MODELLER 8v1, Jun 20, 2005 11:37am PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2005 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, 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, WinXP build 2600 Service Pack 2, HCHOE, uni, x86 Family 15 Model 1 Stepping 2 Date and time of compilation : 06/21/2005 10:55:30 MODELLER executable type : i386-w32 Job starting time (YY/MM/DD HH:MM:SS): 2005/09/01 18:42:08.535 openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['1lp1', 'aav5_1'], atom_files=[], file='aav5_1.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open aav5_1.ali Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124923 2075.120 2.026 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2126623 2076.780 2.028 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2130023 2080.101 2.031 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2136823 2086.741 2.038 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2150423 2100.022 2.051 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2177623 2126.585 2.077 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2232023 2179.710 2.129 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2340823 2285.960 2.232 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2558423 2498.460 2.440 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2993623 2923.460 2.855 Dynamically allocated memory at amaxalignment [B,kB,MB]: 3864023 3773.460 3.685 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26231701 25616.895 25.016 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26232597 25617.770 25.017 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26233493 25618.645 25.018 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26234389 25619.520 25.019 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26235285 25620.395 25.020 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26236181 25621.270 25.021 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26237077 25622.145 25.022 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26237973 25623.020 25.022 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26238869 25623.895 25.023 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26239765 25624.770 25.024 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26240661 25625.645 25.025 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26241557 25626.520 25.026 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26242453 25627.395 25.027 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26243349 25628.270 25.028 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26244245 25629.145 25.028 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26245141 25630.020 25.029 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26246037 25630.895 25.030 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26246933 25631.770 25.031 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26247829 25632.645 25.032 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26248725 25633.520 25.033 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26249621 25634.395 25.034 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26250517 25635.270 25.034 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26251413 25636.145 25.035 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26252309 25637.020 25.036 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26253205 25637.895 25.037 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26254101 25638.770 25.038 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26254997 25639.645 25.039 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26255893 25640.520 25.040 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26256789 25641.395 25.040 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26257685 25642.270 25.041 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26258581 25643.145 25.042 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26259477 25644.020 25.043 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26260373 25644.895 25.044 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26261269 25645.770 25.045 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26262165 25646.645 25.046 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26263061 25647.520 25.046 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26263957 25648.395 25.047 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26264853 25649.270 25.048 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26265749 25650.145 25.049 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26266645 25651.020 25.050 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26267541 25651.895 25.051 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26268437 25652.770 25.052 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26269333 25653.645 25.052 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26270229 25654.520 25.053 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26271125 25655.395 25.054 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26272021 25656.270 25.055 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26272917 25657.145 25.056 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26273813 25658.020 25.057 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26274709 25658.895 25.058 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26275605 25659.770 25.058 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26276501 25660.645 25.059 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26277397 25661.520 25.060 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26278293 25662.395 25.061 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26279189 25663.270 25.062 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26280085 25664.145 25.063 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26280981 25665.020 25.063 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26281877 25665.895 25.064 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26282773 25666.770 25.065 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26283669 25667.645 25.066 Dynamically allocated memory at amaxalignment [B,kB,MB]: 26284565 25668.520 25.067 Read the alignment from file : aav5_1.ali Total number of alignment positions: 31500 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1lp1 31140 60 1lp1 undefined 2 aav5_1 31080 60 aav5_1 runcmd______> alignment.check() check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL 1lp1.pdb Dynamically allocated memory at amaxstructure [B,kB,MB]: 44159345 43124.359 42.114 openf5__224_> Open 11 OLD SEQUENTIAL 1lp1.pdb 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 ---------------------------------------------- 240 1 316 323 G V 16.933 525 1 598 80 L G 66.821 765 1 316 323 G V 16.932 1050 1 598 80 L G 66.822 1290 1 316 323 G V 16.933 1575 1 598 80 L G 66.819 1815 1 316 323 G V 16.933 2100 1 598 80 L G 66.819 2340 1 316 323 G V 16.932 2625 1 598 80 L G 145.795 2865 1 316 323 G V 16.932 3150 1 598 80 L G 66.822 3390 1 316 323 G V 16.933 3675 1 598 80 L G 66.821 3915 1 316 323 G V 16.932 4200 1 598 80 L G 66.823 4440 1 316 323 G V 16.933 4725 1 598 80 L G 66.819 4965 1 316 323 G V 16.932 5250 1 598 80 L G 34.593 5490 1 316 323 G V 16.933 5775 1 598 80 L G 66.819 6015 1 316 323 G V 16.933 6300 1 598 80 L G 66.822 6540 1 316 323 G V 16.933 6825 1 598 80 L G 66.822 7065 1 316 323 G V 16.933 7350 1 598 80 L G 66.823 7590 1 316 323 G V 16.933 7875 1 598 80 L G 145.794 8115 1 316 323 G V 16.932 8400 1 598 80 L G 66.819 8640 1 316 323 G V 16.933 8925 1 598 80 L G 66.822 9165 1 316 323 G V 16.933 9450 1 598 80 L G 66.821 9690 1 316 323 G V 16.933 9975 1 598 80 L G 66.822 10215 1 316 323 G V 16.932 10500 1 598 80 L G 136.027 10740 1 316 323 G V 16.933 11025 1 598 80 L G 66.821 11265 1 316 323 G V 16.933 11550 1 598 80 L G 66.823 11790 1 316 323 G V 16.932 12075 1 598 80 L G 66.819 12315 1 316 323 G V 16.932 12600 1 598 80 L G 66.819 12840 1 316 323 G V 16.932 13125 1 598 80 L G 145.795 13365 1 316 323 G V 16.934 13650 1 598 80 L G 66.822 13890 1 316 323 G V 16.932 14175 1 598 80 L G 66.821 14415 1 316 323 G V 16.933 14700 1 598 80 L G 66.823 14940 1 316 323 G V 16.932 15225 1 598 80 L G 66.819 15465 1 316 323 G V 16.931 15750 1 598 80 L G 34.593 15990 1 316 323 G V 16.932 16275 1 598 80 L G 66.819 16515 1 316 323 G V 16.933 16800 1 598 80 L G 66.822 17040 1 316 323 G V 16.932 17325 1 598 80 L G 66.821 17565 1 316 323 G V 16.933 17850 1 598 80 L G 66.823 18090 1 316 323 G V 16.933 18375 1 598 80 L G 145.793 18615 1 316 323 G V 16.932 18900 1 598 80 L G 66.818 19140 1 316 323 G V 16.932 19425 1 598 80 L G 66.822 19665 1 316 323 G V 16.932 19950 1 598 80 L G 66.822 20190 1 316 323 G V 16.933 20475 1 598 80 L G 66.823 20715 1 316 323 G V 16.933 21000 1 598 80 L G 136.028 21240 1 316 323 G V 16.933 21525 1 598 80 L G 66.822 21765 1 316 323 G V 16.933 22050 1 598 80 L G 66.822 22290 1 316 323 G V 16.932 22575 1 598 80 L G 66.820 22815 1 316 323 G V 16.933 23100 1 598 80 L G 66.819 23340 1 316 323 G V 16.932 23625 1 598 80 L G 145.795 23865 1 316 323 G V 16.932 24150 1 598 80 L G 66.823 24390 1 316 323 G V 16.933 24675 1 598 80 L G 66.821 24915 1 316 323 G V 16.933 25200 1 598 80 L G 66.822 25440 1 316 323 G V 16.933 25725 1 598 80 L G 66.819 25965 1 316 323 G V 16.932 26250 1 598 80 L G 34.592 26490 1 316 323 G V 16.932 26775 1 598 80 L G 66.819 27015 1 316 323 G V 16.933 27300 1 598 80 L G 66.823 27540 1 316 323 G V 16.933 27825 1 598 80 L G 66.821 28065 1 316 323 G V 16.932 28350 1 598 80 L G 66.823 28590 1 316 323 G V 16.933 28875 1 598 80 L G 145.793 29115 1 316 323 G V 16.933 29400 1 598 80 L G 66.819 29640 1 316 323 G V 16.933 29925 1 598 80 L G 66.823 30165 1 316 323 G V 16.933 30450 1 598 80 L G 66.821 30690 1 316 323 G V 16.933 30975 1 598 80 L G 66.823 31215 1 316 323 G V 16.933 END OF TABLE check_a_344_> << END OF COMMAND runcmd______> topology.append(file='${LIB}/top_heav.lib', add_topology=True) openf5__224_> Open 11 OLD SEQUENTIAL ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL8v1}/modlib/models.lib runcmd______> parameters.append(file='${LIB}/par.lib') openf5__224_> Open 11 OLD SEQUENTIAL ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,kB,MB]: 44195749 43159.910 42.148 openf5__224_> Open 11 OLD SEQUENTIAL ${LIB}/par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 runcmd______> model.generate_topology(add_segment=False, sequence='aav5_1', (def)patch_default=True) Dynamically allocated memory at amaxmodel [B,kB,MB]: 44285707 43247.762 42.234 Dynamically allocated memory at amaxmodel [B,kB,MB]: 44798943 43748.969 42.724 Dynamically allocated memory at amaxmodel [B,kB,MB]: 44863359 43811.875 42.785 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 518 atom names : C +N atom indices : 4119 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 518 atom names : C CA +N O atom indices : 4119 4114 0 4120 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 518 4120 4248 0 0 1902 Dynamically allocated memory at amaxmodel [B,kB,MB]: 45044239 43988.516 42.958 patch_______> segment topology patched using RTF: 1 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 1 518 4120 4248 5805 6953 1902 Dynamically allocated memory at amaxmodel [B,kB,MB]: 45235095 44174.898 43.140 patch_______> segment topology patched using RTF: 518 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 1 518 4121 4249 5807 6955 1903 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 518 4121 4249 5807 6955 1903 Dynamically allocated memory at amaxmodel [B,kB,MB]: 45235127 44174.930 43.140 Dynamically allocated memory at amaxmodel [B,kB,MB]: 45325259 44262.949 43.226 Dynamically allocated memory at amaxmodel [B,kB,MB]: 45836263 44761.977 43.713 Dynamically allocated memory at amaxmodel [B,kB,MB]: 45900703 44824.906 43.774 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 1036 atom names : C +N atom indices : 8240 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 1036 atom names : C CA +N O atom indices : 8240 8235 0 8241 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1036 8241 8497 5807 6955 3805 Dynamically allocated memory at amaxmodel [B,kB,MB]: 46081611 45001.574 43.947 patch_______> segment topology patched using RTF: 519 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 2 1036 8241 8497 11612 13908 3805 Dynamically allocated memory at amaxmodel [B,kB,MB]: 46286427 45201.590 44.142 patch_______> segment topology patched using RTF: 1036 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1036 8242 8498 11614 13910 3806 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1036 8242 8498 11614 13910 3806 Dynamically allocated memory at amaxmodel [B,kB,MB]: 46286459 45201.621 44.142 Dynamically allocated memory at amaxmodel [B,kB,MB]: 46376591 45289.641 44.228 Dynamically allocated memory at amaxmodel [B,kB,MB]: 46887595 45788.668 44.715 Dynamically allocated memory at amaxmodel [B,kB,MB]: 46952035 45851.598 44.777 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 1554 atom names : C +N atom indices : 12361 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 1554 atom names : C CA +N O atom indices : 12361 12356 0 12362 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1554 12362 12746 11614 13910 5708 Dynamically allocated memory at amaxmodel [B,kB,MB]: 47132943 46028.266 44.949 patch_______> segment topology patched using RTF: 1037 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 3 1554 12362 12746 17419 20863 5708 Dynamically allocated memory at amaxmodel [B,kB,MB]: 47306999 46198.242 45.115 patch_______> segment topology patched using RTF: 1554 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1554 12363 12747 17421 20865 5709 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1554 12363 12747 17421 20865 5709 Dynamically allocated memory at amaxmodel [B,kB,MB]: 47307031 46198.273 45.116 Dynamically allocated memory at amaxmodel [B,kB,MB]: 47397163 46286.293 45.201 Dynamically allocated memory at amaxmodel [B,kB,MB]: 47908167 46785.320 45.689 Dynamically allocated memory at amaxmodel [B,kB,MB]: 47972607 46848.250 45.750 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 2072 atom names : C +N atom indices : 16482 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 2072 atom names : C CA +N O atom indices : 16482 16477 0 16483 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2072 16483 16995 17421 20865 7611 Dynamically allocated memory at amaxmodel [B,kB,MB]: 48153515 47024.918 45.923 patch_______> segment topology patched using RTF: 1555 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 4 2072 16483 16995 23226 27818 7611 Dynamically allocated memory at amaxmodel [B,kB,MB]: 48267451 47136.184 46.031 patch_______> segment topology patched using RTF: 2072 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2072 16484 16996 23228 27820 7612 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2072 16484 16996 23228 27820 7612 Dynamically allocated memory at amaxmodel [B,kB,MB]: 48267483 47136.215 46.031 Dynamically allocated memory at amaxmodel [B,kB,MB]: 48357615 47224.234 46.117 Dynamically allocated memory at amaxmodel [B,kB,MB]: 48868619 47723.262 46.605 Dynamically allocated memory at amaxmodel [B,kB,MB]: 48933059 47786.191 46.666 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 2590 atom names : C +N atom indices : 20603 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 2590 atom names : C CA +N O atom indices : 20603 20598 0 20604 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2590 20604 21244 23228 27820 9514 Dynamically allocated memory at amaxmodel [B,kB,MB]: 49113967 47962.859 46.839 patch_______> segment topology patched using RTF: 2073 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 5 2590 20604 21244 29033 34773 9514 Dynamically allocated memory at amaxmodel [B,kB,MB]: 49414703 48256.547 47.126 patch_______> segment topology patched using RTF: 2590 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2590 20605 21245 29035 34775 9515 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2590 20605 21245 29035 34775 9515 Dynamically allocated memory at amaxmodel [B,kB,MB]: 49414735 48256.578 47.126 Dynamically allocated memory at amaxmodel [B,kB,MB]: 49504867 48344.598 47.212 Dynamically allocated memory at amaxmodel [B,kB,MB]: 50015871 48843.625 47.699 Dynamically allocated memory at amaxmodel [B,kB,MB]: 50080311 48906.555 47.760 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 3108 atom names : C +N atom indices : 24724 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 3108 atom names : C CA +N O atom indices : 24724 24719 0 24725 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3108 24725 25493 29035 34775 11417 Dynamically allocated memory at amaxmodel [B,kB,MB]: 50261219 49083.223 47.933 patch_______> segment topology patched using RTF: 2591 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 6 3108 24725 25493 34840 41728 11417 Dynamically allocated memory at amaxmodel [B,kB,MB]: 50458075 49275.465 48.121 patch_______> segment topology patched using RTF: 3108 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3108 24726 25494 34842 41730 11418 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3108 24726 25494 34842 41730 11418 Dynamically allocated memory at amaxmodel [B,kB,MB]: 50458107 49275.496 48.121 Dynamically allocated memory at amaxmodel [B,kB,MB]: 50548239 49363.516 48.207 Dynamically allocated memory at amaxmodel [B,kB,MB]: 51059243 49862.543 48.694 Dynamically allocated memory at amaxmodel [B,kB,MB]: 51136555 49938.043 48.768 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 3626 atom names : C +N atom indices : 28845 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 3626 atom names : C CA +N O atom indices : 28845 28840 0 28846 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3626 28846 29742 34842 41730 13320 Dynamically allocated memory at amaxmodel [B,kB,MB]: 51317463 50114.711 48.940 patch_______> segment topology patched using RTF: 3109 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 7 3626 28846 29742 40647 48683 13320 Dynamically allocated memory at amaxmodel [B,kB,MB]: 51317519 50114.766 48.940 patch_______> segment topology patched using RTF: 3626 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3626 28847 29743 40649 48685 13321 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3626 28847 29743 40649 48685 13321 Dynamically allocated memory at amaxmodel [B,kB,MB]: 51317551 50114.797 48.940 Dynamically allocated memory at amaxmodel [B,kB,MB]: 51407683 50202.816 49.026 Dynamically allocated memory at amaxmodel [B,kB,MB]: 51918687 50701.844 49.514 Dynamically allocated memory at amaxmodel [B,kB,MB]: 52011471 50792.453 49.602 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 4144 atom names : C +N atom indices : 32966 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 4144 atom names : C CA +N O atom indices : 32966 32961 0 32967 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4144 32967 33991 40649 48685 15223 Dynamically allocated memory at amaxmodel [B,kB,MB]: 52192379 50969.121 49.775 patch_______> segment topology patched using RTF: 3627 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 8 4144 32967 33991 46454 55638 15223 Dynamically allocated memory at amaxmodel [B,kB,MB]: 52428595 51199.801 50.000 patch_______> segment topology patched using RTF: 4144 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4144 32968 33992 46456 55640 15224 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4144 32968 33992 46456 55640 15224 Dynamically allocated memory at amaxmodel [B,kB,MB]: 52428627 51199.832 50.000 Dynamically allocated memory at amaxmodel [B,kB,MB]: 52518759 51287.852 50.086 Dynamically allocated memory at amaxmodel [B,kB,MB]: 53029763 51786.879 50.573 Dynamically allocated memory at amaxmodel [B,kB,MB]: 53141107 51895.613 50.679 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 4662 atom names : C +N atom indices : 37087 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 4662 atom names : C CA +N O atom indices : 37087 37082 0 37088 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4662 37088 38240 46456 55640 17126 Dynamically allocated memory at amaxmodel [B,kB,MB]: 53322015 52072.281 50.852 patch_______> segment topology patched using RTF: 4145 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 9 4662 37088 38240 52261 62593 17126 Dynamically allocated memory at amaxmodel [B,kB,MB]: 53605471 52349.094 51.122 patch_______> segment topology patched using RTF: 4662 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4662 37089 38241 52263 62595 17127 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4662 37089 38241 52263 62595 17127 Dynamically allocated memory at amaxmodel [B,kB,MB]: 53605503 52349.125 51.122 Dynamically allocated memory at amaxmodel [B,kB,MB]: 53695635 52437.145 51.208 Dynamically allocated memory at amaxmodel [B,kB,MB]: 54206639 52936.172 51.695 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 5180 atom names : C +N atom indices : 41208 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 5180 atom names : C CA +N O atom indices : 41208 41203 0 41209 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5180 41209 42489 52263 62595 19029 Dynamically allocated memory at amaxmodel [B,kB,MB]: 54387547 53112.840 51.868 patch_______> segment topology patched using RTF: 4663 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 10 5180 41209 42489 58068 69548 19029 Dynamically allocated memory at amaxmodel [B,kB,MB]: 54387603 53112.895 51.868 patch_______> segment topology patched using RTF: 5180 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5180 41210 42490 58070 69550 19030 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5180 41210 42490 58070 69550 19030 Dynamically allocated memory at amaxmodel [B,kB,MB]: 54387635 53112.926 51.868 Dynamically allocated memory at amaxmodel [B,kB,MB]: 54477767 53200.945 51.954 Dynamically allocated memory at amaxmodel [B,kB,MB]: 54988771 53699.973 52.441 Dynamically allocated memory at amaxmodel [B,kB,MB]: 55122371 53830.441 52.569 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 5698 atom names : C +N atom indices : 45329 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 5698 atom names : C CA +N O atom indices : 45329 45324 0 45330 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5698 45330 46738 58070 69550 20932 Dynamically allocated memory at amaxmodel [B,kB,MB]: 55303279 54007.109 52.741 patch_______> segment topology patched using RTF: 5181 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 11 5698 45330 46738 63875 76503 20932 Dynamically allocated memory at amaxmodel [B,kB,MB]: 55643415 54339.273 53.066 patch_______> segment topology patched using RTF: 5698 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5698 45331 46739 63877 76505 20933 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5698 45331 46739 63877 76505 20933 Dynamically allocated memory at amaxmodel [B,kB,MB]: 55643447 54339.305 53.066 Dynamically allocated memory at amaxmodel [B,kB,MB]: 55733579 54427.324 53.152 Dynamically allocated memory at amaxmodel [B,kB,MB]: 56244583 54926.352 53.639 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 6216 atom names : C +N atom indices : 49450 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 6216 atom names : C CA +N O atom indices : 49450 49445 0 49451 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6216 49451 50987 63877 76505 22835 Dynamically allocated memory at amaxmodel [B,kB,MB]: 56425491 55103.020 53.812 patch_______> segment topology patched using RTF: 5699 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 12 6216 49451 50987 69682 83458 22835 Dynamically allocated memory at amaxmodel [B,kB,MB]: 56425547 55103.074 53.812 patch_______> segment topology patched using RTF: 6216 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6216 49452 50988 69684 83460 22836 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6216 49452 50988 69684 83460 22836 Dynamically allocated memory at amaxmodel [B,kB,MB]: 56425579 55103.105 53.812 Dynamically allocated memory at amaxmodel [B,kB,MB]: 56515711 55191.125 53.898 Dynamically allocated memory at amaxmodel [B,kB,MB]: 57026715 55690.152 54.385 Dynamically allocated memory at amaxmodel [B,kB,MB]: 57187035 55846.715 54.538 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 6734 atom names : C +N atom indices : 53571 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 6734 atom names : C CA +N O atom indices : 53571 53566 0 53572 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6734 53572 55236 69684 83460 24738 Dynamically allocated memory at amaxmodel [B,kB,MB]: 57367943 56023.383 54.710 patch_______> segment topology patched using RTF: 6217 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 13 6734 53572 55236 75489 90413 24738 Dynamically allocated memory at amaxmodel [B,kB,MB]: 57776079 56421.953 55.100 patch_______> segment topology patched using RTF: 6734 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6734 53573 55237 75491 90415 24739 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6734 53573 55237 75491 90415 24739 Dynamically allocated memory at amaxmodel [B,kB,MB]: 57776111 56421.984 55.100 Dynamically allocated memory at amaxmodel [B,kB,MB]: 57866243 56510.004 55.186 Dynamically allocated memory at amaxmodel [B,kB,MB]: 58377247 57009.031 55.673 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 7252 atom names : C +N atom indices : 57692 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 7252 atom names : C CA +N O atom indices : 57692 57687 0 57693 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7252 57693 59485 75491 90415 26641 Dynamically allocated memory at amaxmodel [B,kB,MB]: 58558155 57185.699 55.845 patch_______> segment topology patched using RTF: 6735 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 14 7252 57693 59485 81296 97368 26641 Dynamically allocated memory at amaxmodel [B,kB,MB]: 58558211 57185.754 55.845 patch_______> segment topology patched using RTF: 7252 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7252 57694 59486 81298 97370 26642 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7252 57694 59486 81298 97370 26642 Dynamically allocated memory at amaxmodel [B,kB,MB]: 58558243 57185.785 55.845 Dynamically allocated memory at amaxmodel [B,kB,MB]: 58648375 57273.805 55.931 Dynamically allocated memory at amaxmodel [B,kB,MB]: 59159379 57772.832 56.419 Dynamically allocated memory at amaxmodel [B,kB,MB]: 59351763 57960.707 56.602 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 7770 atom names : C +N atom indices : 61813 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 7770 atom names : C CA +N O atom indices : 61813 61808 0 61814 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 15 7770 61814 63734 81298 97370 28544 Dynamically allocated memory at amaxmodel [B,kB,MB]: 59532671 58137.375 56.775 patch_______> segment topology patched using RTF: 7253 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 15 7770 61814 63734 87103 104323 28544 Dynamically allocated memory at amaxmodel [B,kB,MB]: 60022447 58615.672 57.242 patch_______> segment topology patched using RTF: 7770 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 15 7770 61815 63735 87105 104325 28545 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 15 7770 61815 63735 87105 104325 28545 Dynamically allocated memory at amaxmodel [B,kB,MB]: 60022479 58615.703 57.242 Dynamically allocated memory at amaxmodel [B,kB,MB]: 60112611 58703.723 57.328 Dynamically allocated memory at amaxmodel [B,kB,MB]: 60623615 59202.750 57.815 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 8288 atom names : C +N atom indices : 65934 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 8288 atom names : C CA +N O atom indices : 65934 65929 0 65935 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 16 8288 65935 67983 87105 104325 30447 Dynamically allocated memory at amaxmodel [B,kB,MB]: 60804523 59379.418 57.988 patch_______> segment topology patched using RTF: 7771 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 16 8288 65935 67983 92910 111278 30447 Dynamically allocated memory at amaxmodel [B,kB,MB]: 60804579 59379.473 57.988 patch_______> segment topology patched using RTF: 8288 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 16 8288 65936 67984 92912 111280 30448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 16 8288 65936 67984 92912 111280 30448 Dynamically allocated memory at amaxmodel [B,kB,MB]: 60804611 59379.504 57.988 Dynamically allocated memory at amaxmodel [B,kB,MB]: 60894743 59467.523 58.074 Dynamically allocated memory at amaxmodel [B,kB,MB]: 61405747 59966.551 58.561 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 8806 atom names : C +N atom indices : 70055 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 8806 atom names : C CA +N O atom indices : 70055 70050 0 70056 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 17 8806 70056 72232 92912 111280 32350 Dynamically allocated memory at amaxmodel [B,kB,MB]: 61586655 60143.219 58.734 patch_______> segment topology patched using RTF: 8289 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 17 8806 70056 72232 98717 118233 32350 Dynamically allocated memory at amaxmodel [B,kB,MB]: 61586711 60143.273 58.734 patch_______> segment topology patched using RTF: 8806 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 17 8806 70057 72233 98719 118235 32351 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 17 8806 70057 72233 98719 118235 32351 Dynamically allocated memory at amaxmodel [B,kB,MB]: 61586743 60143.305 58.734 Dynamically allocated memory at amaxmodel [B,kB,MB]: 61676875 60231.324 58.820 Dynamically allocated memory at amaxmodel [B,kB,MB]: 62187879 60730.352 59.307 Dynamically allocated memory at amaxmodel [B,kB,MB]: 62418743 60955.805 59.527 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 9324 atom names : C +N atom indices : 74176 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 9324 atom names : C CA +N O atom indices : 74176 74171 0 74177 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 18 9324 74177 76481 98719 118235 34253 Dynamically allocated memory at amaxmodel [B,kB,MB]: 62599651 61132.473 59.700 patch_______> segment topology patched using RTF: 8807 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 18 9324 74177 76481 104524 125188 34253 Dynamically allocated memory at amaxmodel [B,kB,MB]: 63187347 61706.395 60.260 patch_______> segment topology patched using RTF: 9324 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 18 9324 74178 76482 104526 125190 34254 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 18 9324 74178 76482 104526 125190 34254 Dynamically allocated memory at amaxmodel [B,kB,MB]: 63187379 61706.426 60.260 Dynamically allocated memory at amaxmodel [B,kB,MB]: 63277511 61794.445 60.346 Dynamically allocated memory at amaxmodel [B,kB,MB]: 63788515 62293.473 60.833 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 9842 atom names : C +N atom indices : 78297 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 9842 atom names : C CA +N O atom indices : 78297 78292 0 78298 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 19 9842 78298 80730 104526 125190 36156 Dynamically allocated memory at amaxmodel [B,kB,MB]: 63969423 62470.141 61.006 patch_______> segment topology patched using RTF: 9325 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 19 9842 78298 80730 110331 132143 36156 Dynamically allocated memory at amaxmodel [B,kB,MB]: 63969479 62470.195 61.006 patch_______> segment topology patched using RTF: 9842 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 19 9842 78299 80731 110333 132145 36157 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 19 9842 78299 80731 110333 132145 36157 Dynamically allocated memory at amaxmodel [B,kB,MB]: 63969511 62470.227 61.006 Dynamically allocated memory at amaxmodel [B,kB,MB]: 64059643 62558.246 61.092 Dynamically allocated memory at amaxmodel [B,kB,MB]: 64570647 63057.273 61.579 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 10360 atom names : C +N atom indices : 82418 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 10360 atom names : C CA +N O atom indices : 82418 82413 0 82419 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 20 10360 82419 84979 110333 132145 38059 Dynamically allocated memory at amaxmodel [B,kB,MB]: 64751555 63233.941 61.752 patch_______> segment topology patched using RTF: 9843 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 20 10360 82419 84979 116138 139098 38059 Dynamically allocated memory at amaxmodel [B,kB,MB]: 64751611 63233.996 61.752 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 20 10360 82420 84980 116140 139100 38060 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 20 10360 82420 84980 116140 139100 38060 Dynamically allocated memory at amaxmodel [B,kB,MB]: 64751643 63234.027 61.752 Dynamically allocated memory at amaxmodel [B,kB,MB]: 64841775 63322.047 61.838 Dynamically allocated memory at amaxmodel [B,kB,MB]: 65352779 63821.074 62.325 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 10878 atom names : C +N atom indices : 86539 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 10878 atom names : C CA +N O atom indices : 86539 86534 0 86540 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 21 10878 86540 89228 116140 139100 39962 Dynamically allocated memory at amaxmodel [B,kB,MB]: 65533687 63997.742 62.498 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 21 10878 86540 89228 121945 146053 39962 Dynamically allocated memory at amaxmodel [B,kB,MB]: 65533743 63997.797 62.498 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 21 10878 86541 89229 121947 146055 39963 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 21 10878 86541 89229 121947 146055 39963 Dynamically allocated memory at amaxmodel [B,kB,MB]: 65533775 63997.828 62.498 Dynamically allocated memory at amaxmodel [B,kB,MB]: 65623907 64085.848 62.584 Dynamically allocated memory at amaxmodel [B,kB,MB]: 66134911 64584.875 63.071 Dynamically allocated memory at amaxmodel [B,kB,MB]: 66411951 64855.422 63.335 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 11396 atom names : C +N atom indices : 90660 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 11396 atom names : C CA +N O atom indices : 90660 90655 0 90661 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 22 11396 90661 93477 121947 146055 41865 Dynamically allocated memory at amaxmodel [B,kB,MB]: 66592859 65032.090 63.508 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 22 11396 90661 93477 127752 153008 41865 Dynamically allocated memory at amaxmodel [B,kB,MB]: 67298115 65720.812 64.180 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 22 11396 90662 93478 127754 153010 41866 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 22 11396 90662 93478 127754 153010 41866 Dynamically allocated memory at amaxmodel [B,kB,MB]: 67298147 65720.844 64.181 Dynamically allocated memory at amaxmodel [B,kB,MB]: 67388279 65808.867 64.266 Dynamically allocated memory at amaxmodel [B,kB,MB]: 67899283 66307.891 64.754 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 11914 atom names : C +N atom indices : 94781 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 11914 atom names : C CA +N O atom indices : 94781 94776 0 94782 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 23 11914 94782 97726 127754 153010 43768 Dynamically allocated memory at amaxmodel [B,kB,MB]: 68080191 66484.562 64.926 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 23 11914 94782 97726 133559 159963 43768 Dynamically allocated memory at amaxmodel [B,kB,MB]: 68080247 66484.617 64.926 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 23 11914 94783 97727 133561 159965 43769 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 23 11914 94783 97727 133561 159965 43769 Dynamically allocated memory at amaxmodel [B,kB,MB]: 68080279 66484.648 64.926 Dynamically allocated memory at amaxmodel [B,kB,MB]: 68170411 66572.664 65.012 Dynamically allocated memory at amaxmodel [B,kB,MB]: 68681415 67071.695 65.500 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 12432 atom names : C +N atom indices : 98902 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 12432 atom names : C CA +N O atom indices : 98902 98897 0 98903 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 24 12432 98903 ***** 133561 159965 45671 Dynamically allocated memory at amaxmodel [B,kB,MB]: 68862323 67248.359 65.672 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 24 12432 98903 ***** 139366 166918 45671 Dynamically allocated memory at amaxmodel [B,kB,MB]: 68862379 67248.414 65.672 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 24 12432 98904 ***** 139368 166920 45672 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 24 12432 98904 ***** 139368 166920 45672 Dynamically allocated memory at amaxmodel [B,kB,MB]: 68862411 67248.445 65.672 Dynamically allocated memory at amaxmodel [B,kB,MB]: 68952543 67336.469 65.758 Dynamically allocated memory at amaxmodel [B,kB,MB]: 69463547 67835.492 66.246 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 12950 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 12950 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 25 12950 ***** ***** 139368 166920 47574 Dynamically allocated memory at amaxmodel [B,kB,MB]: 69644455 68012.164 66.418 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 25 12950 ***** ***** 145173 173873 47574 Dynamically allocated memory at amaxmodel [B,kB,MB]: 69644511 68012.219 66.418 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 25 12950 ***** ***** 145175 173875 47575 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 25 12950 ***** ***** 145175 173875 47575 Dynamically allocated memory at amaxmodel [B,kB,MB]: 69644543 68012.250 66.418 Dynamically allocated memory at amaxmodel [B,kB,MB]: 69734675 68100.266 66.504 Dynamically allocated memory at amaxmodel [B,kB,MB]: 70245679 68599.297 66.992 Dynamically allocated memory at amaxmodel [B,kB,MB]: 70578127 68923.953 67.309 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 13468 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 13468 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 26 13468 ***** ***** 145175 173875 49477 Dynamically allocated memory at amaxmodel [B,kB,MB]: 70759035 69100.617 67.481 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 26 13468 ***** ***** 150980 180828 49477 Dynamically allocated memory at amaxmodel [B,kB,MB]: 71605331 69927.078 68.288 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 26 13468 ***** ***** 150982 180830 49478 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 26 13468 ***** ***** 150982 180830 49478 Dynamically allocated memory at amaxmodel [B,kB,MB]: 71605363 69927.109 68.288 Dynamically allocated memory at amaxmodel [B,kB,MB]: 71695495 70015.133 68.374 Dynamically allocated memory at amaxmodel [B,kB,MB]: 72206499 70514.156 68.861 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 13986 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 13986 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 27 13986 ***** ***** 150982 180830 51380 Dynamically allocated memory at amaxmodel [B,kB,MB]: 72387407 70690.828 69.034 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 27 13986 ***** ***** 156787 187783 51380 Dynamically allocated memory at amaxmodel [B,kB,MB]: 72387463 70690.883 69.034 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 27 13986 ***** ***** 156789 187785 51381 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 27 13986 ***** ***** 156789 187785 51381 Dynamically allocated memory at amaxmodel [B,kB,MB]: 72387495 70690.914 69.034 Dynamically allocated memory at amaxmodel [B,kB,MB]: 72477627 70778.930 69.120 Dynamically allocated memory at amaxmodel [B,kB,MB]: 72988631 71277.961 69.607 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 14504 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 14504 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 28 14504 ***** ***** 156789 187785 53283 Dynamically allocated memory at amaxmodel [B,kB,MB]: 73169539 71454.625 69.780 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 28 14504 ***** ***** 162594 194738 53283 Dynamically allocated memory at amaxmodel [B,kB,MB]: 73169595 71454.680 69.780 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 28 14504 ***** ***** 162596 194740 53284 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 28 14504 ***** ***** 162596 194740 53284 Dynamically allocated memory at amaxmodel [B,kB,MB]: 73169627 71454.711 69.780 Dynamically allocated memory at amaxmodel [B,kB,MB]: 73259759 71542.734 69.866 Dynamically allocated memory at amaxmodel [B,kB,MB]: 73770763 72041.758 70.353 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 15022 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 15022 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 29 15022 ***** ***** 162596 194740 55186 Dynamically allocated memory at amaxmodel [B,kB,MB]: 73951671 72218.430 70.526 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 29 15022 ***** ***** 168401 201693 55186 Dynamically allocated memory at amaxmodel [B,kB,MB]: 73951727 72218.484 70.526 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 29 15022 ***** ***** 168403 201695 55187 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 29 15022 ***** ***** 168403 201695 55187 Dynamically allocated memory at amaxmodel [B,kB,MB]: 73951759 72218.516 70.526 Dynamically allocated memory at amaxmodel [B,kB,MB]: 74041891 72306.531 70.612 Dynamically allocated memory at amaxmodel [B,kB,MB]: 74552895 72805.562 71.099 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 15540 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 15540 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 30 15540 ***** ***** 168403 201695 57089 Dynamically allocated memory at amaxmodel [B,kB,MB]: 74733803 72982.227 71.272 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 30 15540 ***** ***** 174208 208648 57089 Dynamically allocated memory at amaxmodel [B,kB,MB]: 74733859 72982.281 71.272 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 30 15540 ***** ***** 174210 208650 57090 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 30 15540 ***** ***** 174210 208650 57090 Dynamically allocated memory at amaxmodel [B,kB,MB]: 74733891 72982.312 71.272 Dynamically allocated memory at amaxmodel [B,kB,MB]: 74824023 73070.336 71.358 Dynamically allocated memory at amaxmodel [B,kB,MB]: 75335027 73569.359 71.845 Dynamically allocated memory at amaxmodel [B,kB,MB]: 75733955 73958.938 72.226 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 16058 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 16058 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 31 16058 ***** ***** 174210 208650 58992 Dynamically allocated memory at amaxmodel [B,kB,MB]: 75914863 74135.609 72.398 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 31 16058 ***** ***** 180015 215603 58992 Dynamically allocated memory at amaxmodel [B,kB,MB]: 76930399 75127.344 73.367 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 31 16058 ***** ***** 180017 215605 58993 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 31 16058 ***** ***** 180017 215605 58993 Dynamically allocated memory at amaxmodel [B,kB,MB]: 76930431 75127.375 73.367 Dynamically allocated memory at amaxmodel [B,kB,MB]: 77020563 75215.391 73.453 Dynamically allocated memory at amaxmodel [B,kB,MB]: 77531567 75714.422 73.940 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 16576 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 16576 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 32 16576 ***** ***** 180017 215605 60895 Dynamically allocated memory at amaxmodel [B,kB,MB]: 77712475 75891.086 74.112 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 32 16576 ***** ***** 185822 222558 60895 Dynamically allocated memory at amaxmodel [B,kB,MB]: 77712531 75891.141 74.112 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 32 16576 ***** ***** 185824 222560 60896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 32 16576 ***** ***** 185824 222560 60896 Dynamically allocated memory at amaxmodel [B,kB,MB]: 77712563 75891.172 74.112 Dynamically allocated memory at amaxmodel [B,kB,MB]: 77802695 75979.195 74.198 Dynamically allocated memory at amaxmodel [B,kB,MB]: 78313699 76478.219 74.686 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 17094 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 17094 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 33 17094 ***** ***** 185824 222560 62798 Dynamically allocated memory at amaxmodel [B,kB,MB]: 78494607 76654.891 74.858 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 33 17094 ***** ***** 191629 229513 62798 Dynamically allocated memory at amaxmodel [B,kB,MB]: 78494663 76654.945 74.858 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 33 17094 ***** ***** 191631 229515 62799 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 33 17094 ***** ***** 191631 229515 62799 Dynamically allocated memory at amaxmodel [B,kB,MB]: 78494695 76654.977 74.858 Dynamically allocated memory at amaxmodel [B,kB,MB]: 78584827 76742.992 74.944 Dynamically allocated memory at amaxmodel [B,kB,MB]: 79095831 77242.023 75.432 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 17612 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 17612 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 34 17612 ***** ***** 191631 229515 64701 Dynamically allocated memory at amaxmodel [B,kB,MB]: 79276739 77418.688 75.604 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 34 17612 ***** ***** 197436 236468 64701 Dynamically allocated memory at amaxmodel [B,kB,MB]: 79276795 77418.742 75.604 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 34 17612 ***** ***** 197438 236470 64702 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 34 17612 ***** ***** 197438 236470 64702 Dynamically allocated memory at amaxmodel [B,kB,MB]: 79276827 77418.773 75.604 Dynamically allocated memory at amaxmodel [B,kB,MB]: 79366959 77506.797 75.690 Dynamically allocated memory at amaxmodel [B,kB,MB]: 79877963 78005.820 76.178 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 18130 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 18130 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 35 18130 ***** ***** 197438 236470 66604 Dynamically allocated memory at amaxmodel [B,kB,MB]: 80058871 78182.492 76.350 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 35 18130 ***** ***** 203243 243423 66604 Dynamically allocated memory at amaxmodel [B,kB,MB]: 80058927 78182.547 76.350 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 35 18130 ***** ***** 203245 243425 66605 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 35 18130 ***** ***** 203245 243425 66605 Dynamically allocated memory at amaxmodel [B,kB,MB]: 80058959 78182.578 76.350 Dynamically allocated memory at amaxmodel [B,kB,MB]: 80149091 78270.594 76.436 Dynamically allocated memory at amaxmodel [B,kB,MB]: 80660095 78769.625 76.923 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 18648 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 18648 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 36 18648 ***** ***** 203245 243425 68507 Dynamically allocated memory at amaxmodel [B,kB,MB]: 80841003 78946.289 77.096 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 36 18648 ***** ***** 209050 250378 68507 Dynamically allocated memory at amaxmodel [B,kB,MB]: 80841059 78946.344 77.096 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 36 18648 ***** ***** 209052 250380 68508 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 36 18648 ***** ***** 209052 250380 68508 Dynamically allocated memory at amaxmodel [B,kB,MB]: 80841091 78946.375 77.096 Dynamically allocated memory at amaxmodel [B,kB,MB]: 80931223 79034.398 77.182 Dynamically allocated memory at amaxmodel [B,kB,MB]: 81442227 79533.422 77.669 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 19166 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 19166 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 37 19166 ***** ***** 209052 250380 70410 Dynamically allocated memory at amaxmodel [B,kB,MB]: 81623135 79710.094 77.842 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 37 19166 ***** ***** 214857 257333 70410 Dynamically allocated memory at amaxmodel [B,kB,MB]: 82841751 80900.148 79.004 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 37 19166 ***** ***** 214859 257335 70411 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 37 19166 ***** ***** 214859 257335 70411 Dynamically allocated memory at amaxmodel [B,kB,MB]: 82841783 80900.180 79.004 Dynamically allocated memory at amaxmodel [B,kB,MB]: 82931915 80988.195 79.090 Dynamically allocated memory at amaxmodel [B,kB,MB]: 83442919 81487.227 79.577 Dynamically allocated memory at amaxmodel [B,kB,MB]: 83921639 81954.727 80.034 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 19684 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 19684 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 38 19684 ***** ***** 214859 257335 72313 Dynamically allocated memory at amaxmodel [B,kB,MB]: 84102547 82131.391 80.206 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 38 19684 ***** ***** 220664 264288 72313 Dynamically allocated memory at amaxmodel [B,kB,MB]: 84102603 82131.445 80.206 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 38 19684 ***** ***** 220666 264290 72314 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 38 19684 ***** ***** 220666 264290 72314 Dynamically allocated memory at amaxmodel [B,kB,MB]: 84102635 82131.477 80.207 Dynamically allocated memory at amaxmodel [B,kB,MB]: 84192767 82219.500 80.292 Dynamically allocated memory at amaxmodel [B,kB,MB]: 84703771 82718.523 80.780 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 20202 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 20202 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 39 20202 ***** ***** 220666 264290 74216 Dynamically allocated memory at amaxmodel [B,kB,MB]: 84884679 82895.195 80.952 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 39 20202 ***** ***** 226471 271243 74216 Dynamically allocated memory at amaxmodel [B,kB,MB]: 84884735 82895.250 80.952 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 39 20202 ***** ***** 226473 271245 74217 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 39 20202 ***** ***** 226473 271245 74217 Dynamically allocated memory at amaxmodel [B,kB,MB]: 84884767 82895.281 80.952 Dynamically allocated memory at amaxmodel [B,kB,MB]: 84974899 82983.297 81.038 Dynamically allocated memory at amaxmodel [B,kB,MB]: 85485903 83482.328 81.526 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 20720 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 20720 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 40 20720 ***** ***** 226473 271245 76119 Dynamically allocated memory at amaxmodel [B,kB,MB]: 85666811 83658.992 81.698 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 40 20720 ***** ***** 232278 278198 76119 Dynamically allocated memory at amaxmodel [B,kB,MB]: 85666867 83659.047 81.698 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 40 20720 ***** ***** 232280 278200 76120 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 40 20720 ***** ***** 232280 278200 76120 Dynamically allocated memory at amaxmodel [B,kB,MB]: 85666899 83659.078 81.698 Dynamically allocated memory at amaxmodel [B,kB,MB]: 85757031 83747.102 81.784 Dynamically allocated memory at amaxmodel [B,kB,MB]: 86268035 84246.125 82.272 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 21238 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 21238 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 41 21238 ***** ***** 232280 278200 78022 Dynamically allocated memory at amaxmodel [B,kB,MB]: 86448943 84422.797 82.444 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 41 21238 ***** ***** 238085 285153 78022 Dynamically allocated memory at amaxmodel [B,kB,MB]: 86448999 84422.852 82.444 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 41 21238 ***** ***** 238087 285155 78023 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 41 21238 ***** ***** 238087 285155 78023 Dynamically allocated memory at amaxmodel [B,kB,MB]: 86449031 84422.883 82.444 Dynamically allocated memory at amaxmodel [B,kB,MB]: 86539163 84510.898 82.530 Dynamically allocated memory at amaxmodel [B,kB,MB]: 87050167 85009.930 83.018 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 21756 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 21756 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 42 21756 ***** ***** 238087 285155 79925 Dynamically allocated memory at amaxmodel [B,kB,MB]: 87231075 85186.594 83.190 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 42 21756 ***** ***** 243892 292108 79925 Dynamically allocated memory at amaxmodel [B,kB,MB]: 87231131 85186.648 83.190 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 42 21756 ***** ***** 243894 292110 79926 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 42 21756 ***** ***** 243894 292110 79926 Dynamically allocated memory at amaxmodel [B,kB,MB]: 87231163 85186.680 83.190 Dynamically allocated memory at amaxmodel [B,kB,MB]: 87321295 85274.703 83.276 Dynamically allocated memory at amaxmodel [B,kB,MB]: 87832299 85773.727 83.763 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 22274 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 22274 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 43 22274 ***** ***** 243894 292110 81828 Dynamically allocated memory at amaxmodel [B,kB,MB]: 88013207 85950.398 83.936 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 43 22274 ***** ***** 249699 299063 81828 Dynamically allocated memory at amaxmodel [B,kB,MB]: 88013263 85950.453 83.936 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 43 22274 ***** ***** 249701 299065 81829 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 43 22274 ***** ***** 249701 299065 81829 Dynamically allocated memory at amaxmodel [B,kB,MB]: 88013295 85950.484 83.936 Dynamically allocated memory at amaxmodel [B,kB,MB]: 88103427 86038.500 84.022 Dynamically allocated memory at amaxmodel [B,kB,MB]: 88614431 86537.531 84.509 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 22792 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 22792 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 44 22792 ***** ***** 249701 299065 83731 Dynamically allocated memory at amaxmodel [B,kB,MB]: 88795339 86714.195 84.682 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 44 22792 ***** ***** 255506 306018 83731 Dynamically allocated memory at amaxmodel [B,kB,MB]: 90257675 88142.258 86.076 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 44 22792 ***** ***** 255508 306020 83732 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 44 22792 ***** ***** 255508 306020 83732 Dynamically allocated memory at amaxmodel [B,kB,MB]: 90257707 88142.289 86.076 Dynamically allocated memory at amaxmodel [B,kB,MB]: 90347839 88230.312 86.162 Dynamically allocated memory at amaxmodel [B,kB,MB]: 90858843 88729.336 86.650 Dynamically allocated memory at amaxmodel [B,kB,MB]: 91433315 89290.344 87.198 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 23310 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 23310 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 45 23310 ***** ***** 255508 306020 85634 Dynamically allocated memory at amaxmodel [B,kB,MB]: 91614223 89467.016 87.370 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 45 23310 ***** ***** 261313 312973 85634 Dynamically allocated memory at amaxmodel [B,kB,MB]: 91614279 89467.070 87.370 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 45 23310 ***** ***** 261315 312975 85635 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 45 23310 ***** ***** 261315 312975 85635 Dynamically allocated memory at amaxmodel [B,kB,MB]: 91614311 89467.102 87.370 Dynamically allocated memory at amaxmodel [B,kB,MB]: 91704443 89555.117 87.456 Dynamically allocated memory at amaxmodel [B,kB,MB]: 92215447 90054.148 87.944 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 23828 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 23828 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 46 23828 ***** ***** 261315 312975 87537 Dynamically allocated memory at amaxmodel [B,kB,MB]: 92396355 90230.812 88.116 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 46 23828 ***** ***** 267120 319928 87537 Dynamically allocated memory at amaxmodel [B,kB,MB]: 92396411 90230.867 88.116 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 46 23828 ***** ***** 267122 319930 87538 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 46 23828 ***** ***** 267122 319930 87538 Dynamically allocated memory at amaxmodel [B,kB,MB]: 92396443 90230.898 88.116 Dynamically allocated memory at amaxmodel [B,kB,MB]: 92486575 90318.922 88.202 Dynamically allocated memory at amaxmodel [B,kB,MB]: 92997579 90817.945 88.689 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 24346 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 24346 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 47 24346 ***** ***** 267122 319930 89440 Dynamically allocated memory at amaxmodel [B,kB,MB]: 93178487 90994.617 88.862 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 47 24346 ***** ***** 272927 326883 89440 Dynamically allocated memory at amaxmodel [B,kB,MB]: 93178543 90994.672 88.862 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 47 24346 ***** ***** 272929 326885 89441 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 47 24346 ***** ***** 272929 326885 89441 Dynamically allocated memory at amaxmodel [B,kB,MB]: 93178575 90994.703 88.862 Dynamically allocated memory at amaxmodel [B,kB,MB]: 93268707 91082.719 88.948 Dynamically allocated memory at amaxmodel [B,kB,MB]: 93779711 91581.750 89.435 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 24864 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 24864 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 48 24864 ***** ***** 272929 326885 91343 Dynamically allocated memory at amaxmodel [B,kB,MB]: 93960619 91758.414 89.608 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 48 24864 ***** ***** 278734 333838 91343 Dynamically allocated memory at amaxmodel [B,kB,MB]: 93960675 91758.469 89.608 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 48 24864 ***** ***** 278736 333840 91344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 48 24864 ***** ***** 278736 333840 91344 Dynamically allocated memory at amaxmodel [B,kB,MB]: 93960707 91758.500 89.608 Dynamically allocated memory at amaxmodel [B,kB,MB]: 94050839 91846.523 89.694 Dynamically allocated memory at amaxmodel [B,kB,MB]: 94561843 92345.547 90.181 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 25382 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 25382 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 49 25382 ***** ***** 278736 333840 93246 Dynamically allocated memory at amaxmodel [B,kB,MB]: 94742751 92522.219 90.354 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 49 25382 ***** ***** 284541 340793 93246 Dynamically allocated memory at amaxmodel [B,kB,MB]: 94742807 92522.273 90.354 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 49 25382 ***** ***** 284543 340795 93247 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 49 25382 ***** ***** 284543 340795 93247 Dynamically allocated memory at amaxmodel [B,kB,MB]: 94742839 92522.305 90.354 Dynamically allocated memory at amaxmodel [B,kB,MB]: 94832971 92610.320 90.440 Dynamically allocated memory at amaxmodel [B,kB,MB]: 95343975 93109.352 90.927 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 25900 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 25900 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 50 25900 ***** ***** 284543 340795 95149 Dynamically allocated memory at amaxmodel [B,kB,MB]: 95524883 93286.016 91.100 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 50 25900 ***** ***** 290348 347748 95149 Dynamically allocated memory at amaxmodel [B,kB,MB]: 95524939 93286.070 91.100 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 50 25900 ***** ***** 290350 347750 95150 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 50 25900 ***** ***** 290350 347750 95150 Dynamically allocated memory at amaxmodel [B,kB,MB]: 95524971 93286.102 91.100 Dynamically allocated memory at amaxmodel [B,kB,MB]: 95615103 93374.125 91.186 Dynamically allocated memory at amaxmodel [B,kB,MB]: 96126107 93873.148 91.673 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 26418 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 26418 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 51 26418 ***** ***** 290350 347750 97052 Dynamically allocated memory at amaxmodel [B,kB,MB]: 96307015 94049.820 91.846 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 51 26418 ***** ***** 296155 354703 97052 Dynamically allocated memory at amaxmodel [B,kB,MB]: 96307071 94049.875 91.846 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 51 26418 ***** ***** 296157 354705 97053 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 51 26418 ***** ***** 296157 354705 97053 Dynamically allocated memory at amaxmodel [B,kB,MB]: 96307103 94049.906 91.846 Dynamically allocated memory at amaxmodel [B,kB,MB]: 96397235 94137.922 91.932 Dynamically allocated memory at amaxmodel [B,kB,MB]: 96908239 94636.953 92.419 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 26936 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 26936 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 52 26936 ***** ***** 296157 354705 98955 Dynamically allocated memory at amaxmodel [B,kB,MB]: 97089147 94813.617 92.591 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 52 26936 ***** ***** 301962 361658 98955 Dynamically allocated memory at amaxmodel [B,kB,MB]: 97089203 94813.672 92.591 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 52 26936 ***** ***** 301964 361660 98956 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 52 26936 ***** ***** 301964 361660 98956 Dynamically allocated memory at amaxmodel [B,kB,MB]: 97089235 94813.703 92.592 Dynamically allocated memory at amaxmodel [B,kB,MB]: 97179367 94901.727 92.677 Dynamically allocated memory at amaxmodel [B,kB,MB]: 97690371 95400.750 93.165 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 27454 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 27454 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 53 27454 ***** ***** 301964 361660 100858 Dynamically allocated memory at amaxmodel [B,kB,MB]: 97871279 95577.422 93.337 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 53 27454 ***** ***** 307769 368613 100858 Dynamically allocated memory at amaxmodel [B,kB,MB]: 99626055 97291.070 95.011 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 53 27454 ***** ***** 307771 368615 100859 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 53 27454 ***** ***** 307771 368615 100859 Dynamically allocated memory at amaxmodel [B,kB,MB]: 99626087 97291.102 95.011 Dynamically allocated memory at amaxmodel [B,kB,MB]: 99716219 97379.117 95.097 Dynamically allocated memory at amaxmodel [B,kB,MB]: 100227223 97878.148 95.584 Dynamically allocated memory at amaxmodel [B,kB,MB]: 100916575 98551.344 96.242 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 27972 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 27972 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 54 27972 ***** ***** 307771 368615 102761 Dynamically allocated memory at amaxmodel [B,kB,MB]: 101097483 98728.008 96.414 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 54 27972 ***** ***** 313576 375568 102761 Dynamically allocated memory at amaxmodel [B,kB,MB]: 101097539 98728.062 96.414 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 54 27972 ***** ***** 313578 375570 102762 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 54 27972 ***** ***** 313578 375570 102762 Dynamically allocated memory at amaxmodel [B,kB,MB]: 101097571 98728.094 96.414 Dynamically allocated memory at amaxmodel [B,kB,MB]: 101187703 98816.117 96.500 Dynamically allocated memory at amaxmodel [B,kB,MB]: 101698707 99315.141 96.987 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 28490 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 28490 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 55 28490 ***** ***** 313578 375570 104664 Dynamically allocated memory at amaxmodel [B,kB,MB]: 101879615 99491.812 97.160 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 55 28490 ***** ***** 319383 382523 104664 Dynamically allocated memory at amaxmodel [B,kB,MB]: 101879671 99491.867 97.160 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 55 28490 ***** ***** 319385 382525 104665 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 55 28490 ***** ***** 319385 382525 104665 Dynamically allocated memory at amaxmodel [B,kB,MB]: 101879703 99491.898 97.160 Dynamically allocated memory at amaxmodel [B,kB,MB]: 101969835 99579.914 97.246 Dynamically allocated memory at amaxmodel [B,kB,MB]: 102480839 100078.945 97.733 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 29008 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 29008 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 56 29008 ***** ***** 319385 382525 106567 Dynamically allocated memory at amaxmodel [B,kB,MB]: 102661747 100255.609 97.906 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 56 29008 ***** ***** 325190 389478 106567 Dynamically allocated memory at amaxmodel [B,kB,MB]: 102661803 100255.664 97.906 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 56 29008 ***** ***** 325192 389480 106568 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 56 29008 ***** ***** 325192 389480 106568 Dynamically allocated memory at amaxmodel [B,kB,MB]: 102661835 100255.695 97.906 Dynamically allocated memory at amaxmodel [B,kB,MB]: 102751967 100343.719 97.992 Dynamically allocated memory at amaxmodel [B,kB,MB]: 103262971 100842.742 98.479 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 29526 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 29526 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 57 29526 ***** ***** 325192 389480 108470 Dynamically allocated memory at amaxmodel [B,kB,MB]: 103443879 101019.414 98.652 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 57 29526 ***** ***** 330997 396433 108470 Dynamically allocated memory at amaxmodel [B,kB,MB]: 103443935 101019.469 98.652 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 57 29526 ***** ***** 330999 396435 108471 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 57 29526 ***** ***** 330999 396435 108471 Dynamically allocated memory at amaxmodel [B,kB,MB]: 103443967 101019.500 98.652 Dynamically allocated memory at amaxmodel [B,kB,MB]: 103534099 101107.516 98.738 Dynamically allocated memory at amaxmodel [B,kB,MB]: 104045103 101606.547 99.225 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 30044 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 30044 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 58 30044 ***** ***** 330999 396435 110373 Dynamically allocated memory at amaxmodel [B,kB,MB]: 104226011 101783.211 99.398 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 58 30044 ***** ***** 336804 403388 110373 Dynamically allocated memory at amaxmodel [B,kB,MB]: 104226067 101783.266 99.398 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 58 30044 ***** ***** 336806 403390 110374 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 58 30044 ***** ***** 336806 403390 110374 Dynamically allocated memory at amaxmodel [B,kB,MB]: 104226099 101783.297 99.398 Dynamically allocated memory at amaxmodel [B,kB,MB]: 104316231 101871.320 99.484 Dynamically allocated memory at amaxmodel [B,kB,MB]: 104827235 102370.344 99.971 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 30562 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 30562 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 59 30562 ***** ***** 336806 403390 112276 Dynamically allocated memory at amaxmodel [B,kB,MB]: 105008143 102547.016 100.144 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 59 30562 ***** ***** 342611 410343 112276 Dynamically allocated memory at amaxmodel [B,kB,MB]: 105008199 102547.070 100.144 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 59 30562 ***** ***** 342613 410345 112277 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 59 30562 ***** ***** 342613 410345 112277 Dynamically allocated memory at amaxmodel [B,kB,MB]: 105008231 102547.102 100.144 Dynamically allocated memory at amaxmodel [B,kB,MB]: 105098363 102635.117 100.230 Dynamically allocated memory at amaxmodel [B,kB,MB]: 105609367 103134.148 100.717 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 31080 atom names : C +N atom indices : ***** 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 31080 atom names : C CA +N O atom indices : ***** ***** 0 ***** mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 60 31080 ***** ***** 342613 410345 114179 Dynamically allocated memory at amaxmodel [B,kB,MB]: 105790275 103310.812 100.889 patch_______> segment topology patched using RTF: **** ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 60 31080 ***** ***** 348418 417298 114179 Dynamically allocated memory at amaxmodel [B,kB,MB]: 105790331 103310.867 100.890 patch_______> segment topology patched using RTF: **** ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 60 31080 ***** ***** 348420 417300 114180 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 60 31080 ***** ***** 348420 417300 114180 runcmd______> model.patch_ss_templates() runcmd______> model.transfer_xyz(cluster_cut=-1.0, (def)cluster_method='RMSD') transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 217740 29520 runcmd______> model.build(build_method='INTERNAL_COORDINATES', initialize_xyz=False) runcmd______> model.write(file='aav5_1.ini', (def)output_directory='', (def)model_format='PDB', (def)no_ter=False, (def)write_all_atoms=True) openf5__224_> Open 14 UNKNOWN SEQUENTIAL aav5_1.ini wrpdb2__568_> Residues, atoms, selected atoms: 31080 247260 247260 runcmd______> restraints.make(residue_span_range=(0, 99999), (def)residue_grouping=1, restraint_type='stereo', (def)restraint_sel_atoms=1, restraint_group=26, (def)basis_pdf_weight='LOCAL', distance_rsr_model=5, (def)maximal_distance=999.0, (def)basis_relative_weight=0.050000000000000003, spline_on_site=True, (def)residue_span_sign=True, (def)intersegment=True, add_restraints=True, (def)dih_lib_only=False, (def)spline_dx=0.5, (def)spline_min_points=5, (def)spline_range=4.0, (def)mnch_lib=1, (def)accessibility_type=8, (def)restraint_stdev=(0.0, 1.0), (def)restraint_stdev2=(0.0, 0.0, 0.0), (def)sheet_h_bonds=7, (def)surftyp=1, (def)restraint_parameters=(3, 1, 3, 3, 4, 2, 0, 0.0, 0.086999999999999994), (def)distance_atoms=('CA', 'CA'), (def)atom_ids=('',), (def)residue_ids='') make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,kB,MB]: 105937739 103454.820 101.030 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 106019659 103534.820 101.108 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 106052427 103566.820 101.139 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 106216267 103726.820 101.296 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 106249035 103758.820 101.327 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 106314571 103822.820 101.389 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 106642251 104142.820 101.702 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 106707787 104206.820 101.764 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 106838859 104334.820 101.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 107494219 104974.820 102.514 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 107625291 105102.820 102.639 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 107887435 105358.820 102.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 109198155 106638.820 104.139 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 109460299 106894.820 104.389 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 109984587 107406.820 104.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 112606027 109966.820 107.389 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 113130315 110478.820 107.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 114178891 111502.820 108.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 119421771 116622.820 113.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 120470347 117646.820 114.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 122567499 119694.820 116.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 124664651 121742.820 118.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 135150411 131982.828 128.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 139344715 136078.828 132.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 143539019 140174.828 136.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 164510539 160654.828 156.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 172899147 168846.828 164.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 181287755 177038.828 172.889 Dynamically allocated memory at amaxrestraints [B,kB,MB]: 223230795 217998.828 212.889 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 254940 348420 404940 111840 Total number of restraints before, now : 0 1120140 make_re_422_> Number of previous, current restraints : 0 1120140 make_re_423_> Number of previous, current selected restraints: 0 1120140 runcmd______> restraints.make(residue_span_range=(0, 99999), (def)residue_grouping=1, restraint_type='phi-psi_binormal', (def)restraint_sel_atoms=1, restraint_group=26, (def)basis_pdf_weight='LOCAL', distance_rsr_model=5, (def)maximal_distance=999.0, (def)basis_relative_weight=0.050000000000000003, spline_on_site=True, (def)residue_span_sign=True, (def)intersegment=True, add_restraints=True, (def)dih_lib_only=False, (def)spline_dx=0.5, (def)spline_min_points=5, (def)spline_range=4.0, (def)mnch_lib=1, (def)accessibility_type=8, (def)restraint_stdev=(0.0, 1.0), (def)restraint_stdev2=(0.0, 0.0, 0.0), (def)sheet_h_bonds=7, (def)surftyp=1, (def)restraint_parameters=(3, 1, 3, 3, 4, 2, 0, 0.0, 0.086999999999999994), (def)distance_atoms=('CA', 'CA'), (def)atom_ids=('',), (def)residue_ids='') make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,kB,MB]: 241032075 235382.891 229.866 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. dihdisn_223E> Internal error: array too small: current maximum, current need: 100 101