WhatCheck Report generated for Modelling Request AAAa010Mt

AC code: Model: Batch.0.pdb
-------------------------------------------------------------

************************************************************************
********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program **********
************************************************************************

Date : 2000-07-17
This report was created by WHAT IF version 19970813-1517

INTRODUCTION
------------

This document contains a report of findings by the WHAT IF program
during the analysis of one or more proteins. It contains a separate section
for each of the proteins that have been analysed. Each reported fact has
an assigned severity, one of:

* error: severe errors encountered during the analyses. Items marked
as errors are considered severe problems requiring immediate
attention.

* warning: Either less severe problems or uncommon structural
features. These still need special attention.

* note: Statistical values, plots, or other verbose results of
tests and analyses that have been performed.
 

If alternate conformations are present, only the first is
evaluated.

Hydrogen atoms are only included if explicitly requested, and even then
they are not used by all checks.

Legend
------
Some notations need a little explanation:

RESIDUE: Residues in tables are normally given in 3-5 parts:
- A number. This is the internal sequence number of the residue used
by WHAT IF.
- The residue name. Normally this is a three letter amino acid name.
- The sequence number, between brackets. This is the residue number
as it was given in the input file. It can be followed by the insertion
code.
- The chain identifier. A single character. If no chain identifier
was given in the input file, this will be invisible.
- A model number (only for NMR structures).

Z-VALUE: To indicate the normality of a score, the score may be
expressed as a Z-value or Z-score. This is just the number of
standard deviations that the score deviates from the expected
value. A property of Z-values is that the root-mean-square of a
group of Z-values (the RMS Z-value) is expected to be 1.0. Z-values
above 4.0 and below -4.0 are very uncommon. If a Z-score is used in
WHAT IF, the accompanying text will explain how the expected value
and standard deviation were obtained.
 
 

========================================================================
==== Compound code Model.pdb ====
========================================================================

# 1 # Error: Missing unit cell information
No SCALE matrix is given in the PDB file.

# 2 # Error: Missing symmetry information
Problem: No CRYST1 card is given in the PDB file.

# 3 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.

# 4 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.

# 5 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.

# 6 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.

# 7 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.

# 8 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.

# 9 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.

# 10 # Note: Phenylalanine torsion conventions OK
No errors were detected in phenylalanine torsion angle conventions.

# 11 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.

# 12 # 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.

304 GLU ( 310 )

# 13 # Note: Heavy atom naming OK
No errors were detected in the atom names for non-hydrogen atoms.

# 14 # 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.

7 LEU ( 13 ) C 5.5 10.0 -0.1
19 GLY ( 25 ) C -4.3 -6.9 0.1
27 VAL ( 33 ) CB 5.4 -21.9 -33.6
32 VAL ( 38 ) CB -4.3 -42.8 -33.6
70 ILE ( 76 ) C 6.3 11.7 -0.2
73 VAL ( 79 ) C 9.3 17.7 -0.3
73 VAL ( 79 ) CB 8.0 -16.4 -33.6
99 THR ( 105 ) C -5.4 -10.2 -0.1
101 GLU ( 107 ) CA -5.2 23.4 34.4
101 GLU ( 107 ) C 12.5 23.2 0.0
104 GLU ( 110 ) C 5.8 10.7 0.0
137 ILE ( 143 ) C 4.1 7.5 -0.2
154 LEU ( 160 ) C 7.5 13.6 -0.1
154 LEU ( 160 ) CG -4.2 -42.4 -34.2
160 ASP ( 166 ) C 6.3 11.1 -0.1
166 VAL ( 172 ) C 4.1 7.7 -0.3
184 LEU ( 190 ) C 5.8 10.6 -0.1
220 LEU ( 226 ) CG -4.4 -42.6 -34.2
233 VAL ( 239 ) C 4.1 7.7 -0.3
237 ILE ( 243 ) CB 6.4 45.9 33.3
242 GLY ( 248 ) C 6.5 10.6 0.1
269 VAL ( 275 ) C -4.9 -9.8 -0.3
273 SER ( 279 ) C 5.3 10.0 0.0
282 LEU ( 288 ) C 7.4 13.5 -0.1
289 GLU ( 295 ) C -4.7 -8.7 0.0
295 TYR ( 301 ) C 6.7 12.1 0.0
296 THR ( 302 ) C 4.7 8.8 -0.1
298 LEU ( 304 ) C 4.6 8.4 -0.1
303 ASN ( 309 ) C 5.4 9.6 -0.1
315 GLN ( 321 ) C 7.9 14.2 -0.1
322 LEU ( 328 ) CG -9.1 -51.8 -34.2
361 LEU ( 367 ) CG 4.8 -25.1 -34.2
371 SER ( 377 ) C 6.0 11.2 0.0
372 THR ( 378 ) C 6.3 11.7 -0.1

# 15 # Warning: High improper dihedral angle deviations
The RMS Z-score for the improper dihedrals in the structure is high.
For well refined structures this number is expected to be around 1.0.
The fact that it is higher than 1.5 in this structure could be an
indication of overrefinement.

Improper dihedral RMS Z-score : 1.790

# 16 # Note: Chain names are OK
All chain names assigned to polymer molecules are unique, and all
residue numbers are strictly increasing within each chain.

# 17 # Note: Weights checked OK
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range.

# 18 # Note: No missing atoms detected
All expected atoms are present.

# 19 # Note: OXT check OK
All required C-terminal oxygen atoms are present.

# 20 # Note: No extra C-terminal groups found
No C-terminal groups are present for non C-terminal residues

# 21 # Note: All bond lengths OK
All bond lengths are in agreement with standard bond lengths using
a tolerance of 4 sigma (both standard values and sigma for amino
acid residues have been taken from Engh and Huber [REF], for
DNA/RNA from Parkinson et al [REF])

# 22 # 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: 0.637
RMS-deviation in bond distances: 0.013

# 23 # Warning: Directionality in bond lengths and no X-ray cell
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.

You have most probably seen symmetry problems earlier. Please
correct these and rerun this check to see the possible implications
on the X-ray cell axes.

# 24 # 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.

7 LEU ( 13 ) CD1 CG CD2 101.267 -4.3
21 VAL ( 27 ) CG1 CB CG2 94.825 -7.3
27 VAL ( 33 ) CA CB CG2 117.907 4.4
29 ILE ( 35 ) CA CB CG2 100.424 -5.9
29 ILE ( 35 ) CA CB CG1 120.026 5.7
32 VAL ( 38 ) CG1 CB CG2 98.304 -5.7
71 SER ( 77 ) CA CB OG 121.917 5.4
72 SER ( 78 ) N CA C 125.342 5.1
72 SER ( 78 ) N CA CB 95.589 -8.8
73 VAL ( 79 ) <O <C N 114.441 -5.3
73 VAL ( 79 ) CA CB CG1 100.806 -5.7
73 VAL ( 79 ) CA CB CG2 123.443 7.6
73 VAL ( 79 ) CG1 CB CG2 126.028 6.9
74 TYR ( 80 ) <CA <C N 107.446 -4.4
75 LEU ( 81 ) N CA CB 117.806 4.3
75 LEU ( 81 ) CB CG CD1 94.477 -5.4
75 LEU ( 81 ) CD1 CG CD2 93.978 -7.6
100 GLN ( 106 ) CA C O 102.691 -10.7
101 GLU ( 107 ) <O <C N 137.377 9.0
101 GLU ( 107 ) <C N CA 137.247 8.6
101 GLU ( 107 ) N CA C 122.608 4.1
101 GLU ( 107 ) N CA CB 119.121 5.1
104 GLU ( 110 ) N CA CB 117.634 4.2
104 GLU ( 110 ) CB CG CD 97.685 -8.8
105 ASN ( 111 ) ND2 CG OD1 115.764 -6.8
And so on for a total of 78 lines

# 25 # Note: Normal bond angle variability
Bond angles were found to deviate normally from the mean 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, and this is indeed observed for very high
resolution X-ray structures. More common values are around 1.55

RMS Z-score for bond angles: 1.375
RMS-deviation in bond angles: 2.609

# 26 # 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).

105 ASN ( 111 ) 8.361
310 GLN ( 316 ) 7.656
128 GLU ( 134 ) 7.619
305 GLU ( 311 ) 4.193
69 GLN ( 75 ) 4.124

# 27 # Error: Connections to aromatic rings out of plane
The atoms listed in the table below are connected to a planar
aromatic group in the sidechain of a protein residue but were found
to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a
protein residue the distance of the atom to the least squares plane
through the aromatic system was determined. This value was divided
by the standard deviation from a distribution of similar values
from a database of small molecule structures.

364 TYR ( 370 ) OH 5.066

# 28 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.

# 29 # 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.
 

126 PRO ( 132 ) 5.9 envelop N (0 degrees)
244 PRO ( 250 ) 103.2 envelop C-beta (108 degrees)

# 30 # 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.

92 PRO ( 98 ) -2.7635
154 LEU ( 160 ) -2.7625
73 VAL ( 79 ) -2.5702
282 LEU ( 288 ) -2.4800
77 LEU ( 83 ) -2.4474
25 GLY ( 31 ) -2.2473
30 ILE ( 36 ) -2.2313
70 ILE ( 76 ) -2.1861
268 SER ( 274 ) -2.1777
200 VAL ( 206 ) -2.1487
137 ILE ( 143 ) -2.0758
326 ILE ( 332 ) -2.0655
315 GLN ( 321 ) -2.0545
124 VAL ( 130 ) -2.0203

# 31 # 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 GLU ( 26 ) omega poor
21 VAL ( 27 ) omega poor
24 ASP ( 30 ) Poor phi/psi
42 LYS ( 48 ) Poor phi/psi
67 ASP ( 73 ) Poor phi/psi
71 SER ( 77 ) Poor phi/psi
72 SER ( 78 ) omega poor
73 VAL ( 79 ) Poor phi/psi, omega poor
92 PRO ( 98 ) Poor PRO-phi
99 THR ( 105 ) Poor phi/psi, omega poor
118 GLU ( 124 ) Poor phi/psi
126 PRO ( 132 ) Poor PRO-phi
132 ASP ( 138 ) Poor phi/psi
134 GLN ( 140 ) Poor phi/psi
174 LEU ( 180 ) Poor phi/psi
224 LYS ( 230 ) Poor phi/psi
225 VAL ( 231 ) Poor phi/psi
227 PRO ( 233 ) Poor phi/psi
229 ALA ( 235 ) Poor phi/psi
260 GLY ( 266 ) Poor phi/psi
268 SER ( 274 ) Poor phi/psi
282 LEU ( 288 ) Poor phi/psi
321 HIS ( 327 ) omega poor
322 LEU ( 328 ) Poor phi/psi
347 HIS ( 353 ) Poor phi/psi
358 ILE ( 364 ) omega poor
359 THR ( 365 ) Poor phi/psi
362 THR ( 368 ) Poor phi/psi
378 HIS ( 384 ) Poor phi/psi

# 32 # Note: Ramachandran Z-score OK
The score expressing how well the backbone conformations of all residues
are corresponding to the known allowed areas in the Ramachandran plot is
within expected ranges for well-refined structures.

Ramachandran Z-score : -1.230

# 33 # Note: Omega angle restraint OK
The omega angles for trans-peptide bonds in a structure is
expected to give a gaussian distribution with the average around
+178 degrees, and a standard deviation around 5.5. In the current
structure the standard deviation agrees with this expectation.

Standard deviation of omega values : 4.820

# 34 # Note: chi-1/chi-2 angle correlation Z-score OK
The score expressing how well the chi-1/chi-2 angles of all residues
are corresponding to the populated areas in the database is
within expected ranges for well-refined structures.

chi-1/chi-2 correlation Z-score : -1.480

# 35 # Note: Inside/Outside residue distribution normal
The distribution of residue types over the inside and the outside of the
protein is normal.

inside/outside RMS Z-score : 1.026

# 36 # 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.

131 ILE ( 137 ) CG2 -- 148 MET ( 154 ) SD 0.487 2.913 INTRA BF
84 CYS ( 90 ) SG -- 153 HIS ( 159 ) NE2 0.458 2.842 INTRA BF
283 GLN ( 289 ) NE2 -- 286 THR ( 292 ) CB 0.453 2.647 INTRA BF
101 GLU ( 107 ) CA -- 104 GLU ( 110 ) CD 0.429 2.771 INTRA BF
252 LYS ( 258 ) NZ -- 291 ILE ( 297 ) CG1 0.426 2.674 INTRA BF
159 ASN ( 165 ) ND2 -- 163 LYS ( 169 ) NZ 0.417 2.583 INTRA BF
205 ILE ( 211 ) CG2 -- 210 MET ( 216 ) SD 0.415 2.985 INTRA BF
315 GLN ( 321 ) NE2 -- 317 GLY ( 323 ) N 0.414 2.586 INTRA BF
72 SER ( 78 ) CA -- 73 VAL ( 79 ) CB 0.410 2.790 INTRA BF
86 ASN ( 92 ) CG -- 151 LYS ( 157 ) NZ 0.391 2.709 INTRA BF
205 ILE ( 211 ) CA -- 210 MET ( 216 ) SD 0.386 3.014 INTRA BF
73 VAL ( 79 ) C -- 74 TYR ( 80 ) CD1 0.345 2.855 INTRA BF
14 VAL ( 20 ) CG1 -- 35 CYS ( 41 ) SG 0.344 3.056 INTRA BF
38 ARG ( 44 ) CB -- 54 CYS ( 60 ) SG 0.337 3.063 INTRA BF
114 ARG ( 120 ) NH1 -- 154 LEU ( 160 ) CD1 0.316 2.784 INTRA BF
124 VAL ( 130 ) CG2 -- 127 GLN ( 133 ) NE2 0.308 2.792 INTRA BF
101 GLU ( 107 ) C -- 104 GLU ( 110 ) OE1 0.306 2.494 INTRA BF
310 GLN ( 316 ) NE2 -- 315 GLN ( 321 ) CG 0.305 2.795 INTRA BF
114 ARG ( 120 ) NH2 -- 154 LEU ( 160 ) CD1 0.298 2.802 INTRA BF
29 ILE ( 35 ) CG2 -- 361 LEU ( 367 ) CG 0.295 2.905 INTRA BF
315 GLN ( 321 ) NE2 -- 317 GLY ( 323 ) CA 0.293 2.807 INTRA BF
73 VAL ( 79 ) CG1 -- 75 LEU ( 81 ) CD1 0.288 2.912 INTRA BF
237 ILE ( 243 ) CG2 -- 252 LYS ( 258 ) CE 0.286 2.914 INTRA BF
86 ASN ( 92 ) CB -- 151 LYS ( 157 ) NZ 0.286 2.814 INTRA BF
154 LEU ( 160 ) CD2 -- 155 ILE ( 161 ) C 0.281 2.919 INTRA BF
And so on for a total of 268 lines

# 37 # 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.

277 ARG ( 283 ) -8.85
314 ARG ( 320 ) -8.19
42 LYS ( 48 ) -6.56
133 TYR ( 139 ) -6.43
316 GLN ( 322 ) -6.35
174 LEU ( 180 ) -5.99
138 LYS ( 144 ) -5.78
334 GLN ( 340 ) -5.53
255 HIS ( 261 ) -5.47
315 GLN ( 321 ) -5.44
228 TYR ( 234 ) -5.41
254 ARG ( 260 ) -5.40
171 ARG ( 177 ) -5.32
134 GLN ( 140 ) -5.25
378 HIS ( 384 ) -5.15
274 VAL ( 280 ) -5.13
262 ILE ( 268 ) -5.11
221 ARG ( 227 ) -5.06

# 38 # 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, but 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 score of the series.

40 MET ( 46 ) --- 42 LYS ( 48 ) -4.95
314 ARG ( 320 ) --- 316 GLN ( 322 ) -6.66

# 39 # Note: Structural average packing environment OK
The structural average quality control value is within normal ranges.
 

Average for range 1 - 379 : -1.050

# 40 # 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.

262 ILE ( 268 ) -3.06
322 LEU ( 328 ) -2.75
316 GLN ( 322 ) -2.52

# 41 # 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.

315 GLN ( 321 ) --- 318 VAL ( 324 ) -2.03

# 42 # Note: Structural average packing Z-score OK
The structural average for the second generation quality control
value is within normal ranges.

All contacts : Average = -0.328 Z-score = -2.01
BB-BB contacts : Average = 0.212 Z-score = 1.53
BB-SC contacts : Average = -0.716 Z-score = -3.85
SC-BB contacts : Average = -0.010 Z-score = 0.11
SC-SC contacts : Average = -0.733 Z-score = -3.72

# 43 # 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 constraints on the
neighboring 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!

25 GLY ( 31 ) 2.32 37

# 44 # 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
0.66. 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.

281 SER ( 287 ) 0.34
200 VAL ( 206 ) 0.37
146 VAL ( 152 ) 0.38
112 SER ( 118 ) 0.39

# 45 # 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!

71 SER ( 77 ) 0
73 VAL ( 79 ) 0
98 VAL ( 104 ) 0
99 THR ( 105 ) 0
126 PRO ( 132 ) 0
133 TYR ( 139 ) 0
321 HIS ( 327 ) 0
322 LEU ( 328 ) 0
323 ALA ( 329 ) 0
359 THR ( 365 ) 0
68 CYS ( 74 ) 1
134 GLN ( 140 ) 1
141 VAL ( 147 ) 1
278 PRO ( 284 ) 1
316 GLN ( 322 ) 1
318 VAL ( 324 ) 1
74 TYR ( 80 ) 2
229 ALA ( 235 ) 2
270 GLU ( 276 ) 2
358 ILE ( 364 ) 2

# 46 # Note: Backbone conformation Z-score OK
The backbone conformation analysis gives a score that is normal
for well refined protein structures.

Backbone conformation Z-score : -1.117

# 47 # Warning: Average B-factor problem
The average B-factor for all buried protein atoms normally lies between
10--20. Values around 3--5 are expected for X-ray studies performed
at liquid nitrogen temperature.

Because of the extreme value for the average B-factor, no further analysis
of the B-factors is performed.

Average B-factor for buried atoms : 50.000

# 48 # Warning: Buried unsatisfied hydrogen bond donors and acceptors
The buried hydrogen bond donors and acceptors listed in the table
below are not involved in a hydrogen bond.

Hydrogen bond donors and acceptors that are buried inside the
protein normally form hydrogen bonds within the protein. If there
are any non hydrogen bonded buried hydrogen bond donors/acceptors
in the structure, they will be listed here.

The polar side chain atoms of ARG, LYS, GLU, ASP, HIS, ASN and GLN
are, when they are buried, almost invariably involved in at least
one hydrogen bond. If any of these atoms are listed, an
investigation should be undertaken.

2 LYS ( 8 ) O
8 GLU ( 14 ) OE1
36 PRO ( 42 ) O
40 MET ( 46 ) N
68 CYS ( 74 ) O
71 SER ( 77 ) O
72 SER ( 78 ) N
81 HIS ( 87 ) N
95 GLU ( 101 ) O
96 GLU ( 102 ) N
101 GLU ( 107 ) N
119 HIS ( 125 ) O
123 HIS ( 129 ) ND1
123 HIS ( 129 ) NE2
124 VAL ( 130 ) N
133 TYR ( 139 ) N
138 LYS ( 144 ) N
139 ASN ( 145 ) N
143 LEU ( 149 ) O
145 GLY ( 151 ) N
153 HIS ( 159 ) NE2
158 HIS ( 164 ) N
176 VAL ( 182 ) O
181 PHE ( 187 ) N
220 LEU ( 226 ) N
And so on for a total of 62 lines

# 49 # 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 : -1.375
2nd generation packing quality : -2.014
Ramachandran plot appearance : -1.230
chi-1/chi-2 rotamer normality : -1.480
Backbone conformation : -1.117

RMS Z-scores, should be close to 1.0:
Bond lengths : 0.637 (tight)
Bond angles : 1.375
Omega angle restraints : 0.876
Side chain planarity : 2.001 (loose)
Improper dihedral distribution : 1.790 (loose)
Inside/Outside distribution : 1.026

REFERENCES
==========

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).

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).