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): 2004/09/17 18:56:43.728
check_ali___> Checking pairwise structural superpositions.
Equivalent CA pairs with distance difference larger than 6.0 angstroms:
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------------
END OF TABLE
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
----------------------------------------------
131 1 131 133 A . 17.230
END OF TABLE
delete__442E> One or more atoms absent from MODEL: O: 131: C: 131: N: 132: CA: 132:
delete__443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 14417 13517
>> ENERGY; Differences between the model's features and restraints:
ID1, ID2 : 9999 1
Number of all residues in MODEL : 132
Number of all, selected real atoms : 1053 1053
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13517 13517
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2146
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 : 4768.3096
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 : 1047 1 5 0.012 0.012 40.958 1.000
2 Bond angle potential : 1410 18 23 6.193 6.193 589.08 1.000
3 Stereochemical cosine torsion poten: 628 0 24 53.046 53.046 302.17 1.000
4 Stereochemical improper torsion pot: 420 0 0 1.432 1.432 17.097 1.000
5 Soft-sphere overlap restraints : 2146 2 4 0.012 0.012 39.247 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) : 2180 0 0 0.122 0.122 407.93 1.000
10 Distance restraints 2 (N-O) : 2322 0 0 0.139 0.139 411.63 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: 130 0 0 3.855 3.855 22.788 1.000
14 Sidechain Chi_1 dihedral restraints: 115 0 1 77.384 77.384 33.239 1.000
15 Sidechain Chi_2 dihedral restraints: 79 0 3 62.885 62.885 45.474 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 1 86.433 86.433 36.022 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 84.888 84.888 12.684 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) : 2004 0 1 0.538 0.538 1218.1 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: 129 2 4 22.022 26.105 2.9929 1.000
26 Distance restraints 4 (SDCH-SDCH) : 1105 7 45 1.236 1.236 877.28 1.000
27 Distance restraints 5 (X-Y) : 1893 31 46 0.225 0.225 711.61 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: blbp.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: 14341.6982
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 1 : Bond length potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 998 126R 126R CD CG 986 985 1.70 1.53 0.17 4.74 1.53 0.17 4.74
-------------------------------------------------------------------------------------------------
Feature 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1336 27F 27F CB CG 206 207 152.92 122.30 30.62 6.65 122.30 30.62 6.65
2 1859 76D 76D CA CB 590 591 132.61 108.00 24.60 5.70 108.00 24.60 5.70
3 2396 126R 126R CB CG 984 985 132.57 113.60 18.97 4.66 113.60 18.97 4.66
4 2397 126R 126R CG CD 985 986 131.02 107.50 23.52 6.22 107.50 23.52 6.22
5 2398 126R 126R CD NE 986 987 145.85 120.00 25.85 6.56 120.00 25.85 6.56
-------------------------------------------------------------------------------------------------
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 3624 119F 120G C N 941 943 61.20 78.70 39.79 0.59 82.20 140.45 7.86
1 120G 120G N CA 943 944 -130.37 -166.10 8.50
2 3625 120G 121D C N 945 947 -108.25 -63.30 75.71 8.16 -63.30 75.71 8.16
2 121D 121D N CA 947 948 20.92 -40.00 -40.00
-------------------------------------------------------------------------------------------------
Feature 26 : Distance restraints 4 (SDCH-SDCH)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10716 13S 126R CB NH1 98 989 9.09 3.60 5.49 4.63 3.60 5.49 4.63
2 10726 13S 126R OG NH1 99 989 8.80 3.03 5.76 4.94 3.03 5.76 4.94
3 10738 16F 126R CB NH1 121 989 11.15 4.10 7.05 5.94 4.10 7.05 5.94
4 10747 16F 126R CG NH1 122 989 10.43 3.73 6.70 5.71 3.73 6.70 5.71
5 10761 16F 126R CD1 NH1 123 989 10.18 4.37 5.81 4.87 4.37 5.81 4.87
6 10768 16F 126R CD2 NH1 124 989 10.20 3.40 6.80 5.78 3.40 6.80 5.78
7 10787 16F 126R CE2 NH1 126 989 9.76 3.80 5.96 5.07 3.80 5.96 5.07
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12287 76D 132. OD1 C4 593 1039 8.51 6.75 1.76 8.80 6.75 1.76 8.80
2 12288 76D 132. OD1 C5 593 1040 7.55 5.51 2.04 10.22 5.51 2.04 10.22
3 12289 76D 132. OD1 C6 593 1041 6.25 4.34 1.92 9.58 4.34 1.92 9.58
4 12290 76D 132. OD1 C7 593 1042 5.57 4.26 1.31 6.54 4.26 1.31 6.54
5 12291 76D 132. OD1 C8 593 1043 5.04 3.85 1.18 5.92 3.85 1.18 5.92
6 12343 106R 132. NH2 CA 838 1034 7.48 6.08 1.39 6.97 6.08 1.39 6.97
7 12344 106R 132. NH2 C 838 1035 7.10 5.34 1.76 8.82 5.34 1.76 8.82
8 12345 106R 132. NH2 O 838 1036 6.08 4.35 1.73 8.65 4.35 1.73 8.65
9 12346 106R 132. NH2 OXT 838 1037 8.11 6.12 1.99 9.96 6.12 1.99 9.96
10 12347 106R 132. NH2 C3 838 1038 7.05 6.07 0.98 4.91 6.07 0.98 4.91
11 12395 126R 132. CD C4 986 1039 7.59 6.21 1.38 6.88 6.21 1.38 6.88
12 12401 126R 132. NE C4 987 1039 6.77 5.81 0.96 4.79 5.81 0.96 4.79
13 12407 126R 132. CZ C4 988 1039 7.06 6.16 0.90 4.52 6.16 0.90 4.52
14 12408 126R 132. CZ C14 988 1049 9.11 6.95 2.16 10.78 6.95 2.16 10.78
15 12409 126R 132. CZ C15 988 1050 7.93 6.49 1.44 7.18 6.49 1.44 7.18
16 12422 126R 132. NH2 C13 990 1048 8.29 6.57 1.72 8.58 6.57 1.72 8.58
17 12423 126R 132. NH2 C14 990 1049 7.84 6.02 1.82 9.12 6.02 1.82 9.12
18 12424 126R 132. NH2 C15 990 1050 6.60 5.38 1.22 6.10 5.38 1.22 6.10
19 12452 128Y 132. OH O 1008 1036 4.80 3.54 1.26 6.29 3.54 1.26 6.29
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 1 10 17 60 65 113 73 118 134 135 155
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
ID1, ID2 : 9999 2
Number of all residues in MODEL : 132
Number of all, selected real atoms : 1053 1053
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13517 13517
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2093
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 : 3748.3398
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 : 1047 0 0 0.006 0.006 8.7569 1.000
2 Bond angle potential : 1410 0 5 1.950 1.950 102.88 1.000
3 Stereochemical cosine torsion poten: 628 0 25 53.251 53.251 307.10 1.000
4 Stereochemical improper torsion pot: 420 0 1 1.502 1.502 18.176 1.000
5 Soft-sphere overlap restraints : 2093 0 0 0.003 0.003 2.3897 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) : 2180 0 0 0.128 0.128 407.40 1.000
10 Distance restraints 2 (N-O) : 2322 8 8 0.260 0.260 468.36 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: 130 0 0 4.043 4.043 25.055 1.000
14 Sidechain Chi_1 dihedral restraints: 115 0 7 79.847 79.847 51.855 1.000
15 Sidechain Chi_2 dihedral restraints: 79 0 4 66.084 66.084 47.652 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 2 80.189 80.189 30.804 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 90.807 90.807 9.3879 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) : 2004 0 1 0.480 0.480 1200.5 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: 129 3 7 24.164 30.874 23.155 1.000
26 Distance restraints 4 (SDCH-SDCH) : 1105 0 3 0.876 0.876 704.41 1.000
27 Distance restraints 5 (X-Y) : 1893 8 22 0.156 0.156 340.47 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: blbp.V99990002
# 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: 13399.1904
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 3570 65Q 66L C N 507 509 -45.94 -70.70 128.49 10.70 -70.70 128.49 10.70
1 66L 66L N CA 509 510 -92.32 141.60 141.60
2 3571 66L 67G C N 515 517 -58.76 -62.40 24.21 3.80 82.20 143.30 10.43
2 67G 67G N CA 517 518 -17.26 -41.20 8.50
3 3625 120G 121D C N 945 947 73.28 54.50 34.61 1.74 -63.30 146.08 24.82
3 121D 121D N CA 947 948 11.83 40.90 -40.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12322 78R 132. NH2 C4 613 1039 8.42 6.57 1.85 9.25 6.57 1.85 9.25
2 12323 78R 132. NH2 C5 613 1040 7.55 5.44 2.11 10.55 5.44 2.11 10.55
3 12324 78R 132. NH2 C6 613 1041 6.20 4.10 2.10 10.52 4.10 2.10 10.52
4 12325 78R 132. NH2 C7 613 1042 6.39 4.45 1.93 9.66 4.45 1.93 9.66
5 12326 78R 132. NH2 C8 613 1043 7.22 5.04 2.18 10.90 5.04 2.18 10.90
6 12327 78R 132. NH2 C9 613 1044 7.80 5.89 1.91 9.57 5.89 1.91 9.57
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 1 7 11 54 63 100 80 91 126 140 136
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
ID1, ID2 : 9999 3
Number of all residues in MODEL : 132
Number of all, selected real atoms : 1053 1053
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13517 13517
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2107
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 : 3958.6375
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 : 1047 0 1 0.008 0.008 16.691 1.000
2 Bond angle potential : 1410 12 16 5.674 5.674 510.31 1.000
3 Stereochemical cosine torsion poten: 628 0 27 53.923 53.923 311.66 1.000
4 Stereochemical improper torsion pot: 420 0 2 1.622 1.622 20.744 1.000
5 Soft-sphere overlap restraints : 2107 1 1 0.007 0.007 11.758 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) : 2180 0 0 0.116 0.116 403.33 1.000
10 Distance restraints 2 (N-O) : 2322 0 0 0.160 0.160 416.86 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: 130 0 0 3.842 3.842 22.634 1.000
14 Sidechain Chi_1 dihedral restraints: 115 0 4 77.356 77.356 43.966 1.000
15 Sidechain Chi_2 dihedral restraints: 79 0 4 59.038 59.038 51.959 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 3 80.229 80.229 35.475 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 77.518 77.518 9.7138 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) : 2004 0 1 0.518 0.518 1212.2 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: 129 1 6 23.173 26.994 11.334 1.000
26 Distance restraints 4 (SDCH-SDCH) : 1105 0 1 0.801 0.801 688.98 1.000
27 Distance restraints 5 (X-Y) : 1893 6 16 0.117 0.117 191.06 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: blbp.V99990003
# 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: 12989.4238
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 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1273 20M 20M CA CB 160 161 132.11 113.50 18.62 4.57 113.50 18.62 4.57
2 1726 64F 64F CB CG 491 492 153.46 122.30 31.17 6.77 122.30 31.17 6.77
-------------------------------------------------------------------------------------------------
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 3625 120G 121D C N 945 947 69.77 54.50 43.02 2.18 -63.30 139.14 23.49
1 121D 121D N CA 947 948 0.67 40.90 -40.00
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12343 106R 132. NH2 CA 838 1034 7.57 6.08 1.49 7.45 6.08 1.49 7.45
2 12344 106R 132. NH2 C 838 1035 7.10 5.34 1.76 8.79 5.34 1.76 8.79
3 12345 106R 132. NH2 O 838 1036 6.12 4.35 1.77 8.83 4.35 1.77 8.83
4 12346 106R 132. NH2 OXT 838 1037 8.01 6.12 1.89 9.44 6.12 1.89 9.44
5 12347 106R 132. NH2 C3 838 1038 7.26 6.07 1.19 5.97 6.07 1.19 5.97
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 11 10 52 79 79 72 100 125 122 159
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
ID1, ID2 : 9999 4
Number of all residues in MODEL : 132
Number of all, selected real atoms : 1053 1053
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13517 13517
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2066
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 : 3882.3369
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 : 1047 0 0 0.006 0.006 8.9587 1.000
2 Bond angle potential : 1410 6 9 3.655 3.655 185.13 1.000
3 Stereochemical cosine torsion poten: 628 0 25 53.360 53.360 309.90 1.000
4 Stereochemical improper torsion pot: 420 0 1 1.459 1.459 17.026 1.000
5 Soft-sphere overlap restraints : 2066 0 0 0.003 0.003 1.6301 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) : 2180 0 0 0.122 0.122 408.09 1.000
10 Distance restraints 2 (N-O) : 2322 2 8 0.201 0.201 464.20 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: 130 0 0 4.021 4.021 24.785 1.000
14 Sidechain Chi_1 dihedral restraints: 115 0 9 77.833 77.833 59.158 1.000
15 Sidechain Chi_2 dihedral restraints: 79 0 5 62.450 62.450 50.230 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 1 84.613 84.613 32.980 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 79.980 79.980 10.715 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) : 2004 0 0 0.491 0.491 1200.6 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: 129 3 7 24.184 31.110 23.599 1.000
26 Distance restraints 4 (SDCH-SDCH) : 1105 0 7 0.939 0.939 723.91 1.000
27 Distance restraints 5 (X-Y) : 1893 14 29 0.161 0.161 361.39 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: blbp.V99990004
# 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: 13431.8262
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 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1273 20M 20M CA CB 160 161 132.10 113.50 18.60 4.57 113.50 18.60 4.57
2 1900 79N 79N ND2 CG 621 619 138.72 122.50 16.22 4.52 122.50 16.22 4.52
-------------------------------------------------------------------------------------------------
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 3570 65Q 66L C N 507 509 -50.01 -70.70 130.54 10.70 -70.70 130.54 10.70
1 66L 66L N CA 509 510 -89.51 141.60 141.60
2 3571 66L 67G C N 515 517 -58.52 -62.40 23.99 3.78 82.20 143.11 10.43
2 67G 67G N CA 517 518 -17.53 -41.20 8.50
3 3624 119F 120G C N 941 943 58.54 78.70 36.70 0.59 82.20 145.88 8.25
3 120G 120G N CA 943 944 -135.44 -166.10 8.50
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12416 126R 132. NH2 CA 990 1034 5.34 3.99 1.35 6.75 3.99 1.35 6.75
2 12417 126R 132. NH2 C 990 1035 5.60 3.88 1.72 8.61 3.88 1.72 8.61
3 12418 126R 132. NH2 O 990 1036 6.81 4.97 1.85 9.23 4.97 1.85 9.23
4 12419 126R 132. NH2 OXT 990 1037 4.75 2.97 1.78 8.90 2.97 1.78 8.90
5 12420 126R 132. NH2 C3 990 1038 6.54 5.19 1.35 6.74 5.19 1.35 6.74
6 12423 126R 132. NH2 C14 990 1049 6.98 6.02 0.96 4.81 6.02 0.96 4.81
7 12424 126R 132. NH2 C15 990 1050 6.81 5.38 1.44 7.19 5.38 1.44 7.19
8 12425 126R 132. NH2 C16 990 1051 7.52 5.85 1.67 8.34 5.85 1.67 8.34
9 12426 126R 132. NH2 C17 990 1052 8.22 6.23 1.99 9.94 6.23 1.99 9.94
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 8 12 45 72 92 70 100 120 134 143
<< end of ENERGY.
>> ENERGY; Differences between the model's features and restraints:
ID1, ID2 : 9999 5
Number of all residues in MODEL : 132
Number of all, selected real atoms : 1053 1053
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13517 13517
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2083
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 : 4079.9014
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 : 1047 0 1 0.008 0.008 18.974 1.000
2 Bond angle potential : 1410 10 15 5.204 5.204 463.41 1.000
3 Stereochemical cosine torsion poten: 628 0 23 53.188 53.188 307.72 1.000
4 Stereochemical improper torsion pot: 420 0 0 1.317 1.317 14.188 1.000
5 Soft-sphere overlap restraints : 2083 1 1 0.007 0.007 11.900 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) : 2180 0 0 0.125 0.125 407.13 1.000
10 Distance restraints 2 (N-O) : 2322 1 5 0.195 0.195 434.76 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: 130 0 1 4.089 4.089 25.631 1.000
14 Sidechain Chi_1 dihedral restraints: 115 0 1 72.060 72.060 36.432 1.000
15 Sidechain Chi_2 dihedral restraints: 79 0 3 58.988 58.988 43.455 1.000
16 Sidechain Chi_3 dihedral restraints: 37 0 0 59.339 59.339 29.336 1.000
17 Sidechain Chi_4 dihedral restraints: 18 0 0 84.343 84.343 12.639 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) : 2004 0 0 0.521 0.521 1211.1 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: 129 6 8 25.642 38.318 24.229 1.000
26 Distance restraints 4 (SDCH-SDCH) : 1105 1 4 0.906 0.906 692.72 1.000
27 Distance restraints 5 (X-Y) : 1893 14 22 0.157 0.157 346.31 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: blbp.V99990005
# 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: 13214.6035
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 2 : Bond angle potential
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 1336 27F 27F CB CG 206 207 152.92 122.30 30.63 6.66 122.30 30.63 6.66
2 1411 34N 34N ND2 CG 263 261 138.91 122.50 16.41 4.57 122.50 16.41 4.57
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 6201 1V 46G N O 1 353 12.61 9.64 2.97 4.51 9.64 2.97 4.51
-------------------------------------------------------------------------------------------------
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 3550 45E 46G C N 348 350 -62.66 -80.20 54.66 1.38 78.70 158.45 8.88
1 46G 46G N CA 350 351 122.33 174.10 -166.10
2 3551 46G 47G C N 352 354 76.40 82.20 27.51 1.62 -62.40 140.67 25.93
2 47G 47G N CA 354 355 -18.39 8.50 -41.20
3 3602 97W 98D C N 770 772 53.80 -70.90 141.94 11.91 54.50 177.19 12.97
3 98D 98D N CA 772 773 -141.91 150.30 40.90
4 3603 98D 99G C N 778 780 -74.04 -62.40 16.01 2.27 82.20 160.97 11.96
4 99G 99G N CA 780 781 -30.22 -41.20 8.50
5 3624 119F 120G C N 941 943 61.65 78.70 38.87 0.58 82.20 141.18 7.87
5 120G 120G N CA 943 944 -131.17 -166.10 8.50
6 3625 120G 121D C N 945 947 -107.87 -63.30 75.36 8.12 -63.30 75.36 8.12
6 121D 121D N CA 947 948 20.77 -40.00 -40.00
-------------------------------------------------------------------------------------------------
Feature 26 : Distance restraints 4 (SDCH-SDCH)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 10653 9K 129E NZ OE2 70 1017 9.07 2.77 6.30 4.61 2.77 6.30 4.61
-------------------------------------------------------------------------------------------------
Feature 27 : Distance restraints 5 (X-Y)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12416 126R 132. NH2 CA 990 1034 5.50 3.99 1.51 7.55 3.99 1.51 7.55
2 12417 126R 132. NH2 C 990 1035 5.65 3.88 1.77 8.85 3.88 1.77 8.85
3 12418 126R 132. NH2 O 990 1036 6.82 4.97 1.86 9.28 4.97 1.86 9.28
4 12419 126R 132. NH2 OXT 990 1037 4.70 2.97 1.73 8.67 2.97 1.73 8.67
5 12420 126R 132. NH2 C3 990 1038 6.72 5.19 1.53 7.63 5.19 1.53 7.63
6 12421 126R 132. NH2 C4 990 1039 7.08 5.92 1.16 5.82 5.92 1.16 5.82
7 12424 126R 132. NH2 C15 990 1050 6.66 5.38 1.29 6.43 5.38 1.29 6.43
8 12425 126R 132. NH2 C16 990 1051 7.41 5.85 1.56 7.79 5.85 1.56 7.79
9 12426 126R 132. NH2 C17 990 1052 8.02 6.23 1.79 8.93 6.23 1.79 8.93
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 9 12 53 54 89 69 87 122 131 154
<< end of ENERGY.
Dynamically allocated memory at finish [B,kB,MB]: 8601123 8399.534 8.203
Starting time : 2004/09/17 18:56:43.728
Closing time : 2004/09/17 19:00:20.870
Total CPU time [seconds] : 216.67