WHAT IF Check report

This file was created 2000-10-28 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please read the introduction 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 1E4F

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped. 
  12 ARG  (  18 ) T
  70 ARG  (  76 ) T
  84 ARG  (  90 ) T
  91 ARG  (  97 ) T
  98 ARG  ( 104 ) T
 130 ARG  ( 136 ) T
 137 ARG  ( 143 ) T
 200 ARG  ( 206 ) T
 252 ARG  ( 258 ) T
 273 ARG  ( 279 ) T
 345 ARG  ( 357 ) T

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0 
  13 TYR  (  19 ) T
 227 TYR  ( 233 ) T
 349 TYR  ( 361 ) T

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0. 
   3 PHE  (   9 ) T
  50 PHE  (  56 ) T
  73 PHE  (  79 ) T
  82 PHE  (  88 ) T
 167 PHE  ( 173 ) T
 170 PHE  ( 176 ) T
 340 PHE  ( 352 ) T
 369 PHE  ( 381 ) T
 373 PHE  ( 385 ) T

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. 
   8 ASP  (  14 ) T
  46 ASP  (  52 ) T
  92 ASP  (  98 ) T
 134 ASP  ( 140 ) T
 135 ASP  ( 141 ) T
 144 ASP  ( 150 ) T
 244 ASP  ( 250 ) T
 276 ASP  ( 282 ) T
 366 ASP  ( 378 ) T

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. 
  41 GLU  (  47 ) T
  43 GLU  (  49 ) T
  63 GLU  (  69 ) T
  83 GLU  (  89 ) T
  85 GLU  (  91 ) T
 107 GLU  ( 113 ) T
 118 GLU  ( 124 ) T
 136 GLU  ( 142 ) T
 153 GLU  ( 159 ) T
 197 GLU  ( 203 ) T
 269 GLU  ( 275 ) T
 298 GLU  ( 304 ) T
 311 GLU  ( 317 ) T
 362 GLU  ( 374 ) T

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value. 

  23 ASP  (  29 ) T    C        4.5      8.1      0.0

Geometric checks

Warning: C-terminal oxygen atoms missing

The C-atoms listed in the table below belong to a C-terminal residue in a protein chain, but the C-terminal oxygen ("O2" or "OXT") that it should be bound to was not found. 
 314 ILE  ( 320 ) T    C

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 sigma 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 "--SS", the disulphide bridge has a deviating length. 

  21 LYS  (  27 ) T      N   -C     0.934 -19.8

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be around 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong constraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.454
RMS-deviation in bond distances: 0.010

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. 
  21 LYS  (  27 ) T     -O   -C    N    84.818 -23.9
  21 LYS  (  27 ) T     -CA  -C    N   155.082  18.4
  21 LYS  (  27 ) T     -C    N    CA  149.081  15.2

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be around 1.0 for a normally restrained data set. More common values are around 1.55. The fact that it is lower than 0.667 in this structure might indicate that too-strong constraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.554
RMS-deviation in bond angles: 1.255

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value (0.0). 
  25 GLU  (  31 ) T   5.313

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. 

 283 THR  ( 289 ) T -2.8297
 317 PRO  ( 329 ) T -2.6521
 245 THR  ( 251 ) T -2.2146
 202 VAL  ( 208 ) T -2.1027
 316 ILE  ( 328 ) T -2.0942
 142 PRO  ( 148 ) T -2.0563
 201 GLY  ( 207 ) T -2.0238

Warning: Backbone torsion angle evaluation shows 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. 

  20 GLY  (  26 ) T omega poor
  21 LYS  (  27 ) T Poor phi/psi
  23 ASP  (  29 ) T Poor phi/psi
  66 GLN  (  72 ) T Poor phi/psi
 123 PRO  ( 129 ) T Poor PRO-phi
 136 GLU  ( 142 ) T Poor phi/psi
 142 PRO  ( 148 ) T Poor PRO-phi
 144 ASP  ( 150 ) T Poor phi/psi
 176 LYS  ( 182 ) T Poor phi/psi
 219 ASN  ( 225 ) T Poor phi/psi
 226 SER  ( 232 ) T Poor phi/psi
 229 PRO  ( 235 ) T Poor phi/psi
 316 ILE  ( 328 ) T Poor phi/psi
 317 PRO  ( 329 ) T Poor PRO-phi
 331 ARG  ( 343 ) T Poor phi/psi
 359 ASN  ( 371 ) T Poor phi/psi

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.919

Note: Ramachandran plot

In this Ramachandran plot X-signs represent glycines, squares represent prolines and small plus-signs represent the other residues. If too many plus-signs fall outside the contoured areas then the molecule is poorly refined (or worse).

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. "Allowed" regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green.

Chain identifier: T

Accessibility related checks

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: T

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

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 centers of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterium was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1--3 and 1--4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably aren't there anyway.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. 

  70 ARG  (  76 ) T    NH1  --  297 ARG  ( 303 ) T    NE     0.458   2.542 INTER BF
  22 ARG  (  28 ) T    O    --   24 GLN  (  30 ) T    N      0.440   2.260 INTRA BF
  22 ARG  (  28 ) T    O    --   23 ASP  (  29 ) T    C      0.429   2.371 INTRA BF
  43 GLU  (  49 ) T    CD   --  385 HOH  (HOH  ) A     21    0.414   2.786 INTRA BF
  22 ARG  (  28 ) T    N    --   25 GLU  (  31 ) T    O      0.329   2.221 INTRA BF
  20 GLY  (  26 ) T    O    --   21 LYS  (  27 ) T    N      0.324   1.476 INTRA B2
 378 ALA  ( 390 ) T    CB   --  380 HOH  (HOH  ) A     62    0.294   2.906 INTRA
 182 LYS  ( 188 ) T    NZ   --  378 ALA  ( 390 ) T    CB     0.293   2.807 INTRA
 293 HIS  ( 299 ) T    CE1  --  383 HOH  (HOH  ) A    110    0.282   2.918 INTRA
 125 HIS  ( 131 ) T    CE1  --  183 SER  ( 189 ) T    N      0.262   2.838 INTRA
 316 ILE  ( 328 ) T    CG1  --  317 PRO  ( 329 ) T    N      0.258   2.842 INTRA
 382 HOH  (HOH  ) A    115  --  383 HOH  (HOH  ) A    103    0.244   2.806 INTER HB
  21 LYS  (  27 ) T    CA   --   25 GLU  (  31 ) T    O      0.244   2.556 INTRA BF
 231 GLY  ( 237 ) T    N    --  234 HIS  ( 240 ) T    CD2    0.240   2.860 INTRA
 325 GLY  ( 337 ) T    N    --  383 HOH  (HOH  ) A    116    0.231   2.719 INTRA HB
 380 HOH  (HOH  ) A    129  --  380 HOH  (HOH  ) A    130    0.230   2.820 INTRA HB
  42 GLY  (  48 ) T    N    --  381 HOH  (HOH  ) A     19    0.229   2.721 INTRA HB
 331 ARG  ( 343 ) T    N    --  382 HOH  (HOH  ) A    120    0.226   2.724 INTRA HB
  70 ARG  (  76 ) T    NH1  --  297 ARG  ( 303 ) T    CD     0.226   2.874 INTER BF
  37 ARG  (  43 ) T    NH2  --   52 GLU  (  58 ) T    CB     0.221   2.879 INTRA BF
 371 ALA  ( 383 ) T    N    --  380 HOH  (HOH  ) A    138    0.217   2.733 INTRA HB
  21 LYS  (  27 ) T    CG   --   26 TRP  (  32 ) T    CE2    0.212   2.988 INTRA BF
 338 GLU  ( 350 ) T    CD   --  383 HOH  (HOH  ) A    110    0.208   2.992 INTRA
 207 LEU  ( 213 ) T    CA   --  383 HOH  (HOH  ) A     70    0.206   2.994 INTRA
 200 ARG  ( 206 ) T    NH2  --  383 HOH  (HOH  ) A     81    0.202   2.748 INTER HB
And so on for a total of 139 lines

3D-database related checks

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. 

 140 PHE  ( 146 ) T  -6.18
 257 HIS  ( 263 ) T  -5.67
 200 ARG  ( 206 ) T  -5.59
 317 PRO  ( 329 ) T  -5.58
 275 LEU  ( 281 ) T  -5.54
 176 LYS  ( 182 ) T  -5.40
 341 LYS  ( 353 ) T  -5.32
 351 ASN  ( 363 ) T  -5.24

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 quality 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. 
 358 ILE  ( 370 ) T  -2.72

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: T

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. 

  33 SER  (  39 ) T   0.35
 259 ASN  ( 265 ) T   0.36
 202 VAL  ( 208 ) T   0.37
 128 SER  ( 134 ) T   0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighboring 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 center.

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! 

  23 ASP  (  29 ) T  0
  24 GLN  (  30 ) T  0
 135 ASP  ( 141 ) T  0
 136 GLU  ( 142 ) T  0
 348 CYS  ( 360 ) T  0
  22 ARG  (  28 ) T  1
  93 PHE  (  99 ) T  1
  95 GLU  ( 101 ) T  1
 140 PHE  ( 146 ) T  2
 176 LYS  ( 182 ) T  2

Water related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file. 
 380 HOH  (HOH  ) A    141
 383 HOH  (HOH  ) A     87
 384 HOH  (HOH  ) A     50

B-factor analysis

Note: B-factor plot

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

Chain identifier: T

Hydrogen bond 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 favorable 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. If a residue is marked ``flexible'' the flipped conformation is only slightly better than the non-flipped conformation. 
  24 GLN  (  30 ) T
  64 GLN  (  70 ) T
  66 GLN  (  72 ) T
 125 HIS  ( 131 ) T
 219 ASN  ( 225 ) T
 234 HIS  ( 240 ) T
 259 ASN  ( 265 ) T
 293 HIS  ( 299 ) T
 333 ASN  ( 345 ) T
 365 ASN  ( 377 ) T

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. 

   5 THR  (  11 ) T    OG1
  11 SER  (  17 ) T    OG
  37 ARG  (  43 ) T    NE
  44 ILE  (  50 ) T    N
  64 GLN  (  70 ) T    NE2
  79 SER  (  85 ) T    N
  82 PHE  (  88 ) T    N
 103 ASP  ( 109 ) T    N
 130 ARG  ( 136 ) T    NH1
 137 ARG  ( 143 ) T    NE
 154 TYR  ( 160 ) T    OH
 156 SER  ( 162 ) T    OG
 183 SER  ( 189 ) T    OG
 210 ASN  ( 216 ) T    ND2
 211 PHE  ( 217 ) T    N
 268 GLU  ( 274 ) T    N
 276 ASP  ( 282 ) T    N
 286 LYS  ( 292 ) T    N
 305 LYS  ( 311 ) T    N
 308 ARG  ( 314 ) T    NE
 315 GLY  ( 327 ) T    N
 316 ILE  ( 328 ) T    N
 333 ASN  ( 345 ) T    ND2
 354 ARG  ( 366 ) T    NH2
 360 ALA  ( 372 ) T    N
 368 SER  ( 380 ) T    OG
 378 ALA  ( 390 ) T    N

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 that are 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. 

  25 GLU  (  31 ) T    OE2

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 constraint values. The first part of the table shows a number of constraint-independent quality indicators.
 

Structure Z-scores, positive is better than average: 

  1st generation packing quality :   0.749
  2nd generation packing quality :   1.161
  Ramachandran plot appearance   :  -0.117
  chi-1/chi-2 rotamer normality  :   1.288
  Backbone conformation          :  -0.155
RMS Z-scores, should be close to 1.0: 
  Bond lengths                   :   0.454 (tight)
  Bond angles                    :   0.554 (tight)
  Omega angle restraints         :   0.349 (tight)
  Side chain planarity           :   0.634 (tight)
  Improper dihedral distribution :   0.466
  B-factor distribution          :   0.558
  Inside/Outside distribution    :   0.985

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.

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

Resolution found in PDB file : 1.90
 

Structure Z-scores, positive is better than average: 

  1st generation packing quality :   1.3
  2nd generation packing quality :   0.4
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :   1.7
  Backbone conformation          :  -0.5
RMS Z-scores, should be close to 1.0: 
  Bond lengths                   :   0.454 (tight)
  Bond angles                    :   0.554 (tight)
  Omega angle restraints         :   0.349 (tight)
  Side chain planarity           :   0.634 (tight)
  Improper dihedral distribution :   0.466
  B-factor distribution          :   0.558
  Inside/Outside distribution    :   0.985