WHAT IF Check report

This file was created 2012-01-05 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 pdb1o1b.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 : 7.707
CA-only RMS fit for the two chains : 7.699

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 : 12.435
CA-only RMS fit for the two chains : 12.462

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 J

All-atom RMS fit for the two chains : 17.480
CA-only RMS fit for the two chains : 17.528

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 J

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  -
 503 GLU   ( 506-)  A  -
 534 GLU   ( 537-)  A  -
 540 PRO   ( 543-)  A  -
 553 ASP   ( 556-)  A  -
 626 GLU   ( 629-)  A  -
 629 GLY   ( 632-)  A  -
 630 GLY   ( 633-)  A  -
 634 LYS   ( 637-)  A  -
 635 GLY   ( 638-)  A  -
 639 LYS   ( 642-)  A  -
 729 ILE   ( 732-)  A  -
 733 GLN   ( 736-)  A  -
 758 GLY   ( 761-)  A  -
 759 HIS   ( 762-)  A  -
 768 LEU   ( 771-)  A  -
 816 ASN   ( 819-)  A  -
 933 SER   ( 111-)  B  -
 959 TRP   ( 137-)  B  -
 982 GLY   ( 160-)  B  -
 987 LYS   (   4-)  C  -
1344 GLN   ( 215-)  D  -
And so on for a total of 121 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: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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

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

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 178 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: J

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: K

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: L

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

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

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.

 984 ARG   (  19-)  C
1000 ARG   (  35-)  C
1057 ARG   (  92-)  C
1073 ARG   ( 108-)  C
2099 ARG   (  19-)  F
2115 ARG   (  35-)  F
2172 ARG   (  92-)  F
2188 ARG   ( 108-)  F
3213 ARG   (  19-)  I
3229 ARG   (  35-)  I
3286 ARG   (  92-)  I
3302 ARG   ( 108-)  I
4323 ARG   (  19-)  L
4339 ARG   (  35-)  L
4396 ARG   (  92-)  L
4412 ARG   ( 108-)  L

Warning: Tyrosine convention problem

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

 955 TYR   ( 150-)  B
1104 TYR   ( 139-)  C
2070 TYR   ( 150-)  E
2219 TYR   ( 139-)  F
3184 TYR   ( 150-)  H
3333 TYR   ( 139-)  I
4294 TYR   ( 150-)  K
4443 TYR   ( 139-)  L

Warning: Phenylalanine convention problem

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

 839 PHE   (  31-)  B
 888 PHE   (  80-)  B
 908 PHE   ( 101-)  B
 923 PHE   ( 116-)  B
 947 PHE   ( 140-)  B
 979 PHE   (  14-)  C
 982 PHE   (  17-)  C
1030 PHE   (  65-)  C
1052 PHE   (  87-)  C
1059 PHE   (  94-)  C
1954 PHE   (  31-)  E
2003 PHE   (  80-)  E
2023 PHE   ( 101-)  E
2037 PHE   ( 116-)  E
2061 PHE   ( 140-)  E
2094 PHE   (  14-)  F
2097 PHE   (  17-)  F
2145 PHE   (  65-)  F
2167 PHE   (  87-)  F
2174 PHE   (  94-)  F
3067 PHE   (  31-)  H
3116 PHE   (  80-)  H
3137 PHE   ( 101-)  H
3152 PHE   ( 116-)  H
3176 PHE   ( 140-)  H
3208 PHE   (  14-)  I
3211 PHE   (  17-)  I
3259 PHE   (  65-)  I
3281 PHE   (  87-)  I
3288 PHE   (  94-)  I
4177 PHE   (  31-)  K
4226 PHE   (  80-)  K
4247 PHE   ( 101-)  K
4262 PHE   ( 116-)  K
4285 PHE   ( 140-)  K
4318 PHE   (  14-)  L
4321 PHE   (  17-)  L
4369 PHE   (  65-)  L
4391 PHE   (  87-)  L
4398 PHE   (  94-)  L

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.

 828 ASP   (  20-)  B
 834 ASP   (  26-)  B
 853 ASP   (  45-)  B
 854 ASP   (  46-)  B
 902 ASP   (  95-)  B
 954 ASP   ( 149-)  B
 967 ASP   ( 162-)  B
 973 ASP   (   8-)  C
 997 ASP   (  32-)  C
1051 ASP   (  86-)  C
1060 ASP   (  95-)  C
1943 ASP   (  20-)  E
1949 ASP   (  26-)  E
1968 ASP   (  45-)  E
1969 ASP   (  46-)  E
2017 ASP   (  95-)  E
2069 ASP   ( 149-)  E
2082 ASP   ( 162-)  E
2088 ASP   (   8-)  F
2112 ASP   (  32-)  F
2166 ASP   (  86-)  F
2175 ASP   (  95-)  F
3056 ASP   (  20-)  H
3062 ASP   (  26-)  H
3081 ASP   (  45-)  H
3082 ASP   (  46-)  H
3131 ASP   (  95-)  H
3183 ASP   ( 149-)  H
3196 ASP   ( 162-)  H
3202 ASP   (   8-)  I
3226 ASP   (  32-)  I
3280 ASP   (  86-)  I
3289 ASP   (  95-)  I
4166 ASP   (  20-)  K
4172 ASP   (  26-)  K
4191 ASP   (  45-)  K
4192 ASP   (  46-)  K
4241 ASP   (  95-)  K
4293 ASP   ( 149-)  K
4306 ASP   ( 162-)  K
4312 ASP   (   8-)  L
4336 ASP   (  32-)  L
4390 ASP   (  86-)  L
4399 ASP   (  95-)  L

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.

 831 GLU   (  23-)  B
 833 GLU   (  25-)  B
 837 GLU   (  29-)  B
 857 GLU   (  49-)  B
 878 GLU   (  70-)  B
 894 GLU   (  86-)  B
 977 GLU   (  12-)  C
1032 GLU   (  67-)  C
1050 GLU   (  85-)  C
1054 GLU   (  89-)  C
1071 GLU   ( 106-)  C
1081 GLU   ( 116-)  C
1085 GLU   ( 120-)  C
1086 GLU   ( 121-)  C
1096 GLU   ( 131-)  C
1946 GLU   (  23-)  E
1948 GLU   (  25-)  E
1952 GLU   (  29-)  E
1972 GLU   (  49-)  E
1993 GLU   (  70-)  E
2009 GLU   (  86-)  E
2092 GLU   (  12-)  F
2147 GLU   (  67-)  F
2165 GLU   (  85-)  F
2169 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    4.1
  72 ASP   (  75-)  A      CG   OD1   1.34    4.7
  83 ASP   (  86-)  A      CG   OD1   1.34    4.6
  95 HIS   (  98-)  A      CB   CG    1.44   -4.4
 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    1.68    7.7
 216 GLU   ( 219-)  A      N   -C     1.21   -5.8
 238 ASP   ( 241-)  A      CG   OD1   1.34    4.6
 285 PHE   ( 288-)  A      CA   C     1.44   -4.2
 303 THR   ( 306-)  A      CB   OG1   1.36   -4.6
 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    4.4
 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    4.8
 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 281 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

 |  1.002462  0.000071  0.000010|
 |  0.000071  1.002424  0.000024|
 |  0.000010  0.000024  1.001531|
Proposed new scale matrix

 |  0.003325  0.000000  0.000000|
 |  0.000000  0.003325  0.000000|
 |  0.000000  0.000000  0.003328|
With corresponding cell

    A    = 300.769  B   = 300.757  C    = 300.489
    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: 1424.697
(Under-)estimated Z-score: 27.818

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  118.49    4.4
  35 VAL   (  38-)  A      N    CA   CB  102.69   -4.6
  44 PHE   (  47-)  A      C    CA   CB  101.02   -4.8
  68 THR   (  71-)  A      N    CA   CB  117.36    4.0
  72 ASP   (  75-)  A      N    CA   CB  122.91    7.3
  72 ASP   (  75-)  A      C    CA   CB  117.73    4.0
  79 PRO   (  82-)  A      N    CA   CB  109.34    5.8
  85 ILE   (  88-)  A      CB   CG1  CD1 101.48   -5.9
  95 HIS   (  98-)  A      C    CA   CB   87.30  -12.0
  95 HIS   (  98-)  A      CD2  CG   ND1 110.34    4.2
 101 TYR   ( 104-)  A      C    CA   CB  117.93    4.1
 115 TYR   ( 118-)  A      C    CA   CB  101.49   -4.5
 125 PRO   ( 128-)  A      N    CA   CB  108.13    4.7
 134 PRO   ( 137-)  A     -CA  -C    N   108.49   -5.6
 138 LEU   ( 141-)  A      C    CA   CB   97.94   -6.4
 150 PRO   ( 153-)  A      N    CA   CB  107.46    4.1
 158 ASN   ( 161-)  A      CA   CB   CG  107.62   -5.0
 158 ASN   ( 161-)  A      ND2  CG   OD1 127.29    4.7
 162 PHE   ( 165-)  A      N    CA   CB  100.31   -6.0
 162 PHE   ( 165-)  A      CA   CB   CG  108.82   -5.0
 169 ASN   ( 172-)  A      N    CA   CB  118.15    4.5
 170 GLN   ( 173-)  A      N    CA   CB  102.92   -4.5
 177 GLU   ( 180-)  A      N    CA   CB  118.47    4.7
 189 VAL   ( 192-)  A      CA   CB   CG1 101.92   -5.0
 193 PHE   ( 196-)  A      CA   CB   CG  108.26   -5.5
And so on for a total of 2709 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.

 828 ASP   (  20-)  B
 831 GLU   (  23-)  B
 833 GLU   (  25-)  B
 834 ASP   (  26-)  B
 837 GLU   (  29-)  B
 853 ASP   (  45-)  B
 854 ASP   (  46-)  B
 857 GLU   (  49-)  B
 878 GLU   (  70-)  B
 894 GLU   (  86-)  B
 902 ASP   (  95-)  B
 954 ASP   ( 149-)  B
 967 ASP   ( 162-)  B
 973 ASP   (   8-)  C
 977 GLU   (  12-)  C
 984 ARG   (  19-)  C
 997 ASP   (  32-)  C
1000 ARG   (  35-)  C
1032 GLU   (  67-)  C
1050 GLU   (  85-)  C
1051 ASP   (  86-)  C
1054 GLU   (  89-)  C
1057 ARG   (  92-)  C
1060 ASP   (  95-)  C
1071 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     9.30    33.73
  95 HIS   (  98-)  A      CA     8.3    49.45    34.11
  95 HIS   (  98-)  A      C      8.6    12.99     0.15
 134 PRO   ( 137-)  A      N      6.1    17.47    -2.48
 261 ASP   ( 264-)  A      CA     7.8    49.28    33.73
 337 LEU   ( 341-)  A      CA    -8.5    21.14    34.19
 443 GLN   ( 447-)  A      CA   -12.3    10.23    33.96
 476 ILE   ( 480-)  A      CB     6.5    40.82    32.31
 616 THR   ( 625-)  A      CB     6.6    48.78    34.09
 619 GLY   ( 628-)  A      C     -6.3    -8.21     0.06
 627 LYS   ( 637-)  A      C    -17.4   -26.20     0.11
 636 THR   ( 648-)  A      CB   -13.7     3.47    34.09
 637 VAL   ( 649-)  A      C      7.9    10.97     0.15
 637 VAL   ( 649-)  A      CB   -35.1   -78.97   -32.96
 686 ASN   ( 698-)  A      C     -6.0    -9.18     0.27
 742 THR   ( 756-)  A      CA     6.6    44.82    33.84
 747 HIS   ( 762-)  A      CA    -7.2    20.95    34.11
 816 MET   ( 832-)  A      CA    -7.5    20.60    34.17
 823 PRO   ( 840-)  A      N     -6.2   -22.78    -2.48
 829 GLU   (  21-)  B      C      6.5     9.45    -0.03
 830 THR   (  22-)  B      C      7.5    11.48     0.30
 832 ILE   (  24-)  B      C      6.4     8.36     0.03
 852 LYS   (  44-)  B      C      6.0     9.20     0.11
 853 ASP   (  45-)  B      C      6.3     9.67    -0.01
 860 ALA   (  52-)  B      C      6.2     9.60     0.08
And so on for a total of 209 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.

4786 ARG   ( 335-)  0    7.44
6272 ARG   ( 335-)  4    7.40
6643 ARG   ( 335-)  5    7.40
5901 ARG   ( 335-)  3    7.39
9578 ARG   ( 335-)  Z    7.38
5529 ARG   ( 335-)  2    7.38
5158 ARG   ( 335-)  1    7.36
9207 ARG   ( 335-)  Y    7.36
7014 ARG   ( 335-)  7    7.34
8836 ARG   ( 335-)  X    7.34
4107 ALA   ( 784-)  J    6.65
1882 ALA   ( 784-)  D    6.63
 768 ALA   ( 784-)  A    6.63
9391 ARG   ( 147-)  Z    6.54
2997 ALA   ( 784-)  G    6.52
3559 GLU   ( 219-)  J    6.29
2444 GLU   ( 219-)  G    6.28
 216 GLU   ( 219-)  A    6.24
1330 GLU   ( 219-)  D    6.18
5931 ALA   ( 365-)  3    6.08
7406 ALA   ( 365-)  8    6.08
7044 ALA   ( 365-)  7    6.07
6302 ALA   ( 365-)  4    6.07
5559 ALA   ( 365-)  2    6.07
7772 ALA   ( 365-)  9    6.06
And so on for a total of 277 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 : 1.714

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.

3184 TYR   ( 150-)  H   15.55
2070 TYR   ( 150-)  E   15.55
 955 TYR   ( 150-)  B   15.34
4294 TYR   ( 150-)  K   15.32
4322 ASP   (  18-)  L    9.77
3212 ASP   (  18-)  I    9.71
2098 ASP   (  18-)  F    9.70
 983 ASP   (  18-)  C    9.65
2029 ASP   ( 107-)  E    8.35
 914 ASP   ( 107-)  B    8.26
4253 ASP   ( 107-)  K    8.20
3143 ASP   ( 107-)  H    8.12
4393 GLU   (  89-)  L    7.02
3283 GLU   (  89-)  I    6.88
1054 GLU   (  89-)  C    6.81
2169 GLU   (  89-)  F    6.77
2186 GLU   ( 106-)  F    5.76
 966 GLU   ( 161-)  B    5.71
4305 GLU   ( 161-)  K    5.70
4410 GLU   ( 106-)  L    5.67
2081 GLU   ( 161-)  E    5.63
3319 GLU   ( 125-)  I    5.63
1071 GLU   ( 106-)  C    5.62
3195 GLU   ( 161-)  H    5.61
2205 GLU   ( 125-)  F    5.53
And so on for a total of 73 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.

 614 PHE   ( 623-)  A      CB   7.02
1729 PHE   ( 623-)  D      CB   7.00
3958 PHE   ( 623-)  J      CB   7.00
2845 PHE   ( 623-)  G      CB   6.97
6679 HIS   ( 371-)  5      CB   5.61
7778 HIS   ( 371-)  9      CB   5.60
9243 HIS   ( 371-)  Y      CB   5.59
5194 HIS   ( 371-)  1      CB   5.59
5937 HIS   ( 371-)  3      CB   5.59
7050 HIS   ( 371-)  7      CB   5.59
8140 HIS   ( 371-)  V      CB   5.59
8503 HIS   ( 371-)  W      CB   5.59
7412 HIS   ( 371-)  8      CB   5.58
4822 HIS   ( 371-)  0      CB   5.58
9614 HIS   ( 371-)  Z      CB   5.57
8872 HIS   ( 371-)  X      CB   5.56
6308 HIS   ( 371-)  4      CB   5.55
5565 HIS   ( 371-)  2      CB   5.55
7583 HIS   ( 173-)  9      CB   4.18
4626 HIS   ( 173-)  0      CB   4.18
7948 HIS   ( 173-)  V      CB   4.18
7219 HIS   ( 173-)  8      CB   4.17
9046 HIS   ( 173-)  Y      CB   4.17
6482 HIS   ( 173-)  5      CB   4.17
9417 HIS   ( 173-)  Z      CB   4.17
4996 HIS   ( 173-)  1      CB   4.17
8312 HIS   ( 173-)  W      CB   4.17
5739 HIS   ( 173-)  3      CB   4.17
6853 HIS   ( 173-)  7      CB   4.17
6111 HIS   ( 173-)  4      CB   4.17
5368 HIS   ( 173-)  2      CB   4.16
8676 HIS   ( 173-)  X      CB   4.16
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -4.339

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 : -4.339

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.

3177 PRO   ( 141-)  H    -2.9
 948 PRO   ( 141-)  B    -2.9
4286 PRO   ( 141-)  K    -2.9
2062 PRO   ( 141-)  E    -2.9
 814 PRO   ( 830-)  A    -2.9
3041 PRO   ( 830-)  G    -2.9
1928 PRO   ( 830-)  D    -2.9
4152 PRO   ( 830-)  J    -2.9
2355 TYR   ( 129-)  G    -2.8
3469 TYR   ( 129-)  J    -2.8
 126 TYR   ( 129-)  A    -2.8
1240 TYR   ( 129-)  D    -2.8
8982 PRO   ( 109-)  Y    -2.8
6789 PRO   ( 109-)  7    -2.8
8612 PRO   ( 109-)  X    -2.8
5675 PRO   ( 109-)  3    -2.8
8248 PRO   ( 109-)  W    -2.8
7157 PRO   ( 109-)  8    -2.8
9353 PRO   ( 109-)  Z    -2.8
5304 PRO   ( 109-)  2    -2.8
4562 PRO   ( 109-)  0    -2.8
7884 PRO   ( 109-)  V    -2.8
6418 PRO   ( 109-)  5    -2.8
4932 PRO   ( 109-)  1    -2.8
7520 PRO   ( 109-)  9    -2.8
And so on for a total of 547 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
 134 PRO   ( 137-)  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
 501 GLY   ( 507-)  A  Poor phi/psi
 551 GLY   ( 560-)  A  Poor phi/psi
 563 LYS   ( 572-)  A  Poor phi/psi
 568 ALA   ( 577-)  A  omega poor
 637 VAL   ( 649-)  A  omega poor
 638 SER   ( 650-)  A  Poor phi/psi
And so on for a total of 322 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 : -4.639

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.

 333 SER   ( 336-)  A    0.33
1447 SER   ( 336-)  D    0.33
2561 SER   ( 336-)  G    0.33
3676 SER   ( 336-)  J    0.33
 156 SER   ( 159-)  A    0.36
1270 SER   ( 159-)  D    0.36
2385 SER   ( 159-)  G    0.36
3499 SER   ( 159-)  J    0.36
 416 SER   ( 420-)  A    0.37
1529 SER   ( 420-)  D    0.37
2645 SER   ( 420-)  G    0.37
3758 SER   ( 420-)  J    0.37
4732 SER   ( 281-)  0    0.40
5104 SER   ( 281-)  1    0.40
5476 SER   ( 281-)  2    0.40
5847 SER   ( 281-)  3    0.40
6218 SER   ( 281-)  4    0.40
6589 SER   ( 281-)  5    0.40
6961 SER   ( 281-)  7    0.40
7327 SER   ( 281-)  8    0.40
7690 SER   ( 281-)  9    0.40
8055 SER   ( 281-)  V    0.40
8419 SER   ( 281-)  W    0.40
8783 SER   ( 281-)  X    0.40
9153 SER   ( 281-)  Y    0.40
9524 SER   ( 281-)  Z    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 3729 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!

2293 GLY   (  67-)  G   2.50   80
3407 GLY   (  67-)  J   2.50   80
1178 GLY   (  67-)  D   2.49   80
  64 GLY   (  67-)  A   2.49   80
2754 PRO   ( 529-)  G   2.29   11
1638 PRO   ( 529-)  D   2.29   11
 523 PRO   ( 529-)  A   2.29   11
3867 PRO   ( 529-)  J   2.29   11
3620 PRO   ( 280-)  J   2.20   10
2505 PRO   ( 280-)  G   2.20   10
1391 PRO   ( 280-)  D   2.20   10
 277 PRO   ( 280-)  A   2.20   10
 403 GLY   ( 407-)  A   2.04   15
2632 GLY   ( 407-)  G   2.04   15
3746 GLY   ( 407-)  J   2.04   15
1517 GLY   ( 407-)  D   2.03   16
8649 GLY   ( 146-)  X   1.59   80
6084 GLY   ( 146-)  4   1.58   80
4969 GLY   ( 146-)  1   1.58   80
6455 GLY   ( 146-)  5   1.58   80
9390 GLY   ( 146-)  Z   1.58   80
4599 GLY   ( 146-)  0   1.58   80
9019 GLY   ( 146-)  Y   1.58   80
5712 GLY   ( 146-)  3   1.58   80
6826 GLY   ( 146-)  7   1.58   80
8285 GLY   ( 146-)  W   1.58   80
5341 GLY   ( 146-)  2   1.58   80
7921 GLY   ( 146-)  V   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    0.12 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    0.11 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
 523 PRO   ( 529-)  A    0.13 LOW
 536 PRO   ( 543-)  A    0.06 LOW
 559 PRO   ( 568-)  A    0.02 LOW
 561 PRO   ( 570-)  A    0.07 LOW
 593 PRO   ( 602-)  A    0.03 LOW
 657 PRO   ( 669-)  A    0.13 LOW
 665 PRO   ( 677-)  A    0.02 LOW
And so on for a total of 212 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   156.5 half-chair C-alpha/N (162 degrees)
 948 PRO   ( 141-)  B  -160.1 half-chair N/C-delta (-162 degrees)
1006 PRO   (  41-)  C   -10.4 half-chair C-alpha/N (-18 degrees)
1264 PRO   ( 153-)  D   171.2 envelop N (180 degrees)
1928 PRO   ( 830-)  D   156.4 half-chair C-alpha/N (162 degrees)
2062 PRO   ( 141-)  E  -160.3 half-chair N/C-delta (-162 degrees)
2121 PRO   (  41-)  F   -10.7 half-chair C-alpha/N (-18 degrees)
2379 PRO   ( 153-)  G   171.5 envelop N (180 degrees)
3041 PRO   ( 830-)  G   156.9 half-chair C-alpha/N (162 degrees)
3177 PRO   ( 141-)  H  -159.6 half-chair N/C-delta (-162 degrees)
3235 PRO   (  41-)  I   -10.9 half-chair C-alpha/N (-18 degrees)
3493 PRO   ( 153-)  J   171.6 envelop N (180 degrees)
4152 PRO   ( 830-)  J   156.7 half-chair C-alpha/N (162 degrees)
4286 PRO   ( 141-)  K  -160.4 half-chair N/C-delta (-162 degrees)
4345 PRO   (  41-)  L   -10.4 half-chair C-alpha/N (-18 degrees)
4562 PRO   ( 109-)  0   112.4 envelop C-beta (108 degrees)
4932 PRO   ( 109-)  1   112.4 envelop C-beta (108 degrees)
5304 PRO   ( 109-)  2   112.3 envelop C-beta (108 degrees)
5675 PRO   ( 109-)  3   112.3 envelop C-beta (108 degrees)
6047 PRO   ( 109-)  4   112.4 envelop C-beta (108 degrees)
6418 PRO   ( 109-)  5   112.4 envelop C-beta (108 degrees)
6789 PRO   ( 109-)  7   112.3 envelop C-beta (108 degrees)
7157 PRO   ( 109-)  8   112.3 envelop C-beta (108 degrees)
7520 PRO   ( 109-)  9   112.2 envelop C-beta (108 degrees)
7884 PRO   ( 109-)  V   112.4 envelop C-beta (108 degrees)
8248 PRO   ( 109-)  W   112.3 envelop C-beta (108 degrees)
8612 PRO   ( 109-)  X   112.2 envelop C-beta (108 degrees)
8982 PRO   ( 109-)  Y   112.3 envelop C-beta (108 degrees)
9353 PRO   ( 109-)  Z   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.

2042 LEU   ( 121-)  E      CD1  <->  2049 PHE   ( 128-)  E      CD2  2.62    0.58  INTRA
3157 LEU   ( 121-)  H      CD1  <->  3164 PHE   ( 128-)  H      CD2  2.62    0.58  INTRA
 928 LEU   ( 121-)  B      CD1  <->   935 PHE   ( 128-)  B      CD2  2.62    0.58  INTRA
4267 LEU   ( 121-)  K      CD1  <->  4274 PHE   ( 128-)  K      CD2  2.61    0.59  INTRA
1893 ARG   ( 795-)  D      CD   <->  2115 ARG   (  35-)  F      NH2  2.60    0.50  INTRA
2861 LYS   ( 642-)  G      CE   <->  8114 SER   ( 344-)  V      CB   2.46    0.74  INTRA
1743 LYS   ( 642-)  D      CE   <->  7751 SER   ( 344-)  9      CB   2.45    0.75  INTRA
 632 LYS   ( 642-)  A      CE   <->  7387 SER   ( 344-)  8      CB   2.45    0.75  INTRA
4655 THR   ( 202-)  0      N    <->  9159 ILE   ( 287-)  Y      CD1  2.35    0.75  INTRA
1813 SER   ( 713-)  D      OG   <->  1869 LEU   ( 771-)  D      CD2  2.32    0.48  INTRA
2058 TRP   ( 137-)  E      CH2  <->  2066 GLY   ( 146-)  E      N    2.29    0.81  INTRA
 944 TRP   ( 137-)  B      CH2  <->   952 GLY   ( 146-)  B      N    2.29    0.81  INTRA
3173 TRP   ( 137-)  H      CH2  <->  3181 GLY   ( 146-)  H      N    2.29    0.81  INTRA
1737 GLY   ( 632-)  D      C    <->  7436 ASP   (  25-)  9      N    2.19    0.91  INTRA
8792 LYS   ( 291-)  X      CB   <->  9487 ASP   ( 244-)  Z      CB   2.19    1.01  INTRA
 547 ASP   ( 556-)  A      C    <->  7824 GLN   (  49-)  V      N    2.14    0.96  INTRA
2319 MET   (  93-)  G      CG   <->  2977 MLY   ( 764-)  G      CD   2.14    1.06  INTRA
1326 GLN   ( 215-)  D      CD   <->  1450 ILE   ( 340-)  D      N    2.12    0.98  INTRA
3555 GLN   ( 215-)  J      CD   <->  3679 ILE   ( 340-)  J      N    2.12    0.98  INTRA
 212 GLN   ( 215-)  A      CD   <->   336 ILE   ( 340-)  A      N    2.11    0.99  INTRA
1660 MLY   ( 553-)  D      CH2  <->  8186 VAL   (  45-)  W      CG2  2.08    1.12  INTRA
1866 MLY   ( 768-)  D      O    <->  1869 LEU   ( 771-)  D      CD1  2.08    0.72  INTRA
3909 LYS   ( 574-)  J      NZ   <->  3924 ASP   ( 589-)  J      OD2  2.06    0.64  INTRA
2796 LYS   ( 574-)  G      NZ   <->  2811 ASP   ( 589-)  G      OD2  2.06    0.64  INTRA
 565 LYS   ( 574-)  A      NZ   <->   580 ASP   ( 589-)  A      OD2  2.06    0.64  INTRA
And so on for a total of 5693 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: 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

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

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.

2099 ARG   (  19-)  F      -7.75
4323 ARG   (  19-)  L      -7.70
3213 ARG   (  19-)  I      -7.69
 984 ARG   (  19-)  C      -7.67
7817 GLN   (  41-)  V      -7.51
8545 GLN   (  41-)  X      -7.51
8914 GLN   (  41-)  Y      -7.51
7452 GLN   (  41-)  9      -7.51
4864 GLN   (  41-)  1      -7.51
4494 GLN   (  41-)  0      -7.51
7089 GLN   (  41-)  8      -7.51
6350 GLN   (  41-)  5      -7.51
8182 GLN   (  41-)  W      -7.51
9285 GLN   (  41-)  Z      -7.50
6721 GLN   (  41-)  7      -7.50
5607 GLN   (  41-)  3      -7.50
5979 GLN   (  41-)  4      -7.50
 126 TYR   ( 129-)  A      -7.41
3469 TYR   ( 129-)  J      -7.41
1240 TYR   ( 129-)  D      -7.40
2355 TYR   ( 129-)  G      -7.40
5236 GLN   (  41-)  2      -7.33
 367 ARG   ( 371-)  A      -6.99
3710 ARG   ( 371-)  J      -6.99
1481 ARG   ( 371-)  D      -6.99
And so on for a total of 227 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.

 567 GLU   ( 576-)  A       569 - HIS    578- ( A)         -4.28
1682 GLU   ( 576-)  D      1684 - HIS    578- ( D)         -4.28
2798 GLU   ( 576-)  G      2800 - HIS    578- ( G)         -4.27
3911 GLU   ( 576-)  J      3913 - HIS    578- ( J)         -4.25
4492 ARG   (  39-)  0      4494 - GLN     41- ( 0)         -6.72
4862 ARG   (  39-)  1      4864 - GLN     41- ( 1)         -6.74
5234 ARG   (  39-)  2      5236 - GLN     41- ( 2)         -6.67
5605 ARG   (  39-)  3      5607 - GLN     41- ( 3)         -6.73
5977 ARG   (  39-)  4      5979 - GLN     41- ( 4)         -6.72
6348 ARG   (  39-)  5      6350 - GLN     41- ( 5)         -6.72
6719 ARG   (  39-)  7      6721 - GLN     41- ( 7)         -6.72
7087 ARG   (  39-)  8      7089 - GLN     41- ( 8)         -6.71
7450 ARG   (  39-)  9      7452 - GLN     41- ( 9)         -6.72
7815 ARG   (  39-)  V      7817 - GLN     41- ( V)         -6.72
8180 ARG   (  39-)  W      8182 - GLN     41- ( W)         -6.71
8543 ARG   (  39-)  X      8545 - GLN     41- ( X)         -6.75
8912 ARG   (  39-)  Y      8914 - GLN     41- ( Y)         -6.73
9283 ARG   (  39-)  Z      9285 - GLN     41- ( Z)         -6.69

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: 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

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

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.

 971 ALA   (   6-)  C   -3.14
2086 ALA   (   6-)  F   -3.14
3200 ALA   (   6-)  I   -3.14
1223 ALA   ( 112-)  D   -2.88
 109 ALA   ( 112-)  A   -2.88
8248 PRO   ( 109-)  W   -2.85
8612 PRO   ( 109-)  X   -2.85
7884 PRO   ( 109-)  V   -2.85
4932 PRO   ( 109-)  1   -2.85
9353 PRO   ( 109-)  Z   -2.85
4562 PRO   ( 109-)  0   -2.85
8982 PRO   ( 109-)  Y   -2.85
6349 HIS   (  40-)  5   -2.84
7839 ILE   (  64-)  V   -2.68
2070 TYR   ( 150-)  E   -2.67
7475 ILE   (  64-)  9   -2.66
6744 ILE   (  64-)  7   -2.62
3728 LEU   ( 389-)  J   -2.62
 385 LEU   ( 389-)  A   -2.62
2614 LEU   ( 389-)  G   -2.62
1499 LEU   ( 389-)  D   -2.61
1573 ILE   ( 464-)  D   -2.61
 460 ILE   ( 464-)  A   -2.61
3802 ILE   ( 464-)  J   -2.61
7112 ILE   (  64-)  8   -2.57
3912 ALA   ( 577-)  J   -2.55
5978 HIS   (  40-)  4   -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.

 586 TRP   ( 595-)  A     -  589 MLY   ( 598-)  A      -251.21
1701 TRP   ( 595-)  D     - 1704 MLY   ( 598-)  D      -251.21
1740 GLY   ( 639-)  D     - 1744 GLY   ( 643-)  D        -1.69
2817 TRP   ( 595-)  G     - 2820 MLY   ( 598-)  G      -251.21
3051 PRO   ( 840-)  G     - 3054 LYS   ( 843-)  G        -2.00
3930 TRP   ( 595-)  J     - 3933 MLY   ( 598-)  J      -251.21
9612 ILE   ( 369-)  Z     - 9615 ARG   ( 372-)  Z        -1.72

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: 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

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

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
 582 ASN   ( 591-)  A
 646 ASN   ( 658-)  A
1238 ASN   ( 127-)  D
1590 ASN   ( 481-)  D
1697 ASN   ( 591-)  D
1758 ASN   ( 658-)  D
1889 GLN   ( 791-)  D
2353 ASN   ( 127-)  G
2706 ASN   ( 481-)  G
2813 ASN   ( 591-)  G
2875 ASN   ( 658-)  G
2905 HIS   ( 688-)  G
3234 ASN   (  40-)  I
3467 ASN   ( 127-)  J
3819 ASN   ( 481-)  J
3926 ASN   ( 591-)  J
3986 ASN   ( 658-)  J
4502 GLN   (  49-)  0
4872 GLN   (  49-)  1
5244 GLN   (  49-)  2
5368 HIS   ( 173-)  2
5615 GLN   (  49-)  3
5625 GLN   (  59-)  3
And so on for a total of 51 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
  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
  82 TYR   (  85-)  A      OH
  98 ALA   ( 101-)  A      N
 106 ARG   ( 109-)  A      NH1
 109 ALA   ( 112-)  A      N
 110 TRP   ( 113-)  A      NE1
 112 ILE   ( 115-)  A      N
 115 TYR   ( 118-)  A      OH
 118 LEU   ( 121-)  A      N
 119 PHE   ( 122-)  A      N
 120 CYS   ( 123-)  A      N
 122 THR   ( 125-)  A      OG1
 131 VAL   ( 134-)  A      N
 132 TYR   ( 135-)  A      N
 133 ASN   ( 136-)  A      N
 135 MLY   ( 138-)  A      N
 138 LEU   ( 141-)  A      N
And so on for a total of 1410 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
 580 ASP   ( 589-)  A      OD2
 590 ASN   ( 599-)  A      OD1
 643 GLU   ( 655-)  A      OE2
 676 HIS   ( 688-)  A      ND1
 686 ASN   ( 698-)  A      OD1
 707 ASP   ( 719-)  A      OD1
 843 ASP   (  35-)  B      OD1
 844 GLN   (  36-)  B      OE1
 954 ASP   ( 149-)  B      OD1
1022 GLU   (  57-)  C      OE2
1060 ASP   (  95-)  C      OD2
1197 ASP   (  86-)  D      OD2
1207 HIS   (  96-)  D      ND1
1209 HIS   (  98-)  D      ND1
And so on for a total of 265 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
 532 GLU   ( 539-)  A   H-bonding suggests Gln
 596 GLU   ( 605-)  A   H-bonding suggests Gln
 792 GLU   ( 808-)  A   H-bonding suggests Gln
 833 GLU   (  25-)  B   H-bonding suggests Gln; but Alt-Rotamer
 834 ASP   (  26-)  B   H-bonding suggests Asn; but Alt-Rotamer
 837 GLU   (  29-)  B   H-bonding suggests Gln
 843 ASP   (  35-)  B   H-bonding suggests Asn; but Alt-Rotamer
 857 GLU   (  49-)  B   H-bonding suggests Gln
 873 ASP   (  65-)  B   H-bonding suggests Asn
 894 GLU   (  86-)  B   H-bonding suggests Gln
 899 ASP   (  92-)  B   H-bonding suggests Asn
 912 ASP   ( 105-)  B   H-bonding suggests Asn
 926 GLU   ( 119-)  B   H-bonding suggests Gln
 954 ASP   ( 149-)  B   H-bonding suggests Asn
 966 GLU   ( 161-)  B   H-bonding suggests Gln
 977 GLU   (  12-)  C   H-bonding suggests Gln; but Alt-Rotamer
 983 ASP   (  18-)  C   H-bonding suggests Asn; but Alt-Rotamer
1054 GLU   (  89-)  C   H-bonding suggests Gln; but Alt-Rotamer
1060 ASP   (  95-)  C   H-bonding suggests Asn
1089 GLU   ( 124-)  C   H-bonding suggests Gln
And so on for a total of 179 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 :  -1.633
  2nd generation packing quality :  -1.722
  Ramachandran plot appearance   :  -4.339 (bad)
  chi-1/chi-2 rotamer normality  :  -4.639 (bad)
  Backbone conformation          :  -0.789

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.948
  Bond angles                    :   1.575
  Omega angle restraints         :   0.751
  Side chain planarity           :   1.374
  Improper dihedral distribution :   1.767 (loose)
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.008

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                   :   0.948
  Bond angles                    :   1.575
  Omega angle restraints         :   0.751
  Side chain planarity           :   1.374
  Improper dihedral distribution :   1.767 (loose)
  B-factor distribution          :   0.362
  Inside/Outside distribution    :   1.008
==============

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.