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 pdb3h3w.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.

1624 HIS   ( 663-)  E  -
1625 HIS   ( 664-)  E  -

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

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 631 LEU   ( 646-)  B
3229 LEU   ( 646-)  J

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 VAL   ( 340-)  A    High
   2 THR   ( 341-)  A    High
   3 ALA   ( 342-)  A    High
   4 THR   ( 343-)  A    High
   5 ASP   ( 344-)  A    High
   6 TYR   ( 345-)  A    High
   7 ASP   ( 346-)  A    High
   8 THR   ( 347-)  A    High
   9 PHE   ( 348-)  A    High
  11 SER   ( 350-)  A    High
  12 GLU   ( 351-)  A    High
  13 ARG   ( 352-)  A    High
  14 PHE   ( 353-)  A    High
  15 GLY   ( 354-)  A    High
  16 SER   ( 355-)  A    High
  17 ILE   ( 356-)  A    High
  18 ILE   ( 357-)  A    High
  19 GLN   ( 358-)  A    High
  20 ALA   ( 359-)  A    High
  26 ASP   ( 365-)  A    High
  29 LYS   ( 368-)  A    High
  31 GLY   ( 370-)  A    High
  32 TYR   ( 371-)  A    High
  37 ALA   ( 376-)  A    High
  38 LYS   ( 377-)  A    High
And so on for a total of 1678 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

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Nomenclature related problems

Warning: Tyrosine convention problem

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

  32 TYR   ( 371-)  A
  56 TYR   ( 395-)  A
  60 TYR   ( 399-)  A
  74 TYR   ( 413-)  A
 128 TYR   ( 467-)  A
 197 TYR   ( 536-)  A
 251 TYR   ( 590-)  A
 285 TYR   ( 624-)  A
 311 TYR   ( 650-)  A
 356 TYR   ( 371-)  B
 398 TYR   ( 413-)  B
 433 TYR   ( 448-)  B
 452 TYR   ( 467-)  B
 521 TYR   ( 536-)  B
 574 TYR   ( 589-)  B
 582 TYR   ( 597-)  B
 588 TYR   ( 603-)  B
 609 TYR   ( 624-)  B
 635 TYR   ( 650-)  B
 682 TYR   ( 371-)  C
 706 TYR   ( 395-)  C
 710 TYR   ( 399-)  C
 724 TYR   ( 413-)  C
 778 TYR   ( 467-)  C
 847 TYR   ( 536-)  C
And so on for a total of 114 lines.

Warning: Phenylalanine convention problem

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

  14 PHE   ( 353-)  A
  24 PHE   ( 363-)  A
  34 PHE   ( 373-)  A
 120 PHE   ( 459-)  A
 176 PHE   ( 515-)  A
 277 PHE   ( 616-)  A
 303 PHE   ( 642-)  A
 338 PHE   ( 353-)  B
 348 PHE   ( 363-)  B
 440 PHE   ( 455-)  B
 500 PHE   ( 515-)  B
 543 PHE   ( 558-)  B
 562 PHE   ( 577-)  B
 618 PHE   ( 633-)  B
 627 PHE   ( 642-)  B
 664 PHE   ( 353-)  C
 674 PHE   ( 363-)  C
 684 PHE   ( 373-)  C
 770 PHE   ( 459-)  C
 826 PHE   ( 515-)  C
 927 PHE   ( 616-)  C
 953 PHE   ( 642-)  C
 988 PHE   ( 353-)  D
 998 PHE   ( 363-)  D
1088 PHE   ( 455-)  D
And so on for a total of 90 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.

 106 ASP   ( 445-)  A
 131 ASP   ( 470-)  A
 194 ASP   ( 533-)  A
 205 ASP   ( 544-)  A
 223 ASP   ( 562-)  A
 248 ASP   ( 587-)  A
 261 ASP   ( 600-)  A
 287 ASP   ( 626-)  A
 297 ASP   ( 636-)  A
 383 ASP   ( 398-)  B
 430 ASP   ( 445-)  B
 455 ASP   ( 470-)  B
 529 ASP   ( 544-)  B
 572 ASP   ( 587-)  B
 611 ASP   ( 626-)  B
 621 ASP   ( 636-)  B
 756 ASP   ( 445-)  C
 781 ASP   ( 470-)  C
 844 ASP   ( 533-)  C
 855 ASP   ( 544-)  C
 873 ASP   ( 562-)  C
 898 ASP   ( 587-)  C
 911 ASP   ( 600-)  C
 937 ASP   ( 626-)  C
 947 ASP   ( 636-)  C
And so on for a total of 95 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.

 172 GLU   ( 511-)  A
 192 GLU   ( 531-)  A
 255 GLU   ( 594-)  A
 283 GLU   ( 622-)  A
 304 GLU   ( 643-)  A
 317 GLU   ( 656-)  A
 496 GLU   ( 511-)  B
 579 GLU   ( 594-)  B
 599 GLU   ( 614-)  B
 607 GLU   ( 622-)  B
 628 GLU   ( 643-)  B
 641 GLU   ( 656-)  B
 647 GLU   ( 662-)  B
 822 GLU   ( 511-)  C
 842 GLU   ( 531-)  C
 905 GLU   ( 594-)  C
 933 GLU   ( 622-)  C
 954 GLU   ( 643-)  C
 967 GLU   ( 656-)  C
1144 GLU   ( 511-)  D
1227 GLU   ( 594-)  D
1247 GLU   ( 614-)  D
1255 GLU   ( 622-)  D
1276 GLU   ( 643-)  D
1289 GLU   ( 656-)  D
And so on for a total of 78 lines.

Geometric checks

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

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

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

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  48 VAL   ( 387-)  A     -C    N    CA  129.31    4.2
  92 GLU   ( 431-)  A      C    CA   CB  101.26   -4.7
 117 ASN   ( 456-)  A      C    CA   CB   92.97   -9.0
 118 SER   ( 457-)  A      N    CA   C    94.57   -5.9
 118 SER   ( 457-)  A      N    CA   CB  124.93    8.5
 136 VAL   ( 475-)  A     -C    N    CA  130.02    4.6
 136 VAL   ( 475-)  A      N    CA   C   124.35    4.7
 187 PRO   ( 526-)  A     -C    N    CD  107.61   -4.2
 189 THR   ( 528-)  A     -C    N    CA  106.36   -8.5
 249 LYS   ( 588-)  A      N    CA   C    97.95   -4.7
 295 THR   ( 634-)  A      N    CA   C    99.19   -4.3
 306 ASP   ( 645-)  A      C    CA   CB  126.16    8.5
 307 LEU   ( 646-)  A      N    CA   CB   89.47  -12.4
 323 GLU   ( 662-)  A     -C    N    CA  109.92   -6.5
 324 HIS   ( 663-)  A      CG   ND1  CE1 109.61    4.0
 332 THR   ( 347-)  B      C    CA   CB  102.35   -4.1
 351 SER   ( 366-)  B     -C    N    CA  113.97   -4.3
 351 SER   ( 366-)  B      N    CA   C    97.79   -4.8
 352 THR   ( 367-)  B      C    CA   CB   97.13   -6.8
 383 ASP   ( 398-)  B      C    CA   CB  126.34    8.5
 386 LEU   ( 401-)  B      C    CA   CB  119.49    4.9
 388 PRO   ( 403-)  B      C    CA   CB  117.96    4.1
 391 PRO   ( 406-)  B     -O   -C    N   127.62    4.0
 391 PRO   ( 406-)  B     -C    N    CD   56.81  -16.6
 392 SER   ( 407-)  B      N    CA   C    98.12   -4.7
And so on for a total of 252 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.

 106 ASP   ( 445-)  A
 131 ASP   ( 470-)  A
 172 GLU   ( 511-)  A
 192 GLU   ( 531-)  A
 194 ASP   ( 533-)  A
 205 ASP   ( 544-)  A
 223 ASP   ( 562-)  A
 248 ASP   ( 587-)  A
 255 GLU   ( 594-)  A
 261 ASP   ( 600-)  A
 283 GLU   ( 622-)  A
 287 ASP   ( 626-)  A
 297 ASP   ( 636-)  A
 304 GLU   ( 643-)  A
 317 GLU   ( 656-)  A
 383 ASP   ( 398-)  B
 430 ASP   ( 445-)  B
 455 ASP   ( 470-)  B
 496 GLU   ( 511-)  B
 529 ASP   ( 544-)  B
 572 ASP   ( 587-)  B
 579 GLU   ( 594-)  B
 599 GLU   ( 614-)  B
 607 GLU   ( 622-)  B
 611 ASP   ( 626-)  B
And so on for a total of 173 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.

 187 PRO   ( 526-)  A      N     12.2    37.38    -2.48
 306 ASP   ( 645-)  A      CA   -12.1     9.60    33.73
 307 LEU   ( 646-)  A      CA     8.7    47.51    34.19
 352 THR   ( 367-)  B      CA     7.0    45.59    33.84
 354 PRO   ( 369-)  B      N      7.8    23.12    -2.48
 391 PRO   ( 406-)  B      N     25.0    79.54    -2.48
 459 SER   ( 474-)  B      CA     6.2    45.79    34.32
 519 VAL   ( 534-)  B      CA    11.5    49.90    33.23
 533 LYS   ( 548-)  B      CA    -7.9    20.80    33.92
 837 PRO   ( 526-)  C      N     12.2    37.38    -2.48
 956 ASP   ( 645-)  C      CA   -12.1     9.57    33.73
 957 LEU   ( 646-)  C      CA     8.7    47.49    34.19
1002 THR   ( 367-)  D      CA     7.0    45.58    33.84
1004 PRO   ( 369-)  D      N      7.8    23.02    -2.48
1039 PRO   ( 406-)  D      N     25.0    79.51    -2.48
1107 SER   ( 474-)  D      CA     6.2    45.79    34.32
1167 VAL   ( 534-)  D      CA    11.5    49.90    33.23
1181 LYS   ( 548-)  D      CA    -7.8    20.89    33.92
1485 PRO   ( 526-)  E      N     12.1    37.28    -2.48
1604 ASP   ( 645-)  E      CA   -12.1     9.59    33.73
1605 LEU   ( 646-)  E      CA     8.7    47.52    34.19
1650 THR   ( 367-)  F      CA     7.0    45.57    33.84
1652 PRO   ( 369-)  F      N      7.8    23.03    -2.48
1689 PRO   ( 406-)  F      N     25.0    79.51    -2.48
1757 SER   ( 474-)  F      CA     6.2    45.79    34.32
And so on for a total of 54 lines.

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 533 LYS   ( 548-)  B   10.23
1181 LYS   ( 548-)  D   10.22
3781 LYS   ( 548-)  L   10.21
1831 LYS   ( 548-)  F   10.20
2481 LYS   ( 548-)  H   10.20
3131 LYS   ( 548-)  J   10.20
1416 SER   ( 457-)  E    6.53
2066 SER   ( 457-)  G    6.51
 768 SER   ( 457-)  C    6.51
3366 SER   ( 457-)  K    6.51
 118 SER   ( 457-)  A    6.50
2716 SER   ( 457-)  I    6.50
3130 SER   ( 547-)  J    6.43
3780 SER   ( 547-)  L    6.42
1180 SER   ( 547-)  D    6.41
1830 SER   ( 547-)  F    6.41
2480 SER   ( 547-)  H    6.41
 532 SER   ( 547-)  B    6.41
1434 VAL   ( 475-)  E    5.54
 786 VAL   ( 475-)  C    5.54
3384 VAL   ( 475-)  K    5.53
2734 VAL   ( 475-)  I    5.53
 136 VAL   ( 475-)  A    5.53
2084 VAL   ( 475-)  G    5.51
1001 SER   ( 366-)  D    5.28
And so on for a total of 84 lines.

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.510

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.378

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.

3294 THR   ( 385-)  K    -3.4
  46 THR   ( 385-)  A    -3.4
1994 THR   ( 385-)  G    -3.4
2644 THR   ( 385-)  I    -3.4
1344 THR   ( 385-)  E    -3.4
 696 THR   ( 385-)  C    -3.4
2923 HIS   ( 664-)  I    -3.2
 975 HIS   ( 664-)  C    -3.2
 325 HIS   ( 664-)  A    -3.2
1623 HIS   ( 664-)  E    -3.2
2273 HIS   ( 664-)  G    -3.2
3573 HIS   ( 664-)  K    -3.2
 837 PRO   ( 526-)  C    -3.1
2785 PRO   ( 526-)  I    -3.1
 187 PRO   ( 526-)  A    -3.1
3435 PRO   ( 526-)  K    -3.1
2135 PRO   ( 526-)  G    -3.1
1485 PRO   ( 526-)  E    -3.1
3642 ILE   ( 409-)  L    -2.8
2342 ILE   ( 409-)  H    -2.8
 394 ILE   ( 409-)  B    -2.8
1042 ILE   ( 409-)  D    -2.8
1692 ILE   ( 409-)  F    -2.8
2992 ILE   ( 409-)  J    -2.8
2244 ARG   ( 635-)  G    -2.8
And so on for a total of 402 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 THR   ( 341-)  A  Poor phi/psi
   9 PHE   ( 348-)  A  Poor phi/psi
  14 PHE   ( 353-)  A  Poor phi/psi
  15 GLY   ( 354-)  A  Poor phi/psi
  40 LYS   ( 379-)  A  Poor phi/psi
  49 GLN   ( 388-)  A  Poor phi/psi
  50 ARG   ( 389-)  A  Poor phi/psi
  51 GLU   ( 390-)  A  Poor phi/psi
  53 ILE   ( 392-)  A  Poor phi/psi
  58 LYS   ( 397-)  A  Poor phi/psi
  61 ASN   ( 400-)  A  Poor phi/psi
  63 ALA   ( 402-)  A  Poor phi/psi
 135 SER   ( 474-)  A  Poor phi/psi, omega poor
 163 ASN   ( 502-)  A  Poor phi/psi
 169 ARG   ( 508-)  A  Poor phi/psi
 192 GLU   ( 531-)  A  Poor phi/psi
 193 GLU   ( 532-)  A  Poor phi/psi
 210 GLY   ( 549-)  A  omega poor
 217 GLY   ( 556-)  A  PRO omega poor
 221 SER   ( 560-)  A  omega poor
 227 ASN   ( 566-)  A  Poor phi/psi
 237 ASP   ( 576-)  A  Poor phi/psi
 238 PHE   ( 577-)  A  Poor phi/psi
 248 ASP   ( 587-)  A  Poor phi/psi
 256 ILE   ( 595-)  A  omega poor
And so on for a total of 469 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 : -5.629

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!

  13 ARG   ( 352-)  A      0
  14 PHE   ( 353-)  A      0
  16 SER   ( 355-)  A      0
  17 ILE   ( 356-)  A      0
  19 GLN   ( 358-)  A      0
  29 LYS   ( 368-)  A      0
  30 PRO   ( 369-)  A      0
  40 LYS   ( 379-)  A      0
  41 SER   ( 380-)  A      0
  43 LEU   ( 382-)  A      0
  45 LEU   ( 384-)  A      0
  46 THR   ( 385-)  A      0
  47 THR   ( 386-)  A      0
  48 VAL   ( 387-)  A      0
  49 GLN   ( 388-)  A      0
  50 ARG   ( 389-)  A      0
  51 GLU   ( 390-)  A      0
  52 ASP   ( 391-)  A      0
  58 LYS   ( 397-)  A      0
  59 ASP   ( 398-)  A      0
  61 ASN   ( 400-)  A      0
  62 LEU   ( 401-)  A      0
  63 ALA   ( 402-)  A      0
  64 PRO   ( 403-)  A      0
  68 SER   ( 407-)  A      0
And so on for a total of 1827 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

2129 GLY   ( 520-)  G   1.94   34
 181 GLY   ( 520-)  A   1.94   34
3429 GLY   ( 520-)  K   1.94   34
1479 GLY   ( 520-)  E   1.94   34
2779 GLY   ( 520-)  I   1.94   34
 831 GLY   ( 520-)  C   1.94   34
3614 GLY   ( 381-)  L   1.68   19
2314 GLY   ( 381-)  H   1.68   19
1664 GLY   ( 381-)  F   1.68   19
 366 GLY   ( 381-)  B   1.68   19
2964 GLY   ( 381-)  J   1.63   18
1016 GLY   ( 381-)  D   1.63   18

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].

 187 PRO   ( 526-)  A   154.7 half-chair C-alpha/N (162 degrees)
 218 PRO   ( 557-)  A    44.7 envelop C-delta (36 degrees)
 232 PRO   ( 571-)  A    44.0 envelop C-delta (36 degrees)
 309 PRO   ( 648-)  A    47.8 half-chair C-delta/C-gamma (54 degrees)
 318 PRO   ( 657-)  A    49.8 half-chair C-delta/C-gamma (54 degrees)
 354 PRO   ( 369-)  B   -13.2 half-chair C-alpha/N (-18 degrees)
 363 PRO   ( 378-)  B   100.3 envelop C-beta (108 degrees)
 391 PRO   ( 406-)  B    -1.3 envelop N (0 degrees)
 633 PRO   ( 648-)  B    30.2 envelop C-delta (36 degrees)
 837 PRO   ( 526-)  C   154.7 half-chair C-alpha/N (162 degrees)
 868 PRO   ( 557-)  C    44.7 envelop C-delta (36 degrees)
 882 PRO   ( 571-)  C    44.1 envelop C-delta (36 degrees)
 959 PRO   ( 648-)  C    47.8 half-chair C-delta/C-gamma (54 degrees)
 968 PRO   ( 657-)  C    49.7 half-chair C-delta/C-gamma (54 degrees)
1004 PRO   ( 369-)  D   -13.2 half-chair C-alpha/N (-18 degrees)
1013 PRO   ( 378-)  D   100.3 envelop C-beta (108 degrees)
1039 PRO   ( 406-)  D    -1.4 envelop N (0 degrees)
1281 PRO   ( 648-)  D    30.3 envelop C-delta (36 degrees)
1485 PRO   ( 526-)  E   154.6 half-chair C-alpha/N (162 degrees)
1516 PRO   ( 557-)  E    44.6 envelop C-delta (36 degrees)
1530 PRO   ( 571-)  E    44.1 envelop C-delta (36 degrees)
1607 PRO   ( 648-)  E    47.8 half-chair C-delta/C-gamma (54 degrees)
1616 PRO   ( 657-)  E    49.7 half-chair C-delta/C-gamma (54 degrees)
1652 PRO   ( 369-)  F   -13.2 half-chair C-alpha/N (-18 degrees)
1661 PRO   ( 378-)  F   100.4 envelop C-beta (108 degrees)
And so on for a total of 54 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.

1957 PHE   ( 348-)  G      CZ   <->  2923 HIS   ( 664-)  I      NE2  1.62    1.48  INTRA BF
 325 HIS   ( 664-)  A      CE1  <->  3309 ASN   ( 400-)  K      ND2  1.62    1.48  INTRA BF
1359 ASN   ( 400-)  E      ND2  <->  2273 HIS   ( 664-)  G      CE1  1.61    1.49  INTRA BF
  50 ARG   ( 389-)  A      O    <->    52 ASP   ( 391-)  A      N    1.61    1.09  INTRA BF
1998 ARG   ( 389-)  G      O    <->  2000 ASP   ( 391-)  G      N    1.61    1.09  INTRA BF
1348 ARG   ( 389-)  E      O    <->  1350 ASP   ( 391-)  E      N    1.61    1.09  INTRA BF
3298 ARG   ( 389-)  K      O    <->  3300 ASP   ( 391-)  K      N    1.61    1.09  INTRA BF
 700 ARG   ( 389-)  C      O    <->   702 ASP   ( 391-)  C      N    1.61    1.09  INTRA BF
2648 ARG   ( 389-)  I      O    <->  2650 ASP   ( 391-)  I      N    1.61    1.09  INTRA BF
2010 LEU   ( 401-)  G      CD1  <->  2947 THR   ( 364-)  J      CG2  1.59    1.61  INTRA BF
2012 PRO   ( 403-)  G      CB   <->  2949 SER   ( 366-)  J      CB   1.55    1.65  INTRA BF
2607 PHE   ( 348-)  I      CZ   <->  3573 HIS   ( 664-)  K      NE2  1.54    1.56  INTRA BF
2662 PRO   ( 403-)  I      CB   <->  3599 SER   ( 366-)  L      CB   1.54    1.66  INTRA BF
2660 LEU   ( 401-)  I      CD1  <->  3597 THR   ( 364-)  L      CG2  1.52    1.68  INTRA BF
2009 ASN   ( 400-)  G      ND2  <->  2923 HIS   ( 664-)  I      CE1  1.50    1.60  INTRA BF
2716 SER   ( 457-)  I      O    <->  2893 THR   ( 634-)  I      CG2  1.49    1.31  INTRA BL
1416 SER   ( 457-)  E      O    <->  1593 THR   ( 634-)  E      CG2  1.49    1.31  INTRA BL
 768 SER   ( 457-)  C      O    <->   945 THR   ( 634-)  C      CG2  1.49    1.31  INTRA BL
2066 SER   ( 457-)  G      O    <->  2243 THR   ( 634-)  G      CG2  1.49    1.31  INTRA BL
 118 SER   ( 457-)  A      O    <->   295 THR   ( 634-)  A      CG2  1.49    1.31  INTRA BL
3366 SER   ( 457-)  K      O    <->  3543 THR   ( 634-)  K      CG2  1.49    1.31  INTRA BL
2009 ASN   ( 400-)  G      ND2  <->  2923 HIS   ( 664-)  I      ND1  1.45    1.55  INTRA BF
1307 PHE   ( 348-)  E      CZ   <->  2273 HIS   ( 664-)  G      NE2  1.42    1.68  INTRA BF
1360 LEU   ( 401-)  E      CD1  <->  2297 THR   ( 364-)  H      CG2  1.42    1.78  INTRA BF
2659 ASN   ( 400-)  I      ND2  <->  3573 HIS   ( 664-)  K      CE1  1.41    1.69  INTRA BF
And so on for a total of 2663 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

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.

  60 TYR   ( 399-)  A      -7.30
2658 TYR   ( 399-)  I      -7.30
1358 TYR   ( 399-)  E      -7.30
2008 TYR   ( 399-)  G      -7.26
3308 TYR   ( 399-)  K      -7.25
 710 TYR   ( 399-)  C      -7.21
 712 LEU   ( 401-)  C      -7.07
1293 GLN   ( 660-)  D      -6.98
2593 GLN   ( 660-)  H      -6.96
3893 GLN   ( 660-)  L      -6.96
1943 GLN   ( 660-)  F      -6.96
 645 GLN   ( 660-)  B      -6.96
3243 GLN   ( 660-)  J      -6.96
  62 LEU   ( 401-)  A      -6.24
3310 LEU   ( 401-)  K      -6.20
1360 LEU   ( 401-)  E      -6.19
2660 LEU   ( 401-)  I      -6.08
2010 LEU   ( 401-)  G      -6.06
1687 ILE   ( 404-)  F      -6.04
2987 ILE   ( 404-)  J      -6.03
1037 ILE   ( 404-)  D      -6.02
 389 ILE   ( 404-)  B      -6.02
3637 ILE   ( 404-)  L      -6.02
2337 ILE   ( 404-)  H      -6.02
2363 GLN   ( 430-)  H      -5.88
And so on for a total of 150 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.

  60 TYR   ( 399-)  A        62 - LEU    401- ( A)         -5.94
 321 GLN   ( 660-)  A       325 - HIS    664- ( A)         -5.09
 645 GLN   ( 660-)  B       649 - HIS    664- ( B)         -5.11
 710 TYR   ( 399-)  C       712 - LEU    401- ( C)         -6.18
 971 GLN   ( 660-)  C       975 - HIS    664- ( C)         -5.22
1293 GLN   ( 660-)  D      1297 - HIS    664- ( D)         -5.11
1358 TYR   ( 399-)  E      1360 - LEU    401- ( E)         -5.85
1943 GLN   ( 660-)  F      1947 - HIS    664- ( F)         -5.09
2008 TYR   ( 399-)  G      2010 - LEU    401- ( G)         -5.77
2269 GLN   ( 660-)  G      2273 - HIS    664- ( G)         -5.10
2593 GLN   ( 660-)  H      2597 - HIS    664- ( H)         -5.09
2658 TYR   ( 399-)  I      2660 - LEU    401- ( I)         -5.80
2919 GLN   ( 660-)  I      2923 - HIS    664- ( I)         -5.06
3243 GLN   ( 660-)  J      3247 - HIS    664- ( J)         -5.10
3308 TYR   ( 399-)  K      3310 - LEU    401- ( K)         -5.83
3569 GLN   ( 660-)  K      3573 - HIS    664- ( K)         -5.06
3893 GLN   ( 660-)  L      3897 - HIS    664- ( L)         -5.10

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

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.

 325 HIS   ( 664-)  A   -2.55
2273 HIS   ( 664-)  G   -2.54
 456 ALA   ( 471-)  B   -2.52
3054 ALA   ( 471-)  J   -2.51
1754 ALA   ( 471-)  F   -2.51
1104 ALA   ( 471-)  D   -2.51
3704 ALA   ( 471-)  L   -2.51
2404 ALA   ( 471-)  H   -2.51

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

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.

 321 GLN   ( 660-)  A
 441 ASN   ( 456-)  B
 498 ASN   ( 513-)  B
 581 ASN   ( 596-)  B
 648 HIS   ( 663-)  B
 971 GLN   ( 660-)  C
1089 ASN   ( 456-)  D
1146 ASN   ( 513-)  D
1229 ASN   ( 596-)  D
1296 HIS   ( 663-)  D
1619 GLN   ( 660-)  E
1739 ASN   ( 456-)  F
1796 ASN   ( 513-)  F
1879 ASN   ( 596-)  F
1946 HIS   ( 663-)  F
2269 GLN   ( 660-)  G
2389 ASN   ( 456-)  H
2446 ASN   ( 513-)  H
2529 ASN   ( 596-)  H
2596 HIS   ( 663-)  H
2597 HIS   ( 664-)  H
2919 GLN   ( 660-)  I
3039 ASN   ( 456-)  J
3096 ASN   ( 513-)  J
3179 ASN   ( 596-)  J
3246 HIS   ( 663-)  J
3569 GLN   ( 660-)  K
3689 ASN   ( 456-)  L
3746 ASN   ( 513-)  L
3829 ASN   ( 596-)  L
3896 HIS   ( 663-)  L

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.

  16 SER   ( 355-)  A      N
  18 ILE   ( 357-)  A      N
  26 ASP   ( 365-)  A      N
  28 THR   ( 367-)  A      N
  40 LYS   ( 379-)  A      N
  41 SER   ( 380-)  A      N
  46 THR   ( 385-)  A      OG1
  48 VAL   ( 387-)  A      N
  49 GLN   ( 388-)  A      N
  53 ILE   ( 392-)  A      N
  57 LEU   ( 396-)  A      N
  65 ILE   ( 404-)  A      N
  83 VAL   ( 422-)  A      N
  92 GLU   ( 431-)  A      N
  96 TRP   ( 435-)  A      N
 103 ASP   ( 442-)  A      N
 135 SER   ( 474-)  A      N
 135 SER   ( 474-)  A      OG
 136 VAL   ( 475-)  A      N
 142 THR   ( 481-)  A      N
 153 TYR   ( 492-)  A      N
 158 ALA   ( 497-)  A      N
 183 LYS   ( 522-)  A      N
 206 ARG   ( 545-)  A      N
 209 LYS   ( 548-)  A      N
And so on for a total of 512 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.

 130 ASP   ( 469-)  A      OD2
 133 ASP   ( 472-)  A      OD2
 179 ASN   ( 518-)  A      OD1
 503 ASN   ( 518-)  B      OD1
 547 ASP   ( 562-)  B      OD2
 567 ASN   ( 582-)  B      OD1
 780 ASP   ( 469-)  C      OD2
 829 ASN   ( 518-)  C      OD1
1151 ASN   ( 518-)  D      OD1
1195 ASP   ( 562-)  D      OD2
1215 ASN   ( 582-)  D      OD1
1428 ASP   ( 469-)  E      OD2
1431 ASP   ( 472-)  E      OD2
1477 ASN   ( 518-)  E      OD1
1801 ASN   ( 518-)  F      OD1
1845 ASP   ( 562-)  F      OD2
2078 ASP   ( 469-)  G      OD2
2127 ASN   ( 518-)  G      OD1
2451 ASN   ( 518-)  H      OD1
2495 ASP   ( 562-)  H      OD2
2728 ASP   ( 469-)  I      OD2
2731 ASP   ( 472-)  I      OD2
2777 ASN   ( 518-)  I      OD1
3101 ASN   ( 518-)  J      OD1
3145 ASP   ( 562-)  J      OD2
3165 ASN   ( 582-)  J      OD1
3378 ASP   ( 469-)  K      OD2
3427 ASN   ( 518-)  K      OD1
3751 ASN   ( 518-)  L      OD1
3795 ASP   ( 562-)  L      OD2

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.

   7 ASP   ( 346-)  A   H-bonding suggests Asn; but Alt-Rotamer
  52 ASP   ( 391-)  A   H-bonding suggests Asn
  59 ASP   ( 398-)  A   H-bonding suggests Asn; but Alt-Rotamer
 103 ASP   ( 442-)  A   H-bonding suggests Asn
 112 ASP   ( 451-)  A   H-bonding suggests Asn
 114 GLU   ( 453-)  A   H-bonding suggests Gln
 133 ASP   ( 472-)  A   H-bonding suggests Asn
 193 GLU   ( 532-)  A   H-bonding suggests Gln
 207 ASP   ( 546-)  A   H-bonding suggests Asn; but Alt-Rotamer
 290 ASP   ( 629-)  A   H-bonding suggests Asn; but Alt-Rotamer
 323 GLU   ( 662-)  A   H-bonding suggests Gln; but Alt-Rotamer
 331 ASP   ( 346-)  B   H-bonding suggests Asn
 376 ASP   ( 391-)  B   H-bonding suggests Asn
 430 ASP   ( 445-)  B   H-bonding suggests Asn
 436 ASP   ( 451-)  B   H-bonding suggests Asn; but Alt-Rotamer
 438 GLU   ( 453-)  B   H-bonding suggests Gln
 531 ASP   ( 546-)  B   H-bonding suggests Asn; but Alt-Rotamer
 550 GLU   ( 565-)  B   H-bonding suggests Gln; but Alt-Rotamer
 641 GLU   ( 656-)  B   H-bonding suggests Gln
 657 ASP   ( 346-)  C   H-bonding suggests Asn; but Alt-Rotamer
 702 ASP   ( 391-)  C   H-bonding suggests Asn
 709 ASP   ( 398-)  C   H-bonding suggests Asn; but Alt-Rotamer
 753 ASP   ( 442-)  C   H-bonding suggests Asn
 762 ASP   ( 451-)  C   H-bonding suggests Asn
 764 GLU   ( 453-)  C   H-bonding suggests Gln
And so on for a total of 114 lines.

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.886
  2nd generation packing quality :  -2.658
  Ramachandran plot appearance   :  -4.378 (bad)
  chi-1/chi-2 rotamer normality  :  -5.629 (bad)
  Backbone conformation          :  -1.160

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.462 (tight)
  Bond angles                    :   0.802
  Omega angle restraints         :   1.217
  Side chain planarity           :   0.314 (tight)
  Improper dihedral distribution :   1.201
  B-factor distribution          :   1.196
  Inside/Outside distribution    :   1.020

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 : 12.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -2.2
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.462 (tight)
  Bond angles                    :   0.802
  Omega angle restraints         :   1.217
  Side chain planarity           :   0.314 (tight)
  Improper dihedral distribution :   1.201
  B-factor distribution          :   1.196
  Inside/Outside distribution    :   1.020
==============

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.