MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, 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 sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:42:02 openf___224_> Open ../atom_files/pdb1fas.ent read_mo_297_> Segments, residues, atoms: 1 61 468 read_mo_298_> Segment: 1 1 A 61 A 468 openf___224_> Open ../atom_files/pdb2ctx.ent read_mo_297_> Segments, residues, atoms: 1 71 518 read_mo_298_> Segment: 1 1 A 71 A 518 openf___224_> Open toxin.ali Read the alignment from file : toxin.ali Total number of alignment positions: 75 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1fas 61 1 1fas fasciculin 1 2 2ctx 71 1 2ctx alpha-cobratoxin openf___224_> Open toxin.pap SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fas 2 2ctx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 61 Numb of atoms/sel atoms in MODEL : 468 245 Numb of residues in MODEL2 : 71 Numb of atoms in MODEL2 : 518 Equivalences refinement : F Numb of aligned equiv positions : 228 Numb of aligned equiv distances : 25878 RMS before superposition : 33.4501 RMS after superposition : 3.1866 DRMS : 2.1515 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 180 Numb of equiv cutoff distances : 22796 Cutoff RMS after superposition : 1.5879 Cutoff DRMS : 1.3951 X_new = Rotation * X + Translation Rotation matrix : -0.7500 -0.4856 0.4491 0.0330 -0.7055 -0.7079 0.6607 -0.5161 0.5451 Translation vector: 68.2032 56.9363 13.6700 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fas 2 2ctx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 61 Numb of atoms/sel atoms in MODEL : 468 223 Numb of residues in MODEL2 : 71 Numb of atoms in MODEL2 : 518 Equivalences refinement : F Numb of aligned equiv positions : 100 Numb of aligned equiv distances : 4950 RMS before superposition : 3.4765 RMS after superposition : 3.2429 DRMS : 2.0252 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 82 Numb of equiv cutoff distances : 4526 Cutoff RMS after superposition : 1.8270 Cutoff DRMS : 1.2858 X_new = Rotation * X + Translation Rotation matrix : 0.9915 -0.0249 0.1277 0.0221 0.9995 0.0227 -0.1282 -0.0197 0.9916 Translation vector: -0.5225 -0.8030 5.5097 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fas 2 2ctx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 61 Numb of atoms/sel atoms in MODEL : 468 117 Numb of residues in MODEL2 : 71 Numb of atoms in MODEL2 : 518 Equivalences refinement : F Numb of aligned equiv positions : 104 Numb of aligned equiv distances : 5356 RMS before superposition : 3.2129 RMS after superposition : 3.5662 DRMS : 2.2577 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 81 Numb of equiv cutoff distances : 4680 Cutoff RMS after superposition : 1.5359 Cutoff DRMS : 1.3449 X_new = Rotation * X + Translation Rotation matrix : 0.9878 0.0319 -0.1521 -0.0354 0.9992 -0.0203 0.1513 0.0254 0.9882 Translation vector: 1.3069 1.2867 -6.2626 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fas 2 2ctx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 61 Numb of atoms/sel atoms in MODEL : 468 468 Numb of residues in MODEL2 : 71 Numb of atoms in MODEL2 : 518 Equivalences refinement : F Numb of aligned equiv positions : 328 Numb of aligned equiv distances : 53628 RMS before superposition : 3.3626 RMS after superposition : 3.2363 DRMS : 2.1235 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 262 Numb of equiv cutoff distances : 47708 Cutoff RMS after superposition : 1.6355 Cutoff DRMS : 1.3710 X_new = Rotation * X + Translation Rotation matrix : 0.9989 -0.0242 0.0399 0.0238 0.9997 0.0110 -0.0402 -0.0101 0.9991 Translation vector: 0.1350 -0.8918 1.6561 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fas 2 2ctx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 61 Numb of atoms/sel atoms in MODEL : 468 18 Numb of residues in MODEL2 : 71 Numb of atoms in MODEL2 : 518 Equivalences refinement : F Numb of aligned equiv positions : 17 Numb of aligned equiv distances : 136 RMS before superposition : 4.2631 RMS after superposition : 2.6249 DRMS : 1.8869 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 13 Numb of equiv cutoff distances : 124 Cutoff RMS after superposition : 1.8881 Cutoff DRMS : 1.2531 X_new = Rotation * X + Translation Rotation matrix : 0.8592 -0.0914 0.5034 -0.0292 0.9735 0.2266 -0.5108 -0.2095 0.8338 Translation vector: 5.5943 0.9934 23.2658 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fas 2 2ctx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 61 Numb of atoms/sel atoms in MODEL : 468 25 Numb of residues in MODEL2 : 71 Numb of atoms in MODEL2 : 518 Equivalences refinement : F Numb of aligned equiv positions : 18 Numb of aligned equiv distances : 153 RMS before superposition : 4.2871 RMS after superposition : 1.7319 DRMS : 0.9477 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 17 Numb of equiv cutoff distances : 153 Cutoff RMS after superposition : 1.4771 Cutoff DRMS : 0.9477 X_new = Rotation * X + Translation Rotation matrix : 0.6136 -0.0974 0.7836 0.4071 0.8893 -0.2083 -0.6766 0.4468 0.5853 Translation vector: 11.9730 -9.8026 11.0973 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fas 2 2ctx Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 61 Numb of atoms/sel atoms in MODEL : 468 214 Numb of residues in MODEL2 : 71 Numb of atoms in MODEL2 : 518 Equivalences refinement : F Numb of aligned equiv positions : 153 Numb of aligned equiv distances : 11628 RMS before superposition : 11.2493 RMS after superposition : 2.7584 DRMS : 2.1885 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 125 Numb of equiv cutoff distances : 10388 Cutoff RMS after superposition : 1.6614 Cutoff DRMS : 1.1999 X_new = Rotation * X + Translation Rotation matrix : 0.2413 0.4988 -0.8324 -0.2696 0.8585 0.4363 0.9322 0.1192 0.3416 Translation vector: 14.0467 11.3745 -30.4715 Starting time : 2016/04/05 22:42:02 Closing time : 2016/04/05 22:42:03 Total CPU time [seconds] : 0.22