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 pdb3hoz.ent

Checks that need to be done early-on in validation

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: C 2 2 21
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 456058.469
Volume of the Unit Cell V= 24571336.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 13.469
Vm by authors and this calculated Vm do not agree very well
SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

3970  MG   (2458-)  A  P

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: 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   (   2-)  A    High
  41 ASP   (  42-)  A    High
  42 GLU   (  43-)  A    High
  43 THR   (  44-)  A    High
  44 GLN   (  45-)  A    High
  45 THR   (  46-)  A    High
  46 ARG   (  47-)  A    High
  62 ARG   (  63-)  A    High
  70 GLN   (  71-)  A    High
 106 CYS   ( 107-)  A    High
 107 MET   ( 108-)  A    High
 108 HIS   ( 109-)  A    High
 109 CYS   ( 110-)  A    High
 114 LEU   ( 115-)  A    High
 115 ASP   ( 116-)  A    High
 116 GLU   ( 117-)  A    High
 117 HIS   ( 118-)  A    High
 118 ASN   ( 119-)  A    High
 119 GLU   ( 120-)  A    High
 120 LEU   ( 121-)  A    High
 121 MET   ( 122-)  A    High
 122 ARG   ( 123-)  A    High
 123 GLN   ( 124-)  A    High
 144 LYS   ( 145-)  A    High
 145 MET   ( 146-)  A    High
And so on for a total of 960 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:

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: 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: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

1215 ARG   (1244-)  A

Warning: Tyrosine convention problem

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

 375 TYR   ( 383-)  A
 409 TYR   ( 417-)  A
 420 TYR   ( 428-)  A
 457 TYR   ( 465-)  A
 470 TYR   ( 478-)  A
 796 TYR   ( 804-)  A
 844 TYR   ( 852-)  A
 925 TYR   ( 933-)  A
1027 TYR   (1035-)  A
1100 TYR   (1119-)  A
1135 TYR   (1154-)  A
1250 TYR   (1287-)  A
1312 TYR   (1349-)  A
1316 TYR   (1353-)  A
1328 TYR   (1365-)  A
1416 TYR   (1453-)  A
1554 TYR   ( 202-)  B
1655 TYR   ( 303-)  B
1820 TYR   ( 486-)  B
2014 TYR   ( 692-)  B
2085 TYR   ( 769-)  B
2114 TYR   ( 798-)  B
2367 TYR   (1064-)  B
2395 TYR   (1092-)  B
2495 TYR   (1192-)  B
2501 TYR   (1198-)  B
2705 TYR   ( 180-)  C
2999 TYR   (  28-)  E
3206 TYR   (  88-)  F
3324 TYR   (  51-)  G
3347 TYR   (  74-)  G
3440 TYR   ( 167-)  G
3464 TYR   (  20-)  H
3529 TYR   (  95-)  H
3536 TYR   ( 102-)  H
3550 TYR   ( 116-)  H
3563 TYR   ( 129-)  H
3613 TYR   (  34-)  I
3743 TYR   (  44-)  J
3762 TYR   (  63-)  J
3825 TYR   (  61-)  K
3845 TYR   (  81-)  K
3884 TYR   (  29-)  L

Warning: Phenylalanine convention problem

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

  21 PHE   (  22-)  A
  94 PHE   (  95-)  A
 211 PHE   ( 219-)  A
 220 PHE   ( 228-)  A
 244 PHE   ( 252-)  A
 256 PHE   ( 264-)  A
 460 PHE   ( 468-)  A
 474 PHE   ( 482-)  A
 713 PHE   ( 721-)  A
 769 PHE   ( 777-)  A
 771 PHE   ( 779-)  A
 779 PHE   ( 787-)  A
 806 PHE   ( 814-)  A
 807 PHE   ( 815-)  A
 858 PHE   ( 866-)  A
 934 PHE   ( 942-)  A
 939 PHE   ( 947-)  A
 963 PHE   ( 971-)  A
1045 PHE   (1053-)  A
1155 PHE   (1174-)  A
1191 PHE   (1220-)  A
1295 PHE   (1332-)  A
1373 PHE   (1410-)  A
1437 PHE   (  38-)  B
1510 PHE   ( 129-)  B
And so on for a total of 60 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.

 253 ASP   ( 261-)  A
 299 ASP   ( 307-)  A
 354 ASP   ( 362-)  A
 475 ASP   ( 483-)  A
 530 ASP   ( 538-)  A
 941 ASP   ( 949-)  A
1383 ASP   (1420-)  A
1409 ASP   (1446-)  A
1646 ASP   ( 294-)  B
1738 ASP   ( 394-)  B
1899 ASP   ( 568-)  B
2106 ASP   ( 790-)  B
2153 ASP   ( 837-)  B
2253 ASP   ( 950-)  B
2661 ASP   ( 136-)  C
2878 ASP   ( 127-)  D
2907 ASP   ( 156-)  D
3361 ASP   (  88-)  G
3452 ASP   (   8-)  H

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 488 GLU   ( 496-)  A
 492 GLU   ( 500-)  A
 610 GLU   ( 618-)  A
 628 GLU   ( 636-)  A
 670 GLU   ( 678-)  A
 793 GLU   ( 801-)  A
 871 GLU   ( 879-)  A
 886 GLU   ( 894-)  A
1427 GLU   (  28-)  B
1464 GLU   (  65-)  B
1538 GLU   ( 186-)  B
1561 GLU   ( 209-)  B
1651 GLU   ( 299-)  B
1895 GLU   ( 564-)  B
2021 GLU   ( 699-)  B
2307 GLU   (1004-)  B
2331 GLU   (1028-)  B
2373 GLU   (1070-)  B
2575 GLU   (  50-)  C
2577 GLU   (  52-)  C
2733 GLU   ( 208-)  C
2758 GLU   ( 233-)  C
2845 GLU   (  54-)  D
2969 GLU   ( 218-)  D
3108 GLU   ( 137-)  E
3230 GLU   ( 112-)  F
3232 GLU   ( 114-)  F
3407 GLU   ( 134-)  G
3616 GLU   (  37-)  I
3626 GLU   (  47-)  I
3661 GLU   (  82-)  I
3718 GLU   (  19-)  J
3731 GLU   (  32-)  J
3828 GLU   (  64-)  K

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.

   2 GLY   (   3-)  A      N    CA   C    98.65   -4.8
  54 ASP   (  55-)  A     -C    N    CA  132.12    5.8
  54 ASP   (  55-)  A      N    CA   CB  119.48    5.3
  55 PRO   (  56-)  A      N    CA   C    97.74   -5.6
  56 ARG   (  57-)  A     -C    N    CA  129.93    4.6
 211 PHE   ( 219-)  A      C    CA   CB  102.09   -4.2
 280 ALA   ( 288-)  A      N    CA   C    98.89   -4.4
 303 GLN   ( 311-)  A      N    CA   C   125.17    5.0
 323 GLY   ( 331-)  A      N    CA   C   128.00    5.3
 391 HIS   ( 399-)  A     -C    N    CA  113.05   -4.8
 391 HIS   ( 399-)  A      CG   ND1  CE1 109.65    4.1
 417 GLN   ( 425-)  A      N    CA   C    97.60   -4.9
 427 HIS   ( 435-)  A      CG   ND1  CE1 109.73    4.1
 432 ASP   ( 440-)  A      N    CA   C    99.19   -4.3
 458 SER   ( 466-)  A      N    CA   C   123.75    4.5
 620 GLY   ( 628-)  A      N    CA   C   124.59    4.2
 621 LEU   ( 629-)  A      N    CA   C    98.22   -4.6
1275 ASN   (1312-)  A      N    CA   C    97.96   -4.7
1366 GLU   (1403-)  A      N    CA   C   123.15    4.3
1707 HIS   ( 363-)  B      N    CA   C    97.45   -4.9
1979 HIS   ( 648-)  B      CG   ND1  CE1 109.62    4.0
2003 TRP   ( 681-)  B      N    CA   C    98.83   -4.4
2060 HIS   ( 744-)  B      CG   ND1  CE1 109.69    4.1
2167 PHE   ( 851-)  B      N    CA   C   123.00    4.2
2198 THR   ( 882-)  B      N    CA   C   122.93    4.2
2410 ALA   (1107-)  B      N    CA   C    98.54   -4.5
2433 PHE   (1130-)  B      N    CA   C    96.82   -5.1
2488 CYS   (1185-)  B      N    CA   C    97.06   -5.1
2536 ARG   (  11-)  C      N    CA   C    99.98   -4.0
2564 ALA   (  39-)  C      N    CA   C   128.07    6.0
2708 TRP   ( 183-)  C      N    CA   C    99.35   -4.2
2799 PHE   (   8-)  D      N    CA   C   124.46    4.7
2816 ALA   (  25-)  D      N    CA   C    99.54   -4.2
2817 THR   (  26-)  D      N    CA   C    93.51   -6.3
2976 ASN   (   5-)  E      N    CA   C    99.04   -4.3
3142 LYS   ( 171-)  E      N    CA   C    96.22   -5.3
3189 GLU   (  71-)  F      N    CA   C    96.62   -5.2
3336 PRO   (  63-)  G      N    CA   C   123.45    4.7
3338 ASP   (  65-)  G      N    CA   C    95.01   -5.8
3704 VAL   (   5-)  J      N    CA   C    97.13   -5.0
3743 TYR   (  44-)  J      N    CA   C   123.18    4.3
3913 LYS   (  58-)  L      N    CA   C   123.42    4.4
3923 GLU   (  68-)  L      N    CA   C    99.97   -4.0
3938 DGUA  (  15-)  T      N9   C8   N7  113.33    4.5
3943 DGUA  (  20-)  T      N9   C8   N7  113.38    4.6
3958 OGUA  (   7-)  P      N9   C8   N7  113.26    4.3
3959 OGUA  (   8-)  P      N9   C8   N7  113.19    4.2
3962 OGUA  (  11-)  P      N9   C8   N7  113.26    4.3

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.

 253 ASP   ( 261-)  A
 299 ASP   ( 307-)  A
 354 ASP   ( 362-)  A
 475 ASP   ( 483-)  A
 488 GLU   ( 496-)  A
 492 GLU   ( 500-)  A
 530 ASP   ( 538-)  A
 610 GLU   ( 618-)  A
 628 GLU   ( 636-)  A
 670 GLU   ( 678-)  A
 793 GLU   ( 801-)  A
 871 GLU   ( 879-)  A
 886 GLU   ( 894-)  A
 941 ASP   ( 949-)  A
1215 ARG   (1244-)  A
1383 ASP   (1420-)  A
1409 ASP   (1446-)  A
1427 GLU   (  28-)  B
1464 GLU   (  65-)  B
1538 GLU   ( 186-)  B
1561 GLU   ( 209-)  B
1646 ASP   ( 294-)  B
1651 GLU   ( 299-)  B
1738 ASP   ( 394-)  B
1895 GLU   ( 564-)  B
And so on for a total of 54 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.

 392 PRO   ( 400-)  A      N      6.7    19.50    -2.48
The average deviation= 0.835

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.

2564 ALA   (  39-)  C   11.54
 280 ALA   ( 288-)  A    8.70
 621 LEU   ( 629-)  A    8.57
2939 ALA   ( 188-)  D    7.49
2976 ASN   (   5-)  E    7.39
2003 TRP   ( 681-)  B    7.01
 702 LEU   ( 710-)  A    6.75
3743 TYR   (  44-)  J    6.52
 867 ALA   ( 875-)  A    6.46
1771 ASP   ( 427-)  B    6.35
 285 GLU   ( 293-)  A    6.24
2772 GLY   ( 247-)  C    6.09
 527 THR   ( 535-)  A    6.07
3519 GLY   (  85-)  H    6.06
 258 LEU   ( 266-)  A    5.95
2817 THR   (  26-)  D    5.94
  55 PRO   (  56-)  A    5.92
2829 ILE   (  38-)  D    5.91
 281 ILE   ( 289-)  A    5.88
1150 ILE   (1169-)  A    5.85
  41 ASP   (  42-)  A    5.84
3142 LYS   ( 171-)  E    5.81
2822 GLN   (  31-)  D    5.74
2433 PHE   (1130-)  B    5.55
2488 CYS   (1185-)  B    5.55
And so on for a total of 105 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 : 1.710

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -5.670

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.

2869 THR   ( 118-)  D    -3.7
1368 THR   (1405-)  A    -3.6
2113 TYR   ( 797-)  B    -3.5
3805 THR   (  41-)  K    -3.4
3898 THR   (  43-)  L    -3.3
3665 PHE   (  86-)  I    -3.3
2796 THR   (   5-)  D    -3.3
1340 THR   (1377-)  A    -3.2
2349 PRO   (1046-)  B    -3.1
3336 PRO   (  63-)  G    -3.1
1103 PRO   (1122-)  A    -3.1
2517 PRO   (1214-)  B    -3.1
 304 PRO   ( 312-)  A    -3.1
3881 THR   (  26-)  L    -3.1
 236 PRO   ( 244-)  A    -3.1
1095 PRO   (1114-)  A    -3.1
2146 TYR   ( 830-)  B    -3.1
3461 PRO   (  17-)  H    -3.1
2798 THR   (   7-)  D    -3.0
3867 THR   ( 103-)  K    -3.0
 392 PRO   ( 400-)  A    -3.0
3871 THR   ( 107-)  K    -3.0
2390 PHE   (1087-)  B    -3.0
 388 PRO   ( 396-)  A    -3.0
1105 HIS   (1124-)  A    -2.9
And so on for a total of 289 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

   3 GLN   (   4-)  A  Poor phi/psi
   4 GLN   (   5-)  A  Poor phi/psi
  34 ILE   (  35-)  A  Poor phi/psi
  40 MET   (  41-)  A  Poor phi/psi
  42 GLU   (  43-)  A  Poor phi/psi
  43 THR   (  44-)  A  Poor phi/psi
  44 GLN   (  45-)  A  Poor phi/psi
  47 ALA   (  48-)  A  Poor phi/psi
  50 GLY   (  51-)  A  Poor phi/psi
  53 ASN   (  54-)  A  Poor phi/psi
  54 ASP   (  55-)  A  Poor phi/psi
  56 ARG   (  57-)  A  Poor phi/psi
  57 LEU   (  58-)  A  Poor phi/psi
  60 ILE   (  61-)  A  Poor phi/psi
  61 ASP   (  62-)  A  Poor phi/psi
  62 ARG   (  63-)  A  Poor phi/psi
  65 LYS   (  66-)  A  Poor phi/psi
  66 CYS   (  67-)  A  Poor phi/psi
  68 THR   (  69-)  A  Poor phi/psi
  69 CYS   (  70-)  A  Poor phi/psi
  70 GLN   (  71-)  A  Poor phi/psi
  71 GLU   (  72-)  A  Poor phi/psi
  73 MET   (  74-)  A  Poor phi/psi
  75 GLU   (  76-)  A  Poor phi/psi
 108 HIS   ( 109-)  A  Poor phi/psi
And so on for a total of 447 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 : -5.089

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.

2161 SER   ( 845-)  B    0.35
1268 VAL   (1305-)  A    0.35
2426 SER   (1123-)  B    0.37
2557 SER   (  32-)  C    0.38
 361 SER   ( 369-)  A    0.38
1063 SER   (1071-)  A    0.38
1589 VAL   ( 237-)  B    0.38

Warning: Unusual backbone conformations

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

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

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

   3 GLN   (   4-)  A      0
   4 GLN   (   5-)  A      0
   5 TYR   (   6-)  A      0
   7 SER   (   8-)  A      0
  31 VAL   (  32-)  A      0
  33 LYS   (  34-)  A      0
  34 ILE   (  35-)  A      0
  35 ARG   (  36-)  A      0
  36 PHE   (  37-)  A      0
  39 THR   (  40-)  A      0
  40 MET   (  41-)  A      0
  41 ASP   (  42-)  A      0
  42 GLU   (  43-)  A      0
  43 THR   (  44-)  A      0
  44 GLN   (  45-)  A      0
  46 ARG   (  47-)  A      0
  47 ALA   (  48-)  A      0
  48 LYS   (  49-)  A      0
  49 ILE   (  50-)  A      0
  52 LEU   (  53-)  A      0
  53 ASN   (  54-)  A      0
  54 ASP   (  55-)  A      0
  55 PRO   (  56-)  A      0
  56 ARG   (  57-)  A      0
  57 LEU   (  58-)  A      0
And so on for a total of 1773 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.287

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!

3907 GLY   (  52-)  L   2.16   10
2741 GLY   ( 216-)  C   2.14   10
1615 GLY   ( 263-)  B   1.94   80
3636 GLY   (  57-)  I   1.93   11
3723 LEU   (  24-)  J   1.80   28
1559 GLY   ( 207-)  B   1.78   65
2345 GLY   (1042-)  B   1.76   12
1259 GLY   (1296-)  A   1.72   17
2095 GLY   ( 779-)  B   1.70   15
2308 GLY   (1005-)  B   1.68   80
3777 GLY   (  13-)  K   1.66   33
 764 GLY   ( 772-)  A   1.63   15
3779 GLY   (  15-)  K   1.63   80
 799 GLY   ( 807-)  A   1.63   26
1642 GLY   ( 290-)  B   1.61   21
 250 GLY   ( 258-)  A   1.58   12
2768 VAL   ( 243-)  C   1.58   62
 665 GLY   ( 673-)  A   1.57   17

Warning: Unusual peptide bond conformations

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

  53 ASN   (  54-)  A   2.00
2520 TYR   (1217-)  B   1.92
3411 THR   ( 138-)  G   1.60

Warning: Unusual PRO puckering amplitudes

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

   9 PRO   (  10-)  A    0.45 HIGH
 237 PRO   ( 245-)  A    0.46 HIGH
 313 PRO   ( 321-)  A    0.45 HIGH
 484 PRO   ( 492-)  A    0.46 HIGH
 506 PRO   ( 514-)  A    0.47 HIGH
 970 PRO   ( 978-)  A    0.47 HIGH
1257 PRO   (1294-)  A    0.45 HIGH
1495 PRO   ( 114-)  B    0.46 HIGH
1967 PRO   ( 636-)  B    0.46 HIGH
3096 PRO   ( 125-)  E    0.45 HIGH
3378 PRO   ( 105-)  G    0.46 HIGH

Warning: Unusual PRO puckering phases

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

 236 PRO   ( 244-)  A   100.7 envelop C-beta (108 degrees)
 237 PRO   ( 245-)  A    99.4 envelop C-beta (108 degrees)
 304 PRO   ( 312-)  A    99.9 envelop C-beta (108 degrees)
 359 PRO   ( 367-)  A  -113.6 envelop C-gamma (-108 degrees)
1095 PRO   (1114-)  A   -44.3 envelop C-alpha (-36 degrees)
1103 PRO   (1122-)  A   105.2 envelop C-beta (108 degrees)
1523 PRO   ( 171-)  B  -115.6 envelop C-gamma (-108 degrees)
1548 PRO   ( 196-)  B  -113.5 envelop C-gamma (-108 degrees)
1626 PRO   ( 274-)  B  -119.9 half-chair C-delta/C-gamma (-126 degrees)
1835 PRO   ( 501-)  B  -122.4 half-chair C-delta/C-gamma (-126 degrees)
2034 PRO   ( 712-)  B  -118.3 half-chair C-delta/C-gamma (-126 degrees)
2115 PRO   ( 799-)  B    44.0 envelop C-delta (36 degrees)
2277 PRO   ( 974-)  B  -115.4 envelop C-gamma (-108 degrees)
2317 PRO   (1014-)  B  -117.5 half-chair C-delta/C-gamma (-126 degrees)
2517 PRO   (1214-)  B   -58.9 half-chair C-beta/C-alpha (-54 degrees)
2707 PRO   ( 182-)  C  -113.9 envelop C-gamma (-108 degrees)
3235 PRO   ( 117-)  F  -118.3 half-chair C-delta/C-gamma (-126 degrees)
3293 PRO   (  20-)  G   -33.5 envelop C-alpha (-36 degrees)
3336 PRO   (  63-)  G   -65.9 envelop C-beta (-72 degrees)
3401 PRO   ( 128-)  G    99.6 envelop C-beta (108 degrees)
3830 PRO   (  66-)  K  -113.3 envelop C-gamma (-108 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.

  33 LYS   (  34-)  A      NZ  <->   56 ARG   (  57-)  A      NH2    0.62    2.23  INTRA BL
3886 CYS   (  31-)  L      SG  <-> 3889 CYS   (  34-)  L      SG     0.62    2.83  INTRA BF
3608 CYS   (  29-)  I      SG  <-> 3611 CYS   (  32-)  I      N      0.59    2.71  INTRA BF
3274 MET   (   1-)  G      SD  <-> 3275 PHE   (   2-)  G      N      0.58    2.62  INTRA BL
  41 ASP   (  42-)  A      O   <->   43 THR   (  44-)  A      N      0.57    2.13  INTRA BF
1213 VAL   (1242-)  A      CG1 <-> 1214 VAL   (1243-)  A      N      0.57    2.43  INTRA BF
2691 GLU   ( 166-)  C      C   <-> 3770 ARG   (   6-)  K      NH1    0.56    2.54  INTRA BL
  68 THR   (  69-)  A      O   <->   70 GLN   (  71-)  A      N      0.54    2.16  INTRA BF
 657 GLY   ( 665-)  A      O   <->  659 GLY   ( 667-)  A      N      0.54    2.16  INTRA BL
3752 HIS   (  53-)  J      CD2 <-> 3753 VAL   (  54-)  J      N      0.53    2.47  INTRA BL
3411 THR   ( 138-)  G      CG2 <-> 3412 ILE   ( 139-)  G      N      0.51    2.49  INTRA BL
3274 MET   (   1-)  G      SD  <-> 3352 PHE   (  79-)  G      CD1    0.50    2.90  INTRA BL
  52 LEU   (  53-)  A      CD2 <->   53 ASN   (  54-)  A      N      0.50    2.50  INTRA BL
 391 HIS   ( 399-)  A      O   <->  393 GLY   ( 401-)  A      N      0.50    2.20  INTRA BL
2195 ARG   ( 879-)  B      NH2 <-> 2201 MET   ( 885-)  B      CE     0.50    2.60  INTRA BF
2708 TRP   ( 183-)  C      O   <-> 2710 LYS   ( 185-)  C      N      0.49    2.21  INTRA BF
3657 CYS   (  78-)  I      SG  <-> 3682 CYS   ( 103-)  I      SG     0.49    2.96  INTRA BF
2798 THR   (   7-)  D      O   <-> 2800 GLN   (   9-)  D      N      0.49    2.21  INTRA BF
3523 LEU   (  89-)  H      O   <-> 3525 ASP   (  91-)  H      N      0.48    2.22  INTRA BF
2591 ARG   (  66-)  C      NH1 <-> 3701 ILE   (   2-)  J      CG2    0.47    2.63  INTRA BL
2637 ASN   ( 112-)  C      CB  <-> 2639 TYR   ( 114-)  C      CE1    0.46    2.74  INTRA BL
1491 HIS   ( 110-)  B      CB  <-> 3909 ARG   (  54-)  L      NH2    0.46    2.64  INTRA BF
1471 ILE   (  90-)  B      CD1 <-> 1776 MET   ( 432-)  B      SD     0.46    2.94  INTRA BF
3654 CYS   (  75-)  I      SG  <-> 3658 HIS   (  79-)  I      N      0.46    2.84  INTRA BF
2601 ASP   (  76-)  C      OD2 <-> 2653 ASN   ( 128-)  C      N      0.46    2.24  INTRA BL
And so on for a total of 2492 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.

1215 ARG   (1244-)  A      -8.27
2802 ARG   (  11-)  D      -7.71
1922 ARG   ( 591-)  B      -7.54
2411 ARG   (1108-)  B      -7.49
  46 ARG   (  47-)  A      -7.07
3697 ARG   ( 118-)  I      -7.03
2971 LEU   ( 220-)  D      -6.99
1977 LEU   ( 646-)  B      -6.85
3897 ARG   (  42-)  L      -6.80
  35 ARG   (  36-)  A      -6.73
   3 GLN   (   4-)  A      -6.71
1810 ARG   ( 476-)  B      -6.61
3021 MET   (  50-)  E      -6.57
 995 LYS   (1003-)  A      -6.56
1805 GLN   ( 469-)  B      -6.52
 309 LYS   ( 317-)  A      -6.50
 303 GLN   ( 311-)  A      -6.45
2399 ARG   (1096-)  B      -6.45
3294 ARG   (  21-)  G      -6.37
2184 MET   ( 868-)  B      -6.36
1417 MET   (1454-)  A      -6.28
2432 ARG   (1129-)  B      -6.26
3587 ARG   (   8-)  I      -6.17
3514 ARG   (  80-)  H      -6.16
 324 LYS   ( 332-)  A      -6.13
And so on for a total of 120 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.

1438 ARG   (  39-)  B      1440 - LYS     41- ( B)         -4.82
2045 ILE   ( 729-)  B      2047 - VAL    731- ( B)         -4.98
2658 ILE   ( 133-)  C      2660 - GLN    135- ( C)         -4.32
2802 ARG   (  11-)  D      2805 - ARG     14- ( D)         -6.20
3696 LYS   ( 117-)  I      3698 - THR    119- ( I)         -5.72
3880 ALA   (  25-)  L      3882 - LEU     27- ( L)         -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: 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.

 439 GLN   ( 447-)  A   -3.30
 464 LEU   ( 472-)  A   -3.09
1361 MET   (1398-)  A   -2.84
 496 LEU   ( 504-)  A   -2.83
2455 MET   (1152-)  B   -2.69
 852 LEU   ( 860-)  A   -2.66
2693 ALA   ( 168-)  C   -2.65
1752 LEU   ( 408-)  B   -2.61
1655 TYR   ( 303-)  B   -2.57
2093 ALA   ( 777-)  B   -2.54
2803 ARG   (  12-)  D   -2.52

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.

  17 GLN   (  18-)  A
  67 GLN   (  68-)  A
  82 HIS   (  83-)  A
 159 GLN   ( 160-)  A
 217 ASN   ( 225-)  A
 386 ASN   ( 394-)  A
 443 HIS   ( 451-)  A
 495 GLN   ( 503-)  A
 509 ASN   ( 517-)  A
 595 ASN   ( 603-)  A
 651 HIS   ( 659-)  A
 737 GLN   ( 745-)  A
 749 ASN   ( 757-)  A
 850 ASN   ( 858-)  A
 918 GLN   ( 926-)  A
1109 GLN   (1128-)  A
1111 GLN   (1130-)  A
1121 HIS   (1140-)  A
1293 ASN   (1330-)  A
1395 GLN   (1432-)  A
1567 GLN   ( 215-)  B
1652 HIS   ( 300-)  B
1677 GLN   ( 325-)  B
1701 GLN   ( 357-)  B
1710 GLN   ( 366-)  B
1846 HIS   ( 515-)  B
1849 HIS   ( 518-)  B
2102 ASN   ( 786-)  B
2368 GLN   (1065-)  B
2464 HIS   (1161-)  B
2508 GLN   (1205-)  B
2514 ASN   (1211-)  B
2590 HIS   (  65-)  C
2598 GLN   (  73-)  C
2637 ASN   ( 112-)  C
2814 ASN   (  23-)  D
2883 GLN   ( 132-)  D
2974 GLN   (   3-)  E
3370 HIS   (  97-)  G
3591 ASN   (  12-)  I
3625 HIS   (  46-)  I
3666 GLN   (  87-)  I
3668 GLN   (  89-)  I
3793 ASN   (  29-)  K
3829 HIS   (  65-)  K
3840 GLN   (  76-)  K
3868 ASN   ( 104-)  K

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

   2 GLY   (   3-)  A      N
   6 SER   (   7-)  A      OG
  33 LYS   (  34-)  A      N
  34 ILE   (  35-)  A      N
  36 PHE   (  37-)  A      N
  38 GLU   (  39-)  A      N
  45 THR   (  46-)  A      N
  51 GLY   (  52-)  A      N
  53 ASN   (  54-)  A      N
  53 ASN   (  54-)  A      ND2
  54 ASP   (  55-)  A      N
  56 ARG   (  57-)  A      NH1
  57 LEU   (  58-)  A      N
  58 GLY   (  59-)  A      N
  66 CYS   (  67-)  A      N
  67 GLN   (  68-)  A      N
  70 GLN   (  71-)  A      N
  72 GLY   (  73-)  A      N
  75 GLU   (  76-)  A      N
  79 HIS   (  80-)  A      N
 107 MET   ( 108-)  A      N
 111 LYS   ( 112-)  A      N
 114 LEU   ( 115-)  A      N
 115 ASP   ( 116-)  A      N
 116 GLU   ( 117-)  A      N
And so on for a total of 645 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.

 115 ASP   ( 116-)  A      OD2
 291 HIS   ( 299-)  A      ND1
 354 ASP   ( 362-)  A      OD1
 391 HIS   ( 399-)  A      ND1
 427 HIS   ( 435-)  A      NE2
 450 HIS   ( 458-)  A      ND1
 594 ASP   ( 602-)  A      OD2
 623 HIS   ( 631-)  A      NE2
 707 GLU   ( 715-)  A      OE2
 760 GLN   ( 768-)  A      OE1
 778 HIS   ( 786-)  A      ND1
 862 GLU   ( 870-)  A      OE2
1159 GLN   (1188-)  A      OE1
1266 GLU   (1303-)  A      OE1
1322 ASP   (1359-)  A      OD2
1330 HIS   (1367-)  A      ND1
1389 GLU   (1426-)  A      OE1
1446 GLN   (  47-)  B      OE1
1588 HIS   ( 236-)  B      ND1
1631 ASP   ( 279-)  B      OD1
1684 ASP   ( 332-)  B      OD1
2021 GLU   ( 699-)  B      OE1
2033 GLU   ( 711-)  B      OE1
2060 HIS   ( 744-)  B      ND1
2083 ASN   ( 767-)  B      OD1
2086 GLN   ( 770-)  B      OE1
2158 ASN   ( 842-)  B      OD1
2210 ASP   ( 894-)  B      OD1
2318 HIS   (1015-)  B      NE2
2328 HIS   (1025-)  B      ND1
2379 HIS   (1076-)  B      ND1
2387 GLN   (1084-)  B      OE1
2459 ASP   (1156-)  B      OD1
2498 HIS   (1195-)  B      ND1
2509 GLU   (1206-)  B      OE1
2676 GLN   ( 151-)  C      OE1
2735 GLU   ( 210-)  C      OE1
2875 GLU   ( 124-)  D      OE2
2927 GLU   ( 176-)  D      OE2
3070 HIS   (  99-)  E      ND1
3358 GLU   (  85-)  G      OE1
3358 GLU   (  85-)  G      OE2
3590 ASN   (  11-)  I      OD1
3626 GLU   (  47-)  I      OE2
3662 ASN   (  83-)  I      OD1
3752 HIS   (  53-)  J      ND1
3888 GLU   (  33-)  L      OE1

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+.

3970  MG   (2458-)  A   -.-  -.-  Low probability ion. B=180.4
Since there are no waters, the water check has been skipped.

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.

  41 ASP   (  42-)  A   H-bonding suggests Asn
  54 ASP   (  55-)  A   H-bonding suggests Asn; but Alt-Rotamer
  71 GLU   (  72-)  A   H-bonding suggests Gln
 150 ASP   ( 151-)  A   H-bonding suggests Asn
 188 GLU   ( 196-)  A   H-bonding suggests Gln
 299 ASP   ( 307-)  A   H-bonding suggests Asn; but Alt-Rotamer
 390 GLU   ( 398-)  A   H-bonding suggests Gln
 473 ASP   ( 481-)  A   H-bonding suggests Asn
 492 GLU   ( 500-)  A   H-bonding suggests Gln
 536 ASP   ( 544-)  A   H-bonding suggests Asn
 677 GLU   ( 685-)  A   H-bonding suggests Gln
 716 GLU   ( 724-)  A   H-bonding suggests Gln
 818 ASP   ( 826-)  A   H-bonding suggests Asn
 922 ASP   ( 930-)  A   H-bonding suggests Asn
1005 ASP   (1013-)  A   H-bonding suggests Asn
1035 ASP   (1043-)  A   H-bonding suggests Asn; but Alt-Rotamer
1136 ASP   (1155-)  A   H-bonding suggests Asn; but Alt-Rotamer
1194 ASP   (1223-)  A   H-bonding suggests Asn
1448 ASP   (  49-)  B   H-bonding suggests Asn
1512 ASP   ( 131-)  B   H-bonding suggests Asn
1540 ASP   ( 188-)  B   H-bonding suggests Asn
1690 GLU   ( 346-)  B   H-bonding suggests Gln
1715 GLU   ( 371-)  B   H-bonding suggests Gln
1743 ASP   ( 399-)  B   H-bonding suggests Asn
1771 ASP   ( 427-)  B   H-bonding suggests Asn; but Alt-Rotamer
And so on for a total of 57 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 :  -1.900
  2nd generation packing quality :  -2.318
  Ramachandran plot appearance   :  -5.670 (bad)
  chi-1/chi-2 rotamer normality  :  -5.089 (bad)
  Backbone conformation          :  -0.829

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.439 (tight)
  Bond angles                    :   0.762
  Omega angle restraints         :   0.234 (tight)
  Side chain planarity           :   0.267 (tight)
  Improper dihedral distribution :   0.713
  B-factor distribution          :   0.426
  Inside/Outside distribution    :   1.032

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 3.65


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -2.5
  chi-1/chi-2 rotamer normality  :  -2.5
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.439 (tight)
  Bond angles                    :   0.762
  Omega angle restraints         :   0.234 (tight)
  Side chain planarity           :   0.267 (tight)
  Improper dihedral distribution :   0.713
  B-factor distribution          :   0.426
  Inside/Outside distribution    :   1.032
==============

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.