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 pdb3gw6.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

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

1532 PEG   (   2-)  A  -
1533 PEG   (  17-)  A  -
1534 TAM   (  32-)  A  -
1535 TAM   (  35-)  A  -
1538 PEG   (  13-)  B  -
1541 PEG   (   6-)  E  -
1542 PEG   (  16-)  E  -
1543 PEG   (  18-)  D  -
1544 PEG   (  21-)  E  -
1545 PEG   (  22-)  E  -
1546 PEG   (  27-)  E  -
1547 PEG   (  33-)  E  -
1550 PEG   (   3-)  C  -
1554 PEG   (  14-)  C  -
1555 PEG   (  29-)  C  -
1557 PEG   (  15-)  D  -
1560 PEG   (   5-)  F  -
1561 PEG   (  24-)  F  -
1562 PEG   (  30-)  F  -
1564 PEG   (  34-)  F  -
1565 TAM   (  28-)  C  -

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

   1 HIS   ( 800-)  A  -   CG
   1 HIS   ( 800-)  A  -   CE1
   7 ARG   ( 812-)  A  -   CZ
 119 ASP   ( 924-)  A  -   CG
 168 ASP   ( 973-)  A  -   CG
 169 GLU   ( 974-)  A  -   CD
 172 CYS   ( 979-)  A  -   CB
 173 ARG   ( 980-)  A  -   CZ
 184 ARG   ( 991-)  A  -   NH2
 210 GLU   (1017-)  A  -   CD
 215 GLU   (1022-)  A  -   CD
 221 GLU   (1028-)  A  -   CD
 245 GLU   (1052-)  A  -   CD
 257 HIS   ( 800-)  B  -   CG
 367 ARG   ( 915-)  B  -   CZ
 375 ASP   ( 923-)  B  -   CG
 380 ASP   ( 928-)  B  -   CG
 412 ARG   ( 963-)  B  -   CZ
 413 ASP   ( 964-)  B  -   CG
 423 GLU   ( 974-)  B  -   CG
 423 GLU   ( 974-)  B  -   CD
 426 ASN   ( 978-)  B  -   CG
 428 ARG   ( 980-)  B  -   CZ
 456 GLU   (1008-)  B  -   CB
 456 GLU   (1008-)  B  -   CD
And so on for a total of 98 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 168 ASP   ( 973-)  A  -   C
 202 GLU   (1009-)  A  -   O
 251 LEU   (1058-)  A  -   C
 417 ALA   ( 968-)  B  -   C
 421 MET   ( 972-)  B  -   C
 460 VAL   (1012-)  B  -   CA
 464 GLU   (1016-)  B  -   O
 506 LEU   (1058-)  B  -   C
 510 GLU   (1062-)  B  -   C
 618 ALA   ( 911-)  E  -   C
 627 VAL   ( 920-)  E  -   O
 674 ILE   ( 967-)  E  -   C
 706 GLU   (1001-)  E  -   CA
 709 GLU   (1004-)  E  -   CA
 767 GLU   (1062-)  E  -   C
1020 LEU   (1061-)  C  -   C
1020 LEU   (1061-)  C  -   O
1021 GLU   (1062-)  C  -   C
1022 GLN   (1063-)  C  -   C
1162 GLN   ( 945-)  D  -   CA
1177 GLN   ( 960-)  D  -   C
1180 ARG   ( 963-)  D  -   C
1183 PHE   ( 966-)  D  -   C
1184 ILE   ( 967-)  D  -   C
1214 ILE   (1002-)  D  -   CA
1217 HIS   (1005-)  D  -   C
1222 GLY   (1010-)  D  -   CA
1222 GLY   (1010-)  D  -   C
1264 GLU   (1052-)  D  -   C
1267 GLU   (1055-)  D  -   C
1268 ALA   (1056-)  D  -   C
1413 VAL   ( 944-)  F  -   CA
1415 LEU   ( 946-)  F  -   O
1419 ASP   ( 950-)  F  -   C
1444 SER   ( 976-)  F  -   O
1473 HIS   (1005-)  F  -   C
1482 THR   (1014-)  F  -   C
1530 GLU   (1062-)  F  -   C

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: E

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: F

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

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.

 169 GLU   ( 974-)  A    High
 170 ASN   ( 975-)  A    High
 172 CYS   ( 979-)  A    High
 248 GLU   (1055-)  A    High
 255 GLU   (1062-)  A    High
 257 HIS   ( 800-)  B    High
 422 ASP   ( 973-)  B    High
 424 SER   ( 976-)  B    High
 425 THR   ( 977-)  B    High
 426 ASN   ( 978-)  B    High
 427 CYS   ( 979-)  B    High
 458 GLY   (1010-)  B    High
 459 ASN   (1011-)  B    High
 500 GLU   (1052-)  B    High
 505 ARG   (1057-)  B    High
 508 ALA   (1060-)  B    High
 509 LEU   (1061-)  B    High
 511 GLN   (1063-)  B    High
 627 VAL   ( 920-)  E    High
 631 ASP   ( 924-)  E    High
 674 ILE   ( 967-)  E    High
 681 GLU   ( 974-)  E    High
 707 ILE   (1002-)  E    High
 719 THR   (1014-)  E    High
 762 ARG   (1057-)  E    High
And so on for a total of 52 lines.

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

   1 HIS   ( 800-)  A    0.68
   5 ARG   ( 804-)  A    0.08
  26 ASP   ( 831-)  A    0.71
 145 ASP   ( 950-)  A    0.80
 147 ARG   ( 952-)  A    0.82
 167 MET   ( 972-)  A    0.81
 168 ASP   ( 973-)  A    0.59
 169 GLU   ( 974-)  A    0.84
 170 ASN   ( 975-)  A    0.76
 172 CYS   ( 979-)  A    0.86
 173 ARG   ( 980-)  A    0.37
 184 ARG   ( 991-)  A    0.67
 191 SER   ( 998-)  A    0.81
 194 GLU   (1001-)  A    0.59
 202 GLU   (1009-)  A    0.18
 203 GLY   (1010-)  A    0.42
 204 ASN   (1011-)  A    0.40
 205 VAL   (1012-)  A    0.81
 207 THR   (1014-)  A    0.63
 208 THR   (1015-)  A    0.53
 209 GLU   (1016-)  A    0.62
 210 GLU   (1017-)  A    0.89
 215 GLU   (1022-)  A    0.71
 221 GLU   (1028-)  A    0.44
 243 LYS   (1050-)  A    0.33
And so on for a total of 277 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. 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: 1

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 2.621 over 10585 bonds
Average difference in B over a bond : 2.66
RMS difference in B over a bond : 10.22

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: E

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: F

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.

   7 ARG   ( 812-)  A
 147 ARG   ( 952-)  A
 242 ARG   (1049-)  A
 250 ARG   (1057-)  A
 264 ARG   ( 812-)  B
 497 ARG   (1049-)  B
 519 ARG   ( 812-)  E
 754 ARG   (1049-)  E
 762 ARG   (1057-)  E
 776 ARG   ( 812-)  C
1008 ARG   (1049-)  C
1029 ARG   ( 812-)  D
1261 ARG   (1049-)  D
1281 ARG   ( 812-)  F
1517 ARG   (1049-)  F

Warning: Tyrosine convention problem

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

  16 TYR   ( 821-)  A
  52 TYR   ( 857-)  A
  64 TYR   ( 869-)  A
  79 TYR   ( 884-)  A
  97 TYR   ( 902-)  A
 133 TYR   ( 938-)  A
 174 TYR   ( 981-)  A
 182 TYR   ( 989-)  A
 213 TYR   (1020-)  A
 309 TYR   ( 857-)  B
 321 TYR   ( 869-)  B
 336 TYR   ( 884-)  B
 354 TYR   ( 902-)  B
 437 TYR   ( 989-)  B
 468 TYR   (1020-)  B
 528 TYR   ( 821-)  E
 564 TYR   ( 857-)  E
 576 TYR   ( 869-)  E
 591 TYR   ( 884-)  E
 609 TYR   ( 902-)  E
 642 TYR   ( 935-)  E
 691 TYR   ( 986-)  E
 694 TYR   ( 989-)  E
 725 TYR   (1020-)  E
 785 TYR   ( 821-)  C
And so on for a total of 51 lines.

Warning: Phenylalanine convention problem

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

  18 PHE   ( 823-)  A
 117 PHE   ( 922-)  A
 190 PHE   ( 997-)  A
 275 PHE   ( 823-)  B
 374 PHE   ( 922-)  B
 629 PHE   ( 922-)  E
 886 PHE   ( 922-)  C
 890 PHE   ( 926-)  C
1040 PHE   ( 823-)  D
1139 PHE   ( 922-)  D
1345 PHE   ( 876-)  F
1391 PHE   ( 922-)  F
1395 PHE   ( 926-)  F

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.

 145 ASP   ( 950-)  A
 375 ASP   ( 923-)  B
 455 ASP   (1007-)  B
 630 ASP   ( 923-)  E
 680 ASP   ( 973-)  E
 966 ASP   (1007-)  C

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.

 109 GLU   ( 914-)  A
 169 GLU   ( 974-)  A
 201 GLU   (1008-)  A
 210 GLU   (1017-)  A
 221 GLU   (1028-)  A
 255 GLU   (1062-)  A
 266 GLU   ( 814-)  B
 457 GLU   (1009-)  B
 464 GLU   (1016-)  B
 521 GLU   ( 814-)  E
 580 GLU   ( 873-)  E
 621 GLU   ( 914-)  E
 681 GLU   ( 974-)  E
 706 GLU   (1001-)  E
 727 GLU   (1022-)  E
 733 GLU   (1028-)  E
 878 GLU   ( 914-)  C
 960 GLU   (1001-)  C
 987 GLU   (1028-)  C
1011 GLU   (1052-)  C
1021 GLU   (1062-)  C
1031 GLU   ( 814-)  D
1131 GLU   ( 914-)  D
1213 GLU   (1001-)  D
1313 GLU   ( 844-)  F
1342 GLU   ( 873-)  F
1383 GLU   ( 914-)  F
1443 GLU   ( 974-)  F
1469 GLU   (1001-)  F
1472 GLU   (1004-)  F
1477 GLU   (1009-)  F
1484 GLU   (1016-)  F
1496 GLU   (1028-)  F
1499 GLU   (1031-)  F
1520 GLU   (1052-)  F

Geometric checks

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.

 403 HIS   ( 954-)  B      CG   ND1  CE1 109.83    4.2
 581 HIS   ( 874-)  E      CG   ND1  CE1 109.64    4.0
 704 HIS   ( 999-)  E      CG   ND1  CE1 109.68    4.1
 769 HIS   ( 800-)  C      CG   ND1  CE1 110.27    4.7
 898 HIS   ( 934-)  C      CG   ND1  CE1 109.82    4.2
 964 HIS   (1005-)  C      CG   ND1  CE1 109.70    4.1
1171 HIS   ( 954-)  D      CG   ND1  CE1 109.68    4.1
1186 HIS   ( 969-)  D      CG   ND1  CE1 109.69    4.1

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.

   7 ARG   ( 812-)  A
 109 GLU   ( 914-)  A
 145 ASP   ( 950-)  A
 147 ARG   ( 952-)  A
 169 GLU   ( 974-)  A
 201 GLU   (1008-)  A
 210 GLU   (1017-)  A
 221 GLU   (1028-)  A
 242 ARG   (1049-)  A
 250 ARG   (1057-)  A
 255 GLU   (1062-)  A
 264 ARG   ( 812-)  B
 266 GLU   ( 814-)  B
 375 ASP   ( 923-)  B
 455 ASP   (1007-)  B
 457 GLU   (1009-)  B
 464 GLU   (1016-)  B
 497 ARG   (1049-)  B
 519 ARG   ( 812-)  E
 521 GLU   ( 814-)  E
 580 GLU   ( 873-)  E
 621 GLU   ( 914-)  E
 630 ASP   ( 923-)  E
 680 ASP   ( 973-)  E
 681 GLU   ( 974-)  E
And so on for a total of 56 lines.

Torsion-related checks

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.

 607 THR   ( 900-)  E    -3.5
 864 THR   ( 900-)  C    -3.4
1369 THR   ( 900-)  F    -3.3
  95 THR   ( 900-)  A    -3.2
 352 THR   ( 900-)  B    -3.0
1188 LEU   ( 971-)  D    -2.6
1013 ILE   (1054-)  C    -2.5
 874 THR   ( 910-)  C    -2.5
1405 ILE   ( 936-)  F    -2.5
 700 THR   ( 995-)  E    -2.4
 601 PRO   ( 894-)  E    -2.4
 726 THR   (1021-)  E    -2.4
 131 ILE   ( 936-)  A    -2.4
 643 ILE   ( 936-)  E    -2.4
 367 ARG   ( 915-)  B    -2.3
 208 THR   (1015-)  A    -2.3
 362 THR   ( 910-)  B    -2.3
 251 LEU   (1058-)  A    -2.3
 974 THR   (1015-)  C    -2.3
 766 LEU   (1061-)  E    -2.3
1117 THR   ( 900-)  D    -2.3
 443 THR   ( 995-)  B    -2.2
1187 GLY   ( 970-)  D    -2.2
1266 ILE   (1054-)  D    -2.2
 390 TYR   ( 938-)  B    -2.2
 166 LEU   ( 971-)  A    -2.2
 900 ILE   ( 936-)  C    -2.2
 858 PRO   ( 894-)  C    -2.2
1226 THR   (1014-)  D    -2.2
1470 ILE   (1002-)  F    -2.2
 143 GLY   ( 948-)  A    -2.1
1153 ILE   ( 936-)  D    -2.1
 194 GLU   (1001-)  A    -2.1
1024 VAL   ( 801-)  D    -2.1
 388 ILE   ( 936-)  B    -2.1
1225 THR   (1013-)  D    -2.1
1067 THR   ( 850-)  D    -2.1
 302 THR   ( 850-)  B    -2.1
1347 SER   ( 878-)  F    -2.1
 972 THR   (1013-)  C    -2.1
 980 THR   (1021-)  C    -2.1
1482 THR   (1014-)  F    -2.1
 778 GLU   ( 814-)  C    -2.0
 227 VAL   (1034-)  A    -2.0
 645 TYR   ( 938-)  E    -2.0
1483 THR   (1015-)  F    -2.0
 814 THR   ( 850-)  C    -2.0
  45 THR   ( 850-)  A    -2.0
 736 GLU   (1031-)  E    -2.0

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.

  32 ARG   ( 837-)  A  Poor phi/psi
  60 ARG   ( 865-)  A  Poor phi/psi
  73 SER   ( 878-)  A  Poor phi/psi
  83 VAL   ( 888-)  A  Poor phi/psi
  92 ARG   ( 897-)  A  omega poor
 170 ASN   ( 975-)  A  Poor phi/psi
 289 ARG   ( 837-)  B  Poor phi/psi
 317 ARG   ( 865-)  B  Poor phi/psi
 330 SER   ( 878-)  B  Poor phi/psi
 339 ASN   ( 887-)  B  Poor phi/psi
 447 HIS   ( 999-)  B  Poor phi/psi
 544 ARG   ( 837-)  E  Poor phi/psi
 572 ARG   ( 865-)  E  Poor phi/psi
 585 SER   ( 878-)  E  Poor phi/psi
 594 ASN   ( 887-)  E  Poor phi/psi
 595 VAL   ( 888-)  E  Poor phi/psi
 842 SER   ( 878-)  C  Poor phi/psi
 852 VAL   ( 888-)  C  Poor phi/psi
1054 ARG   ( 837-)  D  Poor phi/psi
1082 ARG   ( 865-)  D  Poor phi/psi
1095 SER   ( 878-)  D  Poor phi/psi
1105 VAL   ( 888-)  D  Poor phi/psi
1114 ARG   ( 897-)  D  omega poor
1165 GLY   ( 948-)  D  omega poor
1187 GLY   ( 970-)  D  omega poor
1211 HIS   ( 999-)  D  omega poor
1222 GLY   (1010-)  D  omega poor
1306 ARG   ( 837-)  F  Poor phi/psi
1334 ARG   ( 865-)  F  Poor phi/psi
1347 SER   ( 878-)  F  Poor phi/psi
1356 ASN   ( 887-)  F  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.114

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.114

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.

 627 VAL   ( 920-)  E    0.33
 993 VAL   (1034-)  C    0.33
 482 VAL   (1034-)  B    0.36
 507 SER   (1059-)  B    0.38
1527 SER   (1059-)  F    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!

   4 ILE   ( 803-)  A      0
   5 ARG   ( 804-)  A      0
   6 ILE   ( 811-)  A      0
   7 ARG   ( 812-)  A      0
  13 GLU   ( 818-)  A      0
  15 GLU   ( 820-)  A      0
  31 GLN   ( 836-)  A      0
  32 ARG   ( 837-)  A      0
  36 CYS   ( 841-)  A      0
  39 GLU   ( 844-)  A      0
  45 THR   ( 850-)  A      0
  58 ASP   ( 863-)  A      0
  59 SER   ( 864-)  A      0
  60 ARG   ( 865-)  A      0
  65 ASN   ( 870-)  A      0
  72 GLN   ( 877-)  A      0
  73 SER   ( 878-)  A      0
  74 ALA   ( 879-)  A      0
  79 TYR   ( 884-)  A      0
  80 ASN   ( 885-)  A      0
  81 ASP   ( 886-)  A      0
  82 ASN   ( 887-)  A      0
  83 VAL   ( 888-)  A      0
  86 LEU   ( 891-)  A      0
  90 SER   ( 895-)  A      0
And so on for a total of 615 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!

1222 GLY   (1010-)  D   1.88   38
 929 ALA   ( 968-)  C   1.60   13
1187 GLY   ( 970-)  D   1.52   34

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].

 229 PRO   (1036-)  A   103.2 envelop C-beta (108 degrees)
 285 PRO   ( 833-)  B  -115.1 envelop C-gamma (-108 degrees)
 335 PRO   ( 883-)  B    52.0 half-chair C-delta/C-gamma (54 degrees)
 371 PRO   ( 919-)  B   100.9 envelop C-beta (108 degrees)
 484 PRO   (1036-)  B   100.9 envelop C-beta (108 degrees)
 540 PRO   ( 833-)  E  -121.4 half-chair C-delta/C-gamma (-126 degrees)
 601 PRO   ( 894-)  E   101.6 envelop C-beta (108 degrees)
 626 PRO   ( 919-)  E    99.6 envelop C-beta (108 degrees)
 847 PRO   ( 883-)  C    45.3 half-chair C-delta/C-gamma (54 degrees)
 949 PRO   ( 990-)  C    42.6 envelop C-delta (36 degrees)
1100 PRO   ( 883-)  D    37.0 envelop C-delta (36 degrees)
1388 PRO   ( 919-)  F  -121.1 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 168 ASP   ( 973-)  A      CG  <->  170 ASN   ( 975-)  A      ND2    0.88    2.22  INTRA BF
 168 ASP   ( 973-)  A      OD1 <->  170 ASN   ( 975-)  A      ND2    0.54    2.16  INTRA BF
1403 HIS   ( 934-)  F      N   <-> 1430 GLN   ( 961-)  F      NE2    0.35    2.50  INTRA BF
 168 ASP   ( 973-)  A      OD2 <->  170 ASN   ( 975-)  A      ND2    0.33    2.37  INTRA BF
 661 HIS   ( 954-)  E      CE1 <-> 1544 PEG   (  21-)  E      C3     0.32    2.88  INTRA BL
 898 HIS   ( 934-)  C      N   <->  922 GLN   ( 961-)  C      NE2    0.30    2.55  INTRA BL
 808 GLU   ( 844-)  C      N   <->  814 THR   ( 850-)  C      CG2    0.30    2.80  INTRA BL
1161 VAL   ( 944-)  D      O   <-> 1165 GLY   ( 948-)  D      N      0.28    2.42  INTRA BF
1203 ARG   ( 991-)  D      NH1 <-> 1570 HOH   ( 123 )  D      O      0.28    2.42  INTRA BL
 129 HIS   ( 934-)  A      N   <->  156 GLN   ( 961-)  A      NE2    0.26    2.59  INTRA BF
 641 HIS   ( 934-)  E      N   <->  668 GLN   ( 961-)  E      NE2    0.25    2.60  INTRA BF
 551 GLU   ( 844-)  E      N   <->  557 THR   ( 850-)  E      CG2    0.23    2.87  INTRA BL
 297 GLY   ( 845-)  B      N   <->  302 THR   ( 850-)  B      CG2    0.23    2.87  INTRA BL
1151 HIS   ( 934-)  D      N   <-> 1178 GLN   ( 961-)  D      NE2    0.22    2.63  INTRA BF
 579 ASP   ( 872-)  E      OD1 <->  829 ARG   ( 865-)  C      NH1    0.22    2.48  INTRA BL
 184 ARG   ( 991-)  A      NH1 <-> 1566 HOH   ( 243 )  A      O      0.22    2.48  INTRA BF
1211 HIS   ( 999-)  D      NE2 <-> 1570 HOH   ( 271 )  D      O      0.22    2.48  INTRA BF
1454 TYR   ( 986-)  F      N   <-> 1571 HOH   ( 122 )  F      O      0.22    2.48  INTRA BF
1299 THR   ( 830-)  F      N   <-> 1564 PEG   (  34-)  F      C2     0.21    2.89  INTRA BL
1314 GLY   ( 845-)  F      N   <-> 1319 THR   ( 850-)  F      CG2    0.20    2.90  INTRA BL
1217 HIS   (1005-)  D      O   <-> 1225 THR   (1013-)  D      N      0.20    2.50  INTRA BF
 710 HIS   (1005-)  E      NE2 <->  720 THR   (1015-)  E      CG2    0.20    2.90  INTRA
 948 TYR   ( 989-)  C      OH  <-> 1129 ASN   ( 912-)  D      ND2    0.18    2.52  INTRA BL
 548 CYS   ( 841-)  E      SG  <->  550 GLY   ( 843-)  E      N      0.18    3.12  INTRA BL
 680 ASP   ( 973-)  E      CG  <->  681 GLU   ( 974-)  E      N      0.18    2.82  INTRA BF
And so on for a total of 258 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: E

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: F

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.

1220 GLU   (1008-)  D      -5.93
 713 GLU   (1008-)  E      -5.82
1476 GLU   (1008-)  F      -5.79
 456 GLU   (1008-)  B      -5.68
 181 LYS   ( 988-)  A      -5.54
 201 GLU   (1008-)  A      -5.53
 967 GLU   (1008-)  C      -5.38
 261 ARG   ( 804-)  B      -5.33
1456 LYS   ( 988-)  F      -5.28
1188 LEU   ( 971-)  D      -5.17
 515 ARG   ( 804-)  E      -5.03
1021 GLU   (1062-)  C      -5.03
 436 LYS   ( 988-)  B      -5.02

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.

 140 GLN   ( 945-)  A       142 - LYS    947- ( A)         -4.42
 652 GLN   ( 945-)  E       654 - LYS    947- ( E)         -4.40
1162 GLN   ( 945-)  D      1164 - LYS    947- ( D)         -4.22
1414 GLN   ( 945-)  F      1416 - LYS    947- ( F)         -4.40

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: 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: 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: F

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.

1128 ALA   ( 911-)  D   -3.35
 849 ASN   ( 885-)  C   -2.80
 985 HIS   (1026-)  C   -2.67
 731 HIS   (1026-)  E   -2.65
  22 SER   ( 827-)  A   -2.63
1494 HIS   (1026-)  F   -2.61
1296 SER   ( 827-)  F   -2.59
1044 SER   ( 827-)  D   -2.56
1238 HIS   (1026-)  D   -2.55
 534 SER   ( 827-)  E   -2.55

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.

 616 VAL   ( 909-)  E     -  619 ASN   ( 912-)  E        -1.44
 873 VAL   ( 909-)  C     -  876 ASN   ( 912-)  C        -1.34
1126 VAL   ( 909-)  D     - 1129 ASN   ( 912-)  D        -1.60

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: E

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: F

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1571 HOH   ( 266 )  F      O    -13.25  -70.77    2.09

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.

  91 ASN   ( 896-)  A
 107 ASN   ( 912-)  A
 144 ASN   ( 949-)  A
 198 HIS   (1005-)  A
 348 ASN   ( 896-)  B
 418 HIS   ( 969-)  B
 539 ASN   ( 832-)  E
 603 ASN   ( 896-)  E
 619 ASN   ( 912-)  E
 656 ASN   ( 949-)  E
 668 GLN   ( 961-)  E
 768 GLN   (1063-)  E
 860 ASN   ( 896-)  C
 876 ASN   ( 912-)  C
 930 HIS   ( 969-)  C
 958 HIS   ( 999-)  C
 970 ASN   (1011-)  C
1113 ASN   ( 896-)  D
1129 ASN   ( 912-)  D
1171 HIS   ( 954-)  D
1275 HIS   ( 800-)  F
1322 GLN   ( 853-)  F
1329 ASN   ( 860-)  F
1365 ASN   ( 896-)  F
1381 ASN   ( 912-)  F
1430 GLN   ( 961-)  F

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   3 THR   ( 802-)  A      OG1
   5 ARG   ( 804-)  A      NE
   7 ARG   ( 812-)  A      N
   9 GLU   ( 814-)  A      N
  16 TYR   ( 821-)  A      OH
  39 GLU   ( 844-)  A      N
  40 GLY   ( 845-)  A      N
  46 GLY   ( 851-)  A      N
  56 ASN   ( 861-)  A      N
  56 ASN   ( 861-)  A      ND2
  68 GLU   ( 873-)  A      N
  74 ALA   ( 879-)  A      N
  80 ASN   ( 885-)  A      N
  96 ALA   ( 901-)  A      N
 117 PHE   ( 922-)  A      N
 129 HIS   ( 934-)  A      N
 135 TRP   ( 940-)  A      N
 150 PHE   ( 955-)  A      N
 156 GLN   ( 961-)  A      NE2
 158 ARG   ( 963-)  A      NE
 170 ASN   ( 975-)  A      N
 201 GLU   (1008-)  A      N
 242 ARG   (1049-)  A      NE
 242 ARG   (1049-)  A      NH1
 261 ARG   ( 804-)  B      NE
And so on for a total of 147 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.

 149 HIS   ( 954-)  A      ND1
 224 GLU   (1031-)  A      OE1
 230 ASP   (1037-)  A      OD1
 479 GLU   (1031-)  B      OE1
 495 GLN   (1047-)  B      OE1
 613 ASN   ( 906-)  E      OD1
 661 HIS   ( 954-)  E      ND1
 736 GLU   (1031-)  E      OE1
 769 HIS   ( 800-)  C      ND1
 870 ASN   ( 906-)  C      OD1
 990 GLU   (1031-)  C      OE1
1094 GLN   ( 877-)  D      OE1
1123 ASN   ( 906-)  D      OD1
1216 GLU   (1004-)  D      OE1
1243 GLU   (1031-)  D      OE1
1243 GLU   (1031-)  D      OE2
1267 GLU   (1055-)  D      OE2
1274 GLU   (1062-)  D      OE2
1375 ASN   ( 906-)  F      OD1
1423 HIS   ( 954-)  F      NE2
1467 HIS   ( 999-)  F      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1559  CA   (   1-)  F   -.-  -.-  Too few ligands (0)

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

1566 HOH   ( 159 )  A      O  0.99  K  4 NCS 1/1
1566 HOH   ( 191 )  A      O  0.96  K  4 NCS 2/2

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.

 123 ASP   ( 928-)  A   H-bonding suggests Asn
 180 ASP   ( 987-)  A   H-bonding suggests Asn
 200 ASP   (1007-)  A   H-bonding suggests Asn; but Alt-Rotamer
 248 GLU   (1055-)  A   H-bonding suggests Gln
 380 ASP   ( 928-)  B   H-bonding suggests Asn
 435 ASP   ( 987-)  B   H-bonding suggests Asn
 465 GLU   (1017-)  B   H-bonding suggests Gln; but Alt-Rotamer
 680 ASP   ( 973-)  E   H-bonding suggests Asn
 712 ASP   (1007-)  E   H-bonding suggests Asn
 757 GLU   (1052-)  E   H-bonding suggests Gln
 892 ASP   ( 928-)  C   H-bonding suggests Asn; but Alt-Rotamer
 925 ASP   ( 964-)  C   H-bonding suggests Asn
1021 GLU   (1062-)  C   H-bonding suggests Gln
1145 ASP   ( 928-)  D   H-bonding suggests Asn
1219 ASP   (1007-)  D   H-bonding suggests Asn; but Alt-Rotamer
1243 GLU   (1031-)  D   H-bonding suggests Gln
1433 ASP   ( 964-)  F   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.259
  2nd generation packing quality :  -1.118
  Ramachandran plot appearance   :  -1.885
  chi-1/chi-2 rotamer normality  :  -3.114 (poor)
  Backbone conformation          :   0.373

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.188 (tight)
  Bond angles                    :   0.467 (tight)
  Omega angle restraints         :   0.917
  Side chain planarity           :   0.176 (tight)
  Improper dihedral distribution :   0.416
  B-factor distribution          :   2.621 (loose)
  Inside/Outside distribution    :   1.082

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :   0.3
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -0.8
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.188 (tight)
  Bond angles                    :   0.467 (tight)
  Omega angle restraints         :   0.917
  Side chain planarity           :   0.176 (tight)
  Improper dihedral distribution :   0.416
  B-factor distribution          :   2.621 (loose)
  Inside/Outside distribution    :   1.082
==============

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.