WHAT IF Check report

This file was created 2012-09-07 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 pdb3k7a.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: I 2 2 2
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: 425378.781
Volume of the Unit Cell V= 18586854.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 10.924
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 4.570 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)

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: E

Note: Ramachandran plot

Chain identifier: F

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

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'.

 411 SER   ( 418-)  A      OG
 412 LYS   ( 419-)  A      CG
 412 LYS   ( 419-)  A      CD
 412 LYS   ( 419-)  A      CE
 412 LYS   ( 419-)  A      NZ
 413 ARG   ( 420-)  A      CG
 413 ARG   ( 420-)  A      CD
 413 ARG   ( 420-)  A      NE
 413 ARG   ( 420-)  A      CZ
 413 ARG   ( 420-)  A      NH1
 413 ARG   ( 420-)  A      NH2
 416 ASP   ( 423-)  A      CG
 416 ASP   ( 423-)  A      OD1
 416 ASP   ( 423-)  A      OD2
1677 ARG   ( 336-)  B      CG
1677 ARG   ( 336-)  B      CD
1677 ARG   ( 336-)  B      NE
1677 ARG   ( 336-)  B      CZ
1677 ARG   ( 336-)  B      NH1
1677 ARG   ( 336-)  B      NH2
1678 ARG   ( 337-)  B      CG
1678 ARG   ( 337-)  B      CD
1678 ARG   ( 337-)  B      NE
1678 ARG   ( 337-)  B      CZ
1678 ARG   ( 337-)  B      NH1
And so on for a total of 792 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 VAL   (   2-)  A    High
   2 GLY   (   3-)  A    High
   3 GLN   (   4-)  A    High
   4 GLN   (   5-)  A    High
   5 TYR   (   6-)  A    High
   6 SER   (   7-)  A    High
   7 SER   (   8-)  A    High
   8 ALA   (   9-)  A    High
   9 PRO   (  10-)  A    High
  10 LEU   (  11-)  A    High
  11 ARG   (  12-)  A    High
  12 THR   (  13-)  A    High
  13 VAL   (  14-)  A    High
  14 LYS   (  15-)  A    High
  15 GLU   (  16-)  A    High
  16 VAL   (  17-)  A    High
  17 GLN   (  18-)  A    High
  18 PHE   (  19-)  A    High
  19 GLY   (  20-)  A    High
  20 LEU   (  21-)  A    High
  21 PHE   (  22-)  A    High
  22 SER   (  23-)  A    High
  23 PRO   (  24-)  A    High
  24 GLU   (  25-)  A    High
  25 GLU   (  26-)  A    High
And so on for a total of 3744 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) : 93.000

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: E

Note: B-factor plot

Chain identifier: F

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

   5 TYR   (   6-)  A
 369 TYR   ( 376-)  A
 376 TYR   ( 383-)  A
 397 TYR   ( 404-)  A
 410 TYR   ( 417-)  A
 421 TYR   ( 428-)  A
 471 TYR   ( 478-)  A
 797 TYR   ( 804-)  A
 845 TYR   ( 852-)  A
1250 TYR   (1287-)  A
1466 TYR   (  96-)  B
1531 TYR   ( 190-)  B
1543 TYR   ( 202-)  B
1644 TYR   ( 303-)  B
2024 TYR   ( 692-)  B
2095 TYR   ( 769-)  B
2111 TYR   ( 785-)  B
2124 TYR   ( 798-)  B
2137 TYR   ( 811-)  B
2159 TYR   ( 833-)  B
2300 TYR   ( 994-)  B
2370 TYR   (1064-)  B
2498 TYR   (1192-)  B
2610 TYR   (  82-)  C
2642 TYR   ( 114-)  C
2719 TYR   ( 191-)  C
2721 TYR   ( 193-)  C
2757 TYR   ( 229-)  C
2823 TYR   (  28-)  E
2841 TYR   (  46-)  E
2907 TYR   ( 112-)  E
2963 TYR   ( 168-)  E
3027 TYR   (  88-)  F
3113 TYR   (  20-)  H
3176 TYR   (  95-)  H
3183 TYR   ( 102-)  H
3196 TYR   ( 115-)  H
3210 TYR   ( 129-)  H
3260 TYR   (  34-)  I
3408 TYR   (  63-)  J
3491 TYR   (  81-)  K
3529 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.

  18 PHE   (  19-)  A
  21 PHE   (  22-)  A
  94 PHE   (  95-)  A
 212 PHE   ( 219-)  A
 217 PHE   ( 224-)  A
 221 PHE   ( 228-)  A
 245 PHE   ( 252-)  A
 257 PHE   ( 264-)  A
 340 PHE   ( 347-)  A
 461 PHE   ( 468-)  A
 475 PHE   ( 482-)  A
 533 PHE   ( 540-)  A
 584 PHE   ( 591-)  A
 714 PHE   ( 721-)  A
 770 PHE   ( 777-)  A
 772 PHE   ( 779-)  A
 780 PHE   ( 787-)  A
 807 PHE   ( 814-)  A
 808 PHE   ( 815-)  A
 886 PHE   ( 893-)  A
 940 PHE   ( 947-)  A
1035 PHE   (1042-)  A
1157 PHE   (1174-)  A
1193 PHE   (1220-)  A
1295 PHE   (1332-)  A
And so on for a total of 67 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.

 181 ASP   ( 188-)  A
 300 ASP   ( 307-)  A
 355 ASP   ( 362-)  A
 401 ASP   ( 408-)  A
 476 ASP   ( 483-)  A
 709 ASP   ( 716-)  A
 783 ASP   ( 790-)  A
1177 ASP   (1204-)  A
1322 ASP   (1359-)  A
1635 ASP   ( 294-)  B
1737 ASP   ( 396-)  B
2116 ASP   ( 790-)  B
2217 ASP   ( 895-)  B
2242 ASP   ( 936-)  B
2492 ASP   (1186-)  B
2621 ASP   (  93-)  C
2836 ASP   (  41-)  E
2879 ASP   (  84-)  E
3055 ASP   ( 116-)  F
3434 ASP   (  24-)  K

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.

 252 GLU   ( 259-)  A
 479 GLU   ( 486-)  A
 629 GLU   ( 636-)  A
 671 GLU   ( 678-)  A
 794 GLU   ( 801-)  A
 839 GLU   ( 846-)  A
 872 GLU   ( 879-)  A
 924 GLU   ( 931-)  A
 925 GLU   ( 932-)  A
1151 GLU   (1168-)  A
1417 GLU   (  28-)  B
1454 GLU   (  65-)  B
1474 GLU   ( 104-)  B
1550 GLU   ( 209-)  B
1962 GLU   ( 621-)  B
2031 GLU   ( 699-)  B
2334 GLU   (1028-)  B
2376 GLU   (1070-)  B
2438 GLU   (1132-)  B
2455 GLU   (1149-)  B
2578 GLU   (  50-)  C
2580 GLU   (  52-)  C
2694 GLU   ( 166-)  C
2799 GLU   (   4-)  E
2932 GLU   ( 137-)  E
3053 GLU   ( 114-)  F
3207 GLU   ( 126-)  H
3307 GLU   (  82-)  I
3364 GLU   (  19-)  J

Geometric checks

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.997694 -0.000022 -0.000392|
 | -0.000022  0.998201 -0.000150|
 | -0.000392 -0.000150  0.998023|
Proposed new scale matrix

 |  0.004909  0.000000  0.000002|
 |  0.000000  0.004633  0.000000|
 |  0.000000  0.000000  0.002380|
With corresponding cell

    A    = 203.694  B   = 215.827  C    = 420.220
    Alpha=  90.004  Beta=  90.025  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 204.165  B   = 216.216  C    = 421.053
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 503.613
(Under-)estimated Z-score: 16.539

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.

 392 HIS   ( 399-)  A      CG   ND1  CE1 109.67    4.1
 451 HIS   ( 458-)  A      CG   ND1  CE1 109.72    4.1
1362 ARG   (1399-)  A      CB   CG   CD  106.04   -4.0
2539 ARG   (  11-)  C      CB   CG   CD  105.59   -4.3
3660 ASP   ( 120-)  M      N    CA   C   123.53    4.4
3700 GLU   ( 160-)  M      N    CA   C   124.08    4.6
3701 LYS   ( 161-)  M      N    CA   C   124.73    4.8
3705 GLY   ( 165-)  M      N    CA   C   100.02   -4.3
3723 ALA   ( 183-)  M      N    CA   C    97.86   -4.8
3738 VAL   ( 198-)  M      N    CA   C   123.99    4.6

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.

 181 ASP   ( 188-)  A
 252 GLU   ( 259-)  A
 300 ASP   ( 307-)  A
 355 ASP   ( 362-)  A
 401 ASP   ( 408-)  A
 476 ASP   ( 483-)  A
 479 GLU   ( 486-)  A
 629 GLU   ( 636-)  A
 671 GLU   ( 678-)  A
 709 ASP   ( 716-)  A
 783 ASP   ( 790-)  A
 794 GLU   ( 801-)  A
 839 GLU   ( 846-)  A
 872 GLU   ( 879-)  A
 924 GLU   ( 931-)  A
 925 GLU   ( 932-)  A
1151 GLU   (1168-)  A
1177 ASP   (1204-)  A
1322 ASP   (1359-)  A
1417 GLU   (  28-)  B
1454 GLU   (  65-)  B
1474 GLU   ( 104-)  B
1550 GLU   ( 209-)  B
1635 ASP   ( 294-)  B
1737 ASP   ( 396-)  B
1962 GLU   ( 621-)  B
2031 GLU   ( 699-)  B
2116 ASP   ( 790-)  B
2217 ASP   ( 895-)  B
2242 ASP   ( 936-)  B
2334 GLU   (1028-)  B
2376 GLU   (1070-)  B
2438 GLU   (1132-)  B
2455 GLU   (1149-)  B
2492 ASP   (1186-)  B
2578 GLU   (  50-)  C
2580 GLU   (  52-)  C
2621 ASP   (  93-)  C
2694 GLU   ( 166-)  C
2799 GLU   (   4-)  E
2836 ASP   (  41-)  E
2879 ASP   (  84-)  E
2932 GLU   ( 137-)  E
3053 GLU   ( 114-)  F
3055 ASP   ( 116-)  F
3207 GLU   ( 126-)  H
3307 GLU   (  82-)  I
3364 GLU   (  19-)  J
3434 ASP   (  24-)  K

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.

3723 ALA   ( 183-)  M    5.62
3738 VAL   ( 198-)  M    5.39
3701 LYS   ( 161-)  M    5.16
3705 GLY   ( 165-)  M    4.86
1232 GLU   (1269-)  A    4.59
3700 GLU   ( 160-)  M    4.31
3564 LEU   (  64-)  L    4.25
3660 ASP   ( 120-)  M    4.15
 659 ILE   ( 666-)  A    4.11
1637 GLU   ( 296-)  B    4.07

Torsion-related checks

Warning: Ramachandran Z-score low

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

Ramachandran Z-score : -3.771

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.

 589 THR   ( 596-)  A    -3.4
  43 THR   (  44-)  A    -3.2
3162 PRO   (  81-)  H    -3.1
 344 THR   ( 351-)  A    -3.1
  68 THR   (  69-)  A    -3.0
3110 PRO   (  17-)  H    -2.8
1516 ARG   ( 175-)  B    -2.8
 803 PRO   ( 810-)  A    -2.7
2520 PRO   (1214-)  B    -2.7
2202 THR   ( 880-)  B    -2.7
  34 ILE   (  35-)  A    -2.7
3527 LEU   (  27-)  L    -2.7
1105 PRO   (1122-)  A    -2.7
2156 TYR   ( 830-)  B    -2.6
2638 THR   ( 110-)  C    -2.6
2352 PRO   (1046-)  B    -2.6
 444 HIS   ( 451-)  A    -2.6
2922 ILE   ( 127-)  E    -2.6
1589 SER   ( 248-)  B    -2.6
2534 PRO   (   6-)  C    -2.6
 311 SER   ( 318-)  A    -2.6
2978 PRO   ( 183-)  E    -2.6
1028 TYR   (1035-)  A    -2.6
1706 THR   ( 365-)  B    -2.6
1804 THR   ( 463-)  B    -2.5
And so on for a total of 162 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
  31 VAL   (  32-)  A  Poor phi/psi
  33 LYS   (  34-)  A  Poor phi/psi
  40 MET   (  41-)  A  omega poor
  44 GLN   (  45-)  A  Poor phi/psi
  47 ALA   (  48-)  A  Poor phi/psi
  48 LYS   (  49-)  A  Poor phi/psi
  53 ASN   (  54-)  A  Poor phi/psi
  54 ASP   (  55-)  A  PRO omega poor
  56 ARG   (  57-)  A  Poor phi/psi
  60 ILE   (  61-)  A  Poor phi/psi
  62 ARG   (  63-)  A  Poor phi/psi
  66 CYS   (  67-)  A  Poor phi/psi
  68 THR   (  69-)  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
  74 ASN   (  75-)  A  Poor phi/psi
  75 GLU   (  76-)  A  Poor phi/psi
  78 GLY   (  79-)  A  Poor phi/psi
  86 ALA   (  87-)  A  Poor phi/psi
 108 HIS   ( 109-)  A  Poor phi/psi
 157 ARG   ( 164-)  A  Poor phi/psi
 160 CYS   ( 167-)  A  Poor phi/psi
 161 GLY   ( 168-)  A  Poor phi/psi
And so on for a total of 315 lines.

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

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

chi-1/chi-2 correlation Z-score : -3.620

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.

1040 SER   (1047-)  A    0.34
1528 SER   ( 187-)  B    0.34
3365 SER   (  20-)  J    0.36
3503 SER   (  93-)  K    0.36
 198 GLU   ( 205-)  A    0.36
1417 GLU   (  28-)  B    0.36
2560 SER   (  32-)  C    0.38
2466 VAL   (1160-)  B    0.38
1064 SER   (1071-)  A    0.39
2136 GLU   ( 810-)  B    0.39

Warning: Unusual backbone conformations

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

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

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

   5 TYR   (   6-)  A      0
  18 PHE   (  19-)  A      0
  30 SER   (  31-)  A      0
  32 ALA   (  33-)  A      0
  33 LYS   (  34-)  A      0
  34 ILE   (  35-)  A      0
  37 PRO   (  38-)  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
  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
  59 SER   (  60-)  A      0
  60 ILE   (  61-)  A      0
  61 ASP   (  62-)  A      0
  62 ARG   (  63-)  A      0
And so on for a total of 1724 lines.

Warning: Backbone oxygen evaluation

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

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

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

3111 GLY   (  18-)  H   3.50   12
2669 GLY   ( 141-)  C   3.22   11
1588 GLY   ( 247-)  B   3.11   11
1903 GLY   ( 562-)  B   2.72   15
3629 GLY   (  89-)  M   2.43   17
 654 GLY   ( 661-)  A   1.88   11
1259 GLY   (1296-)  A   1.79   68
 666 GLY   ( 673-)  A   1.69   14
 959 ASN   ( 966-)  A   1.65   12
3423 GLY   (  13-)  K   1.53   13

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...

 839 GLU   ( 846-)  A   1.74

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]

3579 PRO   (  25-)  M    0.00 LOW
3585 PRO   (  31-)  M    0.00 LOW
3586 PRO   (  32-)  M    0.00 LOW
3625 PRO   (  85-)  M    0.00 LOW
3683 PRO   ( 143-)  M    0.00 LOW

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].

  23 PRO   (  24-)  A  -138.6 envelop C-delta (-144 degrees)
  55 PRO   (  56-)  A   111.1 envelop C-beta (108 degrees)
  88 PRO   (  89-)  A  -124.4 half-chair C-delta/C-gamma (-126 degrees)
 237 PRO   ( 244-)  A  -123.9 half-chair C-delta/C-gamma (-126 degrees)
 375 PRO   ( 382-)  A  -113.9 envelop C-gamma (-108 degrees)
 556 PRO   ( 563-)  A    50.5 half-chair C-delta/C-gamma (54 degrees)
 561 PRO   ( 568-)  A  -154.7 half-chair N/C-delta (-162 degrees)
 632 PRO   ( 639-)  A  -124.8 half-chair C-delta/C-gamma (-126 degrees)
 787 PRO   ( 794-)  A  -125.6 half-chair C-delta/C-gamma (-126 degrees)
 803 PRO   ( 810-)  A   107.1 envelop C-beta (108 degrees)
1082 PRO   (1099-)  A  -115.0 envelop C-gamma (-108 degrees)
1105 PRO   (1122-)  A    99.5 envelop C-beta (108 degrees)
1257 PRO   (1294-)  A  -115.7 envelop C-gamma (-108 degrees)
1265 PRO   (1302-)  A  -118.8 half-chair C-delta/C-gamma (-126 degrees)
1470 PRO   ( 100-)  B   115.6 envelop C-beta (108 degrees)
1512 PRO   ( 171-)  B  -131.8 half-chair C-delta/C-gamma (-126 degrees)
1537 PRO   ( 196-)  B  -115.7 envelop C-gamma (-108 degrees)
1622 PRO   ( 281-)  B   157.2 half-chair C-alpha/N (162 degrees)
1906 PRO   ( 565-)  B  -148.4 envelop C-delta (-144 degrees)
2044 PRO   ( 712-)  B   -51.8 half-chair C-beta/C-alpha (-54 degrees)
2071 PRO   ( 745-)  B  -115.3 envelop C-gamma (-108 degrees)
2246 PRO   ( 940-)  B   -58.5 half-chair C-beta/C-alpha (-54 degrees)
2280 PRO   ( 974-)  B  -115.7 envelop C-gamma (-108 degrees)
2314 PRO   (1008-)  B   -56.1 half-chair C-beta/C-alpha (-54 degrees)
2320 PRO   (1014-)  B  -125.5 half-chair C-delta/C-gamma (-126 degrees)
2324 PRO   (1018-)  B   106.9 envelop C-beta (108 degrees)
2352 PRO   (1046-)  B   104.0 envelop C-beta (108 degrees)
2424 PRO   (1118-)  B   108.3 envelop C-beta (108 degrees)
2534 PRO   (   6-)  C   166.7 half-chair C-alpha/N (162 degrees)
2570 PRO   (  42-)  C    49.5 half-chair C-delta/C-gamma (54 degrees)
2710 PRO   ( 182-)  C  -114.0 envelop C-gamma (-108 degrees)
2746 PRO   ( 218-)  C    51.6 half-chair C-delta/C-gamma (54 degrees)
2920 PRO   ( 125-)  E   -62.4 half-chair C-beta/C-alpha (-54 degrees)
2946 PRO   ( 151-)  E   -53.2 half-chair C-beta/C-alpha (-54 degrees)
2978 PRO   ( 183-)  E   105.3 envelop C-beta (108 degrees)
3056 PRO   ( 117-)  F  -113.7 envelop C-gamma (-108 degrees)
3070 PRO   ( 131-)  F   -53.7 half-chair C-beta/C-alpha (-54 degrees)
3078 PRO   ( 139-)  F  -112.5 envelop C-gamma (-108 degrees)
3110 PRO   (  17-)  H   -44.9 envelop C-alpha (-36 degrees)
3162 PRO   (  81-)  H    21.6 half-chair N/C-delta (18 degrees)
3163 PRO   (  82-)  H   -60.0 half-chair C-beta/C-alpha (-54 degrees)
3476 PRO   (  66-)  K  -114.3 envelop C-gamma (-108 degrees)
3493 PRO   (  83-)  K  -119.7 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

3303 CYS   (  78-)  I      CB  <-> 3766  ZN   ( 204-)  I     ZN      0.93    2.27  INTRA BF
3300 CYS   (  75-)  I      CB  <-> 3328 CYS   ( 103-)  I      SG     0.68    2.72  INTRA BF
  66 CYS   (  67-)  A      SG  <->   76 CYS   (  77-)  A      SG     0.65    2.80  INTRA BL
3300 CYS   (  75-)  I      SG  <-> 3333 HIS   ( 108-)  I      CD2    0.59    2.81  INTRA BF
 434 PRO   ( 441-)  A      CD  <->  491 ARG   ( 498-)  A      NH2    0.59    2.51  INTRA BL
3548 CYS   (  48-)  L      SG  <-> 3549 LYS   (  49-)  L      N      0.59    2.61  INTRA BF
3233 CYS   (   7-)  I      SG  <-> 3236 CYS   (  10-)  I      SG     0.54    2.91  INTRA BL
  64 LEU   (  65-)  A      CD1 <-> 3573 ASN   (  19-)  M      O      0.49    2.31  INTRA BF
3300 CYS   (  75-)  I      SG  <-> 3333 HIS   ( 108-)  I      CB     0.49    2.91  INTRA BF
1327 ASN   (1364-)  A      ND2 <-> 1329 ARG   (1366-)  A      CG     0.47    2.63  INTRA BL
2469 CYS   (1163-)  B      SG  <-> 2493 ASN   (1187-)  B      ND2    0.43    2.87  INTRA BL
 560 LYS   ( 567-)  A      CB  <->  561 PRO   ( 568-)  A      CD     0.43    2.67  INTRA BF
2469 CYS   (1163-)  B      SG  <-> 2491 CYS   (1185-)  B      SG     0.42    3.03  INTRA BL
2594 ARG   (  66-)  C      NH2 <-> 3348 VAL   (   3-)  J      O      0.42    2.28  INTRA BL
 848 THR   ( 855-)  A      CG2 <->  850 ARG   ( 857-)  A      NE     0.41    2.69  INTRA BL
2621 ASP   (  93-)  C      O   <-> 2655 ARG   ( 127-)  C      NH2    0.41    2.29  INTRA BL
2410 HIS   (1104-)  B      NE2 <-> 2432 GLY   (1126-)  B      O      0.39    2.31  INTRA BL
3163 PRO   (  82-)  H      O   <-> 3165 ALA   (  84-)  H      N      0.38    2.32  INTRA BF
3162 PRO   (  81-)  H      CB  <-> 3163 PRO   (  82-)  H      CD     0.38    2.72  INTRA BF
  66 CYS   (  67-)  A      SG  <->   69 CYS   (  70-)  A      SG     0.37    3.08  INTRA BL
3255 CYS   (  29-)  I      SG  <-> 3258 CYS   (  32-)  I      N      0.36    2.94  INTRA BF
 509 SER   ( 516-)  A      O   <->  511 LYS   ( 518-)  A      N      0.35    2.35  INTRA BL
3643 ASP   ( 103-)  M      O   <-> 3646 PHE   ( 106-)  M      N      0.35    2.35  INTRA BF
2263 ASN   ( 957-)  B      O   <-> 2265 ASP   ( 959-)  B      N      0.35    2.35  INTRA BF
1976 ARG   ( 635-)  B      NH1 <-> 2068 GLU   ( 742-)  B      OE2    0.34    2.36  INTRA BL
And so on for a total of 596 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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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

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.

 410 TYR   ( 417-)  A      -7.95
  46 ARG   (  47-)  A      -7.69
1932 ARG   ( 591-)  B      -7.64
1616 TYR   ( 275-)  B      -7.62
   5 TYR   (   6-)  A      -7.39
 409 ARG   ( 416-)  A      -7.19
2435 ARG   (1129-)  B      -6.93
3112 ARG   (  19-)  H      -6.74
3161 ARG   (  80-)  H      -6.73
2402 ARG   (1096-)  B      -6.66
 304 GLN   ( 311-)  A      -6.66
2430 ARG   (1124-)  B      -6.61
2200 GLN   ( 878-)  B      -6.60
 250 ARG   ( 257-)  A      -6.50
 245 PHE   ( 252-)  A      -6.50
1987 LEU   ( 646-)  B      -6.49
2414 ARG   (1108-)  B      -6.49
3542 ARG   (  42-)  L      -6.44
1618 LYS   ( 277-)  B      -6.40
 107 MET   ( 108-)  A      -6.38
 274 HIS   ( 281-)  A      -6.29
 249 GLN   ( 256-)  A      -6.26
2046 GLU   ( 714-)  B      -6.24
3547 ARG   (  47-)  L      -6.23
 313 ARG   ( 320-)  A      -6.22
And so on for a total of 127 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.

   3 GLN   (   4-)  A         5 - TYR      6- ( A)         -5.24
1428 ARG   (  39-)  B      1430 - LYS     41- ( B)         -4.61
1773 MET   ( 432-)  B      1775 - ARG    434- ( B)         -4.55
2055 ILE   ( 729-)  B      2057 - VAL    731- ( B)         -4.67
2205 LEU   ( 883-)  B      2209 - HIS    887- ( B)         -5.12
3342 LYS   ( 117-)  I      3344 - THR    119- ( I)         -5.03

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: 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: 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

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.

3631 ASN   (  91-)  M   -4.14
3727 ARG   ( 187-)  M   -4.02
3591 ARG   (  37-)  M   -3.98
1845 ARG   ( 504-)  B   -3.89
3610 LEU   (  56-)  M   -3.76
 413 ARG   ( 420-)  A   -3.73
3604 LEU   (  50-)  M   -3.61
 412 LYS   ( 419-)  A   -3.56
1677 ARG   ( 336-)  B   -3.49
3638 LYS   (  98-)  M   -3.45
3572 LEU   (  18-)  M   -3.41
1678 ARG   ( 337-)  B   -3.41
3735 LEU   ( 195-)  M   -3.40
3632 LEU   (  92-)  M   -3.35
3682 LEU   ( 142-)  M   -3.35
3592 PHE   (  38-)  M   -3.21
3213 LEU   ( 132-)  H   -3.19
3644 MET   ( 104-)  M   -3.16
3594 GLU   (  40-)  M   -3.10
3708 MET   ( 168-)  M   -3.08
 465 LEU   ( 472-)  A   -3.05
3614 ARG   (  60-)  M   -3.04
3618 ARG   (  64-)  M   -3.03
1849 LEU   ( 508-)  B   -3.02
3722 ARG   ( 182-)  M   -3.02
And so on for a total of 83 lines.

Warning: Abnormal packing Z-score for sequential residues

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

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

  69 CYS   (  70-)  A     -   72 GLY   (  73-)  A        -1.78
 243 ILE   ( 250-)  A     -  246 ASN   ( 253-)  A        -2.03
 302 ALA   ( 309-)  A     -  307 ALA   ( 314-)  A        -2.00
1780 ALA   ( 439-)  B     - 1783 PHE   ( 442-)  B        -1.83
1847 GLY   ( 506-)  B     - 1850 ALA   ( 509-)  B        -2.23
3270 ARG   (  45-)  I     - 3273 LEU   (  48-)  I        -1.93
3571 ASN   (  17-)  M     - 3576 LEU   (  22-)  M        -2.36
3577 THR   (  23-)  M     - 3592 PHE   (  38-)  M        -2.42
3593 SER   (  39-)  M     - 3599 CYS   (  45-)  M        -2.42
3603 GLY   (  49-)  M     - 3606 LEU   (  52-)  M        -2.38
3607 SER   (  53-)  M     - 3612 ASP   (  58-)  M        -2.54
3615 SER   (  61-)  M     - 3618 ARG   (  64-)  M        -2.46
3623 SER   (  83-)  M     - 3628 ASP   (  88-)  M        -2.13
3629 GLY   (  89-)  M     - 3632 LEU   (  92-)  M        -2.74
3633 SER   (  93-)  M     - 3636 ILE   (  96-)  M        -2.18
3642 THR   ( 102-)  M     - 3646 PHE   ( 106-)  M        -2.27
3647 THR   ( 107-)  M     - 3650 LEU   ( 110-)  M        -2.03
3655 GLY   ( 115-)  M     - 3667 GLN   ( 127-)  M        -2.25
3671 ALA   ( 131-)  M     - 3687 LYS   ( 147-)  M        -2.30
3688 ASP   ( 148-)  M     - 3692 GLU   ( 152-)  M        -2.10
3693 ALA   ( 153-)  M     - 3701 LYS   ( 161-)  M        -2.28
3707 SER   ( 167-)  M     - 3713 ALA   ( 173-)  M        -2.15
3714 ALA   ( 174-)  M     - 3727 ARG   ( 187-)  M        -2.40
3728 THR   ( 188-)  M     - 3733 GLN   ( 193-)  M        -1.97
3734 SER   ( 194-)  M     - 3739 LYS   ( 199-)  M        -2.43
3740 THR   ( 200-)  M     - 3743 PHE   ( 203-)  M        -2.17
3748 ASN   ( 208-)  M     - 3751 LYS   ( 211-)  M        -1.90
3752 ASN   ( 212-)  M     - 3755 ARG   ( 215-)  M        -2.26

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: E

Note: Second generation quality Z-score plot

Chain identifier: F

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

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.

  91 HIS   (  92-)  A
 246 ASN   ( 253-)  A
 249 GLN   ( 256-)  A
 274 HIS   ( 281-)  A
 304 GLN   ( 311-)  A
 383 GLN   ( 390-)  A
 392 HIS   ( 399-)  A
 428 HIS   ( 435-)  A
 496 GLN   ( 503-)  A
 734 ASN   ( 741-)  A
 750 ASN   ( 757-)  A
 779 HIS   ( 786-)  A
 851 ASN   ( 858-)  A
 987 GLN   ( 994-)  A
1111 GLN   (1128-)  A
1395 GLN   (1432-)  A
1556 GLN   ( 215-)  B
1577 HIS   ( 236-)  B
1641 HIS   ( 300-)  B
1707 GLN   ( 366-)  B
1774 GLN   ( 433-)  B
1810 GLN   ( 469-)  B
1856 HIS   ( 515-)  B
1857 ASN   ( 516-)  B
1859 HIS   ( 518-)  B
1879 ASN   ( 538-)  B
2089 GLN   ( 763-)  B
2168 ASN   ( 842-)  B
2263 ASN   ( 957-)  B
2368 HIS   (1062-)  B
2371 GLN   (1065-)  B
2499 GLN   (1193-)  B
2601 GLN   (  73-)  C
2770 GLN   ( 242-)  C
3238 ASN   (  12-)  I
3314 GLN   (  89-)  I
3398 HIS   (  53-)  J
3475 HIS   (  65-)  K
3486 GLN   (  76-)  K
3502 ASN   (  92-)  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.

   3 GLN   (   4-)  A      N
   4 GLN   (   5-)  A      N
   8 ALA   (   9-)  A      N
  11 ARG   (  12-)  A      NE
  24 GLU   (  25-)  A      N
  32 ALA   (  33-)  A      N
  33 LYS   (  34-)  A      N
  34 ILE   (  35-)  A      N
  35 ARG   (  36-)  A      N
  36 PHE   (  37-)  A      N
  38 GLU   (  39-)  A      N
  51 GLY   (  52-)  A      N
  53 ASN   (  54-)  A      N
  54 ASP   (  55-)  A      N
  56 ARG   (  57-)  A      N
  58 GLY   (  59-)  A      N
  62 ARG   (  63-)  A      N
  64 LEU   (  65-)  A      N
  67 GLN   (  68-)  A      NE2
  75 GLU   (  76-)  A      N
  76 CYS   (  77-)  A      N
  78 GLY   (  79-)  A      N
  79 HIS   (  80-)  A      N
  82 HIS   (  83-)  A      N
  87 LYS   (  88-)  A      N
And so on for a total of 662 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.

  17 GLN   (  18-)  A      OE1
  53 ASN   (  54-)  A      OD1
  67 GLN   (  68-)  A      OE1
 115 ASP   ( 116-)  A      OD2
 299 ASN   ( 306-)  A      OD1
 428 HIS   ( 435-)  A      NE2
 438 ASN   ( 445-)  A      OD1
 486 GLN   ( 493-)  A      OE1
 538 GLN   ( 545-)  A      OE1
 760 GLN   ( 767-)  A      OE1
 761 GLN   ( 768-)  A      OE1
 783 ASP   ( 790-)  A      OD2
 847 ASN   ( 854-)  A      OD1
 863 GLU   ( 870-)  A      OE1
 919 GLN   ( 926-)  A      OE1
1123 HIS   (1140-)  A      ND1
1227 GLU   (1264-)  A      OE1
1260 GLU   (1297-)  A      OE1
1293 ASN   (1330-)  A      OD1
1330 HIS   (1367-)  A      ND1
1353 ASN   (1390-)  A      OD1
1436 GLN   (  47-)  B      OE1
1539 ASP   ( 198-)  B      OD2
1557 GLU   ( 216-)  B      OE1
1673 ASP   ( 332-)  B      OD1
2030 GLU   ( 698-)  B      OE1
2043 GLU   ( 711-)  B      OE2
2093 ASN   ( 767-)  B      OD1
2120 ASN   ( 794-)  B      OD1
2147 GLN   ( 821-)  B      OE1
2242 ASP   ( 936-)  B      OD1
2281 GLN   ( 975-)  B      OE1
2290 HIS   ( 984-)  B      ND1
2321 HIS   (1015-)  B      NE2
2331 HIS   (1025-)  B      ND1
2382 HIS   (1076-)  B      ND1
2390 GLN   (1084-)  B      OE1
2462 ASP   (1156-)  B      OD1
2467 HIS   (1161-)  B      ND1
2511 GLN   (1205-)  B      OE1
2512 GLU   (1206-)  B      OE1
2679 GLN   ( 151-)  C      OE1
2759 ASN   ( 231-)  C      OD1
3308 ASN   (  83-)  I      OD1
3446 GLU   (  36-)  K      OE1
3486 GLN   (  76-)  K      OE1

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; but Alt-Rotamer
  54 ASP   (  55-)  A   H-bonding suggests Asn
  71 GLU   (  72-)  A   H-bonding suggests Gln
 150 ASP   ( 151-)  A   H-bonding suggests Asn
 261 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 284 GLU   ( 291-)  A   H-bonding suggests Gln
 298 ASP   ( 305-)  A   H-bonding suggests Asn
 493 GLU   ( 500-)  A   H-bonding suggests Gln; but Alt-Rotamer
 537 ASP   ( 544-)  A   H-bonding suggests Asn
 819 ASP   ( 826-)  A   H-bonding suggests Asn
 924 GLU   ( 931-)  A   H-bonding suggests Gln
 985 ASP   ( 992-)  A   H-bonding suggests Asn; but Alt-Rotamer
1196 ASP   (1223-)  A   H-bonding suggests Asn; but Alt-Rotamer
1232 GLU   (1269-)  A   H-bonding suggests Gln; but Alt-Rotamer
1272 ASP   (1309-)  A   H-bonding suggests Asn
1445 ASP   (  56-)  B   H-bonding suggests Asn
1454 GLU   (  65-)  B   H-bonding suggests Gln
1620 ASP   ( 279-)  B   H-bonding suggests Asn; but Alt-Rotamer
1695 ASP   ( 354-)  B   H-bonding suggests Asn
1712 GLU   ( 371-)  B   H-bonding suggests Gln
1768 ASP   ( 427-)  B   H-bonding suggests Asn; but Alt-Rotamer
1809 GLU   ( 468-)  B   H-bonding suggests Gln
2009 ASP   ( 668-)  B   H-bonding suggests Asn
2028 GLU   ( 696-)  B   H-bonding suggests Gln; but Alt-Rotamer
2043 GLU   ( 711-)  B   H-bonding suggests Gln; but Alt-Rotamer
2231 ASP   ( 909-)  B   H-bonding suggests Asn; but Alt-Rotamer
2242 ASP   ( 936-)  B   H-bonding suggests Asn; but Alt-Rotamer
2462 ASP   (1156-)  B   H-bonding suggests Asn
2547 ASP   (  19-)  C   H-bonding suggests Asn; but Alt-Rotamer
2709 ASP   ( 181-)  C   H-bonding suggests Asn
2843 ASP   (  48-)  E   H-bonding suggests Asn; but Alt-Rotamer
3279 GLU   (  54-)  I   H-bonding suggests Gln; but Alt-Rotamer
3377 GLU   (  32-)  J   H-bonding suggests Gln; but Alt-Rotamer
3432 ASP   (  22-)  K   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.639
  2nd generation packing quality :  -2.640
  Ramachandran plot appearance   :  -3.771 (poor)
  chi-1/chi-2 rotamer normality  :  -3.620 (poor)
  Backbone conformation          :  -1.017

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.468 (tight)
  Bond angles                    :   0.665 (tight)
  Omega angle restraints         :   0.897
  Side chain planarity           :   0.394 (tight)
  Improper dihedral distribution :   0.652
  B-factor distribution          :   1.455
  Inside/Outside distribution    :   1.064

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 : 3.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.468 (tight)
  Bond angles                    :   0.665 (tight)
  Omega angle restraints         :   0.897
  Side chain planarity           :   0.394 (tight)
  Improper dihedral distribution :   0.652
  B-factor distribution          :   1.455
  Inside/Outside distribution    :   1.064
==============

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.