WHAT IF Check report

This file was created 2011-12-16 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 pdb3iyd.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

4186 CMP   ( 680-)  H  -
4187 CMP   ( 679-)  G  -

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

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.

 503 GLU   ( 181-)  B
2155 GLU   ( 523-)  D
3801 SER   (  25-)  H

Warning: Missing atoms

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

  44 ARG   (  45-)  A      CG
  44 ARG   (  45-)  A      CD
  44 ARG   (  45-)  A      NE
  44 ARG   (  45-)  A      CZ
  44 ARG   (  45-)  A      NH1
  44 ARG   (  45-)  A      NH2
 367 ARG   (  45-)  B      CG
 367 ARG   (  45-)  B      CD
 367 ARG   (  45-)  B      NE
 367 ARG   (  45-)  B      CZ
 367 ARG   (  45-)  B      NH1
 367 ARG   (  45-)  B      NH2

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 GLN   (   2-)  A    Zero
   2 GLY   (   3-)  A    Zero
   3 SER   (   4-)  A    Zero
   4 VAL   (   5-)  A    Zero
   5 THR   (   6-)  A    Zero
   6 GLU   (   7-)  A    Zero
   7 PHE   (   8-)  A    Zero
   8 LEU   (   9-)  A    Zero
   9 LYS   (  10-)  A    Zero
  10 PRO   (  11-)  A    Zero
  11 ARG   (  12-)  A    Zero
  12 LEU   (  13-)  A    Zero
  13 VAL   (  14-)  A    Zero
  14 ASP   (  15-)  A    Zero
  15 ILE   (  16-)  A    Zero
  16 GLU   (  17-)  A    Zero
  17 GLN   (  18-)  A    Zero
  18 VAL   (  19-)  A    Zero
  19 SER   (  20-)  A    Zero
  20 SER   (  21-)  A    Zero
  21 THR   (  22-)  A    Zero
  22 HIS   (  23-)  A    Zero
  23 ALA   (  24-)  A    Zero
  24 LYS   (  25-)  A    Zero
  25 VAL   (  26-)  A    Zero
And so on for a total of 4180 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 : 99.98

Note: B-factor plot

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

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: C

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

 390 TYR   (  68-)  B
 507 TYR   ( 185-)  B
 595 TYR   (  47-)  C
 610 TYR   (  62-)  C
 720 TYR   ( 172-)  C
1035 TYR   ( 578-)  C
1041 TYR   ( 584-)  C
1071 TYR   ( 614-)  C
1109 TYR   ( 652-)  C
1183 TYR   ( 726-)  C
1208 TYR   ( 751-)  C
1213 TYR   ( 756-)  C
1267 TYR   ( 810-)  C
1517 TYR   (1213-)  C
1533 TYR   (1229-)  C
1589 TYR   (1285-)  C
1707 TYR   (  75-)  D
1772 TYR   ( 140-)  D
1901 TYR   ( 269-)  D
1981 TYR   ( 349-)  D
2089 TYR   ( 457-)  D
2143 TYR   ( 511-)  D
2241 TYR   ( 609-)  D
2404 TYR   ( 772-)  D
2731 TYR   (1099-)  D
2873 TYR   (1241-)  D
2914 TYR   (1282-)  D
3200 TYR   ( 228-)  F
3366 TYR   ( 394-)  F
3393 TYR   ( 421-)  F
3598 TYR   (  23-)  G
3615 TYR   (  40-)  G
3638 TYR   (  63-)  G
3674 TYR   (  99-)  G
3839 TYR   (  63-)  H
3875 TYR   (  99-)  H

Warning: Phenylalanine convention problem

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

 628 PHE   (  80-)  C
 684 PHE   ( 136-)  C
 704 PHE   ( 156-)  C
 705 PHE   ( 157-)  C
 734 PHE   ( 186-)  C
 736 PHE   ( 188-)  C
 743 PHE   ( 195-)  C
 794 PHE   ( 337-)  C
 842 PHE   ( 385-)  C
 862 PHE   ( 405-)  C
1102 PHE   ( 645-)  C
1363 PHE   ( 906-)  C
1391 PHE   ( 934-)  C
1491 PHE   (1187-)  C
1525 PHE   (1221-)  C
1569 PHE   (1265-)  C
1681 PHE   (  49-)  D
1689 PHE   (  57-)  D
1694 PHE   (  62-)  D
1773 PHE   ( 141-)  D
1808 PHE   ( 176-)  D
1892 PHE   ( 260-)  D
2009 PHE   ( 377-)  D
2012 PHE   ( 380-)  D
2069 PHE   ( 437-)  D
2093 PHE   ( 461-)  D
2252 PHE   ( 620-)  D
2405 PHE   ( 773-)  D
2567 PHE   ( 935-)  D
2732 PHE   (1100-)  D
2831 PHE   (1199-)  D
2951 PHE   (1319-)  D
3030 PHE   (  17-)  E
3494 PHE   ( 522-)  F
3589 PHE   (  14-)  G
3644 PHE   (  69-)  G
3677 PHE   ( 102-)  G
3790 PHE   (  14-)  H
3845 PHE   (  69-)  H
3912 PHE   ( 136-)  H

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.

 629 ASP   (  81-)  C
3165 ASP   ( 173-)  F
3628 ASP   (  53-)  G
3643 ASP   (  68-)  G
3686 ASP   ( 111-)  G
3713 ASP   ( 138-)  G
3736 ASP   ( 161-)  G
3767 ASP   ( 192-)  G
3829 ASP   (  53-)  H
3844 ASP   (  68-)  H
3887 ASP   ( 111-)  H
3914 ASP   ( 138-)  H
3937 ASP   ( 161-)  H
3968 ASP   ( 192-)  H

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.

1593 GLU   (1289-)  C
1774 GLU   ( 142-)  D
3069 GLU   (  56-)  E
3587 GLU   (  12-)  G
3609 GLU   (  34-)  G
3612 GLU   (  37-)  G
3629 GLU   (  54-)  G
3633 GLU   (  58-)  G
3653 GLU   (  78-)  G
3656 GLU   (  81-)  G
3668 GLU   (  93-)  G
3671 GLU   (  96-)  G
3746 GLU   ( 171-)  G
3756 GLU   ( 181-)  G
3766 GLU   ( 191-)  G
3788 GLU   (  12-)  H
3810 GLU   (  34-)  H
3813 GLU   (  37-)  H
3830 GLU   (  54-)  H
3834 GLU   (  58-)  H
3854 GLU   (  78-)  H
3857 GLU   (  81-)  H
3869 GLU   (  93-)  H
3872 GLU   (  96-)  H
3947 GLU   ( 171-)  H
3957 GLU   ( 181-)  H
3967 GLU   ( 191-)  H

Geometric checks

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.

3987 DGUA  (   2-)  I      N9   C8   N7  113.46    4.7
3991 DTHY  (   6-)  I      O4   C4   N3  122.33    4.1
3995 DTHY  (  10-)  I      O4   C4   N3  122.33    4.0
3996 DGUA  (  11-)  I      N9   C8   N7  113.47    4.7
3997 DTHY  (  12-)  I      O4   C4   N3  122.34    4.1
3998 DGUA  (  13-)  I      N9   C8   N7  113.55    4.9
4000 DTHY  (  15-)  I      O4   C4   N3  122.32    4.0
4004 DGUA  (  19-)  I      N9   C8   N7  113.54    4.9
4006 DTHY  (  21-)  I      O4   C4   N3  122.35    4.1
4011 DTHY  (  26-)  I      O4   C4   N3  122.31    4.0
4013 DTHY  (  28-)  I      O4   C4   N3  122.34    4.1
4016 DGUA  (  31-)  I      N9   C8   N7  113.51    4.8
4017 DGUA  (  32-)  I      N9   C8   N7  113.48    4.8
4025 DGUA  (  40-)  I      N9   C8   N7  113.49    4.8
4026 DGUA  (  41-)  I      N9   C8   N7  113.65    5.1
4028 DTHY  (  43-)  I      O4   C4   N3  122.32    4.0
4035 DTHY  (  50-)  I      O4   C4   N3  122.33    4.0
4036 DTHY  (  51-)  I      O4   C4   N3  122.37    4.1
4037 DTHY  (  52-)  I      O4   C4   N3  122.36    4.1
4039 DTHY  (  54-)  I      O4   C4   N3  122.36    4.1
4040 DGUA  (  55-)  I      N9   C8   N7  113.45    4.7
4043 DTHY  (  58-)  I      O4   C4   N3  122.30    4.0
4046 DGUA  (  61-)  I      N9   C8   N7  113.47    4.7
4047 DGUA  (  62-)  I      N9   C8   N7  113.49    4.8
4049 DTHY  (  64-)  I      O4   C4   N3  122.31    4.0
And so on for a total of 77 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.

 629 ASP   (  81-)  C
1593 GLU   (1289-)  C
1774 GLU   ( 142-)  D
3069 GLU   (  56-)  E
3165 ASP   ( 173-)  F
3587 GLU   (  12-)  G
3609 GLU   (  34-)  G
3612 GLU   (  37-)  G
3628 ASP   (  53-)  G
3629 GLU   (  54-)  G
3633 GLU   (  58-)  G
3643 ASP   (  68-)  G
3653 GLU   (  78-)  G
3656 GLU   (  81-)  G
3668 GLU   (  93-)  G
3671 GLU   (  96-)  G
3686 ASP   ( 111-)  G
3713 ASP   ( 138-)  G
3736 ASP   ( 161-)  G
3746 GLU   ( 171-)  G
3756 GLU   ( 181-)  G
3766 GLU   ( 191-)  G
3767 ASP   ( 192-)  G
3788 GLU   (  12-)  H
3810 GLU   (  34-)  H
3813 GLU   (  37-)  H
3829 ASP   (  53-)  H
3830 GLU   (  54-)  H
3834 GLU   (  58-)  H
3844 ASP   (  68-)  H
3854 GLU   (  78-)  H
3857 GLU   (  81-)  H
3869 GLU   (  93-)  H
3872 GLU   (  96-)  H
3887 ASP   ( 111-)  H
3914 ASP   ( 138-)  H
3937 ASP   ( 161-)  H
3947 GLU   ( 171-)  H
3957 GLU   ( 181-)  H
3967 GLU   ( 191-)  H
3968 ASP   ( 192-)  H

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 : -4.852

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.

3018 THR   (   5-)  E    -3.4
2199 THR   ( 567-)  D    -3.4
 712 THR   ( 164-)  C    -3.3
1052 THR   ( 595-)  C    -3.1
 813 THR   ( 356-)  C    -2.9
1251 LEU   ( 794-)  C    -2.8
 854 LEU   ( 397-)  C    -2.8
 556 LEU   ( 234-)  B    -2.7
1412 LEU   (1054-)  C    -2.7
3477 ILE   ( 505-)  F    -2.7
 533 ILE   ( 211-)  B    -2.7
1334 VAL   ( 877-)  C    -2.7
 241 PRO   ( 247-)  A    -2.7
2043 ILE   ( 411-)  D    -2.6
2317 ILE   ( 685-)  D    -2.6
1767 ILE   ( 135-)  D    -2.6
3362 ILE   ( 390-)  F    -2.6
1060 ILE   ( 603-)  C    -2.6
   4 VAL   (   5-)  A    -2.6
  26 THR   (  27-)  A    -2.6
2158 VAL   ( 526-)  D    -2.5
1450 THR   (1092-)  C    -2.5
1246 THR   ( 789-)  C    -2.5
 570 LEU   (  22-)  C    -2.5
2710 LEU   (1078-)  D    -2.5
And so on for a total of 145 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.

   3 SER   (   4-)  A  Poor phi/psi
  42 LEU   (  43-)  A  Poor phi/psi
  48 SER   (  49-)  A  Poor phi/psi
  51 PRO   (  52-)  A  Poor phi/psi
  60 ILE   (  61-)  A  Poor phi/psi
 146 GLN   ( 147-)  A  Poor phi/psi
 151 TYR   ( 152-)  A  Poor phi/psi
 157 ARG   ( 158-)  A  Poor phi/psi
 164 ARG   ( 170-)  A  Poor phi/psi
 173 PRO   ( 179-)  A  Poor phi/psi
 181 VAL   ( 187-)  A  Poor phi/psi
 182 GLU   ( 188-)  A  Poor phi/psi
 189 ARG   ( 195-)  A  Poor phi/psi
 196 VAL   ( 202-)  A  Poor phi/psi
 203 GLY   ( 209-)  A  Poor phi/psi
 222 LEU   ( 228-)  A  Poor phi/psi
 227 ASP   ( 233-)  A  Poor phi/psi
 229 ARG   ( 235-)  A  Poor phi/psi
 234 PRO   ( 240-)  A  Poor phi/psi
 255 GLU   ( 261-)  A  Poor phi/psi
 268 ALA   ( 274-)  A  Poor phi/psi
 287 PRO   ( 293-)  A  Poor phi/psi
 289 LEU   ( 295-)  A  Poor phi/psi
 315 TRP   ( 321-)  A  PRO omega poor
 317 PRO   ( 323-)  A  Poor phi/psi
And so on for a total of 383 lines.

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 SER   (   4-)  A      0
   4 VAL   (   5-)  A      0
   5 THR   (   6-)  A      0
  17 GLN   (  18-)  A      0
  18 VAL   (  19-)  A      0
  29 PRO   (  30-)  A      0
  32 ARG   (  33-)  A      0
  46 LEU   (  47-)  A      0
  47 LEU   (  48-)  A      0
  48 SER   (  49-)  A      0
  49 SER   (  50-)  A      0
  51 PRO   (  52-)  A      0
  53 CYS   (  54-)  A      0
  57 GLU   (  58-)  A      0
  59 GLU   (  60-)  A      0
  60 ILE   (  61-)  A      0
  61 ASP   (  62-)  A      0
  65 HIS   (  66-)  A      0
  71 GLU   (  72-)  A      0
  74 GLN   (  75-)  A      0
  92 GLN   (  93-)  A      0
 102 ASN   ( 103-)  A      0
 104 SER   ( 105-)  A      0
 106 ILE   ( 107-)  A      0
 114 ILE   ( 115-)  A      0
And so on for a total of 2061 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.203

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!

3070 GLY   (  57-)  E   3.28   16
3047 GLY   (  34-)  E   2.86   15
 163 GLY   ( 169-)  A   2.28   80
2245 GLY   ( 613-)  D   2.16   29
2762 GLY   (1130-)  D   2.13   18
2154 GLY   ( 522-)  D   2.01   18
1426 GLY   (1068-)  C   1.91   24
3938 GLY   ( 162-)  H   1.85   11
3211 GLY   ( 239-)  F   1.78   17
1449 GLY   (1091-)  C   1.68   57
3649 GLY   (  74-)  G   1.67   27
2744 GLY   (1112-)  D   1.65   58
 471 GLY   ( 149-)  B   1.60   33
1231 GLY   ( 774-)  C   1.60   10
2294 ALA   ( 662-)  D   1.58   17
2646 GLY   (1014-)  D   1.58   35
 107 GLY   ( 108-)  A   1.57   26
3737 GLY   ( 162-)  G   1.57   17
2769 GLY   (1137-)  D   1.57   16
 688 GLY   ( 140-)  C   1.53   13
3850 GLY   (  74-)  H   1.53   30
3976 GLY   ( 200-)  H   1.52   24
 930 ARG   ( 473-)  C   1.51   17

Warning: Unusual PRO puckering phases

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

  51 PRO   (  52-)  A  -114.4 envelop C-gamma (-108 degrees)
 108 PRO   ( 109-)  A  -115.9 envelop C-gamma (-108 degrees)
 207 PRO   ( 213-)  A  -115.6 envelop C-gamma (-108 degrees)
 241 PRO   ( 247-)  A   100.4 envelop C-beta (108 degrees)
 250 PRO   ( 256-)  A  -113.5 envelop C-gamma (-108 degrees)
 333 PRO   (  11-)  B  -113.4 envelop C-gamma (-108 degrees)
 374 PRO   (  52-)  B  -113.3 envelop C-gamma (-108 degrees)
 573 PRO   (  25-)  C  -112.6 envelop C-gamma (-108 degrees)
 738 PRO   ( 190-)  C  -113.0 envelop C-gamma (-108 degrees)
 832 PRO   ( 375-)  C  -120.8 half-chair C-delta/C-gamma (-126 degrees)
 954 PRO   ( 497-)  C  -115.4 envelop C-gamma (-108 degrees)
1233 PRO   ( 776-)  C  -112.5 envelop C-gamma (-108 degrees)
1354 PRO   ( 897-)  C  -118.1 half-chair C-delta/C-gamma (-126 degrees)
1528 PRO   (1224-)  C  -118.9 half-chair C-delta/C-gamma (-126 degrees)
2134 PRO   ( 502-)  D    99.8 envelop C-beta (108 degrees)
2216 PRO   ( 584-)  D  -114.5 envelop C-gamma (-108 degrees)
2382 PRO   ( 750-)  D  -119.0 half-chair C-delta/C-gamma (-126 degrees)
2483 PRO   ( 851-)  D  -116.2 envelop C-gamma (-108 degrees)
2708 PRO   (1076-)  D  -113.6 envelop C-gamma (-108 degrees)
2734 PRO   (1102-)  D  -114.8 envelop C-gamma (-108 degrees)
3476 PRO   ( 504-)  F    48.5 half-chair C-delta/C-gamma (54 degrees)
3482 PRO   ( 510-)  F  -117.1 half-chair C-delta/C-gamma (-126 degrees)
3584 PRO   (   9-)  G  -117.5 half-chair C-delta/C-gamma (-126 degrees)
3599 PRO   (  24-)  G  -113.8 envelop C-gamma (-108 degrees)
3685 PRO   ( 110-)  G  -113.3 envelop C-gamma (-108 degrees)
3729 PRO   ( 154-)  G  -114.4 envelop C-gamma (-108 degrees)
3735 PRO   ( 160-)  G  -118.1 half-chair C-delta/C-gamma (-126 degrees)
3785 PRO   (   9-)  H  -116.9 envelop C-gamma (-108 degrees)
3800 PRO   (  24-)  H  -114.2 envelop C-gamma (-108 degrees)
3886 PRO   ( 110-)  H  -113.5 envelop C-gamma (-108 degrees)
3930 PRO   ( 154-)  H  -114.5 envelop C-gamma (-108 degrees)
3936 PRO   ( 160-)  H  -118.1 half-chair C-delta/C-gamma (-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.

3010 ALA   (1378-)  D      N   <-> 3011 PRO   (1379-)  D      CD     0.40    2.60  INTRA BL
3052 VAL   (  39-)  E      N   <-> 3053 PRO   (  40-)  E      CD     0.29    2.71  INTRA BL
2557 GLU   ( 925-)  D      N   <-> 2558 PRO   ( 926-)  D      CD     0.26    2.74  INTRA BL
3049 ASP   (  36-)  E      N   <-> 3050 PRO   (  37-)  E      CD     0.24    2.76  INTRA BL
3013 ALA   (1381-)  D      N   <-> 3014 PRO   (1382-)  D      CD     0.22    2.78  INTRA BL
2344 GLN   ( 712-)  D      CD  <-> 2345 GLU   ( 713-)  D      N      0.20    2.80  INTRA BL
2351 PHE   ( 719-)  D      CG  <-> 2352 ASN   ( 720-)  D      N      0.17    2.83  INTRA BL
3072 ILE   (  59-)  E      CG1 <-> 3073 ASN   (  60-)  E      N      0.17    2.83  INTRA BL
3995 DTHY  (  10-)  I      N3  <-> 4172 DADE  (  89-)  J      N1     0.14    2.86  INTRA BL
3538 ASP   ( 566-)  F      CG  <-> 3539 MET   ( 567-)  F      N      0.14    2.86  INTRA BL
 590 ASP   (  42-)  C      N   <->  591 PRO   (  43-)  C      CD     0.14    2.86  INTRA BL
2089 TYR   ( 457-)  D      C   <-> 2090 ASN   ( 458-)  D      ND2    0.13    2.87  INTRA BL
 945 MET   ( 488-)  C      N   <->  946 PRO   ( 489-)  C      CD     0.13    2.87  INTRA BL
 486 ASP   ( 164-)  B      CG  <->  487 GLU   ( 165-)  B      N      0.13    2.87  INTRA BL
 806 GLU   ( 349-)  C      CD  <->  807 THR   ( 350-)  C      N      0.13    2.87  INTRA BL
2905 ASP   (1273-)  D      CG  <-> 2906 PHE   (1274-)  D      N      0.12    2.88  INTRA BL
2247 LYS   ( 615-)  D      N   <-> 2248 PRO   ( 616-)  D      CD     0.12    2.88  INTRA BL
3072 ILE   (  59-)  E      CG2 <-> 3073 ASN   (  60-)  E      N      0.12    2.88  INTRA BL
2770 LEU   (1138-)  D      N   <-> 2771 PRO   (1139-)  D      CD     0.12    2.88  INTRA BL
1577 MET   (1273-)  C      SD  <-> 2430 ARG   ( 798-)  D      NH1    0.11    3.19  INTRA BL
2215 VAL   ( 583-)  D      N   <-> 2216 PRO   ( 584-)  D      CD     0.11    2.89  INTRA BL
2527 CYS   ( 895-)  D      SG  <-> 2530 CYS   ( 898-)  D      SG     0.11    3.34  INTRA BL
1508 LEU   (1204-)  C      N   <-> 1509 PRO   (1205-)  C      CD     0.11    2.89  INTRA BL
1492 ASP   (1188-)  C      CG  <-> 1493 GLY   (1189-)  C      N      0.10    2.90  INTRA BL
1461 VAL   (1103-)  C      N   <-> 1462 PRO   (1104-)  C      CD     0.10    2.90  INTRA BL
And so on for a total of 188 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

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.

 828 ARG   ( 371-)  C      -8.48
 727 TYR   ( 179-)  C      -8.45
3103 ARG   (  90-)  E      -8.30
3082 ARG   (  69-)  E      -8.26
 610 TYR   (  62-)  C      -8.06
3397 TYR   ( 425-)  F      -7.90
 311 ARG   ( 317-)  A      -7.79
1198 MET   ( 741-)  C      -7.65
1520 ARG   (1216-)  C      -7.53
 232 ARG   ( 238-)  A      -7.51
2035 ARG   ( 403-)  D      -7.39
2170 ARG   ( 538-)  D      -7.36
1944 ARG   ( 312-)  D      -7.29
1393 ARG   ( 936-)  C      -7.25
1427 ARG   (1069-)  C      -7.24
 149 ARG   ( 150-)  A      -7.20
3448 ARG   ( 476-)  F      -7.20
1329 TYR   ( 872-)  C      -7.18
 999 ARG   ( 542-)  C      -7.04
3065 ARG   (  52-)  E      -7.03
3539 MET   ( 567-)  F      -6.96
2575 ARG   ( 943-)  D      -6.93
1713 ARG   (  81-)  D      -6.92
1156 LEU   ( 699-)  C      -6.89
2524 PHE   ( 892-)  D      -6.85
And so on for a total of 266 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.

 187 GLU   ( 193-)  A       189 - ARG    195- ( A)         -5.49
 231 VAL   ( 237-)  A       233 - GLN    239- ( A)         -5.63
 329 GLU   (   7-)  B       331 - LEU      9- ( B)         -4.82
 563 PHE   (  15-)  C       566 - ARG     18- ( C)         -5.45
 621 TYR   (  73-)  C       623 - LEU     75- ( C)         -5.19
 788 LYS   ( 331-)  C       791 - GLU    334- ( C)         -5.04
 870 GLU   ( 413-)  C       872 - GLU    415- ( C)         -4.54
 995 LEU   ( 538-)  C       997 - ARG    540- ( C)         -4.86
1417 ARG   (1059-)  C      1419 - GLN   1061- ( C)         -5.05
1618 GLN   (1314-)  C      1620 - GLU   1316- ( C)         -5.57
1802 GLU   ( 170-)  D      1804 - PHE    172- ( D)         -5.33
2049 ARG   ( 417-)  D      2051 - HIS    419- ( D)         -4.27
2149 CYS   ( 517-)  D      2151 - ASN    519- ( D)         -4.26
2157 MET   ( 525-)  D      2160 - THR    528- ( D)         -5.12
2457 VAL   ( 825-)  D      2459 - GLU    827- ( D)         -4.73
2462 ASP   ( 830-)  D      2465 - GLU    833- ( D)         -4.68
2505 GLU   ( 873-)  D      2507 - ASN    875- ( D)         -4.56
2567 PHE   ( 935-)  D      2569 - ILE    937- ( D)         -5.79
2575 ARG   ( 943-)  D      2577 - ALA    945- ( D)         -5.12
2585 LYS   ( 953-)  D      2587 - LYS    955- ( D)         -5.01
2824 LYS   (1192-)  D      2826 - ARG   1194- ( D)         -4.29
3001 ARG   (1369-)  D      3004 - ARG   1372- ( D)         -4.90
3067 ILE   (  54-)  E      3069 - GLU     56- ( E)         -4.92
3163 GLU   ( 171-)  F      3166 - LEU    174- ( F)         -5.13
3594 HIS   (  19-)  G      3596 - HIS     21- ( G)         -4.36

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 - 4181 : -2.143

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

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.

  44 ARG   (  45-)  A   -3.52
 367 ARG   (  45-)  B   -3.32
2562 LEU   ( 930-)  D   -3.23
2120 ASN   ( 488-)  D   -3.23
2115 LEU   ( 483-)  D   -3.11
 289 LEU   ( 295-)  A   -3.04
2535 LEU   ( 903-)  D   -3.03
1398 LYS   ( 941-)  C   -3.02
2853 LEU   (1221-)  D   -2.84
2058 ALA   ( 426-)  D   -2.81
1146 ALA   ( 689-)  C   -2.80
3004 ARG   (1372-)  D   -2.78
2195 LEU   ( 563-)  D   -2.78
2786 ALA   (1154-)  D   -2.75
3838 SER   (  62-)  H   -2.74
3776 LYS   ( 201-)  G   -2.71
1313 ASN   ( 856-)  C   -2.70
1543 VAL   (1239-)  C   -2.69
1918 ALA   ( 286-)  D   -2.68
 254 LEU   ( 260-)  A   -2.67
1004 VAL   ( 547-)  C   -2.67
2424 ASN   ( 792-)  D   -2.66
2799 LYS   (1167-)  D   -2.63
 630 VAL   (  82-)  C   -2.62
 608 GLN   (  60-)  C   -2.62
2482 LYS   ( 850-)  D   -2.61
3003 ARG   (1371-)  D   -2.58
2430 ARG   ( 798-)  D   -2.58
2784 GLU   (1152-)  D   -2.58
1944 ARG   ( 312-)  D   -2.57
1749 LEU   ( 117-)  D   -2.57
2727 MET   (1095-)  D   -2.56
 732 LEU   ( 184-)  C   -2.56
2246 LEU   ( 614-)  D   -2.56
 721 ASN   ( 173-)  C   -2.56
3369 ARG   ( 397-)  F   -2.55
3751 VAL   ( 176-)  G   -2.55
1750 LYS   ( 118-)  D   -2.55
3557 GLU   ( 585-)  F   -2.55
 330 PHE   (   8-)  B   -2.53
 516 GLN   ( 194-)  B   -2.53
3053 PRO   (  40-)  E   -2.52
1679 ARG   (  47-)  D   -2.52
1362 ILE   ( 905-)  C   -2.50

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.

 749 ARG   ( 201-)  C     -  752 LEU   ( 204-)  C        -1.77
 845 LEU   ( 388-)  C     -  850 ASP   ( 393-)  C        -1.91
1145 GLN   ( 688-)  C     - 1148 PRO   ( 691-)  C        -1.65
1541 HIS   (1237-)  C     - 1544 ASP   (1240-)  C        -2.16
1547 MET   (1243-)  C     - 1550 ARG   (1246-)  C        -1.72
1969 ARG   ( 337-)  D     - 1973 ASN   ( 341-)  D        -1.74
2060 THR   ( 428-)  D     - 2064 LEU   ( 432-)  D        -1.89
2177 HIS   ( 545-)  D     - 2180 VAL   ( 548-)  D        -1.75
2781 ARG   (1149-)  D     - 2784 GLU   (1152-)  D        -1.97
2851 ASP   (1219-)  D     - 2855 LEU   (1223-)  D        -2.00
3001 ARG   (1369-)  D     - 3004 ARG   (1372-)  D        -2.17
3424 ILE   ( 452-)  F     - 3427 HIS   ( 455-)  F        -1.92
3556 ARG   ( 584-)  F     - 3559 ILE   ( 587-)  F        -1.87

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

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.

  22 HIS   (  23-)  A
 277 GLN   ( 283-)  A
 345 HIS   (  23-)  B
 388 HIS   (  66-)  B
 406 ASN   (  84-)  B
 450 HIS   ( 128-)  B
 668 GLN   ( 120-)  C
 800 HIS   ( 343-)  C
 974 GLN   ( 517-)  C
1217 ASN   ( 760-)  C
1255 GLN   ( 798-)  C
1428 HIS   (1070-)  C
1430 ASN   (1072-)  C
1561 GLN   (1257-)  C
1603 ASN   (1299-)  C
1617 HIS   (1313-)  C
1628 ASN   (1324-)  C
1908 ASN   ( 276-)  D
1952 ASN   ( 320-)  D
2056 ASN   ( 424-)  D
2062 HIS   ( 430-)  D
2120 ASN   ( 488-)  D
2121 ASN   ( 489-)  D
2255 GLN   ( 623-)  D
2368 GLN   ( 736-)  D
2424 ASN   ( 792-)  D
2497 HIS   ( 865-)  D
2611 ASN   ( 979-)  D
2827 GLN   (1195-)  D
2884 HIS   (1252-)  D
3042 GLN   (  29-)  E
3161 ASN   ( 169-)  F
3218 GLN   ( 246-)  F
3329 GLN   ( 357-)  F
3334 ASN   ( 362-)  F
3856 GLN   (  80-)  H
3946 GLN   ( 170-)  H

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.

   3 SER   (   4-)  A      N
   8 LEU   (   9-)  A      N
  11 ARG   (  12-)  A      N
  14 ASP   (  15-)  A      N
  16 GLU   (  17-)  A      N
  18 VAL   (  19-)  A      N
  22 HIS   (  23-)  A      N
  23 ALA   (  24-)  A      N
  25 VAL   (  26-)  A      N
  26 THR   (  27-)  A      N
  27 LEU   (  28-)  A      N
  36 HIS   (  37-)  A      N
  39 GLY   (  40-)  A      N
  40 ASN   (  41-)  A      ND2
  42 LEU   (  43-)  A      N
  43 ARG   (  44-)  A      NH1
  43 ARG   (  44-)  A      NH2
  44 ARG   (  45-)  A      N
  46 LEU   (  47-)  A      N
  47 LEU   (  48-)  A      N
  49 SER   (  50-)  A      N
  50 MET   (  51-)  A      N
  54 ALA   (  55-)  A      N
  56 THR   (  57-)  A      OG1
  57 GLU   (  58-)  A      N
And so on for a total of 1190 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.

 127 HIS   ( 128-)  A      ND1
 235 GLU   ( 241-)  A      OE1
 239 GLU   ( 245-)  A      OE1
 253 ASP   ( 259-)  A      OD2
 322 ASP   ( 328-)  A      OD1
 526 GLU   ( 204-)  B      OE1
 562 ASP   (  14-)  C      OD1
 588 GLU   (  40-)  C      OE2
 696 GLN   ( 148-)  C      OE1
 737 ASP   ( 189-)  C      OD1
 811 ASP   ( 354-)  C      OD2
 983 HIS   ( 526-)  C      ND1
1088 GLU   ( 631-)  C      OE2
1111 ASP   ( 654-)  C      OD1
1111 ASP   ( 654-)  C      OD2
1131 ASP   ( 674-)  C      OD1
1256 ASN   ( 799-)  C      OD1
1271 ASP   ( 814-)  C      OD1
1356 GLU   ( 899-)  C      OE1
1438 ASN   (1080-)  C      OD1
1466 ASN   (1108-)  C      OD1
1469 GLN   (1111-)  C      OE1
1544 ASP   (1240-)  C      OD1
1576 GLU   (1272-)  C      OE1
1600 ASP   (1296-)  C      OD1
And so on for a total of 76 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.

  14 ASP   (  15-)  A   H-bonding suggests Asn; but Alt-Rotamer
  95 ASP   (  96-)  A   H-bonding suggests Asn
 175 GLU   ( 181-)  A   H-bonding suggests Gln
 193 ASP   ( 199-)  A   H-bonding suggests Asn; but Alt-Rotamer
 230 ASP   ( 236-)  A   H-bonding suggests Asn; but Alt-Rotamer
 238 GLU   ( 244-)  A   H-bonding suggests Gln
 242 GLU   ( 248-)  A   H-bonding suggests Gln
 244 ASP   ( 250-)  A   H-bonding suggests Asn
 252 ASP   ( 258-)  A   H-bonding suggests Asn
 253 ASP   ( 259-)  A   H-bonding suggests Asn; but Alt-Rotamer
 255 GLU   ( 261-)  A   H-bonding suggests Gln
 389 GLU   (  67-)  B   H-bonding suggests Gln
 551 GLU   ( 229-)  B   H-bonding suggests Gln
 555 ASP   ( 233-)  B   H-bonding suggests Asn
 588 GLU   (  40-)  C   H-bonding suggests Gln
 632 GLU   (  84-)  C   H-bonding suggests Gln
 664 ASP   ( 116-)  C   H-bonding suggests Asn; but Alt-Rotamer
 667 GLU   ( 119-)  C   H-bonding suggests Gln; but Alt-Rotamer
 674 GLU   ( 126-)  C   H-bonding suggests Gln
 708 ASP   ( 160-)  C   H-bonding suggests Asn; but Alt-Rotamer
 737 ASP   ( 189-)  C   H-bonding suggests Asn; but Alt-Rotamer
 740 ASP   ( 192-)  C   H-bonding suggests Asn; but Alt-Rotamer
 797 ASP   ( 340-)  C   H-bonding suggests Asn
 799 ASP   ( 342-)  C   H-bonding suggests Asn
 806 GLU   ( 349-)  C   H-bonding suggests Gln
And so on for a total of 119 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 :  -4.107 (poor)
  2nd generation packing quality :  -4.779 (bad)
  Ramachandran plot appearance   :  -4.852 (bad)
  chi-1/chi-2 rotamer normality  :  -1.404
  Backbone conformation          :  -1.229

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.231 (tight)
  Bond angles                    :   0.437 (tight)
  Omega angle restraints         :   0.219 (tight)
  Side chain planarity           :   0.069 (tight)
  Improper dihedral distribution :   0.270
  Inside/Outside distribution    :   1.105

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 : 19.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.1
  2nd generation packing quality :  -2.4
  Ramachandran plot appearance   :  -2.4
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.231 (tight)
  Bond angles                    :   0.437 (tight)
  Omega angle restraints         :   0.219 (tight)
  Side chain planarity           :   0.069 (tight)
  Improper dihedral distribution :   0.270
  Inside/Outside distribution    :   1.105
==============

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.