WHAT IF Check report

This file was created 2011-12-17 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 pdb3o30.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 437.110  B   = 288.380  C    = 306.560
    Alpha=  90.000  Beta=  99.130  Gamma=  90.000

Dimensions of a reduced cell

    A    = 288.380  B   = 306.560  C    = 437.110
    Alpha=  80.870  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 306.560  B   = 288.380  C    = 437.110
    Alpha=  90.000  Beta=  99.130  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  0.000000 -1.000000|
 |  0.000000 -1.000000  0.000000|
 | -1.000000  0.000000  0.000000|

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: 970321.875
Volume of the Unit Cell V= 38143880.0
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 19.655
Vm by authors and this calculated Vm do not agree very well

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.

4438 OHX   (  22-)  1  G

Warning: Ligands for which topology could not be determined

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

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

4429 OHX   (   2-)  G  -         Atom types
4430 OHX   (   4-)  G  -         Atom types
4431 OHX   (1801-)  1  -         Atom types
4432 OHX   (  10-)  G  -         Atom types
4433 OHX   (1802-)  1  -         Atom types
4434 OHX   (  13-)  G  -         Atom types
4435 OHX   (  16-)  G  -         Atom types
4436 OHX   (  20-)  G  -         Atom types
4437 OHX   (  21-)  G  -         Atom types
4438 OHX   (  22-)  1  G         Atom types
4439 OHX   (  24-)  G  -         Atom types
4440 OHX   (  26-)  G  -         Atom types
4441 OHX   (  28-)  G  -         Atom types
4442 OHX   (  29-)  G  -         Atom types
4443 OHX   (  31-)  G  -         Atom types
4444 OHX   (  32-)  G  -         Atom types
4445 OHX   (  34-)  G  -         Atom types
4446 OHX   (1803-)  1  -         Atom types
4447 OHX   (1804-)  1  -         Atom types
4448 OHX   (  43-)  G  -         Atom types
4449 OHX   (1805-)  1  -         Atom types
4450 OHX   (  45-)  G  -         Atom types
4451 OHX   (  46-)  G  -         Atom types
4452 OHX   (  47-)  G  -         Atom types
4453 OHX   (  48-)  G  -         Atom types
And so on for a total of 360 lines.

Administrative problems that can generate validation failures

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

1368 OURA  (1380-)  1  -             1367 OURA  (1378-)  1  -           2.7

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: Q

Note: Ramachandran plot

Chain identifier: R

Note: Ramachandran plot

Chain identifier: S

Note: Ramachandran plot

Chain identifier: T

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

1789 SER   (   2-)  A      OG
1790 LEU   (   3-)  A      CG
1790 LEU   (   3-)  A      CD1
1790 LEU   (   3-)  A      CD2
1791 PRO   (   4-)  A      CG
1791 PRO   (   4-)  A      CD
1793 THR   (   6-)  A      OG1
1793 THR   (   6-)  A      CG2
1794 PHE   (   7-)  A      CG
1794 PHE   (   7-)  A      CD1
1794 PHE   (   7-)  A      CD2
1794 PHE   (   7-)  A      CE1
1794 PHE   (   7-)  A      CE2
1794 PHE   (   7-)  A      CZ
1795 ASP   (   8-)  A      CG
1795 ASP   (   8-)  A      OD1
1795 ASP   (   8-)  A      OD2
1796 LEU   (   9-)  A      CG
1796 LEU   (   9-)  A      CD1
1796 LEU   (   9-)  A      CD2
1797 THR   (  10-)  A      OG1
1797 THR   (  10-)  A      CG2
1798 PRO   (  11-)  A      CG
1798 PRO   (  11-)  A      CD
1799 GLU   (  12-)  A      CG
And so on for a total of 7721 lines.

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 OURA  (   1-)  1    High
   2 OADE  (   2-)  1    High
   3 OURA  (   3-)  1    High
   4 OCYT  (   4-)  1    High
   5 OURA  (   5-)  1    High
   6 OGUA  (   6-)  1    High
   7 OGUA  (   7-)  1    High
   9 OURA  (   9-)  1    High
  14 OCYT  (  14-)  1    High
  17 OCYT  (  17-)  1    High
  19 OADE  (  19-)  1    High
  20 OGUA  (  20-)  1    High
  21 OURA  (  21-)  1    High
  22 OADE  (  22-)  1    High
  24 OURA  (  24-)  1    High
  25 OCYT  (  25-)  1    High
  26 OADE  (  26-)  1    High
  27 OURA  (  27-)  1    High
  28 OADE  (  28-)  1    High
  29 OURA  (  29-)  1    High
  33 OURA  (  33-)  1    High
  34 OGUA  (  34-)  1    High
  35 OURA  (  35-)  1    High
  36 OCYT  (  36-)  1    High
  37 OURA  (  37-)  1    High
And so on for a total of 3065 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: 0

Crystal temperature (K) : 90.000

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

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: Q

Note: B-factor plot

Chain identifier: R

Note: B-factor plot

Chain identifier: S

Note: B-factor plot

Chain identifier: T

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

   3 OURA  (   3-)  1      C1'  N1    1.43   -4.5
  12 OURA  (  12-)  1      N3   C2    1.34   -4.1
  40 OADE  (  40-)  1      N9   C4    1.35   -4.1
  45 OURA  (  45-)  1      N1   C2    1.42    4.7
  45 OURA  (  45-)  1      C6   C5    1.30   -4.3
  45 OURA  (  45-)  1      N3   C2    1.41    5.4
  61 OADE  (  61-)  1      P    OP2   1.41   -4.6
  62 OADE  (  62-)  1      P    OP2   1.39   -5.8
  79 OCYT  (  79-)  1      C1'  N1    1.52    4.5
  91 OGUA  (  91-)  1      N9   C4    1.34   -4.2
 125 OURA  ( 125-)  1      C1'  N1    1.53    6.4
 127 OGUA  ( 127-)  1      C1'  N9    1.39   -7.5
 129 OURA  ( 129-)  1      C1'  N1    1.57   11.4
 135 OADE  ( 135-)  1      C1'  N9    1.40   -5.7
 243 OGUA  ( 243-)  1      C1'  N9    1.38   -9.2
 259 OURA  ( 259-)  1      C1'  N1    1.54    8.3
 295 OADE  ( 295-)  1      N9   C4    1.35   -4.8
 318 OURA  ( 318-)  1      C1'  N1    1.43   -4.3
 326 OGUA  ( 326-)  1      C6   N1    1.35   -5.7
 326 OGUA  ( 326-)  1      C6   O6    1.20   -4.1
 332 OURA  ( 332-)  1      N3   C2    1.34   -4.5
 336 OGUA  ( 336-)  1      N1   C2    1.34   -4.2
 336 OGUA  ( 336-)  1      C6   N1    1.36   -5.1
 342 OCYT  ( 342-)  1      N1   C6    1.34   -5.1
 373 OGUA  ( 373-)  1      N9   C4    1.33   -5.7
And so on for a total of 105 lines.

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.002119 -0.000028  0.000010|
 | -0.000028  1.002179 -0.000078|
 |  0.000010 -0.000078  1.001955|
Proposed new scale matrix

 |  0.002283  0.000000  0.000367|
 |  0.000000  0.003460  0.000000|
 |  0.000000  0.000000  0.003298|
With corresponding cell

    A    = 437.992  B   = 288.979  C    = 307.155
    Alpha=  90.003  Beta=  99.140  Gamma=  90.004

The CRYST1 cell dimensions

    A    = 437.110  B   = 288.380  C    = 306.560
    Alpha=  90.000  Beta=  99.130  Gamma=  90.000

Variance: 4149.716
(Under-)estimated Z-score: 47.476

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.

   3 OURA  (   3-)  1      N1   C6   C5  120.64   -4.1
   3 OURA  (   3-)  1      C6   N1   C2  125.09    6.8
   4 OCYT  (   4-)  1      C5   C4   N3  124.44    6.4
   6 OGUA  (   6-)  1      N9   C8   N7  113.33    4.5
   7 OGUA  (   7-)  1      N9   C8   N7  113.53    4.9
   8 OURA  (   8-)  1      C1'  N1   C2  123.55    4.9
   8 OURA  (   8-)  1      C5   C4   O4  123.45   -4.1
   8 OURA  (   8-)  1      O4   C4   N3  123.43    5.8
  10 OGUA  (  10-)  1      N9   C8   N7  114.57    6.9
  10 OGUA  (  10-)  1      C5   C6   N1  108.81   -5.4
  12 OURA  (  12-)  1      N1   C6   C5  119.44   -6.5
  13 OCYT  (  13-)  1      C1'  N1   C6  114.57   -5.2
  13 OCYT  (  13-)  1      C1'  N1   C2  124.50    5.2
  15 OURA  (  15-)  1      N1   C6   C5  120.60   -4.2
  15 OURA  (  15-)  1      C5   C4   O4  128.73    4.7
  15 OURA  (  15-)  1      O4   C4   N3  116.32   -4.4
  15 OURA  (  15-)  1      N3   C2   O2  118.96   -4.6
  16 OGUA  (  16-)  1      C1'  N9   C8  118.40   -6.6
  16 OGUA  (  16-)  1      C1'  N9   C4  132.62    4.7
  16 OGUA  (  16-)  1      N9   C4   C5  102.66   -6.8
  16 OGUA  (  16-)  1      N9   C4   N3  130.45    7.4
  16 OGUA  (  16-)  1      C8   N9   C4  108.78    5.9
  16 OGUA  (  16-)  1      N1   C2   N2  110.90   -5.9
  16 OGUA  (  16-)  1      N2   C2   N3  124.20    6.1
  17 OCYT  (  17-)  1      C1'  N1   C6  115.80   -4.2
And so on for a total of 1720 lines.

Error: Tau angle problems

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

2278 ASP   (  57-)  C    6.67
2159 LYS   ( 185-)  B    6.52
2470 ALA   ( 110-)  D    5.70
2915 ARG   ( 130-)  G    5.58
3372 LYS   (  59-)  K    5.41
2822 ILE   (  37-)  G    5.38
3857 LEU   (  33-)  P    5.34
1805 LEU   (  18-)  A    5.24
3853 TYR   (  29-)  P    5.21
3549 TYR   (  55-)  M    5.07
2593 LEU   (  28-)  E    5.05
2634 ARG   (  69-)  E    4.99
2199 LEU   ( 225-)  B    4.87
3734 ILE   (  14-)  O    4.84
3116 LEU   (  60-)  I    4.67
2601 LEU   (  36-)  E    4.60
3856 ARG   (  32-)  P    4.50
2457 LEU   (  97-)  D    4.49
2295 GLN   (  74-)  C    4.47
3917 LEU   (  93-)  P    4.47
3448 PRO   (  76-)  L    4.36
3754 ILE   (  34-)  O    4.32
3752 LYS   (  32-)  O    4.31
3265 LEU   (  89-)  J    4.28
3227 PRO   (  51-)  J    4.26
3757 PHE   (  37-)  O    4.24
2032 LEU   (  58-)  B    4.24
2347 VAL   ( 126-)  C    4.24
2330 LEU   ( 109-)  C    4.23
2030 ILE   (  56-)  B    4.21
2103 ILE   ( 129-)  B    4.19
2482 ASN   ( 122-)  D    4.18
4093 ILE   (  31-)  S    4.17
2535 LEU   ( 175-)  D    4.16
3437 GLU   (  65-)  L    4.13
3599 ASP   ( 131-)  M    4.11
1920 ILE   ( 133-)  A    4.06
2028 GLU   (  54-)  B    4.04
2615 SER   (  50-)  E    4.02
2633 LYS   (  68-)  E    4.02
1842 GLU   (  55-)  A    4.02
1851 ILE   (  64-)  A    4.02

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 : -8.160

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.

3953 GLY   ( 129-)  P    -2.5
3032 GLY   (  97-)  H    -2.4
2702 GLY   ( 137-)  E    -2.4
4164 GLY   (  49-)  T    -2.4
2316 GLY   (  95-)  C    -2.4
3943 GLY   ( 119-)  P    -2.4
3381 GLY   (  68-)  K    -2.4
3500 GLY   ( 135-)  L    -2.4
3932 GLY   ( 108-)  P    -2.4
3546 GLY   (  52-)  M    -2.4
1881 GLY   (  94-)  A    -2.4
4407 GLY   ( 298-)  T    -2.4
4143 GLY   (  28-)  T    -2.4
2176 GLY   ( 202-)  B    -2.3
1812 GLY   (  25-)  A    -2.3
2980 GLY   (  45-)  H    -2.3
1838 GLY   (  51-)  A    -2.2
1973 GLY   ( 186-)  A    -2.2
3589 GLY   ( 121-)  M    -2.2
4014 GLY   (  87-)  Q    -2.2
3532 GLY   (  26-)  M    -2.2
2376 GLY   ( 155-)  C    -2.2
2116 GLY   ( 142-)  B    -2.2
2512 GLY   ( 152-)  D    -2.2
2513 GLY   ( 153-)  D    -2.2
2281 GLY   (  60-)  C    -2.2
4253 GLY   ( 138-)  T    -2.1
2134 GLY   ( 160-)  B    -2.1
2166 GLY   ( 192-)  B    -2.1
2836 GLY   (  51-)  G    -2.1
2086 GLY   ( 112-)  B    -2.1
4212 GLY   (  97-)  T    -2.1
4178 GLY   (  63-)  T    -2.1
4043 GLY   (  20-)  R    -2.1
2800 GLY   ( 126-)  F    -2.1
2137 GLY   ( 163-)  B    -2.1
3657 GLY   (  54-)  N    -2.1
2083 GLY   ( 109-)  B    -2.1
3306 GLY   ( 130-)  J    -2.1
2727 GLY   ( 170-)  E    -2.1
3939 GLY   ( 115-)  P    -2.1
2049 GLY   (  75-)  B    -2.1
4303 GLY   ( 194-)  T    -2.1
3048 GLY   ( 113-)  H    -2.1
3843 GLY   ( 123-)  O    -2.0
3489 GLY   ( 124-)  L    -2.0
4040 GLY   (  17-)  R    -2.0
4413 GLY   ( 304-)  T    -2.0
2123 GLY   ( 149-)  B    -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.

1792 ALA   (   5-)  A  Poor phi/psi
1798 PRO   (  11-)  A  Poor phi/psi
1799 GLU   (  12-)  A  Poor phi/psi
1800 ASP   (  13-)  A  Poor phi/psi
1801 ALA   (  14-)  A  Poor phi/psi, omega poor
1804 LEU   (  17-)  A  omega poor
1808 ASN   (  21-)  A  Poor phi/psi
1811 LEU   (  24-)  A  Poor phi/psi
1812 GLY   (  25-)  A  Poor phi/psi
1813 ALA   (  26-)  A  Poor phi/psi
1816 VAL   (  29-)  A  Poor phi/psi
1817 GLN   (  30-)  A  Poor phi/psi
1820 GLN   (  33-)  A  Poor phi/psi
1823 TYR   (  36-)  A  Poor phi/psi
1824 VAL   (  37-)  A  Poor phi/psi
1825 PHE   (  38-)  A  Poor phi/psi, omega poor
1827 ALA   (  40-)  A  Poor phi/psi
1828 ARG   (  41-)  A  Poor phi/psi
1829 PRO   (  42-)  A  Poor phi/psi
1832 VAL   (  45-)  A  Poor phi/psi
1838 GLY   (  51-)  A  Poor phi/psi
1852 ALA   (  65-)  A  Poor phi/psi
1855 PRO   (  68-)  A  Poor phi/psi
1857 PRO   (  70-)  A  omega poor
1858 GLU   (  71-)  A  Poor phi/psi
And so on for a total of 974 lines.

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.

3326 SER   (  13-)  K    0.35
3472 SER   ( 107-)  L    0.36
3610 GLU   ( 142-)  M    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 OURA  (   3-)  1      0
   4 OCYT  (   4-)  1      0
   5 OURA  (   5-)  1      0
   6 OGUA  (   6-)  1      0
   7 OGUA  (   7-)  1      0
   8 OURA  (   8-)  1      0
   9 OURA  (   9-)  1      0
  10 OGUA  (  10-)  1      0
  11 OADE  (  11-)  1      0
  12 OURA  (  12-)  1      0
  13 OCYT  (  13-)  1      0
  14 OCYT  (  14-)  1      0
  15 OURA  (  15-)  1      0
  16 OGUA  (  16-)  1      0
  17 OCYT  (  17-)  1      0
  18 OCYT  (  18-)  1      0
  19 OADE  (  19-)  1      0
  20 OGUA  (  20-)  1      0
  21 OURA  (  21-)  1      0
  22 OADE  (  22-)  1      0
  23 OGUA  (  23-)  1      0
  24 OURA  (  24-)  1      0
  25 OCYT  (  25-)  1      0
  26 OADE  (  26-)  1      0
  27 OURA  (  27-)  1      0
And so on for a total of 3561 lines.

Warning: Backbone conformation Z-score low

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

Backbone conformation Z-score : -2.841

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.172

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!

4014 GLY   (  87-)  Q   3.55   21
3381 GLY   (  68-)  K   3.34   13
2134 GLY   ( 160-)  B   3.20   15
2116 GLY   ( 142-)  B   2.54   56
2800 GLY   ( 126-)  F   2.52   25
2351 GLY   ( 130-)  C   2.45   63
3904 GLY   (  80-)  P   2.17   51
3882 GLY   (  58-)  P   2.09   10
3247 GLY   (  71-)  J   2.09   11
3758 LEU   (  38-)  O   2.04   80
2254 GLY   (  33-)  C   2.01   10
2060 VAL   (  86-)  B   1.83   11
3437 GLU   (  65-)  L   1.79   10
3875 GLY   (  51-)  P   1.72   46
2404 GLY   ( 183-)  C   1.67   17
3553 ALA   (  59-)  M   1.65   40
2159 LYS   ( 185-)  B   1.58   19
1918 GLN   ( 131-)  A   1.55   10
4240 GLY   ( 125-)  T   1.53   46
3714 GLY   ( 111-)  N   1.53   14
2333 GLY   ( 112-)  C   1.51   80

Warning: Unusual peptide bond conformations

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

3862 PHE   (  38-)  P   2.18
4062 THR   (  39-)  R   1.61

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]

1791 PRO   (   4-)  A    0.00 LOW
1798 PRO   (  11-)  A    0.00 LOW
1822 PRO   (  35-)  A    0.00 LOW
1829 PRO   (  42-)  A    0.00 LOW
1855 PRO   (  68-)  A    0.00 LOW
1857 PRO   (  70-)  A    0.00 LOW
1884 PRO   (  97-)  A    0.00 LOW
1891 PRO   ( 104-)  A    0.00 LOW
1905 PRO   ( 118-)  A    0.00 LOW
1913 PRO   ( 126-)  A    0.00 LOW
1929 PRO   ( 142-)  A    0.00 LOW
1939 PRO   ( 152-)  A    0.00 LOW
1948 PRO   ( 161-)  A    0.00 LOW
1981 PRO   ( 194-)  A    0.00 LOW
1986 PRO   ( 199-)  A    0.00 LOW
1994 PRO   ( 207-)  A    0.00 LOW
2011 PRO   (  37-)  B    0.00 LOW
2036 PRO   (  62-)  B    0.00 LOW
2048 PRO   (  74-)  B    0.00 LOW
2059 PRO   (  85-)  B    0.00 LOW
2112 PRO   ( 138-)  B    0.00 LOW
2125 PRO   ( 151-)  B    0.00 LOW
2145 PRO   ( 171-)  B    0.00 LOW
2147 PRO   ( 173-)  B    0.00 LOW
2156 PRO   ( 182-)  B    0.00 LOW
And so on for a total of 98 lines.

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.

 142 OGUA  ( 142-)  1      N2  <->  173 OADE  ( 173-)  1      C2     1.58    1.52  INTRA BF
 814 OURA  ( 825-)  1      C5  <->  836 OADE  ( 847-)  1      N1     1.26    1.84  INTRA BF
 127 OGUA  ( 127-)  1      N1  <->  179 OADE  ( 179-)  1      N6     1.26    1.59  INTRA BF
 732 OURA  ( 743-)  1      N3  <->  798 OADE  ( 809-)  1      C2     1.24    1.86  INTRA BF
 143 OGUA  ( 143-)  1      O6  <->  172 OCYT  ( 172-)  1      N4     1.09    1.61  INTRA BF
 243 OGUA  ( 243-)  1      O6  <->  250 OCYT  ( 250-)  1      N4     1.09    1.61  INTRA BF
 127 OGUA  ( 127-)  1      N1  <->  179 OADE  ( 179-)  1      C6     1.04    2.06  INTRA BF
 142 OGUA  ( 142-)  1      N2  <->  173 OADE  ( 173-)  1      N1     1.04    1.96  INTRA BF
 127 OGUA  ( 127-)  1      C6  <->  179 OADE  ( 179-)  1      C6     1.03    2.17  INTRA BF
 127 OGUA  ( 127-)  1      C2  <->  179 OADE  ( 179-)  1      N6     1.03    2.07  INTRA BF
 243 OGUA  ( 243-)  1      N1  <->  251 OADE  ( 251-)  1      C6     1.02    2.08  INTRA BF
 732 OURA  ( 743-)  1      N3  <->  798 OADE  ( 809-)  1      N3     1.00    2.00  INTRA BF
 142 OGUA  ( 142-)  1      N1  <->  173 OADE  ( 173-)  1      N1     1.00    2.00  INTRA BF
 142 OGUA  ( 142-)  1      N7  <->  266 OADE  ( 266-)  1      C6     0.96    2.14  INTRA BL
 142 OGUA  ( 142-)  1      C5  <->  266 OADE  ( 266-)  1      N6     0.96    2.14  INTRA BL
 243 OGUA  ( 243-)  1      C6  <->  251 OADE  ( 251-)  1      N6     0.96    2.14  INTRA BF
 650 OURA  ( 650-)  1      N3  <->  673 OADE  ( 684-)  1      N6     0.95    1.90  INTRA BF
 364 OGUA  ( 364-)  1      N2  <->  381 OCYT  ( 381-)  1      N1     0.94    2.06  INTRA BF
 173 OADE  ( 173-)  1      C6  <->  174 OURA  ( 174-)  1      C6     0.92    2.28  INTRA BF
 364 OGUA  ( 364-)  1      N2  <->  381 OCYT  ( 381-)  1      C2     0.92    2.18  INTRA BF
  66 OURA  (  66-)  1      N3  <->   71 OADE  (  71-)  1      N6     0.92    1.93  INTRA BF
 981 OADE  ( 992-)  1      C2  <-> 1001 OURA  (1012-)  1      N3     0.91    2.19  INTRA BL
 243 OGUA  ( 243-)  1      C2  <->  251 OADE  ( 251-)  1      N1     0.90    2.20  INTRA BF
 886 OCYT  ( 897-)  1      N3  <->  903 OGUA  ( 914-)  1      N2     0.88    2.12  INTRA BF
 243 OGUA  ( 243-)  1      C2  <->  251 OADE  ( 251-)  1      C2     0.88    2.32  INTRA BF
And so on for a total of 8554 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

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

inside/outside RMS Z-score : 1.224

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: Q

Note: Inside/Outside RMS Z-score plot

Chain identifier: R

Note: Inside/Outside RMS Z-score plot

Chain identifier: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

Note: Quality value plot

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

Chain identifier: M

Note: Quality value plot

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

Chain identifier: N

Note: Quality value plot

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

Chain identifier: O

Note: Quality value plot

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

Chain identifier: P

Note: Quality value plot

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

Chain identifier: Q

Note: Quality value plot

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

Chain identifier: R

Note: Quality value plot

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

Chain identifier: S

Note: Quality value plot

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

Chain identifier: T

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.

3615 GLN   (  12-)  N   -4.19
4078 LYS   (  16-)  S   -4.18
3617 GLN   (  14-)  N   -4.17
2807 LYS   ( 133-)  F   -4.15
3504 LYS   ( 139-)  L   -4.12
3564 GLN   (  70-)  M   -4.09
3563 LYS   (  69-)  M   -4.07
3619 GLN   (  16-)  N   -4.03
3154 ASN   (  98-)  I   -4.00
3889 ASN   (  65-)  P   -3.97
3985 ARG   (  58-)  Q   -3.95
3933 ARG   ( 109-)  P   -3.95
4045 ARG   (  22-)  R   -3.91
3183 ARG   ( 127-)  I   -3.88
3788 ARG   (  68-)  O   -3.85
2696 GLN   ( 131-)  E   -3.85
3204 LEU   (  28-)  J   -3.84
2065 ARG   (  91-)  B   -3.83
2810 ARG   ( 136-)  F   -3.80
3777 ARG   (  57-)  O   -3.78
3506 THR   ( 141-)  L   -3.77
4102 ARG   (  40-)  S   -3.76
2803 ARG   ( 129-)  F   -3.76
3748 ARG   (  28-)  O   -3.76
3488 ARG   ( 123-)  L   -3.76
And so on for a total of 578 lines.

Warning: Abnormal packing Z-score for sequential residues

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

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

1793 THR   (   6-)  A     - 1796 LEU   (   9-)  A        -1.79
1797 THR   (  10-)  A     - 1800 ASP   (  13-)  A        -1.70
1801 ALA   (  14-)  A     - 1806 ALA   (  19-)  A        -2.00
1813 ALA   (  26-)  A     - 1817 GLN   (  30-)  A        -2.24
1818 VAL   (  31-)  A     - 1821 GLU   (  34-)  A        -2.32
1822 PRO   (  35-)  A     - 1826 ASN   (  39-)  A        -2.13
1853 ALA   (  66-)  A     - 1861 VAL   (  74-)  A        -1.97
1872 ALA   (  85-)  A     - 1876 PHE   (  89-)  A        -1.98
1895 THR   ( 108-)  A     - 1898 ILE   ( 111-)  A        -2.37
1901 SER   ( 114-)  A     - 1904 GLU   ( 117-)  A        -2.25
1905 PRO   ( 118-)  A     - 1908 VAL   ( 121-)  A        -2.09
1911 THR   ( 124-)  A     - 1914 ARG   ( 127-)  A        -2.00
1924 SER   ( 137-)  A     - 1928 ILE   ( 141-)  A        -2.18
1933 LEU   ( 146-)  A     - 1937 ASP   ( 150-)  A        -2.28
1946 ALA   ( 159-)  A     - 1952 ARG   ( 165-)  A        -2.36
1953 GLY   ( 166-)  A     - 1957 ILE   ( 170-)  A        -2.11
1958 GLY   ( 171-)  A     - 1967 GLU   ( 180-)  A        -2.05
1968 VAL   ( 181-)  A     - 1972 ARG   ( 185-)  A        -2.13
1986 PRO   ( 199-)  A     - 1992 ARG   ( 205-)  A        -2.44
1996 GLU   ( 209-)  A     - 2000 GLN   ( 213-)  A        -1.98
2016 GLY   (  42-)  B     - 2020 LYS   (  46-)  B        -2.27
2036 PRO   (  62-)  B     - 2044 ASP   (  70-)  B        -2.32
2054 VAL   (  80-)  B     - 2058 LYS   (  84-)  B        -2.10
2059 PRO   (  85-)  B     - 2063 GLN   (  89-)  B        -2.70
2064 THR   (  90-)  B     - 2069 ARG   (  95-)  B        -2.31
And so on for a total of 217 lines.

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: Q

Note: Second generation quality Z-score plot

Chain identifier: R

Note: Second generation quality Z-score plot

Chain identifier: S

Note: Second generation quality Z-score plot

Chain identifier: T

Water, ion, and hydrogenbond related checks

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.

   6 OGUA  (   6-)  1      N2
  17 OCYT  (  17-)  1      O2'
  30 OGUA  (  30-)  1      N2
  32 OURA  (  32-)  1      N3
  34 OGUA  (  34-)  1      N1
  47 OADE  (  47-)  1      N6
  51 OADE  (  51-)  1      N6
  53 OGUA  (  53-)  1      N2
  81 OGUA  (  81-)  1      N1
  89 OGUA  (  89-)  1      N1
 102 OURA  ( 102-)  1      N3
 105 OADE  ( 105-)  1      N6
 111 OURA  ( 111-)  1      N3
 115 OGUA  ( 115-)  1      N2
 121 OURA  ( 121-)  1      N3
 126 OADE  ( 126-)  1      N6
 139 OCYT  ( 139-)  1      N4
 142 OGUA  ( 142-)  1      N1
 151 OGUA  ( 151-)  1      N1
 174 OURA  ( 174-)  1      N3
 175 OGUA  ( 175-)  1      N2
 186 OCYT  ( 186-)  1      N4
 187 OGUA  ( 187-)  1      N2
 201 OGUA  ( 201-)  1      N1
 214 OGUA  ( 214-)  1      N2
And so on for a total of 436 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:

  2nd generation packing quality : -11.301 (bad)
  Ramachandran plot appearance   :  -8.160 (bad)
  Backbone conformation          :  -2.841

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.862
  Bond angles                    :   1.290
  Omega angle restraints         :   1.304 (loose)
  Side chain planarity           :   0.000 (tight)
  Improper dihedral distribution :   0.688
  B-factor distribution          :   0.448
  Inside/Outside distribution    :   1.224 (unusual)

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 4.00


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -7.5 (bad)
  Ramachandran plot appearance   :  -4.7 (bad)
  Backbone conformation          :  -1.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.862
  Bond angles                    :   1.290
  Omega angle restraints         :   1.304 (loose)
  Side chain planarity           :   0.000 (tight)
  Improper dihedral distribution :   0.688
  B-factor distribution          :   0.448
  Inside/Outside distribution    :   1.224 (unusual)
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.