
3182 PRO   ( 141-)  H  -159.4 half-chair N/C-delta (-162 degrees)
3240 PRO   (  41-)  I   -11.0 half-chair C-alpha/N (-18 degrees)
3497 PRO   ( 153-)  P   171.5 envelop N (180 degrees)
4163 PRO   ( 830-)  P   156.9 half-chair C-alpha/N (162 degrees)
4298 PRO   ( 141-)  Q  -160.4 half-chair N/C-delta (-162 degrees)
4357 PRO   (  41-)  R   -10.4 half-chair C-alpha/N (-18 degrees)
4574 PRO   ( 109-)  7   112.4 envelop C-beta (108 degrees)
4941 PRO   ( 109-)  8   112.2 envelop C-beta (108 degrees)
5303 PRO   ( 109-)  9   112.3 envelop C-beta (108 degrees)
5669 PRO   ( 109-)  V   112.3 envelop C-beta (108 degrees)
6032 PRO   ( 109-)  W   112.3 envelop C-beta (108 degrees)
6401 PRO   ( 109-)  X   112.3 envelop C-beta (108 degrees)
6768 PRO   ( 109-)  Y   112.3 envelop C-beta (108 degrees)
7136 PRO   ( 109-)  Z   112.3 envelop C-beta (108 degrees)
7506 PRO   ( 109-)  0   112.2 envelop C-beta (108 degrees)
7871 PRO   ( 109-)  1   112.4 envelop C-beta (108 degrees)
8241 PRO   ( 109-)  2   112.3 envelop C-beta (108 degrees)
8611 PRO   ( 109-)  3   112.4 envelop C-beta (108 degrees)
8982 PRO   ( 109-)  4   112.4 envelop C-beta (108 degrees)
9354 PRO   ( 109-)  5   112.4 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

2044 LEU   ( 121-)  E      CD1  <->  2050 PHE   ( 128-)  E      CD2  2.62    0.58  INTRA
 929 LEU   ( 121-)  B      CD1  <->   936 PHE   ( 128-)  B      CD2  2.62    0.58  INTRA
3162 LEU   ( 121-)  H      CD1  <->  3169 PHE   ( 128-)  H      CD2  2.62    0.58  INTRA
4279 LEU   ( 121-)  Q      CD1  <->  4286 PHE   ( 128-)  Q      CD2  2.61    0.59  INTRA
1744 LYS   ( 642-)  D      CE   <->  5536 SER   ( 344-)  9      CB   2.45    0.75  INTRA
 632 LYS   ( 642-)  A      CE   <->  5172 SER   ( 344-)  8      CB   2.45    0.75  INTRA
2059 TRP   ( 137-)  E      CH2  <->  2067 GLY   ( 146-)  E      N    2.29    0.81  INTRA
 945 TRP   ( 137-)  B      CH2  <->   953 GLY   ( 146-)  B      N    2.29    0.81  INTRA
3178 TRP   ( 137-)  H      CH2  <->  3186 GLY   ( 146-)  H      N    2.29    0.81  INTRA
1618 ILE   ( 508-)  D      CD1  <->  1865 PHE   ( 766-)  D      CZ   2.28    0.92  INTRA
7509 PRO   ( 112-)  0      CG   <->  7958 GLY   ( 197-)  1      N    2.26    0.84  INTRA
1659 MLY   ( 553-)  D      N    <->  5970 MET   (  47-)  W      CA   2.24    0.86  INTRA
 628 LYS   ( 637-)  A      C    <->  5173 ILE   ( 345-)  8      CD1  2.21    0.99  INTRA
3971 GLY   ( 632-)  P      C    <->  7422 ASP   (  25-)  0      N    2.19    0.91  INTRA
 501 GLU   ( 506-)  A      CG   <->   747 PHE   ( 760-)  A      CB   2.17    1.03  INTRA
 696 CYS   ( 707-)  A      O    <->   703 ARG   ( 714-)  A      NH2  2.14    0.56  INTRA
6575 ASP   ( 286-)  X      CA   <->  7229 THR   ( 202-)  Z      CG2  2.13    1.07  INTRA
4152 ASN   ( 819-)  P      ND2  <->  4250 ASP   (  92-)  Q      CB   2.13    0.97  INTRA
1327 GLN   ( 215-)  D      CD   <->  1451 ILE   ( 340-)  D      N    2.12    0.98  INTRA
3559 GLN   ( 215-)  P      CD   <->  3683 ILE   ( 340-)  P      N    2.11    0.99  INTRA
 212 GLN   ( 215-)  A      CD   <->   336 ILE   ( 340-)  A      N    2.11    0.99  INTRA
3015 LEU   ( 798-)  G      CD1  <->  3325 LEU   ( 126-)  I      CD2  2.10    1.10  INTRA
1659 MLY   ( 553-)  D      CH2  <->  5969 VAL   (  45-)  W      CG2  2.09    1.11  INTRA
3914 LYS   ( 574-)  P      NZ   <->  3929 ASP   ( 589-)  P      OD2  2.06    0.64  INTRA
2797 LYS   ( 574-)  G      NZ   <->  2812 ASP   ( 589-)  G      OD2  2.06    0.64  INTRA
And so on for a total of 5792 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: 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: 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: 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: 1

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: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: 5

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.

2100 ARG   (  19-)  F      -7.72
3218 ARG   (  19-)  I      -7.69
4335 ARG   (  19-)  R      -7.68
 985 ARG   (  19-)  C      -7.68
8914 GLN   (  41-)  4      -7.52
7068 GLN   (  41-)  Z      -7.51
5601 GLN   (  41-)  V      -7.51
6334 GLN   (  41-)  X      -7.51
5235 GLN   (  41-)  9      -7.51
6700 GLN   (  41-)  Y      -7.51
7438 GLN   (  41-)  0      -7.51
4873 GLN   (  41-)  8      -7.51
5965 GLN   (  41-)  W      -7.51
7803 GLN   (  41-)  1      -7.51
8543 GLN   (  41-)  3      -7.51
9286 GLN   (  41-)  5      -7.51
4506 GLN   (  41-)  7      -7.51
 126 TYR   ( 129-)  A      -7.41
3474 TYR   ( 129-)  P      -7.41
1241 TYR   ( 129-)  D      -7.41
2356 TYR   ( 129-)  G      -7.40
3714 ARG   ( 371-)  P      -7.00
 367 ARG   ( 371-)  A      -7.00
2597 ARG   ( 371-)  G      -6.99
1482 ARG   ( 371-)  D      -6.99
And so on for a total of 232 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.

 568 GLU   ( 576-)  A       570 - HIS    578- ( A)         -4.28
1681 GLU   ( 576-)  D      1683 - HIS    578- ( D)         -4.28
1735 GLU   ( 631-)  D      1737 - GLY    633- ( D)         -4.17
2799 GLU   ( 576-)  G      2801 - HIS    578- ( G)         -4.27
2854 GLU   ( 631-)  G      2856 - GLY    633- ( G)         -4.19
3916 GLU   ( 576-)  P      3918 - HIS    578- ( P)         -4.27
4504 ARG   (  39-)  7      4506 - GLN     41- ( 7)         -6.73
4871 ARG   (  39-)  8      4873 - GLN     41- ( 8)         -6.73
5233 ARG   (  39-)  9      5235 - GLN     41- ( 9)         -6.72
5599 ARG   (  39-)  V      5601 - GLN     41- ( V)         -6.72
5963 ARG   (  39-)  W      5965 - GLN     41- ( W)         -6.72
6332 ARG   (  39-)  X      6334 - GLN     41- ( X)         -6.75
6698 ARG   (  39-)  Y      6700 - GLN     41- ( Y)         -6.73
7066 ARG   (  39-)  Z      7068 - GLN     41- ( Z)         -6.70
7436 ARG   (  39-)  0      7438 - GLN     41- ( 0)         -6.73
7801 ARG   (  39-)  1      7803 - GLN     41- ( 1)         -6.75
8172 ARG   (  39-)  2      8174 - GLN     41- ( 2)         -5.72
8541 ARG   (  39-)  3      8543 - GLN     41- ( 3)         -6.73
8912 ARG   (  39-)  4      8914 - GLN     41- ( 4)         -6.73
9227 GLN   ( 354-)  4      9229 - TRP    356- ( 4)         -4.64
9284 ARG   (  39-)  5      9286 - GLN     41- ( 5)         -6.73

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: 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: 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: 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: 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

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

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

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.

 972 ALA   (   6-)  C   -3.14
2087 ALA   (   6-)  F   -3.14
3205 ALA   (   6-)  I   -3.14
 109 ALA   ( 112-)  A   -2.88
1224 ALA   ( 112-)  D   -2.88
3457 ALA   ( 112-)  P   -2.88
7871 PRO   ( 109-)  1   -2.85
7136 PRO   ( 109-)  Z   -2.85
5669 PRO   ( 109-)  V   -2.85
6032 PRO   ( 109-)  W   -2.85
6768 PRO   ( 109-)  Y   -2.85
6401 PRO   ( 109-)  X   -2.85
9285 HIS   (  40-)  5   -2.84
7506 PRO   ( 109-)  0   -2.78
2071 TYR   ( 150-)  E   -2.68
5624 ILE   (  64-)  V   -2.66
5258 ILE   (  64-)  9   -2.65
4529 ILE   (  64-)  7   -2.63
 385 LEU   ( 389-)  A   -2.62
3732 LEU   ( 389-)  P   -2.62
 460 ILE   ( 464-)  A   -2.61
2615 LEU   ( 389-)  G   -2.61
1500 LEU   ( 389-)  D   -2.61
1574 ILE   ( 464-)  D   -2.61
2690 ILE   ( 464-)  G   -2.61
3806 ILE   ( 464-)  P   -2.61
4896 ILE   (  64-)  8   -2.58
8913 HIS   (  40-)  4   -2.52
9564 ALA   ( 319-)  5   -2.52
7638 ASP   ( 244-)  0   -2.51

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.

 587 TRP   ( 595-)  A     -  590 MLY   ( 598-)  A      -251.21
1700 TRP   ( 595-)  D     - 1703 MLY   ( 598-)  D      -251.21
1742 LYS   ( 640-)  D     - 1745 GLY   ( 643-)  D        -1.95
2818 TRP   ( 595-)  G     - 2821 MLY   ( 598-)  G      -251.21
3935 TRP   ( 595-)  P     - 3938 MLY   ( 598-)  P      -251.21

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: 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: 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: 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: 1

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: 4

Note: Second generation quality Z-score plot

Chain identifier: 5

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.

 124 ASN   ( 127-)  A
 477 ASN   ( 481-)  A
 583 ASN   ( 591-)  A
 647 ASN   ( 658-)  A
1239 ASN   ( 127-)  D
1591 ASN   ( 481-)  D
1696 ASN   ( 591-)  D
1760 ASN   ( 658-)  D
1890 GLN   ( 791-)  D
2354 ASN   ( 127-)  G
2376 GLN   ( 149-)  G
2707 ASN   ( 481-)  G
2814 ASN   ( 591-)  G
2878 ASN   ( 658-)  G
2908 HIS   ( 688-)  G
3472 ASN   ( 127-)  P
3823 ASN   ( 481-)  P
3931 ASN   ( 591-)  P
3993 ASN   ( 658-)  P
4023 HIS   ( 688-)  P
4514 GLN   (  49-)  7
4626 HIS   ( 161-)  7
4638 HIS   ( 173-)  7
4834 HIS   ( 371-)  7
4881 GLN   (  49-)  8
And so on for a total of 53 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.

   4 MET   (   7-)  A      N
   5 ALA   (   8-)  A      N
   7 PHE   (  10-)  A      N
   8 GLY   (  11-)  A      N
  22 ILE   (  25-)  A      N
  42 GLN   (  45-)  A      N
  44 PHE   (  47-)  A      N
  46 MLY   (  49-)  A      N
  56 MLY   (  59-)  A      N
  58 THR   (  61-)  A      N
  98 ALA   ( 101-)  A      N
 109 ALA   ( 112-)  A      N
 110 TRP   ( 113-)  A      NE1
 112 ILE   ( 115-)  A      N
 115 TYR   ( 118-)  A      OH
 119 PHE   ( 122-)  A      N
 120 CYS   ( 123-)  A      N
 122 THR   ( 125-)  A      OG1
 131 VAL   ( 134-)  A      N
 133 ASN   ( 136-)  A      N
 135 MLY   ( 138-)  A      N
 138 LEU   ( 141-)  A      N
 141 ARG   ( 144-)  A      NH1
 145 ARG   ( 148-)  A      NE
 146 GLN   ( 149-)  A      N
And so on for a total of 1432 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.

  83 ASP   (  86-)  A      OD2
  93 HIS   (  96-)  A      ND1
  95 HIS   (  98-)  A      ND1
 105 GLU   ( 108-)  A      OE2
 151 HIS   ( 154-)  A      ND1
 227 GLU   ( 230-)  A      OE2
 238 ASP   ( 241-)  A      OD1
 356 HIS   ( 360-)  A      ND1
 407 GLU   ( 411-)  A      OE1
 431 GLU   ( 435-)  A      OE1
 472 GLU   ( 476-)  A      OE2
 495 GLU   ( 499-)  A      OE1
 501 GLU   ( 506-)  A      OE2
 533 GLU   ( 538-)  A      OE2
 581 ASP   ( 589-)  A      OD2
 591 ASN   ( 599-)  A      OD1
 644 GLU   ( 655-)  A      OE2
 677 HIS   ( 688-)  A      ND1
 687 ASN   ( 698-)  A      OD1
 708 ASP   ( 719-)  A      OD1
 844 ASP   (  35-)  B      OD1
 845 GLN   (  36-)  B      OE1
 955 ASP   ( 149-)  B      OD1
1023 GLU   (  57-)  C      OE2
1061 ASP   (  95-)  C      OD2
And so on for a total of 270 lines.

Warning: No crystallisation information

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

Warning: 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.

 216 GLU   ( 219-)  A   H-bonding suggests Gln
 217 ASP   ( 220-)  A   H-bonding suggests Asn
 238 ASP   ( 241-)  A   H-bonding suggests Asn; but Alt-Rotamer
 314 GLU   ( 317-)  A   H-bonding suggests Gln
 380 ASP   ( 384-)  A   H-bonding suggests Asn
 534 GLU   ( 539-)  A   H-bonding suggests Gln
 597 GLU   ( 605-)  A   H-bonding suggests Gln
 792 GLU   ( 808-)  A   H-bonding suggests Gln
 834 GLU   (  25-)  B   H-bonding suggests Gln; but Alt-Rotamer
 835 ASP   (  26-)  B   H-bonding suggests Asn; but Alt-Rotamer
 838 GLU   (  29-)  B   H-bonding suggests Gln
 844 ASP   (  35-)  B   H-bonding suggests Asn; but Alt-Rotamer
 858 GLU   (  49-)  B   H-bonding suggests Gln
 874 ASP   (  65-)  B   H-bonding suggests Asn
 895 GLU   (  86-)  B   H-bonding suggests Gln
 900 ASP   (  92-)  B   H-bonding suggests Asn
 913 ASP   ( 105-)  B   H-bonding suggests Asn
 927 GLU   ( 119-)  B   H-bonding suggests Gln
 955 ASP   ( 149-)  B   H-bonding suggests Asn
 978 GLU   (  12-)  C   H-bonding suggests Gln; but Alt-Rotamer
 984 ASP   (  18-)  C   H-bonding suggests Asn; but Alt-Rotamer
1055 GLU   (  89-)  C   H-bonding suggests Gln
1061 ASP   (  95-)  C   H-bonding suggests Asn
1090 GLU   ( 124-)  C   H-bonding suggests Gln
1091 GLU   ( 125-)  C   H-bonding suggests Gln
And so on for a total of 174 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 :  -1.671
  2nd generation packing quality :  -1.740
  Ramachandran plot appearance   :  -4.361 (bad)
  chi-1/chi-2 rotamer normality  :  -4.622 (bad)
  Backbone conformation          :  -0.795

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.946
  Bond angles                    :   1.576
  Omega angle restraints         :   0.772
  Side chain planarity           :   1.375
  Improper dihedral distribution :   1.777 (loose)
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.006

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 : 70.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -2.2
  chi-1/chi-2 rotamer normality  :  -2.3
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.946
  Bond angles                    :   1.576
  Omega angle restraints         :   0.772
  Side chain planarity           :   1.375
  Improper dihedral distribution :   1.777 (loose)
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.006
==============

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.