Starting phenix.real_space_refine on Sun Mar 17 16:54:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/03_2024/6syt_10347_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/03_2024/6syt_10347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/03_2024/6syt_10347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/03_2024/6syt_10347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/03_2024/6syt_10347_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/03_2024/6syt_10347_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 92 5.16 5 C 11829 2.51 5 N 3270 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 743": "NH1" <-> "NH2" Residue "A ARG 2187": "NH1" <-> "NH2" Residue "A ARG 2366": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "C ARG 264": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ARG 482": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18369 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1896, 13209 Classifications: {'peptide': 1896} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 595} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1840} Chain breaks: 46 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1683 Unresolved non-hydrogen angles: 2213 Unresolved non-hydrogen dihedrals: 1217 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 6, 'ASN:plan1': 21, 'TYR:plan': 5, 'UNK:plan-1': 213, 'TRP:plan': 3, 'ASP:plan': 52, 'PHE:plan': 7, 'GLU:plan': 80, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 1017 Chain: "B" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2719 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 252 Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2373 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 17, 'TRANS': 291} Chain breaks: 3 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.25, per 1000 atoms: 0.56 Number of scatterers: 18369 At special positions: 0 Unit cell: (146.28, 178.08, 138.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 9 15.00 Mg 1 11.99 O 3168 8.00 N 3270 7.00 C 11829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.26 Conformation dependent library (CDL) restraints added in 3.3 seconds 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4988 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 5 sheets defined 65.3% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.43 Creating SS restraints... Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.895A pdb=" N UNK A 153 " --> pdb=" O UNK A 149 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.766A pdb=" N UNK A 167 " --> pdb=" O UNK A 163 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N UNK A 172 " --> pdb=" O UNK A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 removed outlier: 3.637A pdb=" N UNK A 200 " --> pdb=" O UNK A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 223 removed outlier: 3.606A pdb=" N UNK A 213 " --> pdb=" O UNK A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.541A pdb=" N UNK A 255 " --> pdb=" O UNK A 251 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N UNK A 260 " --> pdb=" O UNK A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 284 Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.578A pdb=" N UNK A 297 " --> pdb=" O UNK A 293 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.726A pdb=" N ARG A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 removed outlier: 4.046A pdb=" N LEU A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.541A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.552A pdb=" N ALA A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 446 removed outlier: 3.683A pdb=" N VAL A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 438 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 441 " --> pdb=" O MET A 437 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 443 " --> pdb=" O CYS A 439 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 4.066A pdb=" N ALA A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.754A pdb=" N GLN A 485 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 539 through 554 removed outlier: 3.966A pdb=" N VAL A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 583 removed outlier: 3.859A pdb=" N SER A 582 " --> pdb=" O ASN A 578 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 622 removed outlier: 4.135A pdb=" N PHE A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.599A pdb=" N LEU A 642 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 650 removed outlier: 3.735A pdb=" N HIS A 650 " --> pdb=" O MET A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 653 through 656 No H-bonds generated for 'chain 'A' and resid 653 through 656' Processing helix chain 'A' and resid 658 through 672 Processing helix chain 'A' and resid 676 through 678 No H-bonds generated for 'chain 'A' and resid 676 through 678' Processing helix chain 'A' and resid 707 through 718 removed outlier: 4.036A pdb=" N ASN A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 742 removed outlier: 3.688A pdb=" N LYS A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 738 " --> pdb=" O TRP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 748 No H-bonds generated for 'chain 'A' and resid 746 through 748' Processing helix chain 'A' and resid 750 through 752 No H-bonds generated for 'chain 'A' and resid 750 through 752' Processing helix chain 'A' and resid 755 through 767 removed outlier: 3.784A pdb=" N LYS A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 786 removed outlier: 3.619A pdb=" N GLN A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 805 removed outlier: 3.566A pdb=" N ASP A 800 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.999A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 842 " --> pdb=" O ILE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 870 removed outlier: 4.188A pdb=" N PHE A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 890 removed outlier: 3.512A pdb=" N TYR A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 889 " --> pdb=" O ARG A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 926 removed outlier: 3.611A pdb=" N TRP A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 955 removed outlier: 3.549A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 946 " --> pdb=" O THR A 942 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 952 " --> pdb=" O ARG A 948 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 998 removed outlier: 4.267A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 978 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A 994 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 3.662A pdb=" N THR A1028 " --> pdb=" O GLN A1024 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A1035 " --> pdb=" O ARG A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.501A pdb=" N ARG A1049 " --> pdb=" O ALA A1045 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A1057 " --> pdb=" O ASP A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1083 removed outlier: 4.132A pdb=" N MET A1074 " --> pdb=" O GLU A1070 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A1075 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A1082 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.748A pdb=" N GLY A1091 " --> pdb=" O GLU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1114 removed outlier: 3.518A pdb=" N ASN A1108 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A1111 " --> pdb=" O ASN A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1133 removed outlier: 4.027A pdb=" N VAL A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A1131 " --> pdb=" O GLU A1127 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A1132 " --> pdb=" O HIS A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1147 No H-bonds generated for 'chain 'A' and resid 1144 through 1147' Processing helix chain 'A' and resid 1180 through 1195 removed outlier: 3.631A pdb=" N TYR A1185 " --> pdb=" O GLU A1181 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A1191 " --> pdb=" O GLY A1187 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS A1193 " --> pdb=" O LYS A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.844A pdb=" N GLN A1204 " --> pdb=" O TRP A1200 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A1211 " --> pdb=" O GLN A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1239 removed outlier: 3.784A pdb=" N SER A1236 " --> pdb=" O LYS A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1249 removed outlier: 3.567A pdb=" N GLU A1247 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN A1248 " --> pdb=" O GLU A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1304 removed outlier: 3.600A pdb=" N LEU A1293 " --> pdb=" O ILE A1289 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1300 " --> pdb=" O SER A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1330 removed outlier: 3.685A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A1326 " --> pdb=" O LYS A1322 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A1329 " --> pdb=" O LYS A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1338 Processing helix chain 'A' and resid 1349 through 1364 removed outlier: 4.029A pdb=" N LEU A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A1355 " --> pdb=" O THR A1351 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A1358 " --> pdb=" O LEU A1354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A1360 " --> pdb=" O CYS A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1373 No H-bonds generated for 'chain 'A' and resid 1371 through 1373' Processing helix chain 'A' and resid 1379 through 1383 Processing helix chain 'A' and resid 1391 through 1409 removed outlier: 3.549A pdb=" N GLN A1395 " --> pdb=" O PRO A1392 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA A1396 " --> pdb=" O TRP A1393 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A1397 " --> pdb=" O MET A1394 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A1398 " --> pdb=" O GLN A1395 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET A1401 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR A1402 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A1408 " --> pdb=" O GLN A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.900A pdb=" N GLU A1423 " --> pdb=" O SER A1419 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A1431 " --> pdb=" O THR A1427 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A1435 " --> pdb=" O PHE A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1449 removed outlier: 3.917A pdb=" N ARG A1443 " --> pdb=" O SER A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1466 removed outlier: 3.705A pdb=" N GLN A1464 " --> pdb=" O GLN A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1492 removed outlier: 3.500A pdb=" N ILE A1485 " --> pdb=" O PRO A1481 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A1486 " --> pdb=" O GLU A1482 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A1488 " --> pdb=" O ASP A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1512 removed outlier: 3.638A pdb=" N SER A1506 " --> pdb=" O GLU A1502 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A1510 " --> pdb=" O SER A1506 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A1511 " --> pdb=" O CYS A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1532 removed outlier: 3.732A pdb=" N ALA A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A1527 " --> pdb=" O LYS A1523 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1551 removed outlier: 3.501A pdb=" N VAL A1546 " --> pdb=" O GLN A1542 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A1548 " --> pdb=" O LYS A1544 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A1551 " --> pdb=" O TYR A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1560 through 1569 removed outlier: 3.502A pdb=" N ASN A1564 " --> pdb=" O THR A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 removed outlier: 3.563A pdb=" N VAL A1590 " --> pdb=" O GLU A1587 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N HIS A1591 " --> pdb=" O SER A1588 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A1592 " --> pdb=" O THR A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1610 removed outlier: 3.758A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A1602 " --> pdb=" O ASP A1598 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A1603 " --> pdb=" O PHE A1599 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A1604 " --> pdb=" O ILE A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1634 removed outlier: 3.693A pdb=" N LEU A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A1634 " --> pdb=" O GLY A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1656 removed outlier: 3.680A pdb=" N UNK A1651 " --> pdb=" O UNK A1647 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N UNK A1652 " --> pdb=" O UNK A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1675 removed outlier: 3.590A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1716 removed outlier: 3.587A pdb=" N UNK A1713 " --> pdb=" O UNK A1709 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N UNK A1714 " --> pdb=" O UNK A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1729 through 1740 removed outlier: 3.561A pdb=" N LYS A1735 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A1737 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A1738 " --> pdb=" O ARG A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1756 removed outlier: 3.670A pdb=" N SER A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1798 removed outlier: 3.663A pdb=" N VAL A1786 " --> pdb=" O ASP A1782 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A1787 " --> pdb=" O ASP A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1806 through 1810 Processing helix chain 'A' and resid 1819 through 1821 No H-bonds generated for 'chain 'A' and resid 1819 through 1821' Processing helix chain 'A' and resid 1823 through 1829 removed outlier: 4.015A pdb=" N PHE A1827 " --> pdb=" O ILE A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1849 Processing helix chain 'A' and resid 1857 through 1864 removed outlier: 3.581A pdb=" N ILE A1861 " --> pdb=" O LEU A1857 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A1863 " --> pdb=" O PRO A1859 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1938 removed outlier: 4.385A pdb=" N ASP A1935 " --> pdb=" O SER A1931 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1958 removed outlier: 3.772A pdb=" N ALA A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1977 removed outlier: 3.948A pdb=" N LEU A1971 " --> pdb=" O LEU A1967 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A1972 " --> pdb=" O GLY A1968 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A1975 " --> pdb=" O LEU A1971 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A1976 " --> pdb=" O GLN A1972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2018 Processing helix chain 'A' and resid 2036 through 2055 removed outlier: 4.411A pdb=" N ASN A2043 " --> pdb=" O TRP A2039 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A2046 " --> pdb=" O ASP A2042 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA A2047 " --> pdb=" O ASN A2043 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A2052 " --> pdb=" O ILE A2048 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A2053 " --> pdb=" O GLU A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2082 removed outlier: 4.109A pdb=" N UNK A2076 " --> pdb=" O UNK A2072 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N UNK A2077 " --> pdb=" O UNK A2073 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N UNK A2082 " --> pdb=" O UNK A2078 " (cutoff:3.500A) Processing helix chain 'A' and resid 2162 through 2176 Processing helix chain 'A' and resid 2178 through 2183 removed outlier: 3.517A pdb=" N ARG A2182 " --> pdb=" O ALA A2178 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN A2183 " --> pdb=" O THR A2179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2178 through 2183' Processing helix chain 'A' and resid 2215 through 2231 removed outlier: 4.208A pdb=" N ALA A2227 " --> pdb=" O GLN A2223 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A2231 " --> pdb=" O ALA A2227 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2263 removed outlier: 3.641A pdb=" N UNK A2253 " --> pdb=" O UNK A2249 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N UNK A2254 " --> pdb=" O UNK A2250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N UNK A2257 " --> pdb=" O UNK A2253 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N UNK A2260 " --> pdb=" O UNK A2256 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK A2261 " --> pdb=" O UNK A2257 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2288 removed outlier: 3.947A pdb=" N ALA A2282 " --> pdb=" O HIS A2278 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A2283 " --> pdb=" O VAL A2279 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A2284 " --> pdb=" O MET A2280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A2287 " --> pdb=" O VAL A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2300 No H-bonds generated for 'chain 'A' and resid 2297 through 2300' Processing helix chain 'A' and resid 2308 through 2331 removed outlier: 3.639A pdb=" N ALA A2322 " --> pdb=" O ALA A2318 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A2323 " --> pdb=" O ARG A2319 " (cutoff:3.500A) Processing helix chain 'A' and resid 2362 through 2364 No H-bonds generated for 'chain 'A' and resid 2362 through 2364' Processing helix chain 'A' and resid 2377 through 2380 No H-bonds generated for 'chain 'A' and resid 2377 through 2380' Processing helix chain 'A' and resid 2391 through 2405 removed outlier: 3.755A pdb=" N GLU A2397 " --> pdb=" O ARG A2393 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A2400 " --> pdb=" O CYS A2396 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A2402 " --> pdb=" O GLN A2398 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2418 removed outlier: 3.667A pdb=" N LEU A2413 " --> pdb=" O THR A2409 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A2416 " --> pdb=" O THR A2412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3621 removed outlier: 3.673A pdb=" N VAL A3612 " --> pdb=" O TYR A3608 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A3618 " --> pdb=" O LYS A3614 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A3619 " --> pdb=" O ARG A3615 " (cutoff:3.500A) Processing helix chain 'A' and resid 3633 through 3645 Processing helix chain 'A' and resid 3647 through 3650 No H-bonds generated for 'chain 'A' and resid 3647 through 3650' Processing helix chain 'A' and resid 3655 through 3657 No H-bonds generated for 'chain 'A' and resid 3655 through 3657' Processing helix chain 'B' and resid 65 through 71 Processing helix chain 'B' and resid 159 through 171 removed outlier: 4.638A pdb=" N ARG B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 204 removed outlier: 3.903A pdb=" N CYS B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 removed outlier: 4.824A pdb=" N PHE B 227 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 235 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 238 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 296 through 315 removed outlier: 3.603A pdb=" N ARG B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 359 removed outlier: 4.028A pdb=" N LEU B 352 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 355 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 356 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS B 359 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 422 removed outlier: 3.523A pdb=" N GLN B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 457 removed outlier: 3.898A pdb=" N SER B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 484 removed outlier: 4.000A pdb=" N SER B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 Proline residue: B 505 - end of helix Processing helix chain 'B' and resid 524 through 538 removed outlier: 3.761A pdb=" N VAL B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 537 " --> pdb=" O ARG B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 558 removed outlier: 4.447A pdb=" N MET B 549 " --> pdb=" O HIS B 545 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 243 through 246 No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 296 through 314 removed outlier: 3.567A pdb=" N SER C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 337 removed outlier: 3.921A pdb=" N PHE C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 381 through 394 removed outlier: 4.307A pdb=" N GLN C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 466 through 478 removed outlier: 3.715A pdb=" N SER C 475 " --> pdb=" O SER C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 507 removed outlier: 3.745A pdb=" N PHE C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 Processing sheet with id= A, first strand: chain 'A' and resid 2138 through 2142 removed outlier: 3.520A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A2140 " --> pdb=" O TYR A2152 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A2152 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A2142 " --> pdb=" O TYR A2150 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A2150 " --> pdb=" O PHE A2142 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 2341 through 2343 removed outlier: 3.855A pdb=" N VAL A2351 " --> pdb=" O LEU A2342 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.852A pdb=" N LEU B 210 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 212 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 209 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 53 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY B 54 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 141 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 139 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.466A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL C 317 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU C 210 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE C 319 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL C 368 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLN C 322 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU C 370 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 181 through 184 removed outlier: 6.940A pdb=" N ILE C 256 " --> pdb=" O LEU C 183 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 7.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4884 1.33 - 1.45: 4387 1.45 - 1.57: 9272 1.57 - 1.70: 11 1.70 - 1.82: 139 Bond restraints: 18693 Sorted by residual: bond pdb=" CG LEU A 717 " pdb=" CD2 LEU A 717 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.23e+01 bond pdb=" CG LEU C 223 " pdb=" CD1 LEU C 223 " ideal model delta sigma weight residual 1.521 1.409 0.112 3.30e-02 9.18e+02 1.15e+01 bond pdb=" CG LEU A 790 " pdb=" CD1 LEU A 790 " ideal model delta sigma weight residual 1.521 1.410 0.111 3.30e-02 9.18e+02 1.13e+01 bond pdb=" CG LEU A 826 " pdb=" CD2 LEU A 826 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.11e+01 bond pdb=" CG LYS C 217 " pdb=" CD LYS C 217 " ideal model delta sigma weight residual 1.520 1.421 0.099 3.00e-02 1.11e+03 1.08e+01 ... (remaining 18688 not shown) Histogram of bond angle deviations from ideal: 95.33 - 103.11: 179 103.11 - 110.89: 7467 110.89 - 118.67: 7490 118.67 - 126.45: 10085 126.45 - 134.23: 309 Bond angle restraints: 25530 Sorted by residual: angle pdb=" N THR C 326 " pdb=" CA THR C 326 " pdb=" C THR C 326 " ideal model delta sigma weight residual 110.91 119.87 -8.96 1.17e+00 7.31e-01 5.86e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 132.60 7.27 1.00e+00 1.00e+00 5.29e+01 angle pdb=" C THR C 270 " pdb=" N GLN C 271 " pdb=" CA GLN C 271 " ideal model delta sigma weight residual 120.49 130.13 -9.64 1.42e+00 4.96e-01 4.60e+01 angle pdb=" N TYR A1858 " pdb=" CA TYR A1858 " pdb=" C TYR A1858 " ideal model delta sigma weight residual 112.75 120.74 -7.99 1.36e+00 5.41e-01 3.45e+01 angle pdb=" N GLY A1602 " pdb=" CA GLY A1602 " pdb=" C GLY A1602 " ideal model delta sigma weight residual 112.77 105.81 6.96 1.28e+00 6.10e-01 2.96e+01 ... (remaining 25525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 10988 32.97 - 65.95: 93 65.95 - 98.92: 18 98.92 - 131.89: 6 131.89 - 164.87: 3 Dihedral angle restraints: 11108 sinusoidal: 3530 harmonic: 7578 Sorted by residual: dihedral pdb=" C4 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 60.90 -103.97 164.87 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O12 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O13 IHP A3701 " ideal model delta sinusoidal sigma weight residual 64.08 -87.05 151.13 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C6 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 61.05 -78.11 139.16 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 11105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.993: 3159 0.993 - 1.987: 3 1.987 - 2.980: 1 2.980 - 3.973: 0 3.973 - 4.966: 2 Chirality restraints: 3165 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.45 -4.97 2.00e-01 2.50e+01 6.17e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.45 4.77 2.00e-01 2.50e+01 5.68e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -0.30 2.78 2.00e-01 2.50e+01 1.93e+02 ... (remaining 3162 not shown) Planarity restraints: 3167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 734 " 0.032 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP A 734 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 734 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 734 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 734 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 734 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 734 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 734 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 734 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 734 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 669 " -0.020 2.00e-02 2.50e+03 2.65e-02 1.41e+01 pdb=" CG TYR A 669 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 669 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 669 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 669 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 669 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 669 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 669 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1375 " -0.051 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO A1376 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A1376 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1376 " -0.042 5.00e-02 4.00e+02 ... (remaining 3164 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 54 2.50 - 3.10: 14282 3.10 - 3.70: 26188 3.70 - 4.30: 37564 4.30 - 4.90: 61951 Nonbonded interactions: 140039 Sorted by model distance: nonbonded pdb=" OG SER C 218 " pdb="MG MG C 602 " model vdw 1.903 2.170 nonbonded pdb=" OG1 THR C 253 " pdb="MG MG C 602 " model vdw 1.937 2.170 nonbonded pdb=" OG SER C 218 " pdb=" OD2 ASP C 269 " model vdw 1.996 2.440 nonbonded pdb=" O SER A1297 " pdb=" OH TYR A1402 " model vdw 2.011 2.440 nonbonded pdb=" O PRO A1347 " pdb=" OG1 THR A1351 " model vdw 2.100 2.440 ... (remaining 140034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.420 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 48.390 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.145 18693 Z= 1.191 Angle : 1.232 13.326 25530 Z= 0.704 Chirality : 0.162 4.966 3165 Planarity : 0.006 0.076 3167 Dihedral : 11.022 164.865 6120 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 0.13 % Allowed : 2.26 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.37 (0.13), residues: 2277 helix: -3.76 (0.08), residues: 1372 sheet: -3.78 (0.35), residues: 123 loop : -2.68 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP A 734 HIS 0.014 0.004 HIS A2352 PHE 0.040 0.004 PHE A 760 TYR 0.061 0.005 TYR A 669 ARG 0.019 0.002 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 1.944 Fit side-chains REVERT: A 602 PHE cc_start: 0.6018 (m-10) cc_final: 0.5654 (m-80) REVERT: A 786 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8451 (pp) REVERT: A 809 SER cc_start: 0.8610 (p) cc_final: 0.8404 (p) REVERT: A 847 SER cc_start: 0.8770 (t) cc_final: 0.8472 (m) REVERT: A 2154 PHE cc_start: 0.7853 (m-80) cc_final: 0.7447 (m-80) REVERT: B 456 TYR cc_start: 0.8462 (t80) cc_final: 0.8237 (t80) REVERT: C 389 LEU cc_start: 0.8850 (tp) cc_final: 0.8602 (tp) outliers start: 2 outliers final: 0 residues processed: 350 average time/residue: 0.3458 time to fit residues: 176.2166 Evaluate side-chains 209 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS A 677 HIS A 722 ASN A 725 GLN ** A1344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 GLN ** A2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3649 ASN A3652 GLN B 272 ASN B 333 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18693 Z= 0.208 Angle : 0.587 9.132 25530 Z= 0.290 Chirality : 0.040 0.279 3165 Planarity : 0.005 0.063 3167 Dihedral : 8.712 116.368 2764 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.19 % Allowed : 7.67 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.16), residues: 2277 helix: -1.65 (0.12), residues: 1408 sheet: -2.86 (0.36), residues: 129 loop : -2.19 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2221 HIS 0.006 0.001 HIS A 546 PHE 0.018 0.002 PHE B 495 TYR 0.020 0.002 TYR A2218 ARG 0.004 0.001 ARG A1628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 289 time to evaluate : 2.137 Fit side-chains REVERT: A 431 ASP cc_start: 0.6523 (p0) cc_final: 0.5766 (t70) REVERT: A 583 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8741 (pp) REVERT: A 600 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.7169 (t-90) REVERT: A 843 LEU cc_start: 0.8820 (mm) cc_final: 0.8521 (mp) REVERT: A 847 SER cc_start: 0.9052 (t) cc_final: 0.8744 (m) REVERT: A 867 SER cc_start: 0.8794 (t) cc_final: 0.8565 (p) REVERT: A 1492 TYR cc_start: 0.9035 (t80) cc_final: 0.8810 (t80) REVERT: A 1793 LEU cc_start: 0.8408 (tp) cc_final: 0.8045 (tt) REVERT: A 2198 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7592 (pp) REVERT: A 3614 LYS cc_start: 0.8356 (mtmp) cc_final: 0.8006 (mttt) REVERT: B 198 LEU cc_start: 0.8593 (pp) cc_final: 0.8355 (mt) REVERT: B 456 TYR cc_start: 0.8561 (t80) cc_final: 0.8335 (t80) REVERT: C 433 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: C 487 HIS cc_start: 0.6280 (m-70) cc_final: 0.6058 (m90) outliers start: 19 outliers final: 10 residues processed: 301 average time/residue: 0.2960 time to fit residues: 136.8116 Evaluate side-chains 243 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 229 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 488 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 20.0000 chunk 72 optimal weight: 0.0970 chunk 193 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 232 optimal weight: 0.4980 chunk 251 optimal weight: 0.5980 chunk 207 optimal weight: 0.0870 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 186 optimal weight: 0.7980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS A 722 ASN ** A1344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1551 HIS A1606 HIS A2315 GLN A2337 HIS A2340 ASN B 333 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18693 Z= 0.142 Angle : 0.493 7.588 25530 Z= 0.241 Chirality : 0.037 0.188 3165 Planarity : 0.004 0.044 3167 Dihedral : 7.599 94.877 2762 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.70 % Allowed : 10.38 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 2277 helix: -0.38 (0.14), residues: 1418 sheet: -2.18 (0.40), residues: 129 loop : -1.80 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 254 HIS 0.004 0.001 HIS A 546 PHE 0.019 0.001 PHE C 414 TYR 0.015 0.001 TYR A2218 ARG 0.006 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 268 time to evaluate : 2.184 Fit side-chains REVERT: A 867 SER cc_start: 0.8772 (t) cc_final: 0.8535 (p) REVERT: A 1793 LEU cc_start: 0.8403 (tp) cc_final: 0.8118 (tt) REVERT: A 3614 LYS cc_start: 0.8350 (mtmp) cc_final: 0.8037 (mttt) REVERT: C 199 LEU cc_start: 0.8470 (mp) cc_final: 0.8254 (mt) outliers start: 27 outliers final: 15 residues processed: 277 average time/residue: 0.2960 time to fit residues: 126.8598 Evaluate side-chains 248 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2403 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 403 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN A1395 GLN ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1606 HIS A1832 HIS A1947 GLN A2192 HIS ** A2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2352 HIS B 354 GLN C 281 HIS ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18693 Z= 0.263 Angle : 0.556 7.956 25530 Z= 0.273 Chirality : 0.040 0.196 3165 Planarity : 0.004 0.046 3167 Dihedral : 7.581 89.981 2762 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.70 % Allowed : 11.95 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2277 helix: -0.09 (0.14), residues: 1430 sheet: -1.87 (0.42), residues: 129 loop : -1.58 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 254 HIS 0.004 0.001 HIS A 546 PHE 0.027 0.002 PHE A 405 TYR 0.020 0.002 TYR A1355 ARG 0.005 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 256 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: A 518 SER cc_start: 0.8210 (p) cc_final: 0.7916 (m) REVERT: A 1241 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8367 (mtmm) REVERT: A 1338 SER cc_start: 0.8993 (m) cc_final: 0.8775 (p) REVERT: A 1601 LEU cc_start: 0.8699 (pp) cc_final: 0.8449 (pp) REVERT: A 1603 GLN cc_start: 0.8795 (mt0) cc_final: 0.8506 (mm110) REVERT: A 1793 LEU cc_start: 0.8587 (tp) cc_final: 0.8364 (tt) REVERT: A 1803 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8294 (pp) REVERT: A 2324 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6054 (tpt) REVERT: A 3647 LEU cc_start: 0.8217 (mm) cc_final: 0.7963 (mm) outliers start: 43 outliers final: 26 residues processed: 282 average time/residue: 0.3060 time to fit residues: 132.2250 Evaluate side-chains 253 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1241 LYS Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1784 MET Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2346 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2395 SER Chi-restraints excluded: chain A residue 2403 MET Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 488 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 184 optimal weight: 0.0570 chunk 102 optimal weight: 0.7980 chunk 211 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN A1019 ASN ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 GLN B 272 ASN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS C 303 GLN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18693 Z= 0.185 Angle : 0.514 9.606 25530 Z= 0.247 Chirality : 0.038 0.211 3165 Planarity : 0.003 0.044 3167 Dihedral : 7.317 87.732 2762 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.14 % Allowed : 14.47 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2277 helix: 0.37 (0.14), residues: 1429 sheet: -1.75 (0.43), residues: 131 loop : -1.46 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 254 HIS 0.006 0.001 HIS C 281 PHE 0.019 0.001 PHE C 414 TYR 0.022 0.001 TYR A 565 ARG 0.006 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 258 time to evaluate : 1.956 Fit side-chains REVERT: A 518 SER cc_start: 0.8247 (p) cc_final: 0.7956 (m) REVERT: A 1241 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8324 (mtmm) REVERT: A 1483 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8841 (tp) REVERT: A 1536 TRP cc_start: 0.8361 (t-100) cc_final: 0.8109 (t-100) REVERT: A 1603 GLN cc_start: 0.8814 (mt0) cc_final: 0.8524 (mm-40) REVERT: A 1793 LEU cc_start: 0.8675 (tp) cc_final: 0.8457 (tt) REVERT: A 2324 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6058 (tpt) REVERT: A 3614 LYS cc_start: 0.8403 (mtmp) cc_final: 0.8092 (mttt) outliers start: 34 outliers final: 23 residues processed: 275 average time/residue: 0.2999 time to fit residues: 128.4149 Evaluate side-chains 262 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1241 LYS Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2346 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2395 SER Chi-restraints excluded: chain A residue 2412 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 145 optimal weight: 9.9990 chunk 61 optimal weight: 0.0670 chunk 247 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 130 optimal weight: 20.0000 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN C 252 GLN C 303 GLN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18693 Z= 0.212 Angle : 0.522 9.130 25530 Z= 0.252 Chirality : 0.038 0.209 3165 Planarity : 0.003 0.044 3167 Dihedral : 7.163 87.366 2762 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.77 % Allowed : 14.78 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2277 helix: 0.61 (0.14), residues: 1428 sheet: -1.66 (0.44), residues: 131 loop : -1.34 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 254 HIS 0.003 0.001 HIS A 546 PHE 0.024 0.001 PHE B 335 TYR 0.020 0.001 TYR A 565 ARG 0.006 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 250 time to evaluate : 1.969 Fit side-chains REVERT: A 518 SER cc_start: 0.8293 (p) cc_final: 0.8003 (m) REVERT: A 1241 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: A 1386 LYS cc_start: 0.8512 (mttt) cc_final: 0.8274 (mtpt) REVERT: A 1536 TRP cc_start: 0.8428 (t-100) cc_final: 0.8165 (t-100) REVERT: A 1603 GLN cc_start: 0.8827 (mt0) cc_final: 0.8535 (mm110) REVERT: A 2167 MET cc_start: 0.7397 (mmm) cc_final: 0.6794 (mmm) REVERT: A 2324 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6110 (tpt) REVERT: A 3614 LYS cc_start: 0.8365 (mtmp) cc_final: 0.8025 (mttt) REVERT: A 3647 LEU cc_start: 0.8384 (mm) cc_final: 0.8180 (mm) outliers start: 44 outliers final: 28 residues processed: 275 average time/residue: 0.2886 time to fit residues: 123.1241 Evaluate side-chains 260 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 230 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1241 LYS Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2346 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2395 SER Chi-restraints excluded: chain A residue 2412 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 488 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 246 optimal weight: 0.0010 chunk 154 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS C 303 GLN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18693 Z= 0.155 Angle : 0.492 8.907 25530 Z= 0.237 Chirality : 0.037 0.213 3165 Planarity : 0.003 0.042 3167 Dihedral : 6.899 87.060 2762 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.39 % Allowed : 15.66 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2277 helix: 0.92 (0.14), residues: 1435 sheet: -1.34 (0.47), residues: 119 loop : -1.21 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1629 HIS 0.003 0.001 HIS A 546 PHE 0.017 0.001 PHE B 335 TYR 0.019 0.001 TYR A 565 ARG 0.007 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 262 time to evaluate : 2.024 Fit side-chains REVERT: A 888 TYR cc_start: 0.8788 (m-80) cc_final: 0.8504 (m-80) REVERT: A 1241 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8376 (mtmm) REVERT: A 1386 LYS cc_start: 0.8492 (mttt) cc_final: 0.8247 (mtpt) REVERT: A 1536 TRP cc_start: 0.8465 (t-100) cc_final: 0.8235 (t-100) REVERT: A 1603 GLN cc_start: 0.8768 (mt0) cc_final: 0.8548 (mm-40) REVERT: A 1607 LEU cc_start: 0.9286 (tp) cc_final: 0.9083 (tt) REVERT: A 2324 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6027 (tpt) REVERT: A 3614 LYS cc_start: 0.8356 (mtmp) cc_final: 0.8021 (mttt) REVERT: B 345 GLU cc_start: 0.7234 (pm20) cc_final: 0.6880 (pm20) outliers start: 38 outliers final: 28 residues processed: 280 average time/residue: 0.3000 time to fit residues: 131.0003 Evaluate side-chains 273 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1241 LYS Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2346 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2395 SER Chi-restraints excluded: chain A residue 2412 THR Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1931 > 50: distance: 30 - 35: 10.488 distance: 35 - 36: 11.809 distance: 36 - 37: 18.284 distance: 36 - 39: 15.789 distance: 37 - 38: 33.140 distance: 37 - 46: 7.749 distance: 39 - 40: 7.147 distance: 40 - 41: 37.970 distance: 40 - 42: 15.500 distance: 41 - 43: 37.873 distance: 42 - 44: 35.904 distance: 43 - 45: 16.640 distance: 44 - 45: 36.905 distance: 46 - 47: 8.959 distance: 47 - 48: 17.035 distance: 47 - 50: 27.019 distance: 48 - 49: 9.249 distance: 48 - 57: 9.787 distance: 50 - 51: 10.228 distance: 51 - 52: 25.016 distance: 51 - 53: 34.194 distance: 52 - 54: 30.531 distance: 53 - 55: 17.457 distance: 54 - 56: 26.292 distance: 55 - 56: 25.191 distance: 57 - 58: 4.258 distance: 58 - 59: 8.947 distance: 58 - 61: 6.863 distance: 59 - 60: 25.421 distance: 59 - 69: 14.946 distance: 61 - 62: 7.948 distance: 62 - 63: 21.891 distance: 62 - 64: 25.643 distance: 63 - 65: 19.824 distance: 64 - 66: 4.616 distance: 65 - 67: 20.164 distance: 66 - 67: 11.525 distance: 67 - 68: 25.380 distance: 69 - 70: 16.757 distance: 70 - 71: 20.844 distance: 70 - 73: 4.065 distance: 71 - 72: 21.347 distance: 71 - 76: 28.144 distance: 73 - 74: 21.448 distance: 73 - 75: 22.595 distance: 76 - 77: 23.086 distance: 77 - 78: 15.252 distance: 77 - 80: 25.674 distance: 78 - 79: 32.239 distance: 78 - 84: 21.242 distance: 80 - 81: 28.936 distance: 81 - 82: 5.282 distance: 81 - 83: 16.179 distance: 84 - 85: 16.688 distance: 85 - 86: 17.593 distance: 85 - 88: 11.953 distance: 86 - 87: 40.202 distance: 86 - 95: 38.744 distance: 87 - 117: 40.765 distance: 88 - 89: 26.583 distance: 89 - 90: 15.024 distance: 90 - 91: 17.424 distance: 91 - 92: 42.566 distance: 92 - 93: 41.207 distance: 92 - 94: 53.035 distance: 95 - 96: 23.625 distance: 96 - 97: 25.750 distance: 96 - 99: 26.759 distance: 97 - 98: 25.390 distance: 97 - 104: 13.109 distance: 98 - 126: 15.230 distance: 99 - 100: 42.668 distance: 100 - 101: 6.036 distance: 101 - 102: 15.068 distance: 101 - 103: 21.981 distance: 104 - 105: 23.990 distance: 105 - 106: 29.474 distance: 105 - 108: 6.020 distance: 106 - 107: 26.593 distance: 106 - 111: 35.930 distance: 107 - 131: 21.537 distance: 108 - 109: 27.824 distance: 108 - 110: 26.385 distance: 111 - 112: 25.685 distance: 112 - 113: 21.619 distance: 112 - 115: 26.037 distance: 113 - 114: 24.765 distance: 113 - 117: 40.223 distance: 114 - 137: 32.272 distance: 115 - 116: 28.804 distance: 117 - 118: 19.502 distance: 118 - 119: 3.849 distance: 118 - 121: 10.612 distance: 119 - 126: 34.162 distance: 121 - 122: 40.974 distance: 122 - 123: 28.385 distance: 123 - 124: 34.356 distance: 123 - 125: 10.234