WHAT IF Check report

This file was created 2011-12-21 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 pdb1acz.ent

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 109 GLC   (   1-)  A  1   O4  bound to  110 GLC   (   2-)  A  1   C1
 110 GLC   (   2-)  A  1   O4  bound to  111 GLC   (   3-)  A  1   C1
 111 GLC   (   3-)  A  1   O4  bound to  112 GLC   (   4-)  A  1   C1
 112 GLC   (   4-)  A  1   O4  bound to  113 GLC   (   5-)  A  1   C1
 113 GLC   (   5-)  A  1   O4  bound to  114 GLC   (   6-)  A  1   C1
 114 GLC   (   6-)  A  1   O4  bound to  115 GLC   (   7-)  A  1   C1
 115 GLC   (   7-)  A  1   O4  bound to  109 GLC   (   1-)  A  1   C1
 116 GLC   ( 617B)  A  1   O4  bound to  117 GLC   ( 618B)  A  1   C1
 117 GLC   ( 618B)  A  1   O4  bound to  118 GLC   ( 619B)  A  1   C1
 118 GLC   ( 619B)  A  1   O4  bound to  119 GLC   ( 620B)  A  1   C1
 119 GLC   ( 620B)  A  1   O4  bound to  120 GLC   ( 621B)  A  1   C1
 120 GLC   ( 621B)  A  1   O4  bound to  121 GLC   ( 622B)  A  1   C1
 121 GLC   ( 622B)  A  1   O4  bound to  122 GLC   ( 623B)  A  1   C1
 122 GLC   ( 623B)  A  1   O4  bound to  116 GLC   ( 617B)  A  1   C1
 231 GLC   (   1-)  A  2   O4  bound to  232 GLC   (   2-)  A  2   C1
 232 GLC   (   2-)  A  2   O4  bound to  233 GLC   (   3-)  A  2   C1
 233 GLC   (   3-)  A  2   O4  bound to  234 GLC   (   4-)  A  2   C1
 234 GLC   (   4-)  A  2   O4  bound to  235 GLC   (   5-)  A  2   C1
 235 GLC   (   5-)  A  2   O4  bound to  236 GLC   (   6-)  A  2   C1
 236 GLC   (   6-)  A  2   O4  bound to  237 GLC   (   7-)  A  2   C1
 237 GLC   (   7-)  A  2   O4  bound to  231 GLC   (   1-)  A  2   C1
 238 GLC   ( 617B)  A  2   O4  bound to  239 GLC   ( 618B)  A  2   C1
 239 GLC   ( 618B)  A  2   O4  bound to  240 GLC   ( 619B)  A  2   C1
 240 GLC   ( 619B)  A  2   O4  bound to  241 GLC   ( 620B)  A  2   C1
 241 GLC   ( 620B)  A  2   O4  bound to  242 GLC   ( 621B)  A  2   C1
And so on for a total of 70 lines.

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 CYS   ( 509-)  A    Zero
   2 THR   ( 510-)  A    Zero
   3 THR   ( 511-)  A    Zero
   4 PRO   ( 512-)  A    Zero
   5 THR   ( 513-)  A    Zero
   6 ALA   ( 514-)  A    Zero
   7 VAL   ( 515-)  A    Zero
   8 ALA   ( 516-)  A    Zero
   9 VAL   ( 517-)  A    Zero
  10 THR   ( 518-)  A    Zero
  11 PHE   ( 519-)  A    Zero
  12 ASP   ( 520-)  A    Zero
  13 LEU   ( 521-)  A    Zero
  14 THR   ( 522-)  A    Zero
  15 ALA   ( 523-)  A    Zero
  16 THR   ( 524-)  A    Zero
  17 THR   ( 525-)  A    Zero
  18 THR   ( 526-)  A    Zero
  19 TYR   ( 527-)  A    Zero
  20 GLY   ( 528-)  A    Zero
  21 GLU   ( 529-)  A    Zero
  22 ASN   ( 530-)  A    Zero
  23 ILE   ( 531-)  A    Zero
  24 TYR   ( 532-)  A    Zero
  25 LEU   ( 533-)  A    Zero
And so on for a total of 610 lines.

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.

  33 GLY   ( 541-)  A      N    CA    1.52    4.1
  35 TRP   ( 543-)  A      N   -C     1.24   -4.6
 149 GLY   ( 535-)  A      N    CA    1.52    4.1
 271 GLY   ( 535-)  A      N    CA    1.52    4.6
 279 TRP   ( 543-)  A      N   -C     1.25   -4.1
 393 GLY   ( 535-)  A      N    CA    1.52    4.3
 394 SER   ( 536-)  A      N    CA    1.54    4.2
 516 SER   ( 536-)  A      N    CA    1.54    4.2
 523 TRP   ( 543-)  A      N   -C     1.23   -4.8
 540 ASP   ( 560-)  A      N    CA    1.54    4.2

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.977
Model 2 : 0.948
Model 3 : 0.985
Model 4 : 0.984
Model 5 : 1.012

Warning: Directionality in bond lengths

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

Since this is not an XRAY structure this effect is hard to explain.

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.

  34 ASP   ( 542-)  A      C    CA   CB  101.84   -4.3
  52 ASP   ( 560-)  A      CA   CB   CG  107.75   -4.9
  67 PHE   ( 575-)  A      CA   CB   CG  108.92   -4.9
  71 PHE   ( 579-)  A      CA   CB   CG  108.00   -5.8
 193 PHE   ( 579-)  A      CA   CB   CG  105.06   -8.7
 278 ASP   ( 542-)  A      C    CA   CB  101.59   -4.5
 311 PHE   ( 575-)  A      CA   CB   CG  107.97   -5.8
 315 PHE   ( 579-)  A      CA   CB   CG  108.46   -5.3
 400 ASP   ( 542-)  A      C    CA   CB  101.18   -4.7
 400 ASP   ( 542-)  A      CA   CB   CG  108.37   -4.2
 421 TRP   ( 563-)  A      CA   CB   CG  105.51   -4.3
 437 PHE   ( 579-)  A      CA   CB   CG  108.58   -5.2
 523 TRP   ( 543-)  A      N    CA   CB  101.90   -5.1
 539 SER   ( 559-)  A     -CA  -C    N   125.93    4.9
 542 LEU   ( 562-)  A     -CA  -C    N   124.53    4.2
 555 PHE   ( 575-)  A      CA   CB   CG  108.78   -5.0
 559 PHE   ( 579-)  A      CA   CB   CG  109.08   -4.7

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 1.016
Model 2 : 1.031
Model 3 : 1.030
Model 4 : 1.046
Model 5 : 1.035

Note: Per-model averages for chirality check

The table below gives the per-model improper dihedral RMS Z-scores.

Model 1 : 0.951
Model 2 : 0.955
Model 3 : 0.916
Model 4 : 0.992
Model 5 : 0.956

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. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 230 ARG   ( 616-)  A    8.30
 454 ARG   ( 596-)  A    7.67
 108 ARG   ( 616-)  A    7.48
 576 ARG   ( 596-)  A    7.42
 474 ARG   ( 616-)  A    7.12
 210 ARG   ( 596-)  A    6.42
 561 ARG   ( 581-)  A    6.41
 352 ARG   ( 616-)  A    6.40
  88 ARG   ( 596-)  A    5.38
  73 ARG   ( 581-)  A    4.92
 195 ARG   ( 581-)  A    4.42

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 : -7.599

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -7.165
Model 2 : -7.608
Model 3 : -7.928
Model 4 : -7.303
Model 5 : -7.990

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.

 414 TYR   ( 556-)  A    -3.8
 490 THR   ( 510-)  A    -3.6
 368 THR   ( 510-)  A    -3.6
 491 THR   ( 511-)  A    -3.6
  98 THR   ( 606-)  A    -3.5
 261 THR   ( 525-)  A    -3.5
 300 TYR   ( 564-)  A    -3.4
 249 THR   ( 513-)  A    -3.3
  18 THR   ( 526-)  A    -3.3
 262 THR   ( 526-)  A    -3.3
 178 TYR   ( 564-)  A    -3.3
 578 TYR   ( 598-)  A    -3.3
 464 THR   ( 606-)  A    -3.3
 220 THR   ( 606-)  A    -3.3
 504 THR   ( 524-)  A    -3.2
 369 THR   ( 511-)  A    -3.2
 260 THR   ( 524-)  A    -3.1
 472 THR   ( 614-)  A    -3.1
  17 THR   ( 525-)  A    -3.1
 415 THR   ( 557-)  A    -3.0
 395 ILE   ( 537-)  A    -2.9
 512 TYR   ( 532-)  A    -2.9
 454 ARG   ( 596-)  A    -2.9
 135 LEU   ( 521-)  A    -2.8
 413 LYS   ( 555-)  A    -2.8
And so on for a total of 165 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.

  16 THR   ( 524-)  A  Poor phi/psi
  17 THR   ( 525-)  A  Poor phi/psi
  21 GLU   ( 529-)  A  Poor phi/psi
  33 GLY   ( 541-)  A  Poor phi/psi
  36 GLU   ( 544-)  A  Poor phi/psi
  48 TYR   ( 556-)  A  Poor phi/psi
  49 THR   ( 557-)  A  Poor phi/psi
  51 SER   ( 559-)  A  Poor phi/psi
  52 ASP   ( 560-)  A  Poor phi/psi
  57 VAL   ( 565-)  A  Poor phi/psi
  65 GLU   ( 573-)  A  Poor phi/psi
  87 ASN   ( 595-)  A  Poor phi/psi
  98 THR   ( 606-)  A  Poor phi/psi
 138 THR   ( 524-)  A  Poor phi/psi
 143 GLU   ( 529-)  A  Poor phi/psi
 155 GLY   ( 541-)  A  Poor phi/psi
 156 ASP   ( 542-)  A  Poor phi/psi
 166 SER   ( 552-)  A  Poor phi/psi
 172 SER   ( 558-)  A  Poor phi/psi
 174 ASP   ( 560-)  A  Poor phi/psi
 177 TRP   ( 563-)  A  Poor phi/psi
 178 TYR   ( 564-)  A  Poor phi/psi
 179 VAL   ( 565-)  A  Poor phi/psi
 187 GLU   ( 573-)  A  Poor phi/psi
 197 GLU   ( 583-)  A  Poor phi/psi
And so on for a total of 95 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -7.856

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -7.870
Model 2 : -7.824
Model 3 : -7.595
Model 4 : -8.126
Model 5 : -7.864

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 THR   ( 511-)  A      0
   4 PRO   ( 512-)  A      0
   5 THR   ( 513-)  A      0
  12 ASP   ( 520-)  A      0
  14 THR   ( 522-)  A      0
  15 ALA   ( 523-)  A      0
  17 THR   ( 525-)  A      0
  18 THR   ( 526-)  A      0
  19 TYR   ( 527-)  A      0
  21 GLU   ( 529-)  A      0
  22 ASN   ( 530-)  A      0
  29 ILE   ( 537-)  A      0
  32 LEU   ( 540-)  A      0
  34 ASP   ( 542-)  A      0
  35 TRP   ( 543-)  A      0
  36 GLU   ( 544-)  A      0
  39 ASP   ( 547-)  A      0
  41 ILE   ( 549-)  A      0
  46 ASP   ( 554-)  A      0
  47 LYS   ( 555-)  A      0
  48 TYR   ( 556-)  A      0
  49 THR   ( 557-)  A      0
  51 SER   ( 559-)  A      0
  52 ASP   ( 560-)  A      0
  55 TRP   ( 563-)  A      0
And so on for a total of 437 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 : -2.983

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 2.052

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 1.840
Model 2 : 1.967
Model 3 : 2.074
Model 4 : 2.197
Model 5 : 2.163

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!

 528 GLY   ( 548-)  A   1.64   16
  27 GLY   ( 535-)  A   1.63   10
 284 GLY   ( 548-)  A   1.62   11
 430 GLY   ( 572-)  A   1.58   12

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]

  53 PRO   ( 561-)  A    0.19 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].

   4 PRO   ( 512-)  A   -62.8 half-chair C-beta/C-alpha (-54 degrees)
  93 PRO   ( 601-)  A   -63.8 envelop C-beta (-72 degrees)
 126 PRO   ( 512-)  A   -64.5 envelop C-beta (-72 degrees)
 184 PRO   ( 570-)  A   -65.8 envelop C-beta (-72 degrees)
 208 PRO   ( 594-)  A   -62.9 half-chair C-beta/C-alpha (-54 degrees)
 215 PRO   ( 601-)  A   -63.9 envelop C-beta (-72 degrees)
 248 PRO   ( 512-)  A   -57.9 half-chair C-beta/C-alpha (-54 degrees)
 306 PRO   ( 570-)  A   -58.0 half-chair C-beta/C-alpha (-54 degrees)
 337 PRO   ( 601-)  A   -61.0 half-chair C-beta/C-alpha (-54 degrees)
 370 PRO   ( 512-)  A   -63.0 envelop C-beta (-72 degrees)
 419 PRO   ( 561-)  A   -58.4 half-chair C-beta/C-alpha (-54 degrees)
 428 PRO   ( 570-)  A   -53.8 half-chair C-beta/C-alpha (-54 degrees)
 459 PRO   ( 601-)  A   -61.2 half-chair C-beta/C-alpha (-54 degrees)
 492 PRO   ( 512-)  A   -63.8 envelop C-beta (-72 degrees)
 550 PRO   ( 570-)  A   -50.8 half-chair C-beta/C-alpha (-54 degrees)
 581 PRO   ( 601-)  A   -60.7 half-chair C-beta/C-alpha (-54 degrees)

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 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).

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. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

 533 ALA   ( 553-)  A      N   <->  544 TYR   ( 564-)  A      CE1    0.56    2.54
 148 VAL   ( 534-)  A      CG2 <->  156 ASP   ( 542-)  A      C      0.56    2.64
 263 TYR   ( 527-)  A      CD1 <->  295 SER   ( 559-)  A      N      0.55    2.55
 534 ASP   ( 554-)  A      CA  <->  544 TYR   ( 564-)  A      CD2    0.53    2.67
 315 PHE   ( 579-)  A      CD1 <->  351 TRP   ( 615-)  A      CH2    0.52    2.68
 394 SER   ( 536-)  A      N   <->  400 ASP   ( 542-)  A      OD2    0.50    2.20
 559 PHE   ( 579-)  A      CD1 <->  595 TRP   ( 615-)  A      CH2    0.50    2.70
 400 ASP   ( 542-)  A      CG  <->  401 TRP   ( 543-)  A      CZ2    0.50    2.70
 278 ASP   ( 542-)  A      CG  <->  279 TRP   ( 543-)  A      CZ2    0.50    2.70
 541 PRO   ( 561-)  A      O   <->  543 TRP   ( 563-)  A      CD1    0.49    2.31
 540 ASP   ( 560-)  A      N   <->  541 PRO   ( 561-)  A      CD     0.49    2.51
 437 PHE   ( 579-)  A      CZ  <->  439 ARG   ( 581-)  A      N      0.49    2.61
 437 PHE   ( 579-)  A      CG  <->  438 ILE   ( 580-)  A      N      0.49    2.51
 263 TYR   ( 527-)  A      CE1 <->  294 SER   ( 558-)  A      C      0.49    2.71
  27 GLY   ( 535-)  A      C   <->   34 ASP   ( 542-)  A      CB     0.48    2.72
  22 ASN   ( 530-)  A      ND2 <->   24 TYR   ( 532-)  A      CD1    0.48    2.62
 271 GLY   ( 535-)  A      C   <->  278 ASP   ( 542-)  A      CB     0.48    2.72
 149 GLY   ( 535-)  A      O   <->  157 TRP   ( 543-)  A      CE2    0.48    2.32
 410 SER   ( 552-)  A      C   <->  418 ASP   ( 560-)  A      CB     0.48    2.72
   9 VAL   ( 517-)  A      CG1 <->  103 VAL   ( 611-)  A      CG2    0.48    2.72
 541 PRO   ( 561-)  A      CG  <->  610 GLC   ( 623-)  A      C5     0.48    2.72
 390 TYR   ( 532-)  A      CZ  <->  408 ALA   ( 550-)  A      CB     0.47    2.73
 144 ASN   ( 530-)  A      ND2 <->  146 TYR   ( 532-)  A      CD1    0.47    2.63
 272 SER   ( 536-)  A      N   <->  278 ASP   ( 542-)  A      OD2    0.47    2.23
 400 ASP   ( 542-)  A      CG  <->  401 TRP   ( 543-)  A      CE2    0.47    2.73
And so on for a total of 1469 lines.

Packing, accessibility and threading

Note: Per-model averages for inside/outside residue distributi ...heck





Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Warning: Low packing Z-score for some residues


Warning: Abnormal packing Z-score for sequential residues


Note: Per-model averages for NQA





Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure