WHAT IF Check report

This file was created 2014-07-31 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 pdb3j01.ent

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: 5

Note: Ramachandran plot

Chain identifier: 6

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: V

Note: Ramachandran plot

Chain identifier: W

Note: Ramachandran plot

Chain identifier: X

Note: Ramachandran plot

Chain identifier: Y

Note: Ramachandran plot

Chain identifier: Z

Note: Ramachandran plot

Chain identifier: 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

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.

3791 THR   ( 216-)  5
6945 VAL   (  56-)  Z

Warning: B-factors outside the range 0.0 - 100.0

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

   1 OURA  (   1-)  7    Zero
   2 OGUA  (   2-)  7    Zero
   3 OCYT  (   3-)  7    Zero
   4 OCYT  (   4-)  7    Zero
   5 OURA  (   5-)  7    Zero
   6 OGUA  (   6-)  7    Zero
   7 OGUA  (   7-)  7    Zero
   8 OCYT  (   8-)  7    Zero
   9 OGUA  (   9-)  7    Zero
  10 OGUA  (  10-)  7    Zero
  11 OCYT  (  11-)  7    Zero
  12 OCYT  (  12-)  7    Zero
  13 OGUA  (  13-)  7    Zero
  14 OURA  (  14-)  7    Zero
  15 OADE  (  15-)  7    Zero
  16 OGUA  (  16-)  7    Zero
  17 OCYT  (  17-)  7    Zero
  18 OGUA  (  18-)  7    Zero
  19 OCYT  (  19-)  7    Zero
  20 OGUA  (  20-)  7    Zero
  21 OGUA  (  21-)  7    Zero
  22 OURA  (  22-)  7    Zero
  23 OGUA  (  23-)  7    Zero
  24 OGUA  (  24-)  7    Zero
  25 OURA  (  25-)  7    Zero
And so on for a total of 7205 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: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 100.00

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: A

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: B

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: 5

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: 6

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: D

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: E

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: F

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: G

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: H

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: I

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: J

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: K

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: L

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: M

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: N

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: O

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: P

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: Q

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: R

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: S

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: T

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: U

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: V

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: W

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: X

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: Y

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: Z

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: 0

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: 1

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: 2

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: 3

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: 4

Nomenclature related problems

Warning: Arginine nomenclature problem

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

4094 ARG   (  13-)  D
4114 ARG   (  33-)  D
4140 ARG   (  59-)  D
4158 ARG   (  77-)  D
4164 ARG   (  83-)  D
4250 ARG   ( 169-)  D
4265 ARG   ( 184-)  D
4311 ARG   (  21-)  E
4334 ARG   (  44-)  E
4339 ARG   (  49-)  E
4351 ARG   (  61-)  E
4378 ARG   (  88-)  E
4392 ARG   ( 102-)  E
4452 ARG   ( 162-)  E
4460 ARG   ( 170-)  E
4561 ARG   (  70-)  F
4570 ARG   (  79-)  F
4582 ARG   (  91-)  F
4592 ARG   ( 101-)  F
4600 ARG   ( 109-)  F
4602 ARG   ( 111-)  F
4605 ARG   ( 114-)  F
4623 ARG   ( 132-)  F
4671 ARG   (   2-)  G
4821 ARG   ( 152-)  G
And so on for a total of 90 lines.

Warning: Tyrosine convention problem

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

3139 TYR   ( 122-)  A
3265 TYR   ( 248-)  A
3275 TYR   ( 258-)  A
3326 TYR   ( 309-)  A
3349 TYR   ( 332-)  A
3417 TYR   ( 400-)  A
3446 TYR   ( 429-)  A
3458 TYR   ( 441-)  A
3484 TYR   (  36-)  B
3596 TYR   (  21-)  5
3904 TYR   (  95-)  6
3911 TYR   ( 102-)  6
3969 TYR   ( 160-)  6
4126 TYR   (  45-)  D
4325 TYR   (  35-)  E
4391 TYR   ( 101-)  E
4498 TYR   (   7-)  F
4726 TYR   (  57-)  G
4762 TYR   (  93-)  G
4819 TYR   ( 150-)  G
4825 TYR   ( 156-)  G
5055 TYR   (  61-)  I
5151 TYR   (  16-)  J
5209 TYR   (  74-)  J
5260 TYR   ( 125-)  J
5458 TYR   (  58-)  L
5647 TYR   ( 103-)  M
5792 TYR   ( 112-)  N
5906 TYR   (  99-)  O
6022 TYR   (  98-)  P
6061 TYR   (  23-)  Q
6062 TYR   (  24-)  Q
6082 TYR   (  44-)  Q
6157 TYR   (   2-)  R
6238 TYR   (  83-)  R
6296 TYR   (  38-)  S
6452 TYR   (  84-)  T
6602 TYR   (  31-)  V
6628 TYR   (  57-)  V
6994 TYR   (  47-)  0
6995 TYR   (  48-)  0
7166 TYR   (  63-)  3

Warning: Phenylalanine convention problem

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

3026 PHE   (   9-)  A
3055 PHE   (  38-)  A
3084 PHE   (  67-)  A
3147 PHE   ( 130-)  A
3171 PHE   ( 154-)  A
3249 PHE   ( 232-)  A
3253 PHE   ( 236-)  A
3303 PHE   ( 286-)  A
3348 PHE   ( 331-)  A
3354 PHE   ( 337-)  A
3400 PHE   ( 383-)  A
3416 PHE   ( 399-)  A
3418 PHE   ( 401-)  A
3569 PHE   ( 121-)  B
3575 PHE   ( 127-)  B
3653 PHE   (  78-)  5
3686 PHE   ( 111-)  5
3875 PHE   (  66-)  6
4048 PHE   ( 239-)  6
4096 PHE   (  15-)  D
4149 PHE   (  68-)  D
4171 PHE   (  90-)  D
4182 PHE   ( 101-)  D
4199 PHE   ( 118-)  D
4208 PHE   ( 127-)  D
And so on for a total of 62 lines.

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.

3025 ASP   (   8-)  A
3062 ASP   (  45-)  A
3361 ASP   ( 344-)  A
3410 ASP   ( 393-)  A
3432 ASP   ( 415-)  A
3486 ASP   (  38-)  B
3591 ASP   (  16-)  5
3618 ASP   (  43-)  5
3758 ASP   ( 183-)  5
3880 ASP   (  71-)  6
3906 ASP   (  97-)  6
4072 ASP   ( 263-)  6
4124 ASP   (  43-)  D
4184 ASP   ( 103-)  D
4212 ASP   ( 131-)  D
4257 ASP   ( 176-)  D
4262 ASP   ( 181-)  D
4281 ASP   ( 200-)  D
4297 ASP   (   7-)  E
4312 ASP   (  22-)  E
4381 ASP   (  91-)  E
4430 ASP   ( 140-)  E
4435 ASP   ( 145-)  E
4444 ASP   ( 154-)  E
4458 ASP   ( 168-)  E
And so on for a total of 80 lines.

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.

3193 GLU   ( 176-)  A
3225 GLU   ( 208-)  A
3255 GLU   ( 238-)  A
3377 GLU   ( 360-)  A
3447 GLU   ( 430-)  A
3463 GLU   (  15-)  B
3526 GLU   (  78-)  B
3588 GLU   (  13-)  5
3600 GLU   (  25-)  5
3683 GLU   ( 108-)  5
3887 GLU   (  78-)  6
3890 GLU   (  81-)  6
3953 GLU   ( 144-)  6
3988 GLU   ( 179-)  6
4002 GLU   ( 193-)  6
4007 GLU   ( 198-)  6
4111 GLU   (  30-)  D
4145 GLU   (  64-)  D
4155 GLU   (  74-)  D
4162 GLU   (  81-)  D
4170 GLU   (  89-)  D
4292 GLU   (   2-)  E
4306 GLU   (  16-)  E
4315 GLU   (  25-)  E
4401 GLU   ( 111-)  E
And so on for a total of 89 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.

   2 OGUA  (   2-)  7      C2   N3    1.36    4.9
   2 OGUA  (   2-)  7      N1   C2    1.41    4.1
   3 OCYT  (   3-)  7      C4   N3    1.36    4.1
   6 OGUA  (   6-)  7      C2   N3    1.36    4.2
   8 OCYT  (   8-)  7      C4   N3    1.36    4.3
   9 OGUA  (   9-)  7      C2   N3    1.36    4.3
  10 OGUA  (  10-)  7      C2   N3    1.36    4.4
  10 OGUA  (  10-)  7      N1   C2    1.41    4.2
  12 OCYT  (  12-)  7      C4   N3    1.37    4.4
  13 OGUA  (  13-)  7      C2   N3    1.36    4.2
  13 OGUA  (  13-)  7      N1   C2    1.41    4.0
  15 OADE  (  15-)  7      C1'  C2'   1.49   -4.1
  15 OADE  (  15-)  7      N7   C5    1.36   -4.4
  16 OGUA  (  16-)  7      N1   C2    1.41    4.1
  19 OCYT  (  19-)  7      C4   N3    1.36    4.2
  23 OGUA  (  23-)  7      C2   N3    1.36    4.6
  24 OGUA  (  24-)  7      C2   N3    1.36    4.2
  25 OURA  (  25-)  7      C1'  N1    1.51    4.6
  25 OURA  (  25-)  7      N3   C2    1.40    4.4
  27 OCYT  (  27-)  7      P    O5'   1.55   -4.2
  27 OCYT  (  27-)  7      C4   N3    1.36    4.1
  28 OCYT  (  28-)  7      C4   N3    1.36    4.1
  29 OADE  (  29-)  7      N7   C5    1.36   -4.5
  30 OCYT  (  30-)  7      C1'  N1    1.52    4.0
  32 OURA  (  32-)  7      C1'  N1    1.51    4.1
And so on for a total of 2517 lines.

Warning: Directionality in bond lengths and no X-ray cell

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

You have most probably seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the X-ray cell axes.

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.

   1 OURA  (   1-)  7      O4'  C1'  N1  114.37    6.2
   2 OGUA  (   2-)  7      O4'  C1'  N9  113.33    5.1
   2 OGUA  (   2-)  7      N9   C8   N7  113.28    4.4
   2 OGUA  (   2-)  7      C5   C6   O6  124.23   -7.3
   2 OGUA  (   2-)  7      O6   C6   N1  125.02    8.5
   3 OCYT  (   3-)  7      O4'  C1'  N1  114.54    6.3
   3 OCYT  (   3-)  7      C5   C4   N3  119.94   -4.9
   3 OCYT  (   3-)  7      N4   C4   N3  122.36    6.2
   4 OCYT  (   4-)  7      O4'  C1'  N1  115.10    6.9
   4 OCYT  (   4-)  7      C5   C4   N3  120.05   -4.6
   4 OCYT  (   4-)  7      N4   C4   N3  121.71    5.3
   5 OURA  (   5-)  7      O4'  C1'  N1  113.94    5.7
   6 OGUA  (   6-)  7      O4'  C1'  N9  112.68    4.5
   6 OGUA  (   6-)  7      N9   C8   N7  113.16    4.1
   6 OGUA  (   6-)  7      C5   C6   O6  123.76   -8.1
   6 OGUA  (   6-)  7      O6   C6   N1  125.53    9.4
   7 OGUA  (   7-)  7      O4'  C1'  N9  113.73    5.5
   7 OGUA  (   7-)  7      C5   C6   O6  123.82   -8.0
   7 OGUA  (   7-)  7      O6   C6   N1  125.51    9.3
   8 OCYT  (   8-)  7      O4'  C1'  N1  114.67    6.5
   8 OCYT  (   8-)  7      C5   C4   N3  120.12   -4.5
   8 OCYT  (   8-)  7      N4   C4   N3  122.40    6.3
   9 OGUA  (   9-)  7      N9   C8   N7  113.22    4.2
   9 OGUA  (   9-)  7      C5   C6   O6  123.66   -8.2
   9 OGUA  (   9-)  7      O6   C6   N1  125.82    9.9
And so on for a total of 10515 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.

3025 ASP   (   8-)  A
3062 ASP   (  45-)  A
3193 GLU   ( 176-)  A
3225 GLU   ( 208-)  A
3255 GLU   ( 238-)  A
3361 ASP   ( 344-)  A
3377 GLU   ( 360-)  A
3410 ASP   ( 393-)  A
3432 ASP   ( 415-)  A
3447 GLU   ( 430-)  A
3463 GLU   (  15-)  B
3486 ASP   (  38-)  B
3526 GLU   (  78-)  B
3588 GLU   (  13-)  5
3591 ASP   (  16-)  5
3600 GLU   (  25-)  5
3618 ASP   (  43-)  5
3683 GLU   ( 108-)  5
3758 ASP   ( 183-)  5
3880 ASP   (  71-)  6
3887 GLU   (  78-)  6
3890 GLU   (  81-)  6
3906 ASP   (  97-)  6
3953 GLU   ( 144-)  6
3988 GLU   ( 179-)  6
And so on for a total of 259 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.

3089 LEU   (  72-)  A      CA    -7.0    23.43    34.19
3217 PRO   ( 200-)  A      N     -9.1   -32.31    -2.48
3292 ILE   ( 275-)  A      CA    -6.8    22.98    33.24
3331 GLN   ( 314-)  A      CA    -9.8    15.10    33.96
3369 PHE   ( 352-)  A      CA    -6.0    24.37    33.98
3375 PRO   ( 358-)  A      N     -6.3   -23.17    -2.48
3519 PHE   (  71-)  B      CA    -6.8    23.02    33.98
4877 PRO   (  32-)  H      N      9.3    28.05    -2.48
6517 PRO   (  49-)  U      N     10.4    31.48    -2.48
The average deviation= 1.038

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.

6311 SER   (  53-)  S    6.63
4901 ALA   (  56-)  H    6.26
4396 LYS   ( 106-)  E    6.04
5743 ARG   (  63-)  N    5.86
5660 ALA   ( 116-)  M    5.78
7092 ARG   (  35-)  2    5.59
3332 PRO   ( 315-)  A    5.26
6119 GLY   (  81-)  Q    4.85
5723 GLU   (  43-)  N    4.78
4655 GLU   ( 164-)  F    4.72
6096 GLN   (  58-)  Q    4.68
6436 LYS   (  68-)  T    4.56
4628 PHE   ( 137-)  F    4.54
5236 ILE   ( 101-)  J    4.52
5929 LYS   (   5-)  P    4.51
6814 THR   (  65-)  X    4.43
5600 ALA   (  56-)  M    4.42
4699 GLY   (  30-)  G    4.42
4320 GLN   (  30-)  E    4.38
3100 MET   (  83-)  A    4.36
5996 VAL   (  72-)  P    4.26
6158 ALA   (   3-)  R    4.25
7085 ARG   (  28-)  2    4.25
5823 ARG   (  16-)  O    4.24
6072 ALA   (  34-)  Q    4.23
5107 ALA   ( 113-)  I    4.22
4882 VAL   (  37-)  H    4.20
5944 ARG   (  20-)  P    4.01

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 : 1.587

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.

3209 PHE   ( 192-)  A      CB   4.21

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

1904 OADE  (1784-)  8    0.12
2245 OGUA  (2125-)  8    0.12
2268 OGUA  (2148-)  8    0.11
 147 OGUA  (  27-)  8    0.10
1204 OADE  (1084-)  8    0.10
 281 OADE  ( 161-)  8    0.10
1145 OGUA  (1025-)  8    0.10
 Ramachandran Z-score : -3.921

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.921

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.

4647 THR   ( 156-)  F    -3.4
6898 THR   (   9-)  Z    -3.3
3253 PHE   ( 236-)  A    -3.3
3593 THR   (  18-)  5    -3.3
3379 THR   ( 362-)  A    -3.2
3375 PRO   ( 358-)  A    -3.1
6517 PRO   (  49-)  U    -3.1
3217 PRO   ( 200-)  A    -3.1
4629 PRO   ( 138-)  F    -3.1
3059 PRO   (  42-)  A    -3.1
4824 PRO   ( 155-)  G    -3.1
6674 THR   (   9-)  W    -3.0
4877 PRO   (  32-)  H    -3.0
7025 THR   (  22-)  1    -3.0
3721 THR   ( 146-)  5    -3.0
3391 THR   ( 374-)  A    -3.0
4071 THR   ( 262-)  6    -3.0
3321 THR   ( 304-)  A    -2.9
3295 ILE   ( 278-)  A    -2.9
3329 PRO   ( 312-)  A    -2.9
4035 PRO   ( 226-)  6    -2.9
3932 ILE   ( 123-)  6    -2.9
3830 PRO   (  21-)  6    -2.9
4722 PRO   (  53-)  G    -2.8
3057 PRO   (  40-)  A    -2.8
And so on for a total of 213 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.

3035 GLU   (  18-)  A  Poor phi/psi
3041 LEU   (  24-)  A  omega poor
3054 SER   (  37-)  A  omega poor
3056 ILE   (  39-)  A  Poor phi/psi
3061 ILE   (  44-)  A  Poor phi/psi
3062 ASP   (  45-)  A  omega poor
3063 ALA   (  46-)  A  Poor phi/psi
3064 ALA   (  47-)  A  Poor phi/psi
3065 VAL   (  48-)  A  Poor phi/psi
3071 GLU   (  54-)  A  Poor phi/psi, omega poor
3073 GLN   (  56-)  A  Poor phi/psi
3078 ILE   (  61-)  A  Poor phi/psi, omega poor
3084 PHE   (  67-)  A  omega poor
3085 SER   (  68-)  A  Poor phi/psi
3088 ALA   (  71-)  A  Poor phi/psi, omega poor
3089 LEU   (  72-)  A  Poor phi/psi, omega poor
3090 SER   (  73-)  A  Poor phi/psi
3096 ALA   (  79-)  A  Poor phi/psi, omega poor
3099 ILE   (  82-)  A  Poor phi/psi
3115 VAL   (  98-)  A  omega poor
3116 HIS   (  99-)  A  PRO omega poor
3119 LEU   ( 102-)  A  Poor phi/psi
3124 LYS   ( 107-)  A  Poor phi/psi
3146 ILE   ( 129-)  A  omega poor
3152 ILE   ( 135-)  A  omega poor
And so on for a total of 665 lines.

Warning: Unusual rotamers

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

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

6114 SER   (  76-)  Q    0.33
3179 VAL   ( 162-)  A    0.36
3106 SER   (  89-)  A    0.36
5121 SER   ( 127-)  I    0.36
3812 VAL   (   3-)  6    0.38
4469 SER   ( 179-)  E    0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 OCYT  (   3-)  7      0
   4 OCYT  (   4-)  7      0
   5 OURA  (   5-)  7      0
   6 OGUA  (   6-)  7      0
   7 OGUA  (   7-)  7      0
   8 OCYT  (   8-)  7      0
   9 OGUA  (   9-)  7      0
  10 OGUA  (  10-)  7      0
  11 OCYT  (  11-)  7      0
  12 OCYT  (  12-)  7      0
  13 OGUA  (  13-)  7      0
  14 OURA  (  14-)  7      0
  15 OADE  (  15-)  7      0
  16 OGUA  (  16-)  7      0
  17 OCYT  (  17-)  7      0
  18 OGUA  (  18-)  7      0
  19 OCYT  (  19-)  7      0
  20 OGUA  (  20-)  7      0
  21 OGUA  (  21-)  7      0
  22 OURA  (  22-)  7      0
  23 OGUA  (  23-)  7      0
  24 OGUA  (  24-)  7      0
  25 OURA  (  25-)  7      0
  26 OCYT  (  26-)  7      0
  27 OCYT  (  27-)  7      0
And so on for a total of 5185 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.364

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!

4699 GLY   (  30-)  G   2.87   17
7084 GLY   (  27-)  2   2.37   80
6603 GLY   (  32-)  V   2.29   13
3086 GLY   (  69-)  A   2.24   10
5977 GLY   (  53-)  P   2.20   20
3087 GLY   (  70-)  A   2.02   34
4084 GLY   (   3-)  D   1.95   68
4153 GLY   (  72-)  D   1.92   10
5968 GLY   (  44-)  P   1.83   16
4673 ALA   (   4-)  G   1.71   15
6255 GLY   ( 100-)  R   1.68   18
5431 GLY   (  31-)  L   1.68   10
4897 ALA   (  52-)  H   1.55   22

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].

3160 PRO   ( 143-)  A    99.8 envelop C-beta (108 degrees)
3217 PRO   ( 200-)  A   -27.2 envelop C-alpha (-36 degrees)
3375 PRO   ( 358-)  A   -22.1 half-chair C-alpha/N (-18 degrees)
3837 PRO   (  28-)  6  -156.7 half-chair N/C-delta (-162 degrees)
4026 PRO   ( 217-)  6   103.6 envelop C-beta (108 degrees)
4052 PRO   ( 243-)  6   100.5 envelop C-beta (108 degrees)
4144 PRO   (  63-)  D   103.0 envelop C-beta (108 degrees)
4629 PRO   ( 138-)  F   133.2 half-chair C-beta/C-alpha (126 degrees)
4877 PRO   (  32-)  H   132.5 half-chair C-beta/C-alpha (126 degrees)
5181 PRO   (  46-)  J   110.1 envelop C-beta (108 degrees)
5616 PRO   (  72-)  M  -116.0 envelop C-gamma (-108 degrees)
5945 PRO   (  21-)  P   103.7 envelop C-beta (108 degrees)
6515 PRO   (  47-)  U   101.9 envelop C-beta (108 degrees)
6517 PRO   (  49-)  U   120.8 half-chair C-beta/C-alpha (126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

1202 OURA  (1082-)  8      N3  <-> 1206 OADE  (1086-)  8      N1     0.25    2.75  INTRA BL
1202 OURA  (1082-)  8      N3  <-> 1206 OADE  (1086-)  8      C2     0.22    2.88  INTRA BL
 830 OURA  ( 710-)  8      N3  <->  841 OADE  ( 721-)  8      N1     0.22    2.78  INTRA BL
1382 OADE  (1262-)  8      N1  <-> 2137 OURA  (2017-)  8      N3     0.22    2.78  INTRA BL
 402 OADE  ( 282-)  8      N1  <->  478 OURA  ( 358-)  8      N3     0.21    2.79  INTRA BL
1473 OADE  (1353-)  8      N1  <-> 1499 OURA  (1379-)  8      N3     0.21    2.79  INTRA BL
 406 OURA  ( 286-)  8      N3  <->  474 OADE  ( 354-)  8      N1     0.21    2.79  INTRA BL
1505 OADE  (1385-)  8      N1  <-> 1522 OURA  (1402-)  8      N3     0.20    2.80  INTRA BL
1587 OURA  (1467-)  8      N3  <-> 1645 OADE  (1525-)  8      N1     0.20    2.80  INTRA BL
2214 OADE  (2094-)  8      N1  <-> 2315 OURA  (2195-)  8      N3     0.20    2.80  INTRA BL
1652 OADE  (1532-)  8      N1  <-> 1659 OURA  (1539-)  8      N3     0.20    2.80  INTRA BL
2066 OURA  (1946-)  8      N3  <-> 2080 OADE  (1960-)  8      N1     0.19    2.81  INTRA BL
1604 OURA  (1484-)  8      N3  <-> 1625 OADE  (1505-)  8      N1     0.19    2.81  INTRA BL
1424 OADE  (1304-)  8      N1  <-> 1744 OURA  (1624-)  8      N3     0.19    2.81  INTRA BL
1560 OURA  (1440-)  8      N3  <-> 1671 OADE  (1551-)  8      N1     0.19    2.81  INTRA BL
1210 OADE  (1090-)  8      N1  <-> 1221 OURA  (1101-)  8      N3     0.19    2.81  INTRA BL
1135 OURA  (1015-)  8      N3  <-> 1267 OADE  (1147-)  8      N1     0.18    2.82  INTRA BL
2713 OURA  (2593-)  8      N3  <-> 2720 OADE  (2600-)  8      N1     0.18    2.82  INTRA BL
2636 OADE  (2516-)  8      N1  <-> 2688 OURA  (2568-)  8      N3     0.18    2.82  INTRA BL
2956 OURA  (2836-)  8      N3  <-> 3002 OADE  (2882-)  8      N1     0.18    2.82  INTRA BL
1829 OURA  (1709-)  8      N3  <-> 1869 OADE  (1749-)  8      N1     0.18    2.82  INTRA BL
   5 OURA  (   5-)  7      N3  <->  115 OADE  ( 115-)  7      N1     0.18    2.82  INTRA BL
2573 OADE  (2453-)  8      N1  <-> 2620 OURA  (2500-)  8      N3     0.18    2.82  INTRA BL
1289 OADE  (1169-)  8      N1  <-> 1300 OURA  (1180-)  8      N3     0.18    2.82  INTRA BL
2381 OCYT  (2261-)  8      N3  <-> 2399 OGUA  (2279-)  8      N1     0.17    2.83  INTRA BL
And so on for a total of 1165 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: 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

Note: Inside/Outside RMS Z-score plot

Chain identifier: Z

Note: Inside/Outside RMS Z-score plot

Chain identifier: 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

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.

3458 TYR   ( 441-)  A      -9.35
7166 TYR   (  63-)  3      -9.06
6062 TYR   (  24-)  Q      -8.57
3268 ARG   ( 251-)  A      -8.47
5550 ARG   (   6-)  M      -8.45
6719 ARG   (  54-)  W      -8.43
3374 ARG   ( 357-)  A      -8.38
5560 ARG   (  16-)  M      -8.31
4369 ARG   (  79-)  E      -8.17
3891 TYR   (  82-)  6      -8.09
5447 ARG   (  47-)  L      -8.00
6437 ARG   (  69-)  T      -7.97
5326 ARG   (  49-)  K      -7.97
6441 ARG   (  73-)  T      -7.87
3492 ARG   (  44-)  B      -7.82
5554 ARG   (  10-)  M      -7.79
6235 ARG   (  80-)  R      -7.79
5684 ARG   (   4-)  N      -7.78
5448 ARG   (  48-)  L      -7.77
7132 ARG   (  29-)  3      -7.76
3265 TYR   ( 248-)  A      -7.65
4229 GLN   ( 148-)  D      -7.63
5562 ARG   (  18-)  M      -7.55
5308 ARG   (  31-)  K      -7.54
6675 ARG   (  10-)  W      -7.51
And so on for a total of 380 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.

3069 LEU   (  52-)  A      3074 - ARG     57- ( A)         -5.57
3123 LYS   ( 106-)  A      3125 - GLU    108- ( A)         -5.17
3268 ARG   ( 251-)  A      3270 - GLN    253- ( A)         -7.34
3272 ARG   ( 255-)  A      3275 - TYR    258- ( A)         -6.26
3309 SER   ( 292-)  A      3311 - PHE    294- ( A)         -5.25
3441 MET   ( 424-)  A      3443 - SER    426- ( A)         -4.79
3445 GLN   ( 428-)  A      3452 - LYS    435- ( A)         -5.46
3454 ASN   ( 437-)  A      3459 - GLY    442- ( A)         -5.75
3612 LYS   (  37-)  5      3614 - VAL     39- ( 5)         -4.98
3668 GLU   (  93-)  5      3670 - VAL     95- ( 5)         -4.51
3778 GLN   ( 203-)  5      3780 - LYS    205- ( 5)         -5.05
3916 LYS   ( 107-)  6      3919 - LYS    110- ( 6)         -4.95
4046 ARG   ( 237-)  6      4048 - PHE    239- ( 6)         -5.51
4078 ARG   ( 269-)  6      4080 - SER    271- ( 6)         -5.13
4221 HIS   ( 140-)  D      4223 - VAL    142- ( D)         -4.68
4288 VAL   ( 207-)  D      4290 - ALA    209- ( D)         -5.09
4351 ARG   (  61-)  E      4354 - GLY     64- ( E)         -5.74
4515 VAL   (  24-)  F      4517 - GLN     26- ( F)         -4.59
4625 GLN   ( 134-)  F      4627 - ILE    136- ( F)         -4.49
4638 ARG   ( 147-)  F      4640 - ARG    149- ( F)         -5.49
5043 GLU   (  49-)  I      5046 - LEU     52- ( I)         -5.21
5109 ASP   ( 115-)  I      5111 - THR    117- ( I)         -4.16
5305 SER   (  28-)  K      5309 - TYR     32- ( K)         -5.58
5328 LYS   (  51-)  K      5330 - LYS     53- ( K)         -4.54
5417 LYS   (  17-)  L      5419 - LEU     19- ( L)         -4.83
5441 ARG   (  41-)  L      5443 - GLY     43- ( L)         -5.19
5447 ARG   (  47-)  L      5451 - GLU     51- ( L)         -6.10
5458 TYR   (  58-)  L      5460 - ARG     60- ( L)         -5.97
5549 LYS   (   5-)  M      5558 - LYS     14- ( M)         -6.15
5560 ARG   (  16-)  M      5562 - ARG     18- ( M)         -7.07
5625 ARG   (  81-)  M      5630 - LYS     86- ( M)         -5.47
5682 ARG   (   2-)  N      5686 - SER      6- ( N)         -6.07
5689 GLN   (   9-)  N      5692 - ARG     12- ( N)         -5.20
5973 ILE   (  49-)  P      5976 - ARG     52- ( P)         -5.23
6179 LYS   (  24-)  R      6181 - ASP     26- ( R)         -5.21
6237 HIS   (  82-)  R      6239 - ARG     84- ( R)         -4.63
6440 GLN   (  72-)  T      6442 - ILE     74- ( T)         -6.73
6512 HIS   (  44-)  U      6514 - LYS     46- ( U)         -5.44
6519 LEU   (  51-)  U      6521 - GLN     53- ( U)         -5.31
6667 HIS   (   2-)  W      6669 - LYS      4- ( W)         -5.34
6703 ARG   (  38-)  W      6705 - ARG     40- ( W)         -6.15
6884 ASN   (  58-)  Y      6886 - LYS     60- ( Y)         -4.59
6949 VAL   (   2-)  0      6953 - LYS      6- ( 0)         -5.84
7131 LEU   (  28-)  3      7133 - HIS     30- ( 3)         -5.62
7175 LYS   (   8-)  4      7177 - LEU     10- ( 4)         -5.73

Error: Abnormal average packing environment

The average packing score for the structure is very low.

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

Average for range 1 - 7205 : -2.247

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: 5

Note: Quality value plot

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

Chain identifier: 6

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

Note: Quality value plot

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

Chain identifier: V

Note: Quality value plot

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

Chain identifier: W

Note: Quality value plot

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

Chain identifier: X

Note: Quality value plot

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

Chain identifier: Y

Note: Quality value plot

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

Chain identifier: Z

Note: Quality value plot

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

Chain identifier: 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

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.

3454 ASN   ( 437-)  A   -3.80
6953 LYS   (   6-)  0   -3.45
3451 LYS   ( 434-)  A   -3.42
7060 ARG   (   3-)  2   -3.40
6676 ASN   (  11-)  W   -3.37
7199 LYS   (  32-)  4   -3.32
3854 ASN   (  45-)  6   -3.31
5207 LYS   (  72-)  J   -3.24
4073 LYS   ( 264-)  6   -3.23
6235 ARG   (  80-)  R   -3.23
4061 LYS   ( 252-)  6   -3.21
4070 ARG   ( 261-)  6   -3.19
6952 ASN   (   5-)  0   -3.18
4375 PHE   (  85-)  E   -3.17
5691 ASN   (  11-)  N   -3.16
5448 ARG   (  48-)  L   -3.16
5308 ARG   (  31-)  K   -3.15
5447 ARG   (  47-)  L   -3.09
6769 ALA   (  20-)  X   -3.09
4348 LYS   (  58-)  E   -3.08
3853 ASN   (  44-)  6   -3.07
7063 GLN   (   6-)  2   -3.07
5683 HIS   (   3-)  N   -3.06
7059 LYS   (   2-)  2   -3.06
6950 GLN   (   3-)  0   -3.06
And so on for a total of 149 lines.

Warning: Abnormal packing Z-score for sequential residues

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

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

3255 GLU   ( 238-)  A     - 3258 GLN   ( 241-)  A        -1.74
3368 ALA   ( 351-)  A     - 3371 PRO   ( 354-)  A        -2.02
3372 GLY   ( 355-)  A     - 3375 PRO   ( 358-)  A        -2.04
3452 LYS   ( 435-)  A     - 3456 LYS   ( 439-)  A        -2.44
3575 PHE   ( 127-)  B     - 3579 LEU   (   4-)  5        -1.97
3592 ALA   (  17-)  5     - 3595 GLN   (  20-)  5        -1.69
3740 ASN   ( 165-)  5     - 3743 ASN   ( 168-)  5        -1.85
3851 ARG   (  42-)  6     - 3854 ASN   (  45-)  6        -2.35
3857 ILE   (  48-)  6     - 3860 ARG   (  51-)  6        -1.94
3892 ASP   (  83-)  6     - 3895 ARG   (  86-)  6        -1.72
4042 GLY   ( 233-)  6     - 4046 ARG   ( 237-)  6        -2.13
4047 ASN   ( 238-)  6     - 4051 HIS   ( 242-)  6        -2.44
4058 VAL   ( 249-)  6     - 4064 LYS   ( 255-)  6        -1.97
4196 GLY   ( 115-)  D     - 4200 ALA   ( 119-)  D        -2.09
4203 VAL   ( 122-)  D     - 4206 TRP   ( 125-)  D        -1.90
4214 THR   ( 133-)  D     - 4217 ASN   ( 136-)  D        -2.49
4222 ARG   ( 141-)  D     - 4226 SER   ( 145-)  D        -2.11
4232 THR   ( 151-)  D     - 4237 PHE   ( 156-)  D        -2.23
4251 VAL   ( 170-)  D     - 4254 GLN   ( 173-)  D        -1.99
4328 GLY   (  38-)  E     - 4336 GLN   (  46-)  E        -2.02
4368 TRP   (  78-)  E     - 4371 GLY   (  81-)  E        -2.01
4386 VAL   (  96-)  E     - 4390 MET   ( 100-)  E        -1.78
4452 ARG   ( 162-)  E     - 4455 HIS   ( 165-)  E        -2.16
5083 SER   (  89-)  I     - 5086 PRO   (  92-)  I        -1.69
5411 GLY   (  11-)  L     - 5414 LYS   (  14-)  L        -1.75
5415 ALA   (  15-)  L     - 5419 LEU   (  19-)  L        -1.97
5445 GLY   (  45-)  L     - 5450 PHE   (  50-)  L        -2.63
5451 GLU   (  51-)  L     - 5454 GLN   (  54-)  L        -2.06
5559 GLY   (  15-)  M     - 5566 GLN   (  22-)  M        -2.13
5624 VAL   (  80-)  M     - 5628 LYS   (  84-)  M        -2.27
5680 MET   ( 136-)  M     - 5686 SER   (   6-)  N        -2.32
5689 GLN   (   9-)  N     - 5692 ARG   (  12-)  N        -2.33
6015 VAL   (  91-)  P     - 6019 LYS   (  95-)  P        -2.21
6038 ASN   ( 114-)  P     - 6043 ARG   (   5-)  Q        -2.28
6045 VAL   (   7-)  Q     - 6048 ARG   (  10-)  Q        -2.07
6162 SER   (   7-)  R     - 6165 LYS   (  10-)  R        -1.92
6232 PHE   (  77-)  R     - 6238 TYR   (  83-)  R        -2.25
6342 ARG   (  84-)  S     - 6346 ARG   (  88-)  S        -2.03
6368 ARG   ( 110-)  S     - 6371 ARG   (   3-)  T        -1.83
6427 ASN   (  59-)  T     - 6430 VAL   (  62-)  T        -2.09
6433 GLY   (  65-)  T     - 6438 HIS   (  70-)  T        -2.00
6674 THR   (   9-)  W     - 6679 ASP   (  14-)  W        -2.36
6686 GLY   (  21-)  W     - 6689 ARG   (  24-)  W        -2.09
6947 GLU   (  58-)  Z     - 6954 PRO   (   7-)  0        -2.54
6984 HIS   (  37-)  0     - 6987 HIS   (  40-)  0        -1.94
7057 LYS   (  54-)  1     - 7064 PRO   (   7-)  2        -2.69
7095 GLY   (  38-)  2     - 7098 ARG   (  41-)  2        -1.77
7104 PRO   (   1-)  3     - 7110 ARG   (   7-)  3        -2.19
7130 ASN   (  27-)  3     - 7135 LEU   (  32-)  3        -2.26
7143 LYS   (  40-)  3     - 7147 ARG   (  44-)  3        -1.98

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: 5

Note: Second generation quality Z-score plot

Chain identifier: 6

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

Note: Second generation quality Z-score plot

Chain identifier: Z

Note: Second generation quality Z-score plot

Chain identifier: 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

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.

3163 GLN   ( 146-)  A
3269 GLN   ( 252-)  A
3622 ASN   (  47-)  5
3655 GLN   (  80-)  5
3678 GLN   ( 103-)  5
3714 ASN   ( 139-)  5
3740 ASN   ( 165-)  5
3852 ASN   (  43-)  6
4008 HIS   ( 199-)  6
4047 ASN   ( 238-)  6
4117 GLN   (  36-)  D
4217 ASN   ( 136-)  D
4245 GLN   ( 164-)  D
4319 HIS   (  29-)  E
4320 GLN   (  30-)  E
4513 ASN   (  22-)  F
4553 GLN   (  62-)  F
4617 ASN   ( 126-)  F
4690 GLN   (  21-)  G
4741 ASN   (  72-)  G
4783 HIS   ( 114-)  G
4807 GLN   ( 138-)  G
4978 GLN   ( 133-)  H
5005 GLN   (  11-)  I
5175 HIS   (  40-)  J
5202 ASN   (  67-)  J
5211 HIS   (  76-)  J
5267 HIS   ( 132-)  J
5282 GLN   (   5-)  K
5504 GLN   ( 104-)  L
5683 HIS   (   3-)  N
5964 GLN   (  40-)  P
6108 GLN   (  70-)  Q
6241 GLN   (  86-)  R
6315 ASN   (  57-)  S
6427 ASN   (  59-)  T
6507 ASN   (  39-)  U
6649 GLN   (  78-)  V
6667 HIS   (   2-)  W
6765 ASN   (  16-)  X
7047 GLN   (  44-)  1
7073 HIS   (  16-)  2
7128 HIS   (  25-)  3
7133 HIS   (  30-)  3

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.

  25 OURA  (  25-)  7      N3
  47 OCYT  (  47-)  7      N4
  54 OGUA  (  54-)  7      N2
  73 OADE  (  73-)  7      N6
  74 OURA  (  74-)  7      N3
  75 OGUA  (  75-)  7      N1
  98 OGUA  (  98-)  7      N2
 106 OGUA  ( 106-)  7      N2
 112 OGUA  ( 112-)  7      N2
 129 OGUA  (   9-)  8      N2
 143 OGUA  (  23-)  8      N2
 147 OGUA  (  27-)  8      N1
 172 OADE  (  52-)  8      N6
 182 OURA  (  62-)  8      N3
 186 OCYT  (  66-)  8      N4
 200 OGUA  (  80-)  8      N2
 202 OURA  (  82-)  8      N3
 218 OGUA  (  98-)  8      N2
 232 OURA  ( 112-)  8      N3
 300 OGUA  ( 180-)  8      N1
 301 OADE  ( 181-)  8      N6
 340 OGUA  ( 220-)  8      N2
 342 OADE  ( 222-)  8      N6
 366 OCYT  ( 246-)  8      N4
 367 OGUA  ( 247-)  8      N1
And so on for a total of 1712 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.

3062 ASP   (  45-)  A      OD1
3116 HIS   (  99-)  A      ND1
3193 GLU   ( 176-)  A      OE2
3197 GLU   ( 180-)  A      OE2
3229 GLN   ( 212-)  A      OE1
3264 ASN   ( 247-)  A      OD1
3406 GLU   ( 389-)  A      OE1
3410 ASP   ( 393-)  A      OD2
3560 ASP   ( 112-)  B      OD2
3615 GLU   (  40-)  5      OE2
3618 ASP   (  43-)  5      OD2
3633 ASN   (  58-)  5      OD1
3668 GLU   (  93-)  5      OE2
3687 ASP   ( 112-)  5      OD1
3687 ASP   ( 112-)  5      OD2
3701 GLN   ( 126-)  5      OE1
3741 ASP   ( 166-)  5      OD1
3741 ASP   ( 166-)  5      OD2
3852 ASN   (  43-)  6      OD1
3892 ASP   (  83-)  6      OD2
3906 ASP   (  97-)  6      OD2
3908 GLU   (  99-)  6      OE1
3953 GLU   ( 144-)  6      OE2
3988 GLU   ( 179-)  6      OE2
4040 HIS   ( 231-)  6      NE2
And so on for a total of 108 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.

3025 ASP   (   8-)  A   H-bonding suggests Asn
3193 GLU   ( 176-)  A   H-bonding suggests Gln; but Alt-Rotamer
3197 GLU   ( 180-)  A   H-bonding suggests Gln
3377 GLU   ( 360-)  A   H-bonding suggests Gln
3384 ASP   ( 367-)  A   H-bonding suggests Asn
3406 GLU   ( 389-)  A   H-bonding suggests Gln
3410 ASP   ( 393-)  A   H-bonding suggests Asn
3522 GLU   (  74-)  B   H-bonding suggests Gln
3537 GLU   (  89-)  B   H-bonding suggests Gln
3560 ASP   ( 112-)  B   H-bonding suggests Asn
3615 GLU   (  40-)  5   H-bonding suggests Gln
3626 ASP   (  51-)  5   H-bonding suggests Asn
3677 ASP   ( 102-)  5   H-bonding suggests Asn
3687 ASP   ( 112-)  5   H-bonding suggests Asn
3880 ASP   (  71-)  6   H-bonding suggests Asn
3887 GLU   (  78-)  6   H-bonding suggests Gln
3890 GLU   (  81-)  6   H-bonding suggests Gln; but Alt-Rotamer
4002 GLU   ( 193-)  6   H-bonding suggests Gln; but Alt-Rotamer
4007 GLU   ( 198-)  6   H-bonding suggests Gln; but Alt-Rotamer
4109 GLU   (  28-)  D   H-bonding suggests Gln; but Alt-Rotamer
4111 GLU   (  30-)  D   H-bonding suggests Gln
4124 ASP   (  43-)  D   H-bonding suggests Asn
4170 GLU   (  89-)  D   H-bonding suggests Gln
4184 ASP   ( 103-)  D   H-bonding suggests Asn
4189 ASP   ( 108-)  D   H-bonding suggests Asn
And so on for a total of 114 lines.

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -4.368 (poor)
  2nd generation packing quality :  -4.923 (bad)
  Ramachandran plot appearance   :  -3.921 (poor)
  chi-1/chi-2 rotamer normality  :  -1.552
  Backbone conformation          :  -1.237

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.478
  Bond angles                    :   1.969
  Omega angle restraints         :   1.339 (loose)
  Side chain planarity           :   0.459 (tight)
  Improper dihedral distribution :   0.921
  Inside/Outside distribution    :   1.088

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 : 7.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.2
  2nd generation packing quality :  -2.5
  Ramachandran plot appearance   :  -2.0
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.478
  Bond angles                    :   1.969
  Omega angle restraints         :   1.339 (loose)
  Side chain planarity           :   0.459 (tight)
  Improper dihedral distribution :   0.921
  Inside/Outside distribution    :   1.088
==============

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.