Subject: SwissModel WhatCheck AAAa09xBq Batch.1
Date: Tue, 28 Nov 2000 03:47:59 GMT
From: swissmod@ggr.co.uk
To: lslpc@life.nthu.edu.tw-------------------------------------------------------------
WhatCheck Report generated for your SWISS MODEL request
Project: AAAa09xBq
AC code: Model: Batch.1.pdb
For details about the WhatCheck output, please see:
http://www.sander.embl-heidelberg.de/rob/checkhelp/
-------------------------------------------------------------************************************************************************
********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program **********
************************************************************************Date : 2000-11-28
This report was created by WHAT IF version 19970813-1517INTRODUCTION
------------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.
27 GLU ( 27 )
# 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.
20 ASN ( 20 ) C 5.1 9.1 -0.1
27 GLU ( 27 ) C 4.1 7.6 0.0
29 LEU ( 29 ) C 5.2 9.4 -0.1
59 GLY ( 59 ) C 4.3 7.1 0.1
80 LEU ( 80 ) C 5.2 9.5 -0.1
102 GLY ( 102 ) C 4.4 7.1 0.1
110 ALA ( 110 ) C 4.1 7.0 0.0
113 PHE ( 113 ) C 4.2 7.9 -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 : 1.543
# 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 # 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.
14 TRP ( 14 ) CG CD2 1.328 -5.9
14 TRP ( 14 ) NE1 CE2 1.417 4.3
14 TRP ( 14 ) CE2 CZ2 1.303 -4.3
60 GLN ( 60 ) C O 1.108 -6.1
61 LYS ( 61 ) N <C 1.425 4.8
76 LEU ( 76 ) C O 1.118 -5.7
77 PRO ( 77 ) N <C 1.481 7.6
87 HIS ( 87 ) CG CD2 1.310 -4.2
# 22 # Note: Normal bond length variability
Bond lengths were found to deviate normally from the standard bond
lengths (values for Protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]).
RMS Z-score for bond lengths: 0.923
RMS-deviation in bond distances: 0.018
# 23 # Note: No bond length directionality
Comparison of bond distances with Engh and Huber [REF] standard
values for protein residues and Parkinson et al [REF] values for
DNA/RNA does not show significant systematic deviations.
# 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.
14 TRP ( 14 ) CE2 CZ2 CH2 123.530 4.6
14 TRP ( 14 ) CZ2 CH2 CZ3 115.873 -4.3
20 ASN ( 20 ) N CA CB 92.645 -10.5
20 ASN ( 20 ) CA CB CG 124.988 12.4
20 ASN ( 20 ) CB CG ND2 110.078 -4.2
24 TYR ( 24 ) CD1 CE1 CZ 126.910 4.1
24 TYR ( 24 ) CE1 CZ CE2 111.576 -4.4
44 LEU ( 44 ) CD1 CG CD2 101.127 -4.4
58 HIS ( 58 ) CB CG ND1 127.663 4.0
58 HIS ( 58 ) NE2 CD2 CG 110.801 4.3
60 GLN ( 60 ) CG CD NE2 123.651 4.8
64 ASP ( 64 ) CB CG OD2 108.200 -4.4
83 LEU ( 83 ) CD1 CG CD2 100.782 -4.6
85 HIS ( 85 ) CB CG ND1 127.850 4.2
89 ARG ( 89 ) CB CG CD 104.990 -4.6
105 LEU ( 105 ) CA C O 111.478 -5.5
106 LEU ( 106 ) <CA <C N 126.407 5.1
109 PRO ( 109 ) CG CD N 114.655 7.6
109 PRO ( 109 ) CD N CA 102.309 -6.9
116 ASP ( 116 ) CA CB CG 99.531 -13.1
117 PHE ( 117 ) CA CB CG 107.864 -5.9
139 ASP ( 139 ) CA CB CG 116.778 4.2
# 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: 1.225
RMS-deviation in bond angles: 2.236
# 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).
122 HIS ( 122 ) 9.001
64 ASP ( 64 ) 6.416
# 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.
112 HIS ( 112 ) CB 4.416
# 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.
109 PRO ( 109 ) 115.6 envelop C-beta (108 degrees)
# 30 # Note: Torsion angles OK
All individual residues have normal overall torsion angle scores.
# 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.
2 LEU ( 2 ) 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 : 0.344
# 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 : 5.181
# 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 : 0.593
# 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 : 0.958
# 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.
16 LYS ( 16 ) NZ -- 116 ASP ( 116 ) CG 0.588 2.512 INTRA
31 ARG ( 31 ) NH2 -- 111 ARG ( 111 ) NH1 0.444 2.556 INTRA
77 PRO ( 77 ) CA -- 84 ARG ( 84 ) NH2 0.405 2.695 INTRA
76 LEU ( 76 ) C -- 84 ARG ( 84 ) NH2 0.352 2.748 INTRA
117 PHE ( 117 ) CZ -- 122 HIS ( 122 ) CD2 0.294 2.906 INTRA
105 LEU ( 105 ) O -- 109 PRO ( 109 ) CD 0.292 2.508 INTRA
44 LEU ( 44 ) CD1 -- 45 HIS ( 45 ) N 0.232 2.868 INTRA
77 PRO ( 77 ) CA -- 84 ARG ( 84 ) NH1 0.229 2.871 INTRA
83 LEU ( 83 ) CD2 -- 86 ARG ( 86 ) NH1 0.221 2.879 INTRA
77 PRO ( 77 ) N -- 84 ARG ( 84 ) NH2 0.200 2.800 INTRA
83 LEU ( 83 ) CD2 -- 86 ARG ( 86 ) NH2 0.200 2.900 INTRA
88 VAL ( 88 ) CG2 -- 89 ARG ( 89 ) N 0.179 2.921 INTRA
16 LYS ( 16 ) NZ -- 116 ASP ( 116 ) OD1 0.170 2.530 INTRA
88 VAL ( 88 ) CG2 -- 139 ASP ( 139 ) CB 0.161 3.039 INTRA
108 THR ( 108 ) CB -- 109 PRO ( 109 ) CD 0.142 3.058 INTRA
76 LEU ( 76 ) N -- 77 PRO ( 77 ) CD 0.142 2.858 INTRA
75 ASP ( 75 ) OD1 -- 78 ARG ( 78 ) CB 0.137 2.663 INTRA
27 GLU ( 27 ) CD -- 31 ARG ( 31 ) NE 0.137 2.963 INTRA
29 LEU ( 29 ) CD1 -- 58 HIS ( 58 ) CD2 0.126 3.074 INTRA
111 ARG ( 111 ) NH2 -- 112 HIS ( 112 ) NE2 0.121 2.729 INTRA HB
77 PRO ( 77 ) CA -- 84 ARG ( 84 ) CZ 0.119 3.081 INTRA
24 TYR ( 24 ) CE2 -- 112 HIS ( 112 ) CG 0.115 3.085 INTRA
20 ASN ( 20 ) CB -- 24 TYR ( 24 ) CE1 0.108 3.092 INTRA
45 HIS ( 45 ) NE2 -- 46 LEU ( 46 ) CD1 0.086 3.014 INTRA
85 HIS ( 85 ) NE2 -- 89 ARG ( 89 ) CD 0.085 3.015 INTRA BF
83 LEU ( 83 ) CD2 -- 86 ARG ( 86 ) CZ 0.085 3.115 INTRA
73 LEU ( 73 ) CD2 -- 128 PHE ( 128 ) CE1 0.082 3.118 INTRA
138 SER ( 138 ) C -- 140 SER ( 140 ) N 0.080 2.820 INTRA
21 VAL ( 21 ) CG2 -- 22 GLY ( 22 ) N 0.078 3.022 INTRA
1 ALA ( 1 ) C -- 2 LEU ( 2 ) O 0.070 2.730 INTRA
84 ARG ( 84 ) O -- 88 VAL ( 88 ) CG2 0.069 2.731 INTRA
45 HIS ( 45 ) CD2 -- 46 LEU ( 46 ) CD1 0.068 3.132 INTRA
24 TYR ( 24 ) CE2 -- 112 HIS ( 112 ) CD2 0.068 3.132 INTRA
17 MET ( 17 ) SD -- 113 PHE ( 113 ) CE2 0.061 3.339 INTRA
20 ASN ( 20 ) C -- 24 TYR ( 24 ) CD1 0.058 3.142 INTRA
20 ASN ( 20 ) O -- 21 VAL ( 21 ) C 0.054 2.746 INTRA
7 ARG ( 7 ) CZ -- 74 GLU ( 74 ) OE1 0.045 2.755 INTRA
117 PHE ( 117 ) CZ -- 122 HIS ( 122 ) CG 0.045 3.155 INTRA
85 HIS ( 85 ) CD2 -- 89 ARG ( 89 ) CD 0.043 3.157 INTRA
84 ARG ( 84 ) NH2 -- 135 ALA ( 135 ) CB 0.042 3.058 INTRA BF
9 THR ( 9 ) OG1 -- 124 SER ( 124 ) CB 0.026 2.774 INTRA
1 ALA ( 1 ) C -- 2 LEU ( 2 ) C 0.026 2.774 INTRA B3
24 TYR ( 24 ) CE2 -- 112 HIS ( 112 ) CB 0.020 3.180 INTRA
117 PHE ( 117 ) CZ -- 122 HIS ( 122 ) CB 0.020 3.180 INTRA
76 LEU ( 76 ) O -- 84 ARG ( 84 ) NH2 0.019 2.681 INTRA
9 THR ( 9 ) CB -- 121 LEU ( 121 ) CD2 0.018 3.182 INTRA BF
24 TYR ( 24 ) CZ -- 113 PHE ( 113 ) CE2 0.008 3.192 INTRA
32 MET ( 32 ) SD -- 101 LEU ( 101 ) CD1 0.006 3.394 INTRA
138 SER ( 138 ) O -- 140 SER ( 140 ) N 0.004 2.696 INTRA
29 LEU ( 29 ) O -- 33 PHE ( 33 ) CD2 0.003 2.797 INTRA
# 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.
50 LEU ( 50 ) -6.26
112 HIS ( 112 ) -6.04
# 38 # Note: No series of residues with bad packing environment
There are no stretches of three or more residues each having a quality
control score worse than -4.0.
# 39 # Note: Structural average packing environment OK
The structural average quality control value is within normal ranges.
Average for range 1 - 141 : -0.410
# 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.
45 HIS ( 45 ) -3.05
# 41 # Note: No series of residues with abnormal new packing environment
There are no stretches of four or more residues each having a quality
control Z-score worse than -1.75.
# 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 = 0.423 Z-score = 2.95
BB-BB contacts : Average = 0.594 Z-score = 4.26
BB-SC contacts : Average = -0.091 Z-score = -0.41
SC-BB contacts : Average = 0.616 Z-score = 3.92
SC-SC contacts : Average = -0.196 Z-score = -0.76
# 43 # Note: Backbone oxygen evaluation OK
All residues for which the local backbone conformation could be
found in the WHAT IF database have a normal backbone oxygen
position.
# 44 # Note: Rotamers checked OK
None of the residues that have a normal backbone environment have
abnormal rotamers.
# 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!
17 MET ( 17 ) 0
# 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 : 0.910
# 47 # Note: Average B-factor OK
The average B-factor of buried atoms is within expected values for
a room-temperature X-ray study.
Average B-factor for buried atoms : 11.787
# 48 # Note: Number of buried atoms with low B-factor is OK
For protein structures determined at room temperature, no more than
about 1 percent of the B factors of buried atoms is below 5.0.
Percentage of buried atoms with B less than 5 : 0.00
# 49 # Error: The B-factors of bonded atoms show signs of over-refinement
For each of the bond types in a protein a distribution was derived
for the difference between the square roots of the B-factors of the
two atoms. All bonds in the current protein were scored against
these distributions. The number given below is the RMS Z-score over
the structure. For a structure with completely restrained B-factors
within residues, this value will be around 0.35, for extremely high
resolution structures refined with free isotropic B-factors this
number is expected to be near 1.0. Any value over 1.5 is sign of
severe over-refinement of B-factors.
RMS Z-score : 2.707 over 972 bonds
Average difference in B over a bond : 2.19
RMS difference in B over a bond : 8.96
# 50 # 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.
44 LEU ( 44 ) N
70 VAL ( 70 ) O
76 LEU ( 76 ) N
84 ARG ( 84 ) NE
84 ARG ( 84 ) NH2
89 ARG ( 89 ) NE
105 LEU ( 105 ) O
# 51 # 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 : 0.224
2nd generation packing quality : 2.946
Ramachandran plot appearance : 0.344
chi-1/chi-2 rotamer normality : 0.593
Backbone conformation : 0.910
RMS Z-scores, should be close to 1.0:
Bond lengths : 0.923
Bond angles : 1.225
Omega angle restraints : 0.942
Side chain planarity : 2.158 (loose)
Improper dihedral distribution : 1.543 (loose)
B-factor distribution : 2.707 (loose)
Inside/Outside distribution : 0.958REFERENCES
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Errors in protein structures
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R.Engh and R.Huber,
Accurate bond and angle parameters for X-ray protein structure
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Acta Crystallogr. A47, 392--400 (1991).Bond lengths and angles, DNA/RNA
G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
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Dictionary of protein secondary structure: pattern
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Positioning hydrogen atoms by optimizing hydrogen bond networks
in protein structures
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Solvent content of Protein Crystals
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Verification of protein structures: side-chain planarity
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A general definition of ring puckering coordinates
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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).