MODELLER 7v7, Sep 12, 2004 09:15pm
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2004 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
N. Eswar, F. Alber, B. Oliva, A. Fiser,
R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux synth.compbio.ucsf.edu 2.6.8-1.521smp i686
Date and time of compilation : 09/12/2004 21:24:59
Job starting time (YY/MM/DD HH:MM:SS): 2004/09/19 00:40:16.614
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
delete__443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 13625 12489
>> ENERGY; Differences between the model's features and restraints:
ID1, ID2 : 9999 1
Number of all residues in MODEL : 162
Number of all, selected real atoms : 1267 1267
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 12489 12489
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2486
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 200
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SCHEDULE_STEP, N_SCHEDULE : 10 10
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 797.7318
Symmetry term within energy : 0.0000
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 : 1295 0 0 0.004 0.004 6.4998 1.000
2 Bond angle potential : 1763 0 1 1.838 1.838 116.72 1.000
3 Stereochemical cosine torsion poten: 841 0 25 48.275 48.275 315.09 1.000
4 Stereochemical improper torsion pot: 524 0 0 1.101 1.101 13.835 1.000
5 Soft-sphere overlap restraints : 2486 0 0 0.002 0.002 1.0895 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) : 2795 0 1 0.264 0.264 62.343 1.000
10 Distance restraints 2 (N-O) : 2860 0 1 0.308 0.308 83.649 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: 161 1 1 14.601 14.601 27.881 1.000
14 Sidechain Chi_1 dihedral restraints: 132 0 1 70.754 70.754 27.804 1.000
15 Sidechain Chi_2 dihedral restraints: 97 0 0 62.178 62.178 28.712 1.000
16 Sidechain Chi_3 dihedral restraints: 47 0 0 85.506 85.506 33.127 1.000
17 Sidechain Chi_4 dihedral restraints: 15 0 0 117.065 117.065 10.640 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) : 1461 0 0 0.353 0.353 19.783 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: 160 8 10 26.482 45.842 30.949 1.000
26 Distance restraints 4 (SDCH-SDCH) : 338 0 0 0.681 0.681 19.611 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
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: hvdfr.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 13760.0020
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 4424 1M 2E C N 7 9 -100.57 -117.80 17.25 0.65 -63.60 -178.31 22.40
1 2E 2E N CA 9 10 137.59 136.80 -40.30
2 4444 21L 22P C N 154 156 -66.21 -58.70 27.24 1.73 -64.50 151.53 11.40
2 22P 22P N CA 156 157 -4.32 -30.50 147.20
3 4503 80A 81S C N 617 619 -162.60 -64.10 103.21 13.81 -64.10 103.21 13.81
3 81S 81S N CA 619 620 -65.84 -35.00 -35.00
4 4504 81S 82V C N 623 625 -53.42 -62.40 16.35 1.80 -125.40 176.03 10.00
4 82V 82V N CA 625 626 -56.06 -42.40 143.30
5 4506 83E 84E C N 639 641 -166.42 -117.80 48.76 1.70 -63.60 -153.33 33.24
5 84E 84E N CA 641 642 140.42 136.80 -40.30
6 4514 91S 92L C N 692 694 78.83 -70.70 158.48 15.69 -108.50 -176.67 8.17
6 92L 92L N CA 694 695 -165.88 141.60 132.50
7 4571 148E 149G C N 1151 1153 -136.82 -167.20 31.34 0.46 82.20 -147.92 16.07
7 149G 149G N CA 1153 1154 166.94 174.60 8.50
8 4572 149G 150F C N 1155 1157 -61.10 -63.20 19.79 2.61 -124.20 165.24 8.95
8 150F 150F N CA 1157 1158 -63.98 -44.30 143.30
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 6 9 74 81 99 104 139 158 176 186
<< end of ENERGY.
Dynamically allocated memory at finish [B,kB,MB]: 10090693 9854.192 9.623
Starting time : 2004/09/19 00:40:16.614
Closing time : 2004/09/19 00:40:57.017
Total CPU time [seconds] : 38.41