Fellow Modellers,
I ran the first example in the Modeller tutorial, 1fdx,
and I got several restraint violations in the final structure. I ran the
diagnostics, and I dod not receive any error messages.
Is this as it should be?
Is there anywhere in which one can obtain a standard 1fdx run that can be
used as a "known"?
I know that, based upon faq #23, interpreting restraint violations is
something of an art. I am asking to make sure that I ran the program
correctly, and that the program is running as it should be.
My violated restraints are:
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 379 0 0 0.005 0.005 2.8642 1.000
2 Bond angle potential : 520 0 0 2.444 2.444 59.089 1.000
3 Stereochemical cosine torsion poten: 244 0 10 55.593 55.593 103.81 1.000
4 Stereochemical improper torsion pot: 146 0 0 1.474 1.474 6.3455 1.000
5 Soft-sphere overlap restraints : 663 0 0 0.002 0.002 0.47318 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 804 0 0 0.344 0.344 30.114 1.000
10 Distance restraints 2 (N-O) : 832 0 1 0.467 0.467 37.873 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 53 0 0 4.634 4.634 13.423 1.000
14 Sidechain Chi_1 dihedral restraints: 43 0 1 72.693 72.693 11.147 1.000
15 Sidechain Chi_2 dihedral restraints: 26 0 1 68.739 68.739 16.513 1.000
16 Sidechain Chi_3 dihedral restraints: 9 0 0 37.987 37.987 3.4346 1.000
17 Sidechain Chi_4 dihedral restraints: 1 0 0 124.535 124.535 1.0173 1.000
18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000
20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 553 0 0 0.540 0.540 18.286 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 52 9 5 29.961 67.309 9.4985 1.000
26 Distance restraints 4 (SDCH-SDCH) : 100 0 2 1.196 1.196 15.584 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
openf5__224_> Open 17 UNKNOWN SEQUENTIAL 1fdx.V99990001
# Heavy relative violation of each residue is written to: 1fdx.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1296 7S 8C C N 53 55 -75.51 -117.90 43.16 1.34 -63.00 174.54 20.46
1 8C 8C N CA 55 56 133.00 141.10 -41.10
2 1297 8C 9I C N 59 61 -109.33 -97.30 83.47 8.55 -63.40 99.45 15.16
2 9I 9I N CA 61 62 44.60 127.20 -43.60
3 1298 9I 10A C N 67 69 43.10 55.40 23.15 0.89 -62.50 144.55 28.99
3 10A 10A N CA 69 70 57.81 38.20 -40.90
4 1299 10A 11C C N 72 74 -61.78 -63.00 1.43 0.25 -117.90 -172.86 8.06
4 11C 11C N CA 74 75 -40.37 -41.10 141.10
5 1310 21N 22I C N 146 148 -109.14 -120.60 69.78 3.55 -63.40 114.60 17.55
5 22I 22I N CA 148 149 61.47 130.30 -43.60
6 1313 24Q 25G C N 171 173 98.62 78.70 39.64 0.60 82.20 152.01 8.20
6 25G 25G N CA 173 174 159.62 -166.10 8.50
7 1314 25G 26S C N 175 177 -65.61 -64.10 21.61 1.66 -136.60 167.99 9.49
7 26S 26S N CA 177 178 -56.55 -35.00 151.20
8 1315 26S 27I C N 181 183 -64.03 -63.40 6.55 1.10 -120.60 -171.73 12.88
8 27I 27I N CA 183 184 -50.13 -43.60 130.30
9 1316 27I 28Y C N 189 191 104.14 -124.30 131.89 10.18 -124.30 131.89 10.18
9 28Y 28Y N CA 191 192 126.16 135.40 135.40
Thanks and best wishes,
Rich
--------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Medical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
http://cancercenter.ccc.columbia.edu/~friedman/
In Memoriam, Robert Kanigher