WHAT IF Check report

This file was created 2012-01-30 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3k1q.ent

Administrative problems that can generate validation failures

Warning: Overlapping residues or molecules

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

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

1491 GLY   ( 379-)  B  -
1562 ASP   ( 450-)  B  -
1778 ALA   ( 666-)  B  -
1992 LEU   ( 880-)  B  -
2065 GLY   ( 953-)  B  -
2066 PRO   ( 954-)  B  -
2860 ASP   ( 552-)  C  -
3106 VAL   ( 798-)  C  -
3246 TYR   ( 938-)  C  -
3504 ARG   (1196-)  C  -
3536 TYR   (  14-)  D  -
3574 PRO   (  52-)  D  -
3658 TRP   ( 136-)  D  -
3698 ALA   ( 176-)  D  -
3706 HIS   ( 184-)  D  -
3911 PHE   ( 389-)  D  -
4129 GLN   ( 195-)  E  -
4269 ALA   ( 335-)  E  -
5231 ASP   (  66-)  I  -
5319 ARG   ( 154-)  I  -
5334 MET   ( 169-)  I  -
5367 THR   ( 202-)  I  -
5412 GLU   ( 248-)  I  -
5576 ARG   ( 412-)  I  -
5578 GLN   ( 414-)  I  -
And so on for a total of 129 lines.

Please also see the previous check
Please see the user course on the WHAT CHECK website if you want to know why this table and the previous one have not been merged.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: 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

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

Warning: Rounded coordinates detected

At least two atoms were detected with all three coordinates rounded to 1 decimal place. Since this is highly unlikely to occur accidentally, the atoms listed in the table below were probably not refined. It could also be that ALL atomic coordinates were rounded to 1 or 2 decimal places (resulting in considerable loss of accuracy).

  61 THR   (  61-)  A  -   N   123.500    10.900   272.700
 205 PHE   ( 205-)  A  -   CB   102.300    13.900   272.600
1300 ALA   ( 188-)  B  -   N    66.000     7.300   241.300
1464 THR   ( 352-)  B  -   O    13.700    16.400   270.600
1537 LEU   ( 428-)  B  -   CD2    81.200    22.500   248.000
1642 TRP   ( 535-)  B  -   C    91.600     1.900   251.300
1759 GLN   ( 652-)  B  -   N   104.300     3.000   256.000
1855 GLN   ( 748-)  B  -   NE2   102.700     9.000   251.900
2255 THR   (1149-)  B  -   CB    18.400     0.200   269.400
2262 THR   (1156-)  B  -   N    11.400     3.000   273.000
2273 LEU   (1167-)  B  -   CD2    31.500     5.200   280.300
2476 SER   ( 176-)  C  -   O    50.500    60.300   233.700
2504 PHE   ( 204-)  C  -   O    14.500    67.200   259.100
2559 LEU   ( 259-)  C  -   CB    27.900    59.600   252.800
2595 SER   ( 295-)  C  -   OG    28.700    45.100   264.500
2678 GLU   ( 380-)  C  -   OE1    26.900    91.600   250.700
2734 LEU   ( 436-)  C  -   O    41.800    93.600   255.300
2863 LYS   ( 565-)  C  -   CA    89.100    44.400   244.600
3005 PHE   ( 707-)  C  -   N    98.200    51.900   253.200
3043 PHE   ( 745-)  C  -   O    82.300    68.500   250.400
3333 ASN   (1036-)  C  -   N    13.600    22.200   284.200
3677 ALA   ( 169-)  D  -   CA    74.900    32.000   267.400
4294 VAL   ( 375-)  E  -   CB    62.800   110.600   273.100
7633 THR   (  42-)  N  -   O    67.000    16.800   385.300
7638 THR   (  47-)  N  -   CA    69.100    16.100   379.200
And so on for a total of 66 lines.

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.

2173 VAL   (1067-)  B  -
4764 LEU   ( 158-)  G  -
5856 SER   (  83-)  J  -
7023 VAL   ( 632-)  K  -
1324  LEU  ( 158-) Y  -

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 MET   (   1-)  A  -   Zero
   2 ALA   (   2-)  A  -   Zero
   3 ALA   (   3-)  A  -   Zero
   4 VAL   (   4-)  A  -   Zero
   5 PHE   (   5-)  A  -   Zero
   6 GLY   (   6-)  A  -   Zero
   7 ILE   (   7-)  A  -   Zero
   8 GLN   (   8-)  A  -   Zero
   9 LEU   (   9-)  A  -   Zero
  10 VAL   (  10-)  A  -   Zero
  11 PRO   (  11-)  A  -   Zero
  12 LYS   (  12-)  A  -   Zero
  13 LEU   (  13-)  A  -   Zero
  14 ASN   (  14-)  A  -   Zero
  15 THR   (  15-)  A  -   Zero
  16 SER   (  16-)  A  -   Zero
  17 THR   (  17-)  A  -   Zero
  18 THR   (  18-)  A  -   Zero
  19 ARG   (  19-)  A  -   Zero
  20 ARG   (  20-)  A  -   Zero
  21 THR   (  21-)  A  -   Zero
  22 PHE   (  22-)  A  -   Zero
  23 LEU   (  23-)  A  -   Zero
  24 PRO   (  24-)  A  -   Zero
  25 LEU   (  25-)  A  -   Zero
And so on for a total of 13367 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: 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

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

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.

  19 ARG   (  19-)  A  -
  20 ARG   (  20-)  A  -
  26 ARG   (  26-)  A  -
  33 ARG   (  33-)  A  -
  54 ARG   (  54-)  A  -
 102 ARG   ( 102-)  A  -
 111 ARG   ( 111-)  A  -
 129 ARG   ( 129-)  A  -
 137 ARG   ( 137-)  A  -
 187 ARG   ( 187-)  A  -
 198 ARG   ( 198-)  A  -
 213 ARG   ( 213-)  A  -
 215 ARG   ( 215-)  A  -
 284 ARG   ( 284-)  A  -
 306 ARG   ( 306-)  A  -
 334 ARG   ( 334-)  A  -
 339 ARG   ( 339-)  A  -
 353 ARG   ( 353-)  A  -
 377 ARG   ( 377-)  A  -
 396 ARG   ( 396-)  A  -
 399 ARG   ( 399-)  A  -
 472 ARG   ( 472-)  A  -
 480 ARG   ( 480-)  A  -
 485 ARG   ( 485-)  A  -
 491 ARG   ( 491-)  A  -
And so on for a total of 484 lines.

Warning: Tyrosine convention problem

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

  62 TYR   (  62-)  A  -
 103 TYR   ( 103-)  A  -
 140 TYR   ( 140-)  A  -
 156 TYR   ( 156-)  A  -
 177 TYR   ( 177-)  A  -
 201 TYR   ( 201-)  A  -
 206 TYR   ( 206-)  A  -
 388 TYR   ( 388-)  A  -
 404 TYR   ( 404-)  A  -
 635 TYR   ( 635-)  A  -
 938 TYR   ( 938-)  A  -
 956 TYR   ( 956-)  A  -
1160 TYR   (1160-)  A  -
1227 TYR   (1227-)  A  -
1287 TYR   (1287-)  A  -
1296 TYR   (1296-)  A  -
1386 TYR   ( 274-)  B  -
1632 TYR   ( 525-)  B  -
1644 TYR   ( 537-)  B  -
1800 TYR   ( 693-)  B  -
1853 TYR   ( 746-)  B  -
1944 TYR   ( 837-)  B  -
2044 TYR   ( 938-)  B  -
2193 TYR   (1087-)  B  -
2194 TYR   (1088-)  B  -
And so on for a total of 161 lines.

Warning: Phenylalanine convention problem

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

   5 PHE   (   5-)  A  -
 205 PHE   ( 205-)  A  -
 230 PHE   ( 230-)  A  -
 295 PHE   ( 295-)  A  -
 336 PHE   ( 336-)  A  -
 350 PHE   ( 350-)  A  -
 365 PHE   ( 365-)  A  -
 376 PHE   ( 376-)  A  -
 383 PHE   ( 383-)  A  -
 494 PHE   ( 494-)  A  -
 514 PHE   ( 514-)  A  -
 554 PHE   ( 554-)  A  -
 632 PHE   ( 632-)  A  -
 659 PHE   ( 659-)  A  -
 697 PHE   ( 697-)  A  -
 720 PHE   ( 720-)  A  -
 765 PHE   ( 765-)  A  -
 897 PHE   ( 897-)  A  -
 958 PHE   ( 958-)  A  -
1096 PHE   (1096-)  A  -
1100 PHE   (1100-)  A  -
1125 PHE   (1125-)  A  -
1146 PHE   (1146-)  A  -
1168 PHE   (1168-)  A  -
1194 PHE   (1194-)  A  -
And so on for a total of 172 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.

  28 ASP   (  28-)  A  -
 141 ASP   ( 141-)  A  -
 161 ASP   ( 161-)  A  -
 231 ASP   ( 231-)  A  -
 296 ASP   ( 296-)  A  -
 332 ASP   ( 332-)  A  -
 345 ASP   ( 345-)  A  -
 355 ASP   ( 355-)  A  -
 393 ASP   ( 393-)  A  -
 444 ASP   ( 444-)  A  -
 448 ASP   ( 448-)  A  -
 459 ASP   ( 459-)  A  -
 484 ASP   ( 484-)  A  -
 490 ASP   ( 490-)  A  -
 495 ASP   ( 495-)  A  -
 511 ASP   ( 511-)  A  -
 557 ASP   ( 557-)  A  -
 565 ASP   ( 565-)  A  -
 583 ASP   ( 583-)  A  -
 587 ASP   ( 587-)  A  -
 591 ASP   ( 591-)  A  -
 689 ASP   ( 689-)  A  -
 702 ASP   ( 702-)  A  -
 707 ASP   ( 707-)  A  -
 711 ASP   ( 711-)  A  -
And so on for a total of 248 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.

 321 GLU   ( 321-)  A  -
 419 GLU   ( 419-)  A  -
 468 GLU   ( 468-)  A  -
 654 GLU   ( 654-)  A  -
 803 GLU   ( 803-)  A  -
 821 GLU   ( 821-)  A  -
 862 GLU   ( 862-)  A  -
 948 GLU   ( 948-)  A  -
 962 GLU   ( 962-)  A  -
1095 GLU   (1095-)  A  -
1179 GLU   (1179-)  A  -
1308 GLU   ( 196-)  B  -
1349 GLU   ( 237-)  B  -
1367 GLU   ( 255-)  B  -
1372 GLU   ( 260-)  B  -
1446 GLU   ( 334-)  B  -
1450 GLU   ( 338-)  B  -
1531 GLU   ( 422-)  B  -
1581 GLU   ( 474-)  B  -
1654 GLU   ( 547-)  B  -
1704 GLU   ( 597-)  B  -
1762 GLU   ( 655-)  B  -
2006 GLU   ( 900-)  B  -
2077 GLU   ( 971-)  B  -
2134 GLU   (1028-)  B  -
And so on for a total of 141 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.

8535 ALA   (  56-)  P  -   N    CA    1.17  -15.4
8535 ALA   (  56-)  P  -   CA   C     1.23  -14.2
8535 ALA   (  56-)  P  -   CA   CB    2.05   15.9

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 MET   (   1-)  A  -   C    CA   CB  118.58    4.5
   2 ALA   (   2-)  A  -  -C    N    CA  130.55    4.9
   2 ALA   (   2-)  A  -   N    CA   CB  104.32   -4.1
   2 ALA   (   2-)  A  -   C    CA   CB  119.32    5.9
   4 VAL   (   4-)  A  -  -O   -C    N   130.76    4.9
   4 VAL   (   4-)  A  -   N    CA   CB  118.48    4.7
   5 PHE   (   5-)  A  -  -O   -C    N   130.39    4.6
   5 PHE   (   5-)  A  -   CE1  CZ   CE2 112.65   -4.1
   7 ILE   (   7-)  A  -   CA   CB   CG1 121.28    6.4
   7 ILE   (   7-)  A  -   CB   CG1  CD1 123.47    4.6
  13 LEU   (  13-)  A  -   CA   C    O   112.79   -4.7
  15 THR   (  15-)  A  -   CA   CB   CG2 102.54   -4.7
  15 THR   (  15-)  A  -   CA   CB   OG1 120.14    7.0
  17 THR   (  17-)  A  -   N    CA   C   123.19    4.3
  19 ARG   (  19-)  A  -   CG   CD   NE  117.52    4.1
  20 ARG   (  20-)  A  -   N    CA   CB   99.69   -6.4
  20 ARG   (  20-)  A  -   NH1  CZ   NH2 112.41   -4.1
  21 THR   (  21-)  A  -   CA   CB   OG1 117.92    5.5
  22 PHE   (  22-)  A  -   CA   CB   CG  123.23    9.4
  23 LEU   (  23-)  A  -  -CA  -C    N   104.82   -5.7
  25 LEU   (  25-)  A  -  -O   -C    N   129.98    4.4
  26 ARG   (  26-)  A  -   N    CA   CB  103.60   -4.1
  26 ARG   (  26-)  A  -   CA   CB   CG  123.26    4.6
  26 ARG   (  26-)  A  -   CD   NE   CZ  131.34    5.4
  27 PHE   (  27-)  A  -   CB   CG   CD2 113.44   -4.3
And so on for a total of 11704 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.310
RMS-deviation in bond angles: 4.322

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.

  19 ARG   (  19-)  A  -
  20 ARG   (  20-)  A  -
  26 ARG   (  26-)  A  -
  28 ASP   (  28-)  A  -
  33 ARG   (  33-)  A  -
  54 ARG   (  54-)  A  -
 102 ARG   ( 102-)  A  -
 111 ARG   ( 111-)  A  -
 129 ARG   ( 129-)  A  -
 137 ARG   ( 137-)  A  -
 141 ASP   ( 141-)  A  -
 161 ASP   ( 161-)  A  -
 187 ARG   ( 187-)  A  -
 198 ARG   ( 198-)  A  -
 213 ARG   ( 213-)  A  -
 215 ARG   ( 215-)  A  -
 231 ASP   ( 231-)  A  -
 284 ARG   ( 284-)  A  -
 296 ASP   ( 296-)  A  -
 306 ARG   ( 306-)  A  -
 321 GLU   ( 321-)  A  -
 332 ASP   ( 332-)  A  -
 334 ARG   ( 334-)  A  -
 339 ARG   ( 339-)  A  -
 345 ASP   ( 345-)  A  -
And so on for a total of 873 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.

   4 VAL   (   4-)  A  -   CB    -6.2   -41.12   -32.96
   6 GLY   (   6-)  A  -   C      6.3     8.34     0.06
   7 ILE   (   7-)  A  -   C     -9.8   -12.74     0.03
  11 PRO   (  11-)  A  -   C      7.8    12.77     0.42
  12 LYS   (  12-)  A  -   C     -6.5    -9.69     0.11
  13 LEU   (  13-)  A  -   C     -8.4   -13.07     0.20
  19 ARG   (  19-)  A  -   C     -7.2   -10.82     0.13
  22 PHE   (  22-)  A  -   C     -8.7   -13.98     0.23
  25 LEU   (  25-)  A  -   C     -6.3    -9.77     0.20
  31 LEU   (  31-)  A  -   C      6.9    11.03     0.20
  47 LEU   (  47-)  A  -   C      6.4    10.34     0.20
  51 PRO   (  51-)  A  -   C      9.9    16.00     0.42
  52 VAL   (  52-)  A  -   C      6.3     8.82     0.15
  56 ALA   (  56-)  A  -   CA   -12.4    18.37    34.09
  56 ALA   (  56-)  A  -   C     12.5    19.21     0.08
  58 VAL   (  58-)  A  -   C    -10.3   -14.02     0.15
  65 LEU   (  65-)  A  -   CG    -6.3   -44.06   -33.01
  71 HIS   (  71-)  A  -   CA    -6.4    22.38    34.11
  72 HIS   (  72-)  A  -   C      8.4    12.77     0.15
  73 ALA   (  73-)  A  -   C      7.7    11.83     0.08
  74 PHE   (  74-)  A  -   C      6.7    11.08     0.23
  75 ILE   (  75-)  A  -   CA    -6.3    23.69    33.24
  77 ASN   (  77-)  A  -   C      7.2    11.51     0.27
  80 ASP   (  80-)  A  -   C      7.2    11.01    -0.01
  81 TYR   (  81-)  A  -   CA    -6.9    23.07    34.03
And so on for a total of 4079 lines.

Error: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals 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 2.5 worries us. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 4.460

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.

3684 ALA   ( 176-)  D  -  17.41
1949 ALA   ( 842-)  B  -  15.65
1108  SER  ( 534-) U  -  13.82
8382 SER   ( 534-)  O  -  13.57
1171  SER  ( 534-) V  -  13.53
5673 SER   ( 534-)  I  -  13.50
1234  SER  ( 534-) W  -  13.38
9636 SER   ( 534-)  Q  -  13.36
6299 SER   ( 534-)  J  -  13.28
3095 ALA   ( 797-)  C  -  13.10
9005 SER   ( 534-)  P  -  13.09
6927 SER   ( 534-)  K  -  13.05
1160  PHE  ( 417-) V  -  12.95
6183 PHE   ( 417-)  J  -  12.54
2362 ALA   (  62-)  C  -  12.51
1558 ASP   ( 450-)  B  -  12.09
4111 PHE   ( 192-)  E  -  11.95
8268 PHE   ( 417-)  O  -  11.36
8999 ALA   ( 528-)  P  -  11.26
1097  PHE  ( 417-) U  -  11.22
9630 ALA   ( 528-)  Q  -  11.21
6921 ALA   ( 528-)  K  -  11.19
2947 ASN   ( 649-)  C  -  11.05
5558 PHE   ( 417-)  I  -  10.97
6812 PHE   ( 417-)  K  -  10.86
And so on for a total of 2384 lines.

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 3.058

Error: Side chain planarity problems

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

8721 GLU   ( 248-)  P  -  39.15
6016 GLU   ( 248-)  J  -  38.95
1143  GLU  ( 248-) V  -  38.71
5389 GLU   ( 248-)  I  -  35.55
8100 GLU   ( 248-)  O  -  35.01
6645 GLU   ( 248-)  K  -  34.27
9354 GLU   ( 248-)  Q  -  30.24
1206  GLU  ( 248-) W  -  28.83
6184 ASN   ( 418-)  J  -  28.54
1160  ASN  ( 418-) V  -  28.51
8889 ASN   ( 418-)  P  -  28.47
2850 ASP   ( 552-)  C  -  28.01
1097  ASN  ( 418-) U  -  26.45
1558 ASP   ( 450-)  B  -  26.20
8269 ASN   ( 418-)  O  -  26.15
5559 ASN   ( 418-)  I  -  26.07
8150 PHE   ( 298-)  O  -  23.18
8635 GLN   ( 160-)  P  -  22.14
1085  PHE  ( 298-) U  -  21.92
9267 GLN   ( 160-)  Q  -  21.77
1222  GLN  ( 414-) W  -  21.67
6561 GLN   ( 160-)  K  -  21.60
1197  GLN  ( 160-) W  -  21.08
1002  HIS  (   4-) S  -  20.95
5439 PHE   ( 298-)  I  -  20.64
And so on for a total of 1681 lines.

Error: Connections to aromatic rings out of plane

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

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

 956 TYR   ( 956-)  A  -   OH  19.25
4281 TYR   ( 362-)  E  -   OH  18.80
4044 TYR   ( 125-)  E  -   OH  18.21
3224 TYR   ( 926-)  C  -   OH  18.05
3952 TYR   (  33-)  E  -   OH  16.26
3135 TYR   ( 837-)  C  -   OH  15.85
 404 TYR   ( 404-)  A  -   OH  15.68
 183 TYR   ( 183-)  A  -   OH  15.61
4152 TYR   ( 233-)  E  -   OH  15.41
 388 TYR   ( 388-)  A  -   OH  15.14
 879 TYR   ( 879-)  A  -   OH  14.76
2417 TYR   ( 117-)  C  -   OH  14.51
2700 TYR   ( 402-)  C  -   OH  14.21
  81 TYR   (  81-)  A  -   CB  13.64
1193 HIS   (1193-)  A  -   CB  13.47
 452 TYR   ( 452-)  A  -   OH  13.11
3383 HIS   (1086-)  C  -   CB  13.01
4257 HIS   ( 338-)  E  -   CB  12.95
1096 PHE   (1096-)  A  -   CB  12.73
 140 TYR   ( 140-)  A  -   OH  12.44
1277  TYR  ( 327-) X  -    OH  12.33
1088  TYR  ( 327-) U  -    OH  12.21
1151  TYR  ( 327-) V  -    OH  12.17
3488 TYR   (1191-)  C  -   OH  12.08
7355 TYR   (  40-)  M  -   CB  12.05
And so on for a total of 521 lines.

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 : -5.410

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.

1042 THR   (1042-)  A  -   -3.5
1249  THR  (  44-) X  -   -3.5
1123  THR  (  44-) V  -   -3.4
8525 THR   (  44-)  P  -   -3.4
9152 THR   (  44-)  Q  -   -3.4
5817 THR   (  44-)  J  -   -3.4
7902 THR   (  44-)  O  -   -3.4
6446 THR   (  44-)  K  -   -3.4
 181 TYR   ( 181-)  A  -   -3.3
1198  THR  ( 171-) W  -   -3.3
1135  THR  ( 171-) V  -   -3.3
5943 THR   ( 171-)  J  -   -3.3
8025 THR   ( 171-)  O  -   -3.2
1261  THR  ( 171-) X  -   -3.2
6571 THR   ( 171-)  K  -   -3.2
8646 THR   ( 171-)  P  -   -3.2
1217  THR  ( 362-) W  -   -3.2
6759 THR   ( 362-)  K  -   -3.2
8835 THR   ( 362-)  P  -   -3.2
8214 THR   ( 362-)  O  -   -3.2
1091  THR  ( 362-) U  -   -3.2
1154  THR  ( 362-) V  -   -3.2
5503 THR   ( 362-)  I  -   -3.2
9468 THR   ( 362-)  Q  -   -3.2
1073  THR  ( 171-) U  -   -3.2
And so on for a total of 1215 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.

   2 ALA   (   2-)  A  - Poor phi/psi
   5 PHE   (   5-)  A  - Poor phi/psi
  39 LEU   (  39-)  A  - Poor phi/psi
  40 HIS   (  40-)  A  - Poor phi/psi
  42 VAL   (  42-)  A  - Poor phi/psi
  44 TYR   (  44-)  A  - Poor phi/psi
  55 SER   (  55-)  A  - omega poor
  56 ALA   (  56-)  A  - Poor phi/psi, omega poor
  57 THR   (  57-)  A  - omega poor
  63 PRO   (  63-)  A  - PRO omega poor
  65 LEU   (  65-)  A  - Poor phi/psi
  66 ASN   (  66-)  A  - Poor phi/psi
  68 TRP   (  68-)  A  - omega poor
  69 SER   (  69-)  A  - Poor phi/psi
  76 GLU   (  76-)  A  - Poor phi/psi
  88 ILE   (  88-)  A  - omega poor
 125 PHE   ( 125-)  A  - omega poor
 153 LYS   ( 153-)  A  - Poor phi/psi
 154 PHE   ( 154-)  A  - Poor phi/psi
 155 PRO   ( 155-)  A  - omega poor
 156 TYR   ( 156-)  A  - omega poor
 157 GLN   ( 157-)  A  - Poor phi/psi, omega poor
 162 SER   ( 162-)  A  - Poor phi/psi
 163 ASN   ( 163-)  A  - Poor phi/psi, omega poor
 165 THR   ( 165-)  A  - Poor phi/psi
And so on for a total of 2261 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -5.631

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.

4416 SER   (  86-)  F  -   0.33
5756 SER   ( 621-)  I  -   0.33
7012 SER   ( 621-)  K  -   0.33
9719 SER   ( 621-)  Q  -   0.33
1038  SER  (  86-) T  -   0.33
1180  SER  ( 621-) V  -   0.33
3263 SER   ( 966-)  C  -   0.35
5021 SER   ( 139-)  H  -   0.35
1016  SER  ( 139-) S  -   0.35
4469 SER   ( 139-)  F  -   0.35
7454 SER   ( 139-)  M  -   0.35
7730 SER   ( 139-)  N  -   0.35
1043  SER  ( 139-) T  -   0.35
1323  SER  ( 139-) Y  -   0.35
1317  SER  (  86-) Y  -   0.36
4745 SER   ( 139-)  G  -   0.36
7178 SER   ( 139-)  L  -   0.36
9885 SER   ( 139-)  R  -   0.36
1975 SER   ( 869-)  B  -   0.36
9012 SER   ( 541-)  P  -   0.37
4411 SER   (  81-)  F  -   0.37
4963 SER   (  81-)  H  -   0.37
7120 SER   (  81-)  L  -   0.37
7396 SER   (  81-)  M  -   0.37
7672 SER   (  81-)  N  -   0.37
And so on for a total of 60 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 ALA   (   3-)  A  -     0
   5 PHE   (   5-)  A  -     0
  11 PRO   (  11-)  A  -     0
  14 ASN   (  14-)  A  -     0
  18 THR   (  18-)  A  -     0
  22 PHE   (  22-)  A  -     0
  40 HIS   (  40-)  A  -     0
  42 VAL   (  42-)  A  -     0
  43 LEU   (  43-)  A  -     0
  44 TYR   (  44-)  A  -     0
  50 ASN   (  50-)  A  -     0
  52 VAL   (  52-)  A  -     0
  56 ALA   (  56-)  A  -     0
  57 THR   (  57-)  A  -     0
  58 VAL   (  58-)  A  -     0
  62 TYR   (  62-)  A  -     0
  63 PRO   (  63-)  A  -     0
  64 PRO   (  64-)  A  -     0
  65 LEU   (  65-)  A  -     0
  66 ASN   (  66-)  A  -     0
  67 ALA   (  67-)  A  -     0
  68 TRP   (  68-)  A  -     0
  69 SER   (  69-)  A  -     0
  70 PRO   (  70-)  A  -     0
  71 HIS   (  71-)  A  -     0
And so on for a total of 6892 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 : 9.017

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!

3828 GLY   ( 321-)  D  -  2.85   10
1522 PRO   ( 413-)  B  -  1.91   14
3927 GLY   (   8-)  E  -  1.90   42
1192  GLY  ( 104-) W  -  1.90   13
7960 GLY   ( 104-)  O  -  1.87   12
1255  GLY  ( 104-) X  -  1.87   12
9212 GLY   ( 104-)  Q  -  1.87   12
1066  GLY  ( 104-) U  -  1.87   12
5877 GLY   ( 104-)  J  -  1.87   12
8580 GLY   ( 104-)  P  -  1.87   12
1129  GLY  ( 104-) V  -  1.87   12
6506 GLY   ( 104-)  K  -  1.87   12
5249 GLY   ( 104-)  I  -  1.87   12
3304 GLY   (1007-)  C  -  1.80   25
 386 GLY   ( 386-)  A  -  1.68   49
3824 GLY   ( 317-)  D  -  1.66   28
1031  GLY  (  20-) T  -  1.61   80
4238 GLY   ( 319-)  E  -  1.60   60
7059 GLY   (  20-)  L  -  1.60   80
1311  GLY  (  20-) Y  -  1.60   80
3305 GLY   (1008-)  C  -  1.60   19
4626 GLY   (  20-)  G  -  1.59   80
9766 GLY   (  20-)  R  -  1.59   80
4902 GLY   (  20-)  H  -  1.58   79
7335 GLY   (  20-)  M  -  1.58   79
4350 GLY   (  20-)  F  -  1.58   80
7611 GLY   (  20-)  N  -  1.58   80
1004  GLY  (  20-) S  -  1.58   80
3802 GLY   ( 295-)  D  -  1.56   19
1709 GLY   ( 602-)  B  -  1.54   15
1771 GLY   ( 664-)  B  -  1.53   12
2149 GLY   (1043-)  B  -  1.52   22
2558 GLY   ( 258-)  C  -  1.51   63

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

  43 LEU   (  43-)  A  -  1.69
  53 ASP   (  53-)  A  -  2.27
  74 PHE   (  74-)  A  -  1.56
  82 ARG   (  82-)  A  -  1.57
  99 LEU   (  99-)  A  -  1.61
 106 THR   ( 106-)  A  -  1.74
 107 GLN   ( 107-)  A  -  2.35
 127 ASN   ( 127-)  A  -  2.37
 133 ILE   ( 133-)  A  -  2.18
 162 SER   ( 162-)  A  -  1.86
 172 SER   ( 172-)  A  -  1.72
 180 LEU   ( 180-)  A  -  2.84
 274 ALA   ( 274-)  A  -  2.13
 298 SER   ( 298-)  A  -  1.63
 305 GLN   ( 305-)  A  -  1.67
 372 PHE   ( 372-)  A  -  1.57
 410 THR   ( 410-)  A  -  1.55
 455 ALA   ( 455-)  A  -  1.61
 457 LEU   ( 457-)  A  -  1.81
 485 ARG   ( 485-)  A  -  1.72
 492 ALA   ( 492-)  A  -  1.54
 506 ALA   ( 506-)  A  -  1.99
 523 SER   ( 523-)  A  -  1.80
 528 ALA   ( 528-)  A  -  2.02
 562 SER   ( 562-)  A  -  1.68
And so on for a total of 508 lines.

Warning: Unusual PRO puckering amplitudes

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

  78 PRO   (  78-)  A  -   0.46 HIGH
 104 PRO   ( 104-)  A  -   0.48 HIGH
 297 PRO   ( 297-)  A  -   0.14 LOW
 449 PRO   ( 449-)  A  -   0.53 HIGH
 548 PRO   ( 548-)  A  -   0.14 LOW
 936 PRO   ( 936-)  A  -   0.48 HIGH
1007 PRO   (1007-)  A  -   0.45 HIGH
1034 PRO   (1034-)  A  -   0.19 LOW
1105 PRO   (1105-)  A  -   0.16 LOW
1141 PRO   (1141-)  A  -   0.47 HIGH
1402 PRO   ( 290-)  B  -   0.46 HIGH
1551 PRO   ( 443-)  B  -   0.46 HIGH
1592 PRO   ( 485-)  B  -   0.14 LOW
1627 PRO   ( 520-)  B  -   0.46 HIGH
1730 PRO   ( 623-)  B  -   0.10 LOW
1872 PRO   ( 765-)  B  -   0.50 HIGH
1950 PRO   ( 843-)  B  -   0.47 HIGH
2222 PRO   (1116-)  B  -   0.16 LOW
2228 PRO   (1122-)  B  -   0.20 LOW
2232 PRO   (1126-)  B  -   0.49 HIGH
2414 PRO   ( 114-)  C  -   0.47 HIGH
2533 PRO   ( 233-)  C  -   0.48 HIGH
2536 PRO   ( 236-)  C  -   0.20 LOW
2818 PRO   ( 520-)  C  -   0.48 HIGH
2849 PRO   ( 551-)  C  -   0.11 LOW
And so on for a total of 135 lines.

Warning: Unusual PRO puckering phases

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

  70 PRO   (  70-)  A  - -118.2 half-chair C-delta/C-gamma (-126 degrees)
 142 PRO   ( 142-)  A  - -127.1 half-chair C-delta/C-gamma (-126 degrees)
 185 PRO   ( 185-)  A  -   37.9 envelop C-delta (36 degrees)
 242 PRO   ( 242-)  A  -  103.8 envelop C-beta (108 degrees)
 325 PRO   ( 325-)  A  -  101.2 envelop C-beta (108 degrees)
 367 PRO   ( 367-)  A  -  -64.1 envelop C-beta (-72 degrees)
 397 PRO   ( 397-)  A  - -134.4 half-chair C-delta/C-gamma (-126 degrees)
 454 PRO   ( 454-)  A  -  130.5 half-chair C-beta/C-alpha (126 degrees)
 461 PRO   ( 461-)  A  -  109.5 envelop C-beta (108 degrees)
 503 PRO   ( 503-)  A  - -132.5 half-chair C-delta/C-gamma (-126 degrees)
 571 PRO   ( 571-)  A  -  126.0 half-chair C-beta/C-alpha (126 degrees)
 593 PRO   ( 593-)  A  -  119.0 half-chair C-beta/C-alpha (126 degrees)
 741 PRO   ( 741-)  A  -  114.3 envelop C-beta (108 degrees)
 754 PRO   ( 754-)  A  -  102.1 envelop C-beta (108 degrees)
 806 PRO   ( 806-)  A  -  110.2 envelop C-beta (108 degrees)
 826 PRO   ( 826-)  A  -  106.9 envelop C-beta (108 degrees)
 847 PRO   ( 847-)  A  -  100.2 envelop C-beta (108 degrees)
 869 PRO   ( 869-)  A  -  103.4 envelop C-beta (108 degrees)
 919 PRO   ( 919-)  A  -  103.6 envelop C-beta (108 degrees)
 966 PRO   ( 966-)  A  -  102.6 envelop C-beta (108 degrees)
 972 PRO   ( 972-)  A  -  106.3 envelop C-beta (108 degrees)
 982 PRO   ( 982-)  A  -  -43.5 envelop C-alpha (-36 degrees)
 999 PRO   ( 999-)  A  -  127.5 half-chair C-beta/C-alpha (126 degrees)
1024 PRO   (1024-)  A  -  -65.4 envelop C-beta (-72 degrees)
1039 PRO   (1039-)  A  -  -31.8 envelop C-alpha (-36 degrees)
And so on for a total of 182 lines.

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

3525 TYR   (  14-)  D  -   CZ   <->  8535 ALA   (  56-)  P  -   CB   1.92    1.28  INTRA BL
1102  ARG  ( 472-) U  -    CZ   <->  1233  SER  ( 529-) W  -    CA   1.91    1.29  INTRA BL
8377 ALA   ( 528-)  O  -   C    <->  8943 ARG   ( 472-)  P  -   CZ   1.80    1.40  INTRA BL
5668 ALA   ( 528-)  I  -   C    <->  6238 ARG   ( 472-)  J  -   CZ   1.79    1.41  INTRA BL
1171  ALA  ( 528-) V  -    C    <->  1228  ARG  ( 472-) W  -    CZ   1.76    1.44  INTRA BL
6294 ALA   ( 528-)  J  -   C    <->  6865 ARG   ( 472-)  K  -   CZ   1.76    1.44  INTRA BL
1102  ARG  ( 472-) U  -    CZ   <->  1233  SER  ( 529-) W  -    N    1.75    1.35  INTRA BL
3525 TYR   (  14-)  D  -   CE2  <->  8535 ALA   (  56-)  P  -   CB   1.72    1.48  INTRA BL
3525 TYR   (  14-)  D  -   CE1  <->  8535 ALA   (  56-)  P  -   CB   1.68    1.52  INTRA BL
3525 TYR   (  14-)  D  -   CZ   <->  8535 ALA   (  56-)  P  -   CA   1.62    1.58  INTRA BL
3525 TYR   (  14-)  D  -   CE2  <->  8535 ALA   (  56-)  P  -   CA   1.62    1.58  INTRA BL
3525 TYR   (  14-)  D  -   CZ   <->  8535 ALA   (  56-)  P  -   N    1.59    1.51  INTRA BL
9000 SER   ( 529-)  P  -   CB   <->  9388 VAL   ( 282-)  Q  -   CG2  1.56    1.64  INTRA BL
1108  SER  ( 529-) U  -    CB   <->  1146  VAL  ( 282-) V  -    CG2  1.56    1.64  INTRA BL
8010 ARG   ( 154-)  O  -   CG   <->  8721 GLU   ( 248-)  P  -   CG   1.56    1.64  INTRA BL
5298 ARG   ( 154-)  I  -   CG   <->  6016 GLU   ( 248-)  J  -   CG   1.56    1.64  INTRA BL
5423 VAL   ( 282-)  I  -   CG2  <->  6922 SER   ( 529-)  K  -   CB   1.56    1.64  INTRA BL
8134 VAL   ( 282-)  O  -   CG2  <->  9631 SER   ( 529-)  Q  -   CB   1.55    1.65  INTRA BL
1083  VAL  ( 282-) U  -    CG2  <->  1233  SER  ( 529-) W  -    CB   1.55    1.65  INTRA BL
5927 ARG   ( 154-)  J  -   CG   <->  6645 GLU   ( 248-)  K  -   CG   1.54    1.66  INTRA BL
1134  ARG  ( 154-) V  -    CG   <->  1206  GLU  ( 248-) W  -    CG   1.54    1.66  INTRA BL
8010 ARG   ( 154-)  O  -   CD   <->  8721 GLU   ( 248-)  P  -   CG   1.51    1.69  INTRA BL
5298 ARG   ( 154-)  I  -   CD   <->  6016 GLU   ( 248-)  J  -   CG   1.51    1.69  INTRA BL
5298 ARG   ( 154-)  I  -   CB   <->  6016 GLU   ( 248-)  J  -   CG   1.50    1.70  INTRA BL
8010 ARG   ( 154-)  O  -   CB   <->  8721 GLU   ( 248-)  P  -   CG   1.50    1.70  INTRA BL
And so on for a total of 5422 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

Note: Inside/Outside RMS Z-score plot

Chain identifier: W

Note: Inside/Outside RMS Z-score plot

Chain identifier: X

Note: Inside/Outside RMS Z-score plot

Chain identifier: Y

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.

 235 TYR   ( 235-)  A  -     -7.81
1142 ARG   (1142-)  A  -     -7.58
1300  TYR  ( 562-) X  -     -7.52
1243 TYR   (1243-)  A  -     -7.49
2112 ARG   (1006-)  B  -     -7.41
4026 GLN   ( 107-)  E  -     -7.19
 889 ARG   ( 889-)  A  -     -7.18
 824 ARG   ( 824-)  A  -     -7.15
4012 ARG   (  93-)  E  -     -7.09
 353 ARG   ( 353-)  A  -     -7.08
1233 ARG   (1233-)  A  -     -6.95
3903 GLN   ( 396-)  D  -     -6.86
1138 MET   (1138-)  A  -     -6.83
3178 LEU   ( 880-)  C  -     -6.82
3303 ARG   (1006-)  C  -     -6.81
2557 ARG   ( 257-)  C  -     -6.70
3615 GLN   ( 107-)  D  -     -6.69
2357 GLN   (  57-)  C  -     -6.69
2123 PHE   (1017-)  B  -     -6.61
3976 ARG   (  57-)  E  -     -6.59
 775 ARG   ( 775-)  A  -     -6.59
9033 TYR   ( 562-)  P  -     -6.56
 716 PHE   ( 716-)  A  -     -6.54
6954 TYR   ( 562-)  K  -     -6.52
  79 LEU   (  79-)  A  -     -6.48
And so on for a total of 405 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.

 379 VAL   ( 379-)  A  -    381 - PHE    381- ( A)  -      -4.52
 937 LEU   ( 937-)  A  -    939 - GLU    939- ( A)  -      -4.90
1044 LEU   (1044-)  A  -   1046 - GLN   1046- ( A)  -      -4.51
1543 ILE   ( 434-)  B  -   1545 - LEU    436- ( B)  -      -4.61
2406 MET   ( 106-)  C  -   2408 - VAL    108- ( C)  -      -5.26
2514 HIS   ( 214-)  C  -   2517 - LYS    217- ( C)  -      -4.60
2555 GLU   ( 255-)  C  -   2557 - ARG    257- ( C)  -      -5.62
3223 LEU   ( 925-)  C  -   3225 - GLY    927- ( C)  -      -4.89
3659 SER   ( 151-)  D  -   3661 - GLN    153- ( D)  -      -4.24
5748 LEU   ( 613-)  I  -   5750 - LYS    615- ( I)  -      -4.54
6376 SER   ( 612-)  J  -   6379 - LYS    615- ( J)  -      -4.38
7003 SER   ( 612-)  K  -   7006 - LYS    615- ( K)  -      -4.42
8457 LEU   ( 613-)  O  -   8459 - LYS    615- ( O)  -      -4.54
9082 SER   ( 612-)  P  -   9085 - LYS    615- ( P)  -      -4.40
9711 LEU   ( 613-)  Q  -   9713 - LYS    615- ( Q)  -      -4.56
1116  LEU  ( 613-) U  -    1116 -  LYS   615- (U ) -       -4.63
1179  SER  ( 612-) V  -    1179 -  LYS   615- (V ) -       -4.40
1242  SER  ( 612-) W  -    1242 -  LYS   615- (W ) -       -4.40
1305  SER  ( 612-) X  -    1306 -  LYS   615- (X ) -       -4.64

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

Note: Quality value plot

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

Chain identifier: U

Note: Quality value plot

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

Chain identifier: V

Note: Quality value plot

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

Chain identifier: W

Note: Quality value plot

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

Chain identifier: X

Note: Quality value plot

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

Chain identifier: Y

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.

3931 ASN   (  12-)  E  -  -3.35
 381 PHE   ( 381-)  A  -  -3.12
 150 ALA   ( 150-)  A  -  -3.01
 621 ASN   ( 621-)  A  -  -2.94
4112 ALA   ( 193-)  E  -  -2.91
9630 ALA   ( 528-)  Q  -  -2.87
6921 ALA   ( 528-)  K  -  -2.87
1228  ARG  ( 472-) W  -  -2.86
6865 ARG   ( 472-)  K  -  -2.85
8999 ALA   ( 528-)  P  -  -2.85
1108  ALA  ( 528-) U  -  -2.84
6238 ARG   ( 472-)  J  -  -2.84
8943 ARG   ( 472-)  P  -  -2.83
3422 TYR   (1125-)  C  -  -2.80
1544 SER   ( 435-)  B  -  -2.80
3554 ILE   (  46-)  D  -  -2.79
2928 LEU   ( 630-)  C  -  -2.75
3315 GLY   (1018-)  C  -  -2.69
5574 GLY   ( 433-)  I  -  -2.69
6828 GLY   ( 433-)  K  -  -2.69
1224  GLY  ( 433-) W  -  -2.68
8904 GLY   ( 433-)  P  -  -2.68
6199 GLY   ( 433-)  J  -  -2.68
9537 GLY   ( 433-)  Q  -  -2.68
1161  GLY  ( 433-) V  -  -2.68
8284 GLY   ( 433-)  O  -  -2.68
1098  GLY  ( 433-) U  -  -2.67
 788 GLN   ( 788-)  A  -  -2.67
4297 PRO   ( 378-)  E  -  -2.65
 385 THR   ( 385-)  A  -  -2.64
2535 LEU   ( 235-)  C  -  -2.63
3799 ALA   ( 292-)  D  -  -2.60
1102  ARG  ( 472-) U  -  -2.58
3560 PRO   (  52-)  D  -  -2.57
3420 GLN   (1123-)  C  -  -2.55
3674 MET   ( 166-)  D  -  -2.55
2834 ALA   ( 536-)  C  -  -2.53
3084 ALA   ( 786-)  C  -  -2.53
2961 GLN   ( 663-)  C  -  -2.51

Warning: Abnormal packing Z-score for sequential residues

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

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

1330 GLU   ( 218-)  B  -  - 1335 THR   ( 223-)  B  -     -1.81
2832 SER   ( 534-)  C  -  - 2835 TYR   ( 537-)  C  -     -2.07
3176 GLY   ( 878-)  C  -  - 3179 VAL   ( 881-)  C  -     -1.96
3417 PRO   (1120-)  C  -  - 3420 GLN   (1123-)  C  -     -2.15
3897 ASN   ( 390-)  D  -  - 3901 PHE   ( 394-)  D  -     -1.42
ERROR. Too many residues to use DSSP

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: V

Note: Second generation quality Z-score plot

Chain identifier: W

Note: Second generation quality Z-score plot

Chain identifier: X

Note: Second generation quality Z-score plot

Chain identifier: Y

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.

  35 GLN   (  35-)  A  -
 348 GLN   ( 348-)  A  -
 406 ASN   ( 406-)  A  -
1420 ASN   ( 308-)  B  -
1487 ASN   ( 375-)  B  -
1519 HIS   ( 410-)  B  -
1538 ASN   ( 429-)  B  -
1687 HIS   ( 580-)  B  -
1774 ASN   ( 667-)  B  -
2062 HIS   ( 956-)  B  -
2674 ASN   ( 375-)  C  -
2853 GLN   ( 555-)  C  -
3438 ASN   (1141-)  C  -
3447 ASN   (1150-)  C  -
3551 HIS   (  43-)  D  -
3994 HIS   (  75-)  E  -
4042 ASN   ( 123-)  E  -
4077 HIS   ( 158-)  E  -
4106 GLN   ( 187-)  E  -
4207 GLN   ( 288-)  E  -
4420 GLN   (  90-)  F  -
4589 HIS   ( 259-)  F  -
4665 HIS   (  59-)  G  -
4696 GLN   (  90-)  G  -
4865 HIS   ( 259-)  G  -
And so on for a total of 95 lines.

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   2 ALA   (   2-)  A  -   N
  12 LYS   (  12-)  A  -   N
  27 PHE   (  27-)  A  -   N
  40 HIS   (  40-)  A  -   N
  43 LEU   (  43-)  A  -   N
  65 LEU   (  65-)  A  -   N
  69 SER   (  69-)  A  -   N
  71 HIS   (  71-)  A  -   N
  80 ASP   (  80-)  A  -   N
  81 TYR   (  81-)  A  -   N
 112 TYR   ( 112-)  A  -   N
 127 ASN   ( 127-)  A  -   ND2
 148 ILE   ( 148-)  A  -   N
 153 LYS   ( 153-)  A  -   N
 158 TRP   ( 158-)  A  -   N
 158 TRP   ( 158-)  A  -   NE1
 159 THR   ( 159-)  A  -   N
 165 THR   ( 165-)  A  -   N
 171 THR   ( 171-)  A  -   OG1
 173 ALA   ( 173-)  A  -   N
 179 THR   ( 179-)  A  -   N
 190 THR   ( 190-)  A  -   N
 198 ARG   ( 198-)  A  -   N
 198 ARG   ( 198-)  A  -   NH1
 198 ARG   ( 198-)  A  -   NH2
And so on for a total of 1770 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.

  48 ASP   (  48-)  A  -   OD1
  72 HIS   (  72-)  A  -   ND1
 108 ASN   ( 108-)  A  -   OD1
 124 ASP   ( 124-)  A  -   OD2
 167 ASP   ( 167-)  A  -   OD2
 309 ASN   ( 309-)  A  -   OD1
 316 GLN   ( 316-)  A  -   OE1
 362 GLU   ( 362-)  A  -   OE2
 393 ASP   ( 393-)  A  -   OD1
 711 ASP   ( 711-)  A  -   OD2
 730 ASN   ( 730-)  A  -   OD1
 856 ASP   ( 856-)  A  -   OD1
 856 ASP   ( 856-)  A  -   OD2
 934 ASN   ( 934-)  A  -   OD1
 962 GLU   ( 962-)  A  -   OE2
 989 HIS   ( 989-)  A  -   ND1
1029 ASP   (1029-)  A  -   OD1
1069 GLU   (1069-)  A  -   OE2
1152 ASP   (1152-)  A  -   OD1
1197 ASP   (1197-)  A  -   OD1
1487 ASN   ( 375-)  B  -   OD1
1499 GLU   ( 389-)  B  -   OE1
1538 ASN   ( 429-)  B  -   OD1
1631 ASP   ( 524-)  B  -   OD2
1889 ASN   ( 782-)  B  -   OD1
And so on for a total of 308 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.

  32 ASP   (  32-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
  48 ASP   (  48-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
  76 GLU   (  76-)  A  -  H-bonding suggests Gln
  90 ASP   (  90-)  A  -  H-bonding suggests Asn
 124 ASP   ( 124-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 145 ASP   ( 145-)  A  -  H-bonding suggests Asn
 161 ASP   ( 161-)  A  -  H-bonding suggests Asn
 167 ASP   ( 167-)  A  -  H-bonding suggests Asn
 184 ASP   ( 184-)  A  -  H-bonding suggests Asn
 246 ASP   ( 246-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 286 ASP   ( 286-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 321 GLU   ( 321-)  A  -  H-bonding suggests Gln; but Alt-Rotamer
 415 ASP   ( 415-)  A  -  H-bonding suggests Asn
 420 ASP   ( 420-)  A  -  H-bonding suggests Asn
 444 ASP   ( 444-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 490 ASP   ( 490-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 511 ASP   ( 511-)  A  -  H-bonding suggests Asn
 530 GLU   ( 530-)  A  -  H-bonding suggests Gln
 581 ASP   ( 581-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 586 GLU   ( 586-)  A  -  H-bonding suggests Gln
 702 ASP   ( 702-)  A  -  H-bonding suggests Asn; but Alt-Rotamer
 776 ASP   ( 776-)  A  -  H-bonding suggests Asn
 821 GLU   ( 821-)  A  -  H-bonding suggests Gln
 856 ASP   ( 856-)  A  -  H-bonding suggests Asn
 862 GLU   ( 862-)  A  -  H-bonding suggests Gln
And so on for a total of 340 lines.

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -2.238
  2nd generation packing quality :  -3.228 (poor)
  Ramachandran plot appearance   :  -5.410 (bad)
  chi-1/chi-2 rotamer normality  :  -5.631 (bad)
  Backbone conformation          :  -1.532

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.480 (tight)
  Bond angles                    :   2.310 (loose)
  Omega angle restraints         :   1.640 (loose)
  Side chain planarity           :   5.781 (loose)
  Improper dihedral distribution :   4.460 (loose)
  Inside/Outside distribution    :   1.113

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 : 4.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -3.1 (poor)
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.480 (tight)
  Bond angles                    :   2.310 (loose)
  Omega angle restraints         :   1.640 (loose)
  Side chain planarity           :   5.781 (loose)
  Improper dihedral distribution :   4.460 (loose)
  Inside/Outside distribution    :   1.113
==============

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.