WHAT IF Check report

This file was created 2012-08-12 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 pdb2wse.ent

Checks that need to be done early-on in validation

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

3129 CLA   (1187-)  1  -         Atom types
3130 A10   (1188-)  1  -         Atom types
3131 A11   (1189-)  1  -         Atom types
3132 CLA   (1190-)  1  -         Atom types
3133 A12   (1191-)  1  -         Atom types
3134 A13   (1192-)  1  -         Atom types
3135 A14   (1193-)  1  -         Atom types
3136 A15   (1194-)  1  -         Atom types
3137 A16   (1195-)  1  -         Atom types
3138 A17   (1196-)  1  -         Atom types
3139 A18   (1197-)  1  -         Atom types
3140 A19   (1198-)  1  -         Atom types
3141 LMU   (1200-)  1  -         OK
3142 A20   (1212-)  2  -         Atom types
3143 A21   (1213-)  2  -         Atom types
3144 A22   (1214-)  2  -         Atom types
3145 A23   (1215-)  2  -         Atom types
3146 A24   (1216-)  2  -         Atom types
3147 A25   (1217-)  2  -         Atom types
3148 A26   (1218-)  2  -         Atom types
3149 A27   (1219-)  2  -         Atom types
3150 A28   (1220-)  2  -         Atom types
3151 A29   (1221-)  2  -         Atom types
3152 A30   (1222-)  2  -         Atom types
3153 A31   (1223-)  2  -         Atom types
And so on for a total of 261 lines.

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

  11 LEU   (  27-)  1  -   CG  1706 ARG   ( 314-)  B  -   NH1
  11 LEU   (  27-)  1  -   CD1 1706 ARG   ( 314-)  B  -   CZ
  11 LEU   (  27-)  1  -   CD1 1706 ARG   ( 314-)  B  -   NH1
 392 TRP   (  92-)  3  -   CZ2  892 ILE   ( 249-)  A  -   CD1
 392 TRP   (  92-)  3  -   CH2  892 ILE   ( 249-)  A  -   CD1
 397 ILE   (  98-)  3  -   C   3104 LEU   (  61-)  N  -   CD2
1686 ASN   ( 294-)  B  -   CB  2599 GLN   (  38-)  G  -   CD
1686 ASN   ( 294-)  B  -   CB  2599 GLN   (  38-)  G  -   OE1
1686 ASN   ( 294-)  B  -   CG  2599 GLN   (  38-)  G  -   CG
1686 ASN   ( 294-)  B  -   CG  2599 GLN   (  38-)  G  -   CD
1686 ASN   ( 294-)  B  -   CG  2599 GLN   (  38-)  G  -   OE1
1686 ASN   ( 294-)  B  -   ND2 2599 GLN   (  38-)  G  -   CG
1686 ASN   ( 294-)  B  -   ND2 2599 GLN   (  38-)  G  -   CD
1715 TYR   ( 323-)  B  -   CE2 2609 ASP   (  48-)  G  -   O
1716 ASP   ( 324-)  B  -   CB  2608 GLY   (  47-)  G  -   O
1951 CYS   ( 559-)  B  -   SG  3287 SF4   (1785-)  A  -   S1

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.

  39 PRO   (  55-)  1  -
 170 LEU   (  41-)  2  -
 253 PHE   ( 125-)  2  -
 392 TRP   (  92-)  3  -
 611 ASN   ( 142-)  4  -
 847 ASN   ( 204-)  A  -
1952 ASP   ( 560-)  B  -
2433 LYS   (  23-)  F  -
2599 GLN   (  38-)  G  -
3043 LEU   ( 163-)  L  -

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.

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 561 GLU   (  94-)  4  -   OE2 bound to 3176 A60   (1210-)  4  -   C1B
 589 LYS   ( 122-)  4  -   NZ  bound to  616 LYS   ( 150-)  4  -   CD
 616 LYS   ( 150-)  4  -   NZ  bound to  609 ASN   ( 142-)  4  -   CA

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

1523 ASP   ( 134-)  B  -

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: 1

Note: Ramachandran plot

Chain identifier: 2

Note: Ramachandran plot

Chain identifier: 3

Note: Ramachandran plot

Chain identifier: 4

Note: Ramachandran plot

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: N

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

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'.

  71 LEU   (  94-)  1      CG
  71 LEU   (  94-)  1      CD1
  71 LEU   (  94-)  1      CD2
 122 VAL   ( 145-)  1      CG1
 122 VAL   ( 145-)  1      CG2
 123 LYS   ( 146-)  1      CG
 123 LYS   ( 146-)  1      CD
 123 LYS   ( 146-)  1      CE
 123 LYS   ( 146-)  1      NZ
 210 GLU   (  84-)  2      CG
 210 GLU   (  84-)  2      CD
 210 GLU   (  84-)  2      OE1
 210 GLU   (  84-)  2      OE2
 368 VAL   (  70-)  3      CG1
 368 VAL   (  70-)  3      CG2
 504 LEU   (  37-)  4      CG
 504 LEU   (  37-)  4      CD1
 504 LEU   (  37-)  4      CD2
 861 ARG   ( 220-)  A      CB
 861 ARG   ( 220-)  A      CG
 861 ARG   ( 220-)  A      CD
 861 ARG   ( 220-)  A      NE
 861 ARG   ( 220-)  A      CZ
 861 ARG   ( 220-)  A      NH1
 861 ARG   ( 220-)  A      NH2
 958 ARG   ( 318-)  A      CB
 958 ARG   ( 318-)  A      CG
 958 ARG   ( 318-)  A      CD
 958 ARG   ( 318-)  A      NE
 958 ARG   ( 318-)  A      CZ
 958 ARG   ( 318-)  A      NH1
 958 ARG   ( 318-)  A      NH2
1523 ASP   ( 134-)  B      O
1536 PHE   ( 147-)  B      CG
1536 PHE   ( 147-)  B      CD1
1536 PHE   ( 147-)  B      CD2
1536 PHE   ( 147-)  B      CE1
1536 PHE   ( 147-)  B      CE2
1536 PHE   ( 147-)  B      CZ
2607 LYS   (  52-)  G      CG
2607 LYS   (  52-)  G      CD
2607 LYS   (  52-)  G      CE
2607 LYS   (  52-)  G      NZ
2791 PHE   (  39-)  J      CG
2791 PHE   (  39-)  J      CD1
2791 PHE   (  39-)  J      CD2
2791 PHE   (  39-)  J      CE1
2791 PHE   (  39-)  J      CE2
2791 PHE   (  39-)  J      CZ

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.

 351 TRP   (  53-)  3    High
 355 GLY   (  57-)  3    High
 356 GLU   (  58-)  3    High
 357 ILE   (  59-)  3    High
 358 ILE   (  60-)  3    High
 359 ASN   (  61-)  3    High
 360 GLY   (  62-)  3    High
 361 ARG   (  63-)  3    High
 362 TYR   (  64-)  3    High
 363 ALA   (  65-)  3    High
 364 MET   (  66-)  3    High
 365 LEU   (  67-)  3    High
 366 GLY   (  68-)  3    High
 367 ALA   (  69-)  3    High
 368 VAL   (  70-)  3    High
 369 GLY   (  71-)  3    High
 370 ALA   (  72-)  3    High
 371 ILE   (  73-)  3    High
 372 ALA   (  74-)  3    High
 373 PRO   (  75-)  3    High
 374 GLU   (  76-)  3    High
 375 ILE   (  77-)  3    High
 376 LEU   (  78-)  3    High
 377 GLY   (  79-)  3    High
 378 LYS   (  80-)  3    High
 379 ALA   (  81-)  3    High
 380 GLY   (  82-)  3    High
 381 LEU   (  83-)  3    High
 382 ILE   (  84-)  3    High
 383 PRO   (  85-)  3    High
 384 GLN   (  86-)  3    High
 385 GLU   (  87-)  3    High
 386 THR   (  88-)  3    High
 387 ALA   (  89-)  3    High
 388 LEU   (  90-)  3    High

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: 1

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 2

Note: B-factor plot

Chain identifier: 3

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: 4

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: A

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: B

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: C

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: D

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: E

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: F

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: G

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: H

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: I

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: J

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: K

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: L

Warning: B-factor plot useless

All average B-factors are equal. Plot suppressed.

Chain identifier: N

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.

 516 ARG   (  49-)  4
 571 ARG   ( 104-)  4
 572 ARG   ( 105-)  4
 717 ARG   (  76-)  A
 782 ARG   ( 141-)  A
1059 ARG   ( 427-)  A
1071 ARG   ( 439-)  A
1104 ARG   ( 472-)  A
1196 ARG   ( 564-)  A
1199 ARG   ( 567-)  A
1329 ARG   ( 697-)  A
1430 ARG   (  41-)  B
1705 ARG   ( 317-)  B
1784 ARG   ( 396-)  B
1798 ARG   ( 410-)  B
2071 ARG   ( 684-)  B
2079 ARG   ( 692-)  B
2081 ARG   ( 694-)  B
2140 ARG   (  19-)  C
2187 ARG   (  66-)  C
2222 ARG   (  38-)  D
2345 ARG   (  32-)  E
2354 ARG   (  41-)  E
2482 ARG   (  78-)  F
2583 ARG   (  28-)  G
2918 ARG   (  44-)  L
2949 ARG   (  75-)  L

Warning: Tyrosine convention problem

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

 110 TYR   ( 133-)  1
 213 TYR   (  87-)  2
 309 TYR   ( 183-)  2
 362 TYR   (  64-)  3
 402 TYR   ( 111-)  3
 433 TYR   ( 142-)  3
 449 TYR   ( 158-)  3
 482 TYR   ( 197-)  3
 494 TYR   ( 209-)  3
 567 TYR   ( 100-)  4
 747 TYR   ( 106-)  A
 806 TYR   ( 165-)  A
 918 TYR   ( 277-)  A
 979 TYR   ( 347-)  A
1009 TYR   ( 377-)  A
1016 TYR   ( 384-)  A
1300 TYR   ( 668-)  A
1331 TYR   ( 699-)  A
1370 TYR   ( 738-)  A
1432 TYR   (  43-)  B
1506 TYR   ( 117-)  B
1595 TYR   ( 206-)  B
1622 TYR   ( 233-)  B
1760 TYR   ( 372-)  B
1765 TYR   ( 377-)  B
1786 TYR   ( 398-)  B
1964 TYR   ( 577-)  B
1980 TYR   ( 593-)  B
2189 TYR   (  68-)  C
2230 TYR   (  46-)  D
2285 TYR   ( 101-)  D
2338 TYR   ( 154-)  D
2357 TYR   (  44-)  E
2395 TYR   (  82-)  E
2437 TYR   (  32-)  F
2463 TYR   (  59-)  F
2496 TYR   (  92-)  F
2508 TYR   ( 104-)  F
2545 TYR   ( 141-)  F
2638 TYR   (  83-)  G
2639 TYR   (  84-)  G
2648 TYR   (  93-)  G
2668 TYR   (  24-)  H
2676 TYR   (  32-)  H
2759 TYR   (   7-)  J
2910 TYR   (  36-)  L
2953 TYR   (  79-)  L
3033 TYR   ( 159-)  L
3043 TYR   (   6-)  N
3070 TYR   (  33-)  N

Warning: Phenylalanine convention problem

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

   6 PHE   (  22-)  1
  79 PHE   ( 102-)  1
 138 PHE   ( 161-)  1
 193 PHE   (  67-)  2
 214 PHE   (  88-)  2
 346 PHE   (  48-)  3
 394 PHE   (  97-)  3
 460 PHE   ( 169-)  3
 531 PHE   (  64-)  4
 558 PHE   (  91-)  4
 588 PHE   ( 121-)  4
 605 PHE   ( 138-)  4
 632 PHE   ( 166-)  4
 644 PHE   ( 178-)  4
 720 PHE   (  79-)  A
 744 PHE   ( 103-)  A
 837 PHE   ( 196-)  A
 889 PHE   ( 248-)  A
 903 PHE   ( 262-)  A
 910 PHE   ( 269-)  A
 911 PHE   ( 270-)  A
 921 PHE   ( 280-)  A
 970 PHE   ( 338-)  A
1037 PHE   ( 405-)  A
1084 PHE   ( 452-)  A
And so on for a total of 79 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.

   9 ASP   (  25-)  1
  94 ASP   ( 117-)  1
 106 ASP   ( 129-)  1
 113 ASP   ( 136-)  1
 165 ASP   (  37-)  2
 216 ASP   (  90-)  2
 248 ASP   ( 122-)  2
 339 ASP   (  41-)  3
 463 ASP   ( 172-)  3
 575 ASP   ( 108-)  4
 653 ASP   ( 187-)  4
 664 ASP   (  23-)  A
 666 ASP   (  25-)  A
 690 ASP   (  49-)  A
 706 ASP   (  65-)  A
 711 ASP   (  70-)  A
 776 ASP   ( 135-)  A
 839 ASP   ( 198-)  A
 879 ASP   ( 238-)  A
 894 ASP   ( 253-)  A
 939 ASP   ( 298-)  A
1020 ASP   ( 388-)  A
1053 ASP   ( 421-)  A
1065 ASP   ( 433-)  A
1072 ASP   ( 440-)  A
And so on for a total of 60 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.

  15 GLU   (  31-)  1
  21 GLU   (  37-)  1
  27 GLU   (  43-)  1
  86 GLU   ( 109-)  1
  96 GLU   ( 119-)  1
 118 GLU   ( 141-)  1
 119 GLU   ( 142-)  1
 124 GLU   ( 147-)  1
 152 GLU   ( 175-)  1
 192 GLU   (  66-)  2
 212 GLU   (  86-)  2
 224 GLU   (  98-)  2
 284 GLU   ( 158-)  2
 348 GLU   (  50-)  3
 374 GLU   (  76-)  3
 416 GLU   ( 125-)  3
 464 GLU   ( 173-)  3
 499 GLU   (  32-)  4
 511 GLU   (  44-)  4
 548 GLU   (  81-)  4
 549 GLU   (  82-)  4
 569 GLU   ( 102-)  4
 614 GLU   ( 148-)  4
 617 GLU   ( 151-)  4
 713 GLU   (  72-)  A
And so on for a total of 66 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.

 215 THR   (  89-)  2      CA   CB    1.61    4.0
 308 ILE   ( 182-)  2      CA   CB    1.62    4.7
 390 TRP   (  92-)  3      CB   CG    1.80    9.8
 506 TRP   (  39-)  4      CA   C     1.39   -6.6
 508 VAL   (  41-)  4      CA   CB    1.44   -4.5
 555 SER   (  88-)  4      CA   C     1.63    5.0
 555 SER   (  88-)  4      C    O     1.34    5.4
 560 ILE   (  93-)  4      N    CA    1.54    4.5
 560 ILE   (  93-)  4      CA   C     1.65    5.8
 560 ILE   (  93-)  4      C    O     1.34    5.3
 568 VAL   ( 101-)  4      CA   CB    1.44   -4.5
 719 VAL   (  78-)  A      CA   CB    1.62    4.5
 799 ILE   ( 158-)  A      CA   CB    1.63    5.1
 866 VAL   ( 225-)  A      CA   CB    1.64    5.3
1067 VAL   ( 435-)  A      CA   CB    1.62    4.3
1159 VAL   ( 527-)  A      CA   CB    1.63    4.8
1164 ILE   ( 532-)  A      CA   CB    1.63    5.0
1185 VAL   ( 553-)  A      CA   CB    1.63    4.8
1476 ILE   (  87-)  B      N    CA    1.54    4.4
1476 ILE   (  87-)  B      CA   CB    1.61    4.0
1554 VAL   ( 165-)  B      CA   CB    1.61    4.0
2026 VAL   ( 639-)  B      CA   CB    1.64    5.4
2166 THR   (  45-)  C      CA   CB    1.62    4.5
2193 GLU   (  72-)  C      CG   CD    1.42   -4.0
2193 GLU   (  72-)  C      CD   OE2   1.17   -4.4
2194 THR   (  73-)  C      CA   C     1.41   -5.6
2194 THR   (  73-)  C      CA   CB    1.43   -5.0
2231 VAL   (  47-)  D      CA   CB    1.63    4.8
2403 VAL   (  90-)  E      CA   C     1.43   -4.4
2403 VAL   (  90-)  E      CA   CB    1.44   -4.3
2423 GLU   (  18-)  F      CA   C     1.43   -4.5
2577 VAL   (  22-)  G      CA   C     1.61    4.1
2626 VAL   (  71-)  G      CA   CB    1.62    4.6
3033 TYR   ( 159-)  L      N    CA    1.54    4.2
3033 TYR   ( 159-)  L      CA   C     1.61    4.1
3036 ASP   ( 162-)  L      CA   C     1.43   -4.7
3106 CYS   (  69-)  N      CA   C     1.62    4.3

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.992155 -0.000038  0.000738|
 | -0.000038  0.994795 -0.000077|
 |  0.000738 -0.000077  1.000406|
Proposed new scale matrix

 |  0.008353  0.000000  0.000173|
 |  0.000000  0.005317  0.000000|
 | -0.000006  0.000000  0.007728|
With corresponding cell

    A    = 119.710  B   = 188.087  C    = 129.427
    Alpha=  90.002  Beta=  91.142  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 120.655  B   = 189.086  C    = 129.388
    Alpha=  90.000  Beta=  91.240  Gamma=  90.000

Variance: 2457.115
(Under-)estimated Z-score: 36.532

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.

  30 HIS   (  46-)  1      CG   ND1  CE1 109.80    4.2
  41 ILE   (  57-)  1      N    CA   C   135.32    8.6
  41 ILE   (  57-)  1      C    CA   CB   97.07   -6.9
  42 VAL   (  59-)  1      C    CA   CB   97.07   -6.9
  87 HIS   ( 110-)  1      CG   ND1  CE1 109.76    4.2
 157 HIS   ( 180-)  1      CG   ND1  CE1 109.65    4.1
 163 HIS   ( 186-)  1     -C    N    CA  114.00   -4.3
 163 HIS   ( 186-)  1      N    CA   C    99.42   -4.2
 163 HIS   ( 186-)  1      CG   ND1  CE1 109.61    4.0
 166 PRO   (  38-)  2      N    CA   C    99.85   -4.8
 169 LEU   (  41-)  2      CA   CB   CG  100.24   -4.6
 182 MET   (  56-)  2      N    CA   C   125.41    5.1
 182 MET   (  56-)  2      C    CA   CB  117.90    4.1
 183 LEU   (  57-)  2      CA   CB   CG  130.92    4.2
 193 PHE   (  67-)  2      N    CA   CB  118.28    4.6
 193 PHE   (  67-)  2      C    CA   CB  120.44    5.4
 200 LEU   (  74-)  2      N    CA   C    93.39   -6.4
 207 THR   (  81-)  2      N    CA   C    99.44   -4.2
 211 GLN   (  85-)  2      N    CA   CB  117.34    4.0
 218 THR   (  92-)  2      C    CA   CB  118.96    4.7
 227 PHE   ( 101-)  2      N    CA   CB  122.13    6.8
 241 ASN   ( 115-)  2      N    CA   C   124.10    4.6
 244 CYS   ( 118-)  2     -C    N    CA  128.92    4.0
 249 PRO   ( 123-)  2     -CA  -C    N   122.94    4.0
 251 PHE   ( 125-)  2      N    CA   C   124.64    4.8
And so on for a total of 239 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.

   9 ASP   (  25-)  1
  15 GLU   (  31-)  1
  21 GLU   (  37-)  1
  27 GLU   (  43-)  1
  86 GLU   ( 109-)  1
  94 ASP   ( 117-)  1
  96 GLU   ( 119-)  1
 106 ASP   ( 129-)  1
 113 ASP   ( 136-)  1
 118 GLU   ( 141-)  1
 119 GLU   ( 142-)  1
 124 GLU   ( 147-)  1
 152 GLU   ( 175-)  1
 165 ASP   (  37-)  2
 192 GLU   (  66-)  2
 212 GLU   (  86-)  2
 216 ASP   (  90-)  2
 224 GLU   (  98-)  2
 248 ASP   ( 122-)  2
 284 GLU   ( 158-)  2
 339 ASP   (  41-)  3
 348 GLU   (  50-)  3
 374 GLU   (  76-)  3
 416 GLU   ( 125-)  3
 463 ASP   ( 172-)  3
And so on for a total of 153 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.

  43 PRO   (  60-)  1      N      6.8    19.79    -2.48
 161 PRO   ( 184-)  1      N     -8.6   -30.61    -2.48
 182 MET   (  56-)  2      CA    -8.9    18.11    34.17
 189 PHE   (  63-)  2      CA    -6.2    24.10    33.98
 193 PHE   (  67-)  2      CA   -20.7     0.82    33.98
 211 GLN   (  85-)  2      CA    -6.9    20.58    33.96
 218 THR   (  92-)  2      CA   -12.1    13.60    33.84
 227 PHE   ( 101-)  2      CA   -16.9     6.99    33.98
 251 PHE   ( 125-)  2      CA    -8.7    20.12    33.98
 287 THR   ( 161-)  2      CA   -11.2    15.07    33.84
 291 LYS   ( 165-)  2      CA    -6.9    22.41    33.92
 300 VAL   ( 174-)  2      CA   -16.1     9.85    33.23
 301 MET   ( 175-)  2      CA   -11.3    13.79    34.17
 303 ALA   ( 177-)  2      CA    -8.1    23.83    34.09
 304 TRP   ( 178-)  2      CA    -6.5    23.09    34.04
 326 PRO   ( 200-)  2      N     -8.0   -28.68    -2.48
 396 ASN   ( 105-)  3      CA    -6.5    21.27    33.59
 402 TYR   ( 111-)  3      CA   -10.3    17.68    34.03
 501 PRO   (  34-)  4      N      9.4    28.47    -2.48
 507 PHE   (  40-)  4      CA   -13.7    12.14    33.98
 522 VAL   (  55-)  4      CA    -9.0    20.12    33.23
 555 SER   (  88-)  4      CA    -7.2    20.96    34.32
 567 TYR   ( 100-)  4      CA    -9.1    19.72    34.03
 667 PRO   (  26-)  A      N     12.9    39.77    -2.48
1155 VAL   ( 523-)  A      CA    -8.1    21.55    33.23
2089 ILE   ( 702-)  B      CB    -6.1    24.34    32.31
2437 TYR   (  32-)  F      CA    -6.2    24.29    34.03
2569 LEU   (  14-)  G      CA    -7.9    22.09    34.19
2576 PHE   (  21-)  G      CA   -22.8    -2.42    33.98 Wrong hand
2577 VAL   (  22-)  G      CA    -7.5    22.38    33.23
2673 PRO   (  29-)  H      N     -8.2   -29.49    -2.48
2846 PRO   (  52-)  K      N     10.5    31.95    -2.48
2942 PHE   (  68-)  L      CA    -8.3    20.63    33.98
3027 TRP   ( 153-)  L      CA    -6.1    23.69    34.04
3031 LEU   ( 157-)  L      C     -9.3   -14.56     0.20
3080 PRO   (  43-)  N      N     10.1    30.67    -2.48
The average deviation= 1.468

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.

 560 ILE   (  93-)  4   11.49
2571 LEU   (  16-)  G    9.08
 300 VAL   ( 174-)  2    9.04
  41 ILE   (  57-)  1    8.75
 182 MET   (  56-)  2    8.53
2119 LYS   ( 732-)  B    8.51
 561 GLU   (  94-)  4    8.18
3009 GLY   ( 135-)  L    8.07
2097 LEU   ( 710-)  B    7.80
3070 TYR   (  33-)  N    7.57
 504 LEU   (  37-)  4    7.49
 593 LEU   ( 126-)  4    7.43
2429 LYS   (  24-)  F    7.35
 565 SER   (  98-)  4    7.26
 852 LEU   ( 211-)  A    7.25
 200 LEU   (  74-)  2    7.25
 576 ILE   ( 109-)  4    7.10
3064 ALA   (  27-)  N    6.97
 287 THR   ( 161-)  2    6.61
 735 SER   (  94-)  A    6.54
1576 SER   ( 187-)  B    6.49
 992 ILE   ( 360-)  A    6.49
 226 VAL   ( 100-)  2    6.45
2599 PHE   (  44-)  G    6.34
1085 LEU   ( 453-)  A    6.31
And so on for a total of 208 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 : 2.145

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.

2787 ASP   (  35-)  J    4.01

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 : -7.839

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.

 558 PHE   (  91-)  4    -3.9
 394 PHE   (  97-)  3    -3.9
 402 TYR   ( 111-)  3    -3.8
2882 TYR   (   8-)  L    -3.8
 455 PHE   ( 164-)  3    -3.8
3066 PHE   (  29-)  N    -3.7
2668 TYR   (  24-)  H    -3.7
 195 THR   (  69-)  2    -3.7
 392 THR   (  95-)  3    -3.7
1860 TYR   ( 472-)  B    -3.7
3062 THR   (  25-)  N    -3.7
2700 PHE   (  56-)  H    -3.6
 489 THR   ( 204-)  3    -3.6
1493 PHE   ( 104-)  B    -3.6
1352 THR   ( 720-)  A    -3.6
2392 THR   (  79-)  E    -3.5
 639 THR   ( 173-)  4    -3.5
1916 HIS   ( 528-)  B    -3.5
1494 THR   ( 105-)  B    -3.5
 681 PHE   (  40-)  A    -3.5
 556 THR   (  89-)  4    -3.5
2829 THR   (  35-)  K    -3.4
 984 THR   ( 352-)  A    -3.4
1221 THR   ( 589-)  A    -3.4
 923 THR   ( 282-)  A    -3.4
And so on for a total of 868 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   8 PHE   (  24-)  1  Poor phi/psi
   9 ASP   (  25-)  1  Poor phi/psi
  11 LEU   (  27-)  1  Poor phi/psi
  12 GLY   (  28-)  1  Poor phi/psi
  13 LEU   (  29-)  1  Poor phi/psi
  14 GLY   (  30-)  1  Poor phi/psi
  15 GLU   (  31-)  1  omega poor
  17 PRO   (  33-)  1  omega poor
  19 ASN   (  35-)  1  Poor phi/psi
  31 CYS   (  47-)  1  omega poor
  35 MET   (  51-)  1  omega poor
  39 PRO   (  55-)  1  Poor phi/psi
  40 GLY   (  56-)  1  omega poor
  43 PRO   (  60-)  1  omega poor
  44 GLU   (  61-)  1  Poor phi/psi
  45 ALA   (  62-)  1  omega poor
  46 LEU   (  63-)  1  omega poor
  47 GLY   (  64-)  1  omega poor
  48 TYR   (  65-)  1  Poor phi/psi, omega poor
  54 LEU   (  77-)  1  Poor phi/psi
  56 GLY   (  79-)  1  Poor phi/psi
  60 THR   (  83-)  1  Poor phi/psi
  61 TYR   (  84-)  1  Poor phi/psi
  62 LEU   (  85-)  1  Poor phi/psi
  65 PRO   (  88-)  1  omega poor
And so on for a total of 1472 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 : -7.777

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.

1719 HIS   ( 331-)  B    0.36
2101 SER   ( 714-)  B    0.39

Warning: Unusual backbone conformations

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

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

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

   3 PRO   (  19-)  1      0
   4 GLY   (  20-)  1      0
   5 ASP   (  21-)  1      0
   6 PHE   (  22-)  1      0
   8 PHE   (  24-)  1      0
   9 ASP   (  25-)  1      0
  10 PRO   (  26-)  1      0
  13 LEU   (  29-)  1      0
  16 VAL   (  32-)  1      0
  17 PRO   (  33-)  1      0
  18 ALA   (  34-)  1      0
  19 ASN   (  35-)  1      0
  35 MET   (  51-)  1      0
  39 PRO   (  55-)  1      0
  40 GLY   (  56-)  1      0
  41 ILE   (  57-)  1      0
  42 VAL   (  59-)  1      0
  43 PRO   (  60-)  1      0
  44 GLU   (  61-)  1      0
  46 LEU   (  63-)  1      0
  47 GLY   (  64-)  1      0
  48 TYR   (  65-)  1      0
  49 GLY   (  66-)  1      0
  50 GLU   (  73-)  1      0
  51 TRP   (  74-)  1      0
And so on for a total of 2021 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -3.078

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 : 15.943

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!

2464 GLY   (  60-)  F   3.45   66
2096 GLY   ( 709-)  B   3.34   80
1517 GLY   ( 128-)  B   3.19   80
 736 GLY   (  95-)  A   3.07   80
2310 GLY   ( 126-)  D   3.05   11
 775 GLY   ( 134-)  A   2.95   10
3063 GLY   (  26-)  N   2.75   14
2247 GLY   (  63-)  D   2.58   11
1035 GLY   ( 403-)  A   2.47   42
 769 GLY   ( 128-)  A   2.32   73
1328 GLY   ( 696-)  A   2.29   12
1617 GLY   ( 228-)  B   2.11   80
1706 GLY   ( 318-)  B   2.02   26
 342 GLY   (  44-)  3   1.81   23
2977 GLY   ( 103-)  L   1.81   33
1778 GLY   ( 390-)  B   1.72   80
1570 GLY   ( 181-)  B   1.72   13
2047 GLY   ( 660-)  B   1.67   19
2479 GLY   (  75-)  F   1.67   73
1434 ASN   (  45-)  B   1.62   13
2768 THR   (  16-)  J   1.62   15
1133 GLY   ( 501-)  A   1.53   27
1042 ALA   ( 410-)  A   1.51   80
2706 GLY   (  62-)  H   1.51   80

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...

 316 ASP   ( 190-)  2   1.72
2238 LYS   (  54-)  D   1.65
2634 HIS   (  79-)  G   1.73

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]

 667 PRO   (  26-)  A    0.49 HIGH
 869 PRO   ( 228-)  A    0.20 LOW
1012 PRO   ( 380-)  A    0.11 LOW
1395 PRO   (   6-)  B    0.45 HIGH

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].

  10 PRO   (  26-)  1  -113.3 envelop C-gamma (-108 degrees)
  43 PRO   (  60-)  1   -46.1 half-chair C-beta/C-alpha (-54 degrees)
  55 PRO   (  78-)  1     7.9 envelop N (0 degrees)
  65 PRO   (  88-)  1   118.3 half-chair C-beta/C-alpha (126 degrees)
  67 PRO   (  90-)  1    -4.3 envelop N (0 degrees)
 101 PRO   ( 124-)  1    48.5 half-chair C-delta/C-gamma (54 degrees)
 107 PRO   ( 130-)  1    -8.4 envelop N (0 degrees)
 114 PRO   ( 137-)  1   176.4 envelop N (180 degrees)
 146 PRO   ( 169-)  1   -13.7 half-chair C-alpha/N (-18 degrees)
 150 PRO   ( 173-)  1   -14.3 half-chair C-alpha/N (-18 degrees)
 242 PRO   ( 116-)  2     1.6 envelop N (0 degrees)
 249 PRO   ( 123-)  2   -54.0 half-chair C-beta/C-alpha (-54 degrees)
 252 PRO   ( 126-)  2  -145.4 envelop C-delta (-144 degrees)
 271 PRO   ( 145-)  2    12.1 half-chair N/C-delta (18 degrees)
 314 PRO   ( 188-)  2   160.5 half-chair C-alpha/N (162 degrees)
 326 PRO   ( 200-)  2  -114.8 envelop C-gamma (-108 degrees)
 336 PRO   ( 210-)  2   160.8 half-chair C-alpha/N (162 degrees)
 373 PRO   (  75-)  3    11.2 half-chair N/C-delta (18 degrees)
 383 PRO   (  85-)  3   -23.0 half-chair C-alpha/N (-18 degrees)
 389 PRO   (  91-)  3     6.2 envelop N (0 degrees)
 426 PRO   ( 135-)  3   152.2 envelop C-alpha (144 degrees)
 447 PRO   ( 156-)  3    44.7 envelop C-delta (36 degrees)
 450 PRO   ( 159-)  3   121.1 half-chair C-beta/C-alpha (126 degrees)
 453 PRO   ( 162-)  3   -55.3 half-chair C-beta/C-alpha (-54 degrees)
 493 PRO   ( 208-)  3   139.2 envelop C-alpha (144 degrees)
And so on for a total of 102 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.

2142 CYS   (  21-)  C      SG   <->  3285 B55   (1082-)  C      S2   2.94    0.66  INTRA BL
2126 VAL   (   5-)  C      CG2  <->  2186 VAL   (  65-)  C      CG1  2.14    1.06  INTRA BL
2663 GLY   (  19-)  H      O    <->  2666 ASP   (  22-)  H      OD2  2.10    0.30  INTRA BL
3353 LMU   (7037-)  A      C10  <->  3364 LMU   (7051-)  A      C12  1.84    0.46  INTRA B2
2663 GLY   (  19-)  H      O    <->  2666 ASP   (  22-)  H      CG   1.79    1.01  INTRA BL
 561 GLU   (  94-)  4      OE1  <->  3176 A60   (1210-)  4      NB   1.78    0.92  INTRA BL
3106 CYS   (  69-)  N      SG   <->  3303 LMU   (1086-)  N      C3B  1.70    1.30  INTRA B3
1990 ARG   ( 603-)  B      NH1  <->  2120 PHE   ( 733-)  B      CB   1.68    1.42  INTRA BL
2663 GLY   (  19-)  H      C    <->  2666 ASP   (  22-)  H      OD2  1.67    1.13  INTRA BL
2800 SER   (   6-)  K      O    <->  2804 ILE   (  10-)  K      CD1  1.67    1.13  INTRA BL
3043 TYR   (   6-)  N      O    <->  3045 GLU   (   8-)  N      N    1.54    1.16  INTRA BL
 617 GLU   ( 151-)  4      O    <->   620 ILE   ( 154-)  4      CG1  1.52    1.28  INTRA BL
2535 PHE   ( 131-)  F      CE1  <->  3371 B60   (1158-)  F      C1'  1.48    1.32  INTRA BL
3106 CYS   (  69-)  N      SG   <->  3303 LMU   (1086-)  N      O3B  1.44    0.66  INTRA B2
 423 TRP   ( 132-)  3      CH2  <->   446 GLU   ( 155-)  3      CD   1.44    1.76  INTRA BF
2535 PHE   ( 131-)  F      CZ   <->  3371 B60   (1158-)  F      C1'  1.41    1.79  INTRA BL
 536 ILE   (  69-)  4      CD1  <->   641 LYS   ( 175-)  4      CG   1.39    1.81  INTRA BL
2353 ARG   (  40-)  E      CZ   <->  2399 GLU   (  86-)  E      OE1  1.39    1.41  INTRA BL
 561 GLU   (  94-)  4      CD   <->  3176 A60   (1210-)  4      NB   1.36    1.34  INTRA BL
2119 LYS   ( 732-)  B      CG   <->  2121 GLY   ( 734-)  B      N    1.35    1.75  INTRA BL
2126 VAL   (   5-)  C      CB   <->  2186 VAL   (  65-)  C      CG1  1.33    1.87  INTRA BL
1213 CYS   ( 581-)  A      SG   <->  3281 SF4   (1785-)  B      S3   1.33    1.87  INTRA BL
1990 ARG   ( 603-)  B      NH1  <->  2120 PHE   ( 733-)  B      CA   1.32    1.78  INTRA BL
 536 ILE   (  69-)  4      CD1  <->   641 LYS   ( 175-)  4      CB   1.30    1.90  INTRA BL
2838 GLU   (  44-)  K      CG   <->  2839 SER   (  45-)  K      N    1.29    1.71  INTRA BL
And so on for a total of 4893 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.252

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: 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: 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: N

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.

 449 TYR   ( 158-)  3      -8.92
  48 TYR   (  65-)  1      -8.85
 100 TYR   ( 123-)  1      -8.75
2648 TYR   (  93-)  G      -8.51
 600 TYR   ( 133-)  4      -8.22
2917 TYR   (  43-)  L      -8.22
2278 TYR   (  94-)  D      -8.06
1393 ARG   (   4-)  B      -8.04
 263 TYR   ( 137-)  2      -7.86
2605 ARG   (  50-)  G      -7.85
 970 PHE   ( 338-)  A      -7.85
 145 TYR   ( 168-)  1      -7.82
1860 TYR   ( 472-)  B      -7.81
 206 TYR   (  80-)  2      -7.78
  61 TYR   (  84-)  1      -7.76
2311 ARG   ( 127-)  D      -7.75
2437 TYR   (  32-)  F      -7.64
 543 TYR   (  76-)  4      -7.63
1595 TYR   ( 206-)  B      -7.56
 213 TYR   (  87-)  2      -7.53
 454 PHE   ( 163-)  3      -7.53
   6 PHE   (  22-)  1      -7.50
 455 PHE   ( 164-)  3      -7.44
2793 PHE   (  41-)  J      -7.44
2338 TYR   ( 154-)  D      -7.38
And so on for a total of 326 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.

  91 MET   ( 114-)  1        93 - LYS    116- ( 1)         -5.49
  96 GLU   ( 119-)  1       100 - TYR    123- ( 1)         -6.40
 156 THR   ( 179-)  1       159 - ALA    182- ( 1)         -4.72
 199 ILE   (  73-)  2       201 - ASN     75- ( 2)         -5.45
 211 GLN   (  85-)  2       214 - PHE     88- ( 2)         -6.28
 272 LEU   ( 146-)  2       275 - GLY    149- ( 2)         -4.50
 323 LEU   ( 197-)  2       325 - ASP    199- ( 2)         -4.89
 327 HIS   ( 201-)  2       329 - THR    203- ( 2)         -5.09
 340 PRO   (  42-)  3       343 - THR     45- ( 3)         -4.63
 374 GLU   (  76-)  3       376 - LEU     78- ( 3)         -5.15
 396 ASN   ( 105-)  3       398 - TRP    107- ( 3)         -4.94
 431 LYS   ( 140-)  3       435 - LEU    144- ( 3)         -5.61
 437 LEU   ( 146-)  3       439 - LYS    148- ( 3)         -5.14
 443 GLY   ( 152-)  3       446 - GLU    155- ( 3)         -4.47
 458 LEU   ( 167-)  3       460 - PHE    169- ( 3)         -6.06
 462 LYS   ( 171-)  3       464 - GLU    173- ( 3)         -5.05
 528 PRO   (  61-)  4       531 - PHE     64- ( 4)         -4.85
 536 ILE   (  69-)  4       538 - ASN     71- ( 4)         -4.69
 541 LYS   (  74-)  4       543 - TYR     76- ( 4)         -5.66
 547 LYS   (  80-)  4       551 - PHE     84- ( 4)         -5.82
 612 THR   ( 146-)  4       614 - GLU    148- ( 4)         -4.56
 647 LEU   ( 181-)  4       649 - GLN    183- ( 4)         -5.47
 655 TRP   ( 189-)  4       657 - ASN    191- ( 4)         -5.07
 674 GLN   (  33-)  A       677 - LYS     36- ( A)         -5.34
 916 SER   ( 275-)  A       918 - TYR    277- ( A)         -5.34
And so on for a total of 61 lines.

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 - 3122 : -2.883

Note: Quality value plot

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

Chain identifier: 1

Note: Quality value plot

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

Chain identifier: 2

Note: Quality value plot

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

Chain identifier: 3

Note: Quality value plot

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

Chain identifier: 4

Note: Quality value plot

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

Chain identifier: 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: N

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.

 861 ARG   ( 220-)  A   -3.89
2607 LYS   (  52-)  G   -3.76
3109 LYS   (  72-)  N   -3.62
 381 LEU   (  83-)  3   -3.47
1898 LEU   ( 510-)  B   -3.18
2791 PHE   (  39-)  J   -3.17
1571 LEU   ( 182-)  B   -3.10
2937 LEU   (  63-)  L   -3.08
 220 LEU   (  94-)  2   -3.07
2582 GLN   (  27-)  G   -3.05
1418 HIS   (  29-)  B   -3.04
1698 PRO   ( 310-)  B   -3.03
2788 ALA   (  36-)  J   -3.01
1346 LEU   ( 714-)  A   -2.98
 703 HIS   (  62-)  A   -2.97
 722 ALA   (  81-)  A   -2.94
2049 MET   ( 662-)  B   -2.94
2074 LEU   ( 687-)  B   -2.94
 140 VAL   ( 163-)  1   -2.92
1693 LEU   ( 305-)  B   -2.90
2226 VAL   (  42-)  D   -2.90
2190 LEU   (  69-)  C   -2.87
2914 LEU   (  40-)  L   -2.87
 922 LEU   ( 281-)  A   -2.87
 123 LYS   ( 146-)  1   -2.86
And so on for a total of 83 lines.

Warning: Abnormal packing Z-score for sequential residues

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

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

   1 SER   (  17-)  1     -    4 GLY   (  20-)  1        -1.84
 118 GLU   ( 141-)  1     -  121 LYS   ( 144-)  1        -1.81
 138 PHE   ( 161-)  1     -  141 GLN   ( 164-)  1        -2.14
 173 ALA   (  47-)  2     -  176 VAL   (  50-)  2        -1.77
 361 ARG   (  63-)  3     -  364 MET   (  66-)  3        -1.96
 396 ASN   ( 105-)  3     -  401 SER   ( 110-)  3        -2.04
 422 ASP   ( 131-)  3     -  425 LYS   ( 134-)  3        -1.80
 501 PRO   (  34-)  4     -  504 LEU   (  37-)  4        -1.92
 524 GLY   (  57-)  4     -  527 LEU   (  60-)  4        -1.88
 537 ILE   (  70-)  4     -  540 PRO   (  73-)  4        -1.78
 614 GLU   ( 148-)  4     -  617 GLU   ( 151-)  4        -2.03
 672 PHE   (  31-)  A     -  675 TRP   (  34-)  A        -1.76
 701 ASP   (  60-)  A     -  704 ASP   (  63-)  A        -2.29
 841 GLU   ( 200-)  A     -  844 LEU   ( 203-)  A        -2.04
 889 PHE   ( 248-)  A     -  892 ASN   ( 251-)  A        -1.65
 977 GLY   ( 345-)  A     -  982 LEU   ( 350-)  A        -1.86
1001 THR   ( 369-)  A     - 1004 VAL   ( 372-)  A        -1.83
1051 VAL   ( 419-)  A     - 1054 TYR   ( 422-)  A        -1.84
1112 THR   ( 480-)  A     - 1117 GLN   ( 485-)  A        -1.86
1122 GLN   ( 490-)  A     - 1125 GLN   ( 493-)  A        -2.13
1604 VAL   ( 215-)  B     - 1607 TYR   ( 218-)  B        -1.94
1609 GLN   ( 220-)  B     - 1613 PRO   ( 224-)  B        -1.82
1648 GLY   ( 259-)  B     - 1651 HIS   ( 262-)  B        -2.06
1794 ASN   ( 406-)  B     - 1797 ALA   ( 409-)  B        -1.67
1845 PRO   ( 457-)  B     - 1848 ALA   ( 460-)  B        -1.29
1894 ASN   ( 506-)  B     - 1898 LEU   ( 510-)  B        -2.19
2020 ASN   ( 633-)  B     - 2023 THR   ( 636-)  B        -1.68
2127 LYS   (   6-)  C     - 2131 THR   (  10-)  C        -1.93
2187 ARG   (  66-)  C     - 2190 LEU   (  69-)  C        -2.01
2307 VAL   ( 123-)  D     - 2311 ARG   ( 127-)  D        -1.81
2427 LEU   (  22-)  F     - 2431 GLN   (  26-)  F        -1.83
2574 GLY   (  19-)  G     - 2577 VAL   (  22-)  G        -2.12
2579 PHE   (  24-)  G     - 2584 GLU   (  29-)  G        -1.90
2638 TYR   (  83-)  G     - 2641 LEU   (  86-)  G        -1.88
2958 GLY   (  84-)  L     - 2961 ALA   (  87-)  L        -1.85
3093 LYS   (  56-)  N     - 3096 PRO   (  59-)  N        -1.55
3101 ASP   (  64-)  N     - 3104 LEU   (  67-)  N        -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: 1

Note: Second generation quality Z-score plot

Chain identifier: 2

Note: Second generation quality Z-score plot

Chain identifier: 3

Note: Second generation quality Z-score plot

Chain identifier: 4

Note: Second generation quality Z-score plot

Chain identifier: 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: N

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.

 253 ASN   ( 127-)  2
 254 ASN   ( 128-)  2
 359 ASN   (  61-)  3
 514 ASN   (  47-)  4
 584 GLN   ( 117-)  4
 622 ASN   ( 156-)  4
 646 ASN   ( 180-)  4
 657 ASN   ( 191-)  4
 699 HIS   (  58-)  A
 752 ASN   ( 111-)  A
 770 GLN   ( 129-)  A
 989 GLN   ( 357-)  A
1024 GLN   ( 392-)  A
1030 HIS   ( 398-)  A
1106 GLN   ( 474-)  A
1174 HIS   ( 542-)  A
1273 ASN   ( 641-)  A
1292 GLN   ( 660-)  A
1333 GLN   ( 701-)  A
1344 ASN   ( 712-)  A
1353 GLN   ( 721-)  A
1423 HIS   (  34-)  B
1434 ASN   (  45-)  B
1504 ASN   ( 115-)  B
1582 HIS   ( 193-)  B
1620 ASN   ( 231-)  B
1665 HIS   ( 276-)  B
1715 ASN   ( 327-)  B
1716 ASN   ( 328-)  B
1721 GLN   ( 333-)  B
1762 HIS   ( 374-)  B
1763 HIS   ( 375-)  B
1764 GLN   ( 376-)  B
1794 ASN   ( 406-)  B
1892 ASN   ( 504-)  B
1916 HIS   ( 528-)  B
2041 HIS   ( 654-)  B
2297 HIS   ( 113-)  D
2361 ASN   (  48-)  E
2394 ASN   (  81-)  E
2715 ASN   (  71-)  H
2874 ASN   (  80-)  K
2913 ASN   (  39-)  L
3003 GLN   ( 129-)  L
3082 ASN   (  45-)  N

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.

   9 ASP   (  25-)  1      N
  18 ALA   (  34-)  1      N
  26 SER   (  42-)  1      N
  35 MET   (  51-)  1      N
  36 LEU   (  52-)  1      N
  41 ILE   (  57-)  1      N
  45 ALA   (  62-)  1      N
  68 TRP   (  91-)  1      N
  73 THR   (  96-)  1      N
  77 ILE   ( 100-)  1      N
  79 PHE   ( 102-)  1      N
  82 ILE   ( 105-)  1      N
  83 ALA   ( 106-)  1      N
  97 LYS   ( 120-)  1      N
  99 LYS   ( 122-)  1      N
 100 TYR   ( 123-)  1      N
 115 LYS   ( 138-)  1      N
 117 LEU   ( 140-)  1      N
 121 LYS   ( 144-)  1      NZ
 123 LYS   ( 146-)  1      N
 125 ILE   ( 148-)  1      N
 126 LYS   ( 149-)  1      N
 130 LEU   ( 153-)  1      N
 143 SER   ( 166-)  1      N
 172 GLN   (  46-)  2      N
And so on for a total of 884 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.

  86 GLU   ( 109-)  1      OE1
 106 ASP   ( 129-)  1      OD1
 224 GLU   (  98-)  2      OE1
 224 GLU   (  98-)  2      OE2
 408 GLU   ( 117-)  3      OE2
 566 HIS   (  99-)  4      ND1
 569 GLU   ( 102-)  4      OE1
 574 GLN   ( 107-)  4      OE1
 585 ASP   ( 118-)  4      OD1
 703 HIS   (  62-)  A      ND1
 726 GLN   (  85-)  A      OE1
 748 GLU   ( 107-)  A      OE1
 762 GLN   ( 121-)  A      OE1
 771 GLU   ( 130-)  A      OE2
 826 HIS   ( 185-)  A      NE2
 942 HIS   ( 301-)  A      NE2
 943 HIS   ( 302-)  A      ND1
 944 HIS   ( 303-)  A      ND1
 989 GLN   ( 357-)  A      OE1
 993 ASN   ( 361-)  A      OD1
1006 GLN   ( 374-)  A      OE1
1053 ASP   ( 421-)  A      OD2
1062 ASP   ( 430-)  A      OD1
1072 ASP   ( 440-)  A      OD1
1095 HIS   ( 463-)  A      NE2
And so on for a total of 77 lines.

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.

  21 GLU   (  37-)  1   H-bonding suggests Gln; Ligand-contact
  78 GLU   ( 101-)  1   H-bonding suggests Gln
 106 ASP   ( 129-)  1   H-bonding suggests Asn
 192 GLU   (  66-)  2   H-bonding suggests Gln
 212 GLU   (  86-)  2   H-bonding suggests Gln
 216 ASP   (  90-)  2   H-bonding suggests Asn
 238 ASP   ( 112-)  2   H-bonding suggests Asn; but Alt-Rotamer
 260 ASP   ( 134-)  2   H-bonding suggests Asn; but Alt-Rotamer
 325 ASP   ( 199-)  2   H-bonding suggests Asn
 341 GLU   (  43-)  3   H-bonding suggests Gln
 374 GLU   (  76-)  3   H-bonding suggests Gln
 499 GLU   (  32-)  4   H-bonding suggests Gln
 500 ASP   (  33-)  4   H-bonding suggests Asn; but Alt-Rotamer
 548 GLU   (  81-)  4   H-bonding suggests Gln
 549 GLU   (  82-)  4   H-bonding suggests Gln
 569 GLU   ( 102-)  4   H-bonding suggests Gln; Ligand-contact
 585 ASP   ( 118-)  4   H-bonding suggests Asn; but Alt-Rotamer
 701 ASP   (  60-)  A   H-bonding suggests Asn; but Alt-Rotamer
 711 ASP   (  70-)  A   H-bonding suggests Asn
 714 GLU   (  73-)  A   H-bonding suggests Gln; Ligand-contact
 776 ASP   ( 135-)  A   H-bonding suggests Asn
 802 GLU   ( 161-)  A   H-bonding suggests Gln; but Alt-Rotamer
 879 ASP   ( 238-)  A   H-bonding suggests Asn; but Alt-Rotamer
 939 ASP   ( 298-)  A   H-bonding suggests Asn; but Alt-Rotamer
1053 ASP   ( 421-)  A   H-bonding suggests Asn
And so on for a total of 70 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 :  -5.957 (poor)
  2nd generation packing quality :  -6.519 (bad)
  Ramachandran plot appearance   :  -7.839 (bad)
  chi-1/chi-2 rotamer normality  :  -7.777 (bad)
  Backbone conformation          :  -3.078 (poor)

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.908
  Bond angles                    :   1.129
  Omega angle restraints         :   2.899 (loose)
  Side chain planarity           :   0.632 (tight)
  Improper dihedral distribution :   1.397
  B-factor distribution          :   0.369
  Inside/Outside distribution    :   1.252 (unusual)

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 : 3.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -4.4 (bad)
  2nd generation packing quality :  -3.6 (poor)
  Ramachandran plot appearance   :  -4.5 (bad)
  chi-1/chi-2 rotamer normality  :  -5.1 (bad)
  Backbone conformation          :  -1.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.908
  Bond angles                    :   1.129
  Omega angle restraints         :   2.899 (loose)
  Side chain planarity           :   0.632 (tight)
  Improper dihedral distribution :   1.397
  B-factor distribution          :   0.369
  Inside/Outside distribution    :   1.252 (unusual)
==============

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.