Starting phenix.real_space_refine on Tue Jun 24 08:27:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7t_38109/06_2025/8x7t_38109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7t_38109/06_2025/8x7t_38109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7t_38109/06_2025/8x7t_38109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7t_38109/06_2025/8x7t_38109.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7t_38109/06_2025/8x7t_38109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7t_38109/06_2025/8x7t_38109.cif" } resolution = 3.26 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= 0.002 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 17884 2.51 5 N 5009 2.21 5 O 5365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28329 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5085 Classifications: {'peptide': 671} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 30, 'TRANS': 640} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 126 Chain: "C" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4539 Classifications: {'peptide': 581} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 552} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5176 Classifications: {'peptide': 669} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 30, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 4281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4281 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 28, 'TRANS': 551} Chain breaks: 1 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 184 Chain: "F" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 4804 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 30, 'TRANS': 639} Chain breaks: 1 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 607 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 251 Chain: "A" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4444 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 28, 'TRANS': 553} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 95 Time building chain proxies: 19.21, per 1000 atoms: 0.68 Number of scatterers: 28329 At special positions: 0 Unit cell: (121.136, 170.448, 175.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 5365 8.00 N 5009 7.00 C 17884 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 - 3.00 Amino acid : True - 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: 6.61 Conformation dependent library (CDL) restraints added in 3.9 seconds 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7122 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 35 sheets defined 42.3% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 27 through 36 removed outlier: 3.512A pdb=" N VAL D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.619A pdb=" N ALA D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.599A pdb=" N HIS D 112 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 263 through 276 removed outlier: 3.532A pdb=" N ALA D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 287 Processing helix chain 'D' and resid 294 through 306 Processing helix chain 'D' and resid 335 through 346 Processing helix chain 'D' and resid 380 through 385 Processing helix chain 'D' and resid 399 through 411 removed outlier: 4.890A pdb=" N HIS D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 476 through 492 Processing helix chain 'D' and resid 501 through 515 Processing helix chain 'D' and resid 521 through 538 Processing helix chain 'D' and resid 553 through 571 removed outlier: 3.660A pdb=" N ARG D 571 " --> pdb=" O HIS D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 595 Processing helix chain 'D' and resid 604 through 608 Processing helix chain 'D' and resid 611 through 632 Processing helix chain 'D' and resid 639 through 651 Processing helix chain 'D' and resid 654 through 669 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.605A pdb=" N LEU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 80 removed outlier: 3.507A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.987A pdb=" N ILE C 113 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.532A pdb=" N ARG C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 288 removed outlier: 4.507A pdb=" N ALA C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.646A pdb=" N VAL C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 399 through 412 removed outlier: 4.866A pdb=" N HIS C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLU C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 456 through 461 removed outlier: 3.677A pdb=" N SER C 461 " --> pdb=" O PRO C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 491 removed outlier: 3.503A pdb=" N ALA C 479 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 497 Processing helix chain 'C' and resid 501 through 515 removed outlier: 3.542A pdb=" N ALA C 510 " --> pdb=" O LYS C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 543 removed outlier: 3.828A pdb=" N ARG C 540 " --> pdb=" O ARG C 536 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 541 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 571 removed outlier: 3.789A pdb=" N ARG C 571 " --> pdb=" O HIS C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 594 removed outlier: 3.650A pdb=" N ALA C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 587 " --> pdb=" O ALA C 583 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 14 removed outlier: 3.509A pdb=" N ALA B 8 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 11 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.549A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.501A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.979A pdb=" N LYS B 196 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 294 through 307 Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.649A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 344 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 345 " --> pdb=" O TYR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 Processing helix chain 'B' and resid 399 through 411 removed outlier: 3.649A pdb=" N SER B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLU B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.507A pdb=" N LEU B 460 " --> pdb=" O PRO B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 491 removed outlier: 3.524A pdb=" N GLY B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 501 through 516 removed outlier: 3.602A pdb=" N LYS B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 539 Processing helix chain 'B' and resid 553 through 570 Processing helix chain 'B' and resid 577 through 593 Processing helix chain 'B' and resid 611 through 631 removed outlier: 3.582A pdb=" N LYS B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 630 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 650 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.675A pdb=" N ASP B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 14 removed outlier: 4.226A pdb=" N ILE E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 36 removed outlier: 3.882A pdb=" N THR E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 53 removed outlier: 3.526A pdb=" N LEU E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 63 removed outlier: 4.065A pdb=" N LEU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 80 removed outlier: 3.712A pdb=" N GLN E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 194 through 199 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 265 through 275 removed outlier: 3.727A pdb=" N ALA E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 285 removed outlier: 3.692A pdb=" N ILE E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 306 Processing helix chain 'E' and resid 337 through 346 removed outlier: 3.835A pdb=" N ALA E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 344 " --> pdb=" O ARG E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 386 removed outlier: 4.112A pdb=" N ASP E 386 " --> pdb=" O VAL E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 412 removed outlier: 3.867A pdb=" N ALA E 405 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N HIS E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 474 through 490 removed outlier: 3.685A pdb=" N LEU E 486 " --> pdb=" O ALA E 482 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 497 Processing helix chain 'E' and resid 501 through 515 removed outlier: 3.665A pdb=" N ALA E 510 " --> pdb=" O LYS E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 537 removed outlier: 3.709A pdb=" N ARG E 530 " --> pdb=" O GLU E 526 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 544 Processing helix chain 'E' and resid 553 through 572 removed outlier: 3.501A pdb=" N ARG E 562 " --> pdb=" O GLU E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 594 removed outlier: 3.627A pdb=" N ILE E 587 " --> pdb=" O ALA E 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 14 removed outlier: 4.588A pdb=" N MET F 6 " --> pdb=" O ASP F 2 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 36 removed outlier: 3.767A pdb=" N LEU F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 40 Processing helix chain 'F' and resid 45 through 53 removed outlier: 3.633A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 63 removed outlier: 3.646A pdb=" N ALA F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 81 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.966A pdb=" N HIS F 112 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE F 113 " --> pdb=" O SER F 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 109 through 113' Processing helix chain 'F' and resid 253 through 259 Processing helix chain 'F' and resid 265 through 275 removed outlier: 3.764A pdb=" N ARG F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 286 removed outlier: 3.604A pdb=" N ASP F 285 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 304 Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.651A pdb=" N GLY F 316 " --> pdb=" O LEU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 343 removed outlier: 4.150A pdb=" N LEU F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.542A pdb=" N ALA F 385 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 410 removed outlier: 3.782A pdb=" N ALA F 405 " --> pdb=" O ARG F 401 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU F 408 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 463 removed outlier: 4.098A pdb=" N LEU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG F 462 " --> pdb=" O THR F 458 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE F 463 " --> pdb=" O LEU F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 515 removed outlier: 3.560A pdb=" N ALA F 510 " --> pdb=" O LYS F 506 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR F 511 " --> pdb=" O LYS F 507 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN F 515 " --> pdb=" O TYR F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 539 removed outlier: 3.556A pdb=" N GLU F 527 " --> pdb=" O GLU F 523 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 528 " --> pdb=" O ALA F 524 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET F 535 " --> pdb=" O TYR F 531 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS F 537 " --> pdb=" O VAL F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 568 removed outlier: 3.693A pdb=" N ALA F 559 " --> pdb=" O ARG F 555 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG F 562 " --> pdb=" O GLU F 558 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA F 566 " --> pdb=" O ARG F 562 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS F 567 " --> pdb=" O LEU F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 571 No H-bonds generated for 'chain 'F' and resid 569 through 571' Processing helix chain 'F' and resid 577 through 595 removed outlier: 3.930A pdb=" N ARG F 582 " --> pdb=" O ARG F 578 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA F 583 " --> pdb=" O GLU F 579 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE F 588 " --> pdb=" O ALA F 584 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR F 594 " --> pdb=" O ALA F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 608 Processing helix chain 'F' and resid 611 through 627 removed outlier: 3.612A pdb=" N ASN F 618 " --> pdb=" O SER F 614 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE F 627 " --> pdb=" O LEU F 623 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 650 Processing helix chain 'F' and resid 654 through 669 removed outlier: 3.563A pdb=" N ASN F 663 " --> pdb=" O GLU F 659 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU F 664 " --> pdb=" O LYS F 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.064A pdb=" N ALA A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.975A pdb=" N THR A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.526A pdb=" N ALA A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.591A pdb=" N ASP A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.658A pdb=" N HIS A 112 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 113 " --> pdb=" O SER A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 113' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 278 through 288 removed outlier: 4.706A pdb=" N ALA A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 334 through 344 removed outlier: 4.103A pdb=" N ASN A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 399 through 411 removed outlier: 4.844A pdb=" N HIS A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLU A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.575A pdb=" N LEU A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.771A pdb=" N ARG A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 501 through 515 removed outlier: 3.547A pdb=" N LYS A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 535 Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 553 through 571 removed outlier: 3.613A pdb=" N ARG A 571 " --> pdb=" O HIS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 removed outlier: 3.636A pdb=" N LYS A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 41 through 44 Processing sheet with id=AA2, first strand: chain 'D' and resid 103 through 104 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 116 through 127 current: chain 'D' and resid 180 through 189 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 203 through 209 current: chain 'D' and resid 243 through 252 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 243 through 252 current: chain 'D' and resid 375 through 378 Processing sheet with id=AA3, first strand: chain 'D' and resid 143 through 150 removed outlier: 5.364A pdb=" N ASN D 145 " --> pdb=" O CYS D 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 352 through 353 removed outlier: 6.855A pdb=" N THR D 352 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 433 " --> pdb=" O ALA D 390 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 414 through 417 Processing sheet with id=AA6, first strand: chain 'D' and resid 519 through 520 removed outlier: 6.943A pdb=" N VAL D 519 " --> pdb=" O VAL D 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 671 through 675 removed outlier: 5.044A pdb=" N GLU D 673 " --> pdb=" O ARG D 680 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG D 680 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG D 675 " --> pdb=" O PHE D 678 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 104 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 116 through 123 current: chain 'C' and resid 148 through 150 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 148 through 150 current: chain 'C' and resid 203 through 208 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 203 through 208 current: chain 'C' and resid 243 through 252 Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB1, first strand: chain 'C' and resid 349 through 353 removed outlier: 6.841A pdb=" N ILE C 350 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP C 393 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR C 352 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 392 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 329 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 326 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU C 469 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 328 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 414 through 415 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AB4, first strand: chain 'B' and resid 103 through 104 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 116 through 126 current: chain 'B' and resid 180 through 189 removed outlier: 3.522A pdb=" N LEU B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 203 through 208 current: chain 'B' and resid 245 through 252 Processing sheet with id=AB5, first strand: chain 'B' and resid 135 through 137 Processing sheet with id=AB6, first strand: chain 'B' and resid 349 through 353 removed outlier: 6.257A pdb=" N ILE B 350 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 393 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 352 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 433 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 392 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL B 325 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA B 436 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU B 327 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 365 through 368 Processing sheet with id=AB8, first strand: chain 'B' and resid 414 through 419 Processing sheet with id=AB9, first strand: chain 'B' and resid 597 through 598 Processing sheet with id=AC1, first strand: chain 'B' and resid 671 through 675 removed outlier: 7.187A pdb=" N PHE B 678 " --> pdb=" O PRO B 674 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 41 through 44 Processing sheet with id=AC3, first strand: chain 'E' and resid 130 through 132 removed outlier: 3.571A pdb=" N LEU E 188 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 204 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N LEU E 245 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP E 205 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL E 247 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE E 207 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N HIS E 249 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU E 245 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG E 229 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL E 247 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL E 227 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN E 189 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 125 through 126 Processing sheet with id=AC5, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AC6, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'E' and resid 352 through 353 removed outlier: 7.020A pdb=" N THR E 352 " --> pdb=" O ASP E 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 102 through 104 removed outlier: 7.470A pdb=" N LEU F 103 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N ILE F 122 " --> pdb=" O LEU F 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 116 through 127 current: chain 'F' and resid 179 through 189 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 203 through 209 current: chain 'F' and resid 245 through 249 Processing sheet with id=AC9, first strand: chain 'F' and resid 147 through 149 removed outlier: 3.523A pdb=" N MET F 147 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL F 137 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU F 172 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 325 through 328 removed outlier: 6.316A pdb=" N VAL F 325 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ALA F 436 " --> pdb=" O VAL F 325 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU F 327 " --> pdb=" O ALA F 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 388 through 389 removed outlier: 7.365A pdb=" N GLY F 388 " --> pdb=" O THR F 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 671 through 675 removed outlier: 7.862A pdb=" N PHE F 678 " --> pdb=" O PRO F 674 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AD5, first strand: chain 'A' and resid 116 through 127 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 116 through 127 current: chain 'A' and resid 149 through 150 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 150 current: chain 'A' and resid 203 through 208 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 203 through 208 current: chain 'A' and resid 244 through 249 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 244 through 249 current: chain 'A' and resid 376 through 378 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'A' and resid 349 through 353 removed outlier: 6.205A pdb=" N ILE A 350 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP A 393 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A 352 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 392 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 329 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 414 through 416 Processing sheet with id=AD8, first strand: chain 'A' and resid 519 through 520 removed outlier: 6.680A pdb=" N VAL A 519 " --> pdb=" O VAL A 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 1055 hydrogen bonds defined for protein. 3045 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: 10.92 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9748 1.34 - 1.46: 4510 1.46 - 1.58: 14376 1.58 - 1.70: 0 1.70 - 1.81: 118 Bond restraints: 28752 Sorted by residual: bond pdb=" CA PRO A 456 " pdb=" C PRO A 456 " ideal model delta sigma weight residual 1.514 1.532 -0.018 5.50e-03 3.31e+04 1.01e+01 bond pdb=" CA LYS C 318 " pdb=" C LYS C 318 " ideal model delta sigma weight residual 1.530 1.506 0.024 1.14e-02 7.69e+03 4.54e+00 bond pdb=" C THR A 37 " pdb=" N PRO A 38 " ideal model delta sigma weight residual 1.332 1.349 -0.017 8.90e-03 1.26e+04 3.69e+00 bond pdb=" C PRO F 82 " pdb=" N PRO F 83 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.30e-02 5.92e+03 3.34e+00 bond pdb=" CA PRO F 456 " pdb=" C PRO F 456 " ideal model delta sigma weight residual 1.517 1.501 0.016 9.30e-03 1.16e+04 3.12e+00 ... (remaining 28747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 38532 2.50 - 5.00: 405 5.00 - 7.50: 32 7.50 - 10.00: 1 10.00 - 12.49: 1 Bond angle restraints: 38971 Sorted by residual: angle pdb=" N SER E 336 " pdb=" CA SER E 336 " pdb=" C SER E 336 " ideal model delta sigma weight residual 107.44 119.93 -12.49 1.93e+00 2.68e-01 4.19e+01 angle pdb=" C ALA B 420 " pdb=" CA ALA B 420 " pdb=" CB ALA B 420 " ideal model delta sigma weight residual 116.54 110.43 6.11 1.15e+00 7.56e-01 2.82e+01 angle pdb=" C ALA D 334 " pdb=" CA ALA D 334 " pdb=" CB ALA D 334 " ideal model delta sigma weight residual 116.54 110.45 6.09 1.15e+00 7.56e-01 2.80e+01 angle pdb=" C ARG D 235 " pdb=" CA ARG D 235 " pdb=" CB ARG D 235 " ideal model delta sigma weight residual 117.23 110.26 6.97 1.36e+00 5.41e-01 2.63e+01 angle pdb=" N ARG F 569 " pdb=" CA ARG F 569 " pdb=" C ARG F 569 " ideal model delta sigma weight residual 112.38 106.19 6.19 1.22e+00 6.72e-01 2.58e+01 ... (remaining 38966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 16769 16.54 - 33.08: 870 33.08 - 49.62: 159 49.62 - 66.15: 24 66.15 - 82.69: 18 Dihedral angle restraints: 17840 sinusoidal: 6926 harmonic: 10914 Sorted by residual: dihedral pdb=" CA LEU B 209 " pdb=" C LEU B 209 " pdb=" N ASP B 210 " pdb=" CA ASP B 210 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP D 478 " pdb=" CB ASP D 478 " pdb=" CG ASP D 478 " pdb=" OD1 ASP D 478 " ideal model delta sinusoidal sigma weight residual -30.00 -86.87 56.87 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB MET F 535 " pdb=" CG MET F 535 " pdb=" SD MET F 535 " pdb=" CE MET F 535 " ideal model delta sinusoidal sigma weight residual 180.00 120.61 59.39 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 17837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3625 0.045 - 0.089: 722 0.089 - 0.134: 243 0.134 - 0.178: 8 0.178 - 0.223: 2 Chirality restraints: 4600 Sorted by residual: chirality pdb=" CG LEU B 260 " pdb=" CB LEU B 260 " pdb=" CD1 LEU B 260 " pdb=" CD2 LEU B 260 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA SER E 336 " pdb=" N SER E 336 " pdb=" C SER E 336 " pdb=" CB SER E 336 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 4597 not shown) Planarity restraints: 5115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 81 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO F 82 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 82 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 82 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 82 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO C 83 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 643 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C VAL D 643 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL D 643 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE D 644 " 0.009 2.00e-02 2.50e+03 ... (remaining 5112 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 3119 2.74 - 3.28: 30456 3.28 - 3.82: 47791 3.82 - 4.36: 58463 4.36 - 4.90: 95100 Nonbonded interactions: 234929 Sorted by model distance: nonbonded pdb=" O ARG D 235 " pdb=" CD PRO D 239 " model vdw 2.206 3.440 nonbonded pdb=" OH TYR D 508 " pdb=" O MET D 570 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 102 " pdb=" OE1 GLU A 120 " model vdw 2.234 3.040 nonbonded pdb=" O MET C 200 " pdb=" NH1 ARG C 202 " model vdw 2.235 3.120 nonbonded pdb=" O LYS E 135 " pdb=" OG SER E 178 " model vdw 2.254 3.040 ... (remaining 234924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 11 or (resid 12 through 14 and (name N \ or name CA or name C or name O or name CB )) or (resid 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 31 or (resid 32 through \ 33 and (name N or name CA or name C or name O or name CB )) or resid 34 through \ 35 or (resid 36 through 37 and (name N or name CA or name C or name O or name CB \ )) or resid 38 or (resid 39 and (name N or name CA or name C or name O or name \ CB )) or resid 40 through 41 or (resid 42 through 43 and (name N or name CA or n \ ame C or name O or name CB )) or resid 44 through 45 or (resid 46 through 47 and \ (name N or name CA or name C or name O or name CB )) or resid 48 through 50 or \ (resid 51 and (name N or name CA or name C or name O or name CB )) or resid 52 o \ r (resid 53 and (name N or name CA or name C or name O or name CB )) or resid 54 \ or (resid 55 through 58 and (name N or name CA or name C or name O or name CB ) \ ) or resid 59 through 64 or (resid 65 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 75 or (resid 76 throu \ gh 77 and (name N or name CA or name C or name O or name CB )) or resid 78 or (r \ esid 79 through 81 and (name N or name CA or name C or name O or name CB )) or r \ esid 82 through 85 or (resid 86 through 91 and (name N or name CA or name C or n \ ame O or name CB )) or resid 92 through 94 or (resid 95 through 97 and (name N o \ r name CA or name C or name O or name CB )) or resid 98 or (resid 99 and (name N \ or name CA or name C or name O or name CB )) or resid 100 or (resid 101 and (na \ me N or name CA or name C or name O or name CB )) or resid 102 or (resid 103 thr \ ough 104 and (name N or name CA or name C or name O or name CB )) or resid 105 o \ r (resid 106 through 107 and (name N or name CA or name C or name O or name CB ) \ ) or resid 108 through 110 or (resid 111 and (name N or name CA or name C or nam \ e O or name CB )) or resid 112 through 114 or (resid 115 and (name N or name CA \ or name C or name O or name CB )) or resid 116 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 127 or (r \ esid 128 and (name N or name CA or name C or name O or name CB )) or resid 129 t \ hrough 131 or (resid 132 through 133 and (name N or name CA or name C or name O \ or name CB )) or resid 134 through 136 or (resid 137 and (name N or name CA or n \ ame C or name O or name CB )) or resid 138 through 144 or (resid 145 and (name N \ or name CA or name C or name O or name CB )) or resid 146 through 150 or (resid \ 151 through 152 and (name N or name CA or name C or name O or name CB )) or res \ id 153 through 154 or (resid 155 through 157 and (name N or name CA or name C or \ name O or name CB )) or resid 158 through 161 or (resid 162 and (name N or name \ CA or name C or name O or name CB )) or resid 163 or (resid 164 through 165 and \ (name N or name CA or name C or name O or name CB )) or resid 166 through 173 o \ r (resid 174 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 75 through 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 through 189 or (resid 190 and (name N or name CA or name C or \ name O or name CB )) or resid 191 through 192 or (resid 193 and (name N or name \ CA or name C or name O or name CB )) or resid 194 through 195 or (resid 196 and \ (name N or name CA or name C or name O or name CB )) or resid 197 through 203 o \ r (resid 204 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 05 through 211 or (resid 212 and (name N or name CA or name C or name O or name \ CB )) or resid 213 through 230 or (resid 231 and (name N or name CA or name C or \ name O or name CB )) or resid 232 through 233 or (resid 234 through 238 and (na \ me N or name CA or name C or name O or name CB )) or resid 239 or (resid 240 thr \ ough 241 and (name N or name CA or name C or name O or name CB )) or resid 242 t \ hrough 249 or (resid 250 and (name N or name CA or name C or name O or name CB ) \ ) or resid 251 through 254 or (resid 255 through 257 and (name N or name CA or n \ ame C or name O or name CB )) or resid 258 or (resid 259 and (name N or name CA \ or name C or name O or name CB )) or resid 260 or (resid 261 through 262 and (na \ me N or name CA or name C or name O or name CB )) or resid 263 through 264 or (r \ esid 265 and (name N or name CA or name C or name O or name CB )) or resid 266 t \ hrough 267 or (resid 268 through 269 and (name N or name CA or name C or name O \ or name CB )) or resid 270 or (resid 271 and (name N or name CA or name C or nam \ e O or name CB )) or resid 272 through 274 or (resid 275 through 277 and (name N \ or name CA or name C or name O or name CB )) or resid 278 or (resid 279 and (na \ me N or name CA or name C or name O or name CB )) or resid 280 through 284 or (r \ esid 285 and (name N or name CA or name C or name O or name CB )) or resid 286 t \ hrough 291 or (resid 292 and (name N or name CA or name C or name O or name CB ) \ ) or resid 293 through 296 or (resid 297 through 298 and (name N or name CA or n \ ame C or name O or name CB )) or resid 299 through 314 or (resid 315 and (name N \ or name CA or name C or name O or name CB )) or resid 316 or (resid 317 through \ 320 and (name N or name CA or name C or name O or name CB )) or resid 321 throu \ gh 325 or (resid 326 and (name N or name CA or name C or name O or name CB )) or \ resid 327 or (resid 328 and (name N or name CA or name C or name O or name CB ) \ ) or resid 329 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O or name CB )) or resid 339 or (resid 340 and (name N or name CA or name C or \ name O or name CB )) or resid 341 through 343 or (resid 344 and (name N or name \ CA or name C or name O or name CB )) or resid 345 through 350 or (resid 351 and \ (name N or name CA or name C or name O or name CB )) or resid 352 through 355 o \ r (resid 356 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 57 through 361 or (resid 362 through 366 and (name N or name CA or name C or nam \ e O or name CB )) or resid 367 or (resid 368 through 369 and (name N or name CA \ or name C or name O or name CB )) or resid 370 or (resid 371 and (name N or name \ CA or name C or name O or name CB )) or resid 372 through 374 or (resid 375 thr \ ough 376 and (name N or name CA or name C or name O or name CB )) or resid 377 t \ hrough 390 or (resid 391 and (name N or name CA or name C or name O or name CB ) \ ) or resid 392 through 393 or (resid 394 through 395 and (name N or name CA or n \ ame C or name O or name CB )) or resid 396 or (resid 397 and (name N or name CA \ or name C or name O or name CB )) or resid 398 through 402 or (resid 403 and (na \ me N or name CA or name C or name O or name CB )) or resid 404 through 414 or (r \ esid 415 and (name N or name CA or name C or name O or name CB )) or resid 416 o \ r (resid 417 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 18 through 424 or (resid 425 through 426 and (name N or name CA or name C or nam \ e O or name CB )) or resid 427 through 429 or (resid 430 and (name N or name CA \ or name C or name O or name CB )) or resid 431 through 439 or (resid 440 and (na \ me N or name CA or name C or name O or name CB )) or resid 441 or (resid 442 and \ (name N or name CA or name C or name O or name CB )) or resid 443 through 444 o \ r (resid 445 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 46 through 451 or (resid 452 through 453 and (name N or name CA or name C or nam \ e O or name CB )) or resid 454 through 462 or (resid 463 and (name N or name CA \ or name C or name O or name CB )) or resid 464 through 468 or (resid 469 and (na \ me N or name CA or name C or name O or name CB )) or resid 470 through 471 or (r \ esid 472 and (name N or name CA or name C or name O or name CB )) or resid 473 o \ r (resid 474 through 477 and (name N or name CA or name C or name O or name CB ) \ ) or resid 478 through 485 or (resid 486 through 487 and (name N or name CA or n \ ame C or name O or name CB )) or resid 488 or (resid 489 through 490 and (name N \ or name CA or name C or name O or name CB )) or resid 491 or (resid 492 through \ 496 and (name N or name CA or name C or name O or name CB )) or resid 497 throu \ gh 501 or (resid 502 through 504 and (name N or name CA or name C or name O or n \ ame CB )) or resid 505 or (resid 506 through 508 and (name N or name CA or name \ C or name O or name CB )) or resid 509 through 510 or (resid 511 through 512 and \ (name N or name CA or name C or name O or name CB )) or resid 513 through 520 o \ r (resid 521 through 522 and (name N or name CA or name C or name O or name CB ) \ ) or resid 523 through 527 or (resid 528 through 532 and (name N or name CA or n \ ame C or name O or name CB )) or resid 533 through 536 or (resid 537 and (name N \ or name CA or name C or name O or name CB )) or resid 538 or (resid 539 through \ 541 and (name N or name CA or name C or name O or name CB )) or resid 542 throu \ gh 544 or (resid 545 and (name N or name CA or name C or name O or name CB )) or \ resid 546 through 547 or (resid 548 and (name N or name CA or name C or name O \ or name CB )) or resid 549 through 551 or (resid 552 and (name N or name CA or n \ ame C or name O or name CB )) or resid 553 through 557 or (resid 558 through 560 \ and (name N or name CA or name C or name O or name CB )) or resid 561 through 5 \ 62 or (resid 563 and (name N or name CA or name C or name O or name CB )) or res \ id 564 through 569 or (resid 570 through 572 and (name N or name CA or name C or \ name O or name CB )) or resid 573 through 575 or (resid 576 and (name N or name \ CA or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or \ name CA or name C or name O or name CB )) or resid 579 through 581 or (resid 582 \ through 584 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 85 through 590 or (resid 591 through 593 and (name N or name CA or name C or nam \ e O or name CB )) or resid 594)) selection = (chain 'B' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 11 or (resid 12 through 14 and (name N \ or name CA or name C or name O or name CB )) or (resid 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 or (resid 31 through 33 and (nam \ e N or name CA or name C or name O or name CB )) or resid 34 through 35 or (resi \ d 36 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 through 41 or (resid 42 through 43 and (name N or name CA or name C or name \ O or name CB )) or resid 44 through 45 or (resid 46 through 47 and (name N or n \ ame CA or name C or name O or name CB )) or resid 48 through 50 or (resid 51 and \ (name N or name CA or name C or name O or name CB )) or resid 52 or (resid 53 a \ nd (name N or name CA or name C or name O or name CB )) or resid 54 through 55 o \ r (resid 56 through 58 and (name N or name CA or name C or name O or name CB )) \ or resid 59 through 64 or (resid 65 through 67 and (name N or name CA or name C \ or name O or name CB )) or resid 68 through 71 or (resid 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 through 75 or (resid 76 through \ 77 and (name N or name CA or name C or name O or name CB )) or resid 78 or (res \ id 79 through 81 and (name N or name CA or name C or name O or name CB )) or res \ id 82 through 84 or (resid 85 through 91 and (name N or name CA or name C or nam \ e O or name CB )) or resid 92 through 94 or (resid 95 through 97 and (name N or \ name CA or name C or name O or name CB )) or resid 98 or (resid 99 and (name N o \ r name CA or name C or name O or name CB )) or resid 100 or (resid 101 and (name \ N or name CA or name C or name O or name CB )) or resid 102 or (resid 103 throu \ gh 104 and (name N or name CA or name C or name O or name CB )) or resid 105 or \ (resid 106 through 107 and (name N or name CA or name C or name O or name CB )) \ or resid 108 through 110 or (resid 111 and (name N or name CA or name C or name \ O or name CB )) or resid 112 through 114 or (resid 115 and (name N or name CA or \ name C or name O or name CB )) or resid 116 through 117 or (resid 118 and (name \ N or name CA or name C or name O or name CB )) or resid 119 through 131 or (res \ id 132 through 133 and (name N or name CA or name C or name O or name CB )) or r \ esid 134 through 136 or (resid 137 and (name N or name CA or name C or name O or \ name CB )) or resid 138 or (resid 139 and (name N or name CA or name C or name \ O or name CB )) or resid 140 or (resid 141 and (name N or name CA or name C or n \ ame O or name CB )) or resid 142 through 144 or (resid 145 and (name N or name C \ A or name C or name O or name CB )) or resid 146 or (resid 147 and (name N or na \ me CA or name C or name O or name CB )) or resid 148 or (resid 149 and (name N o \ r name CA or name C or name O or name CB )) or resid 150 or (resid 151 through 1 \ 52 and (name N or name CA or name C or name O or name CB )) or resid 153 through \ 154 or (resid 155 through 157 and (name N or name CA or name C or name O or nam \ e CB )) or resid 158 through 161 or (resid 162 and (name N or name CA or name C \ or name O or name CB )) or resid 163 or (resid 164 through 165 and (name N or na \ me CA or name C or name O or name CB )) or resid 166 through 170 or (resid 171 t \ hrough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 and (name N or name CA or name C or name O or name CB )) or resid \ 175 through 178 or (resid 179 and (name N or name CA or name C or name O or nam \ e CB )) or resid 180 through 189 or (resid 190 and (name N or name CA or name C \ or name O or name CB )) or resid 191 through 192 or (resid 193 and (name N or na \ me CA or name C or name O or name CB )) or resid 194 through 201 or (resid 202 a \ nd (name N or name CA or name C or name O or name CB )) or resid 203 or (resid 2 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 205 through \ 211 or (resid 212 and (name N or name CA or name C or name O or name CB )) or r \ esid 213 through 230 or (resid 231 and (name N or name CA or name C or name O or \ name CB )) or resid 232 through 236 or (resid 237 through 238 and (name N or na \ me CA or name C or name O or name CB )) or resid 239 through 240 or (resid 241 a \ nd (name N or name CA or name C or name O or name CB )) or resid 242 through 245 \ or (resid 246 and (name N or name CA or name C or name O or name CB )) or resid \ 247 through 249 or (resid 250 and (name N or name CA or name C or name O or nam \ e CB )) or resid 251 through 254 or (resid 255 through 257 and (name N or name C \ A or name C or name O or name CB )) or resid 258 or (resid 259 and (name N or na \ me CA or name C or name O or name CB )) or resid 260 or (resid 261 through 262 a \ nd (name N or name CA or name C or name O or name CB )) or resid 263 through 264 \ or (resid 265 and (name N or name CA or name C or name O or name CB )) or resid \ 266 through 267 or (resid 268 through 269 and (name N or name CA or name C or n \ ame O or name CB )) or resid 270 or (resid 271 and (name N or name CA or name C \ or name O or name CB )) or resid 272 through 274 or (resid 275 through 277 and ( \ name N or name CA or name C or name O or name CB )) or resid 278 or (resid 279 a \ nd (name N or name CA or name C or name O or name CB )) or resid 280 through 284 \ or (resid 285 and (name N or name CA or name C or name O or name CB )) or resid \ 286 through 291 or (resid 292 and (name N or name CA or name C or name O or nam \ e CB )) or resid 293 through 296 or (resid 297 through 298 and (name N or name C \ A or name C or name O or name CB )) or resid 299 through 310 or (resid 311 and ( \ name N or name CA or name C or name O or name CB )) or resid 312 or (resid 313 a \ nd (name N or name CA or name C or name O or name CB )) or resid 314 or (resid 3 \ 15 and (name N or name CA or name C or name O or name CB )) or resid 316 or (res \ id 317 through 320 and (name N or name CA or name C or name O or name CB )) or r \ esid 321 through 325 or (resid 326 and (name N or name CA or name C or name O or \ name CB )) or resid 327 or (resid 328 and (name N or name CA or name C or name \ O or name CB )) or resid 329 through 337 or (resid 338 and (name N or name CA or \ name C or name O or name CB )) or resid 339 or (resid 340 and (name N or name C \ A or name C or name O or name CB )) or resid 341 through 343 or (resid 344 and ( \ name N or name CA or name C or name O or name CB )) or resid 345 through 350 or \ (resid 351 and (name N or name CA or name C or name O or name CB )) or resid 352 \ through 355 or (resid 356 and (name N or name CA or name C or name O or name CB \ )) or resid 357 through 361 or (resid 362 through 366 and (name N or name CA or \ name C or name O or name CB )) or resid 367 or (resid 368 through 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 and ( \ name N or name CA or name C or name O or name CB )) or resid 372 through 374 or \ (resid 375 through 376 and (name N or name CA or name C or name O or name CB )) \ or resid 377 through 390 or (resid 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 393 or (resid 394 through 395 and (name N o \ r name CA or name C or name O or name CB )) or resid 396 or (resid 397 and (name \ N or name CA or name C or name O or name CB )) or resid 398 through 402 or (res \ id 403 and (name N or name CA or name C or name O or name CB )) or resid 404 thr \ ough 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) \ or resid 414 or (resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 or (resid 417 and (name N or name CA or name C or name O or nam \ e CB )) or resid 418 through 424 or (resid 425 through 426 and (name N or name C \ A or name C or name O or name CB )) or resid 427 through 429 or (resid 430 and ( \ name N or name CA or name C or name O or name CB )) or resid 431 through 439 or \ (resid 440 and (name N or name CA or name C or name O or name CB )) or resid 441 \ or (resid 442 and (name N or name CA or name C or name O or name CB )) or resid \ 443 through 444 or (resid 445 and (name N or name CA or name C or name O or nam \ e CB )) or resid 446 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 451 or (resid 452 through 453 and ( \ name N or name CA or name C or name O or name CB )) or resid 454 through 462 or \ (resid 463 and (name N or name CA or name C or name O or name CB )) or resid 464 \ through 468 or (resid 469 and (name N or name CA or name C or name O or name CB \ )) or resid 470 through 471 or (resid 472 and (name N or name CA or name C or n \ ame O or name CB )) or resid 473 or (resid 474 through 477 and (name N or name C \ A or name C or name O or name CB )) or resid 478 through 485 or (resid 486 throu \ gh 487 and (name N or name CA or name C or name O or name CB )) or resid 488 or \ (resid 489 through 490 and (name N or name CA or name C or name O or name CB )) \ or resid 491 or (resid 492 through 496 and (name N or name CA or name C or name \ O or name CB )) or resid 497 through 498 or (resid 499 and (name N or name CA or \ name C or name O or name CB )) or resid 500 through 501 or (resid 502 through 5 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 505 or (res \ id 506 through 508 and (name N or name CA or name C or name O or name CB )) or r \ esid 509 through 510 or (resid 511 through 512 and (name N or name CA or name C \ or name O or name CB )) or resid 513 through 520 or (resid 521 through 522 and ( \ name N or name CA or name C or name O or name CB )) or resid 523 through 524 or \ (resid 525 and (name N or name CA or name C or name O or name CB )) or resid 526 \ through 527 or (resid 528 through 532 and (name N or name CA or name C or name \ O or name CB )) or resid 533 or (resid 534 and (name N or name CA or name C or n \ ame O or name CB )) or resid 535 through 536 or (resid 537 and (name N or name C \ A or name C or name O or name CB )) or resid 538 or (resid 539 through 541 and ( \ name N or name CA or name C or name O or name CB )) or resid 542 through 544 or \ (resid 545 and (name N or name CA or name C or name O or name CB )) or resid 546 \ through 547 or (resid 548 and (name N or name CA or name C or name O or name CB \ )) or resid 549 through 551 or (resid 552 and (name N or name CA or name C or n \ ame O or name CB )) or resid 553 through 557 or (resid 558 through 560 and (name \ N or name CA or name C or name O or name CB )) or resid 561 through 562 or (res \ id 563 and (name N or name CA or name C or name O or name CB )) or resid 564 thr \ ough 569 or (resid 570 through 572 and (name N or name CA or name C or name O or \ name CB )) or resid 573 through 575 or (resid 576 and (name N or name CA or nam \ e C or name O or name CB )) or resid 577 or (resid 578 and (name N or name CA or \ name C or name O or name CB )) or resid 579 through 581 or (resid 582 through 5 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 585 through \ 590 or (resid 591 through 593 and (name N or name CA or name C or name O or nam \ e CB )) or resid 594)) selection = (chain 'C' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 11 or (resid 12 through 14 and (name N \ or name CA or name C or name O or name CB )) or (resid 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 or (resid 31 through 33 and (nam \ e N or name CA or name C or name O or name CB )) or resid 34 through 35 or (resi \ d 36 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 and (name N or name CA or name C or name O or name CB )) or re \ sid 40 through 41 or (resid 42 through 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 45 or (resid 46 through 47 and (name N or \ name CA or name C or name O or name CB )) or resid 48 through 50 or (resid 51 a \ nd (name N or name CA or name C or name O or name CB )) or resid 52 or (resid 53 \ and (name N or name CA or name C or name O or name CB )) or resid 54 through 55 \ or (resid 56 through 58 and (name N or name CA or name C or name O or name CB ) \ ) or resid 59 through 64 or (resid 65 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 75 or (resid 76 throu \ gh 77 and (name N or name CA or name C or name O or name CB )) or resid 78 or (r \ esid 79 through 81 and (name N or name CA or name C or name O or name CB )) or r \ esid 82 through 84 or (resid 85 through 91 and (name N or name CA or name C or n \ ame O or name CB )) or resid 92 through 94 or (resid 95 through 97 and (name N o \ r name CA or name C or name O or name CB )) or resid 98 or (resid 99 and (name N \ or name CA or name C or name O or name CB )) or resid 100 or (resid 101 and (na \ me N or name CA or name C or name O or name CB )) or resid 102 or (resid 103 thr \ ough 104 and (name N or name CA or name C or name O or name CB )) or resid 105 o \ r (resid 106 through 107 and (name N or name CA or name C or name O or name CB ) \ ) or resid 108 through 110 or (resid 111 and (name N or name CA or name C or nam \ e O or name CB )) or resid 112 through 114 or (resid 115 and (name N or name CA \ or name C or name O or name CB )) or resid 116 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 127 or (r \ esid 128 and (name N or name CA or name C or name O or name CB )) or resid 129 t \ hrough 131 or (resid 132 through 133 and (name N or name CA or name C or name O \ or name CB )) or resid 134 through 136 or (resid 137 and (name N or name CA or n \ ame C or name O or name CB )) or resid 138 or (resid 139 and (name N or name CA \ or name C or name O or name CB )) or resid 140 through 144 or (resid 145 and (na \ me N or name CA or name C or name O or name CB )) or resid 146 or (resid 147 and \ (name N or name CA or name C or name O or name CB )) or resid 148 or (resid 149 \ and (name N or name CA or name C or name O or name CB )) or resid 150 or (resid \ 151 through 152 and (name N or name CA or name C or name O or name CB )) or res \ id 153 through 154 or (resid 155 through 157 and (name N or name CA or name C or \ name O or name CB )) or resid 158 through 161 or (resid 162 and (name N or name \ CA or name C or name O or name CB )) or resid 163 or (resid 164 through 165 and \ (name N or name CA or name C or name O or name CB )) or resid 166 through 168 o \ r (resid 169 through 172 and (name N or name CA or name C or name O or name CB ) \ ) or resid 173 or (resid 174 and (name N or name CA or name C or name O or name \ CB )) or resid 175 through 176 or (resid 177 and (name N or name CA or name C or \ name O or name CB )) or resid 178 or (resid 179 and (name N or name CA or name \ C or name O or name CB )) or resid 180 through 189 or (resid 190 and (name N or \ name CA or name C or name O or name CB )) or resid 191 through 192 or (resid 193 \ and (name N or name CA or name C or name O or name CB )) or resid 194 through 1 \ 95 or (resid 196 and (name N or name CA or name C or name O or name CB )) or res \ id 197 through 201 or (resid 202 and (name N or name CA or name C or name O or n \ ame CB )) or resid 203 or (resid 204 and (name N or name CA or name C or name O \ or name CB )) or resid 205 through 211 or (resid 212 and (name N or name CA or n \ ame C or name O or name CB )) or resid 213 through 230 or (resid 231 and (name N \ or name CA or name C or name O or name CB )) or resid 232 through 233 or (resid \ 234 through 238 and (name N or name CA or name C or name O or name CB )) or res \ id 239 or (resid 240 through 241 and (name N or name CA or name C or name O or n \ ame CB )) or resid 242 through 245 or (resid 246 and (name N or name CA or name \ C or name O or name CB )) or resid 247 through 249 or (resid 250 and (name N or \ name CA or name C or name O or name CB )) or resid 251 through 254 or (resid 255 \ through 257 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 58 or (resid 259 and (name N or name CA or name C or name O or name CB )) or res \ id 260 or (resid 261 through 262 and (name N or name CA or name C or name O or n \ ame CB )) or resid 263 through 264 or (resid 265 and (name N or name CA or name \ C or name O or name CB )) or resid 266 through 267 or (resid 268 through 269 and \ (name N or name CA or name C or name O or name CB )) or resid 270 or (resid 271 \ and (name N or name CA or name C or name O or name CB )) or resid 272 through 2 \ 74 or (resid 275 through 277 and (name N or name CA or name C or name O or name \ CB )) or resid 278 or (resid 279 and (name N or name CA or name C or name O or n \ ame CB )) or resid 280 through 284 or (resid 285 and (name N or name CA or name \ C or name O or name CB )) or resid 286 through 291 or (resid 292 and (name N or \ name CA or name C or name O or name CB )) or resid 293 through 296 or (resid 297 \ through 298 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 99 through 310 or (resid 311 and (name N or name CA or name C or name O or name \ CB )) or resid 312 or (resid 313 and (name N or name CA or name C or name O or n \ ame CB )) or resid 314 or (resid 315 and (name N or name CA or name C or name O \ or name CB )) or resid 316 or (resid 317 through 320 and (name N or name CA or n \ ame C or name O or name CB )) or resid 321 through 325 or (resid 326 and (name N \ or name CA or name C or name O or name CB )) or resid 327 or (resid 328 and (na \ me N or name CA or name C or name O or name CB )) or resid 329 through 337 or (r \ esid 338 and (name N or name CA or name C or name O or name CB )) or resid 339 o \ r (resid 340 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 41 through 343 or (resid 344 and (name N or name CA or name C or name O or name \ CB )) or resid 345 through 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB )) or resid 352 through 355 or (resid 356 and (name N or name \ CA or name C or name O or name CB )) or resid 357 through 361 or (resid 362 thr \ ough 366 and (name N or name CA or name C or name O or name CB )) or resid 367 o \ r (resid 368 through 369 and (name N or name CA or name C or name O or name CB ) \ ) or resid 370 through 374 or (resid 375 through 376 and (name N or name CA or n \ ame C or name O or name CB )) or resid 377 through 390 or (resid 391 and (name N \ or name CA or name C or name O or name CB )) or resid 392 through 393 or (resid \ 394 through 395 and (name N or name CA or name C or name O or name CB )) or res \ id 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) or \ resid 398 through 402 or (resid 403 and (name N or name CA or name C or name O \ or name CB )) or resid 404 through 412 or (resid 413 and (name N or name CA or n \ ame C or name O or name CB )) or resid 414 or (resid 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 or (resid 417 and (name N or name \ CA or name C or name O or name CB )) or resid 418 or (resid 419 through 420 and \ (name N or name CA or name C or name O or name CB )) or resid 421 through 424 o \ r (resid 425 through 426 and (name N or name CA or name C or name O or name CB ) \ ) or resid 427 through 429 or (resid 430 and (name N or name CA or name C or nam \ e O or name CB )) or resid 431 through 439 or (resid 440 and (name N or name CA \ or name C or name O or name CB )) or resid 441 or (resid 442 and (name N or name \ CA or name C or name O or name CB )) or resid 443 through 444 or (resid 445 and \ (name N or name CA or name C or name O or name CB )) or resid 446 through 447 o \ r (resid 448 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 49 through 451 or (resid 452 through 453 and (name N or name CA or name C or nam \ e O or name CB )) or resid 454 through 462 or (resid 463 and (name N or name CA \ or name C or name O or name CB )) or resid 464 through 468 or (resid 469 and (na \ me N or name CA or name C or name O or name CB )) or resid 470 through 471 or (r \ esid 472 and (name N or name CA or name C or name O or name CB )) or resid 473 o \ r (resid 474 through 477 and (name N or name CA or name C or name O or name CB ) \ ) or resid 478 through 485 or (resid 486 through 487 and (name N or name CA or n \ ame C or name O or name CB )) or resid 488 or (resid 489 through 490 and (name N \ or name CA or name C or name O or name CB )) or resid 491 or (resid 492 through \ 496 and (name N or name CA or name C or name O or name CB )) or resid 497 throu \ gh 498 or (resid 499 and (name N or name CA or name C or name O or name CB )) or \ resid 500 through 501 or (resid 502 through 504 and (name N or name CA or name \ C or name O or name CB )) or resid 505 or (resid 506 through 508 and (name N or \ name CA or name C or name O or name CB )) or resid 509 through 510 or (resid 511 \ through 512 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 13 through 520 or (resid 521 through 522 and (name N or name CA or name C or nam \ e O or name CB )) or resid 523 through 524 or (resid 525 and (name N or name CA \ or name C or name O or name CB )) or resid 526 through 527 or (resid 528 through \ 532 and (name N or name CA or name C or name O or name CB )) or resid 533 or (r \ esid 534 and (name N or name CA or name C or name O or name CB )) or resid 535 t \ hrough 536 or (resid 537 and (name N or name CA or name C or name O or name CB ) \ ) or resid 538 or (resid 539 through 541 and (name N or name CA or name C or nam \ e O or name CB )) or resid 542 through 544 or (resid 545 and (name N or name CA \ or name C or name O or name CB )) or resid 546 through 547 or (resid 548 and (na \ me N or name CA or name C or name O or name CB )) or resid 549 through 551 or (r \ esid 552 and (name N or name CA or name C or name O or name CB )) or resid 553 t \ hrough 557 or (resid 558 through 560 and (name N or name CA or name C or name O \ or name CB )) or resid 561 through 562 or (resid 563 and (name N or name CA or n \ ame C or name O or name CB )) or resid 564 through 569 or (resid 570 through 572 \ and (name N or name CA or name C or name O or name CB )) or resid 573 through 5 \ 75 or (resid 576 and (name N or name CA or name C or name O or name CB )) or res \ id 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) or \ resid 579 through 581 or (resid 582 through 584 and (name N or name CA or name \ C or name O or name CB )) or resid 585 through 590 or (resid 591 through 593 and \ (name N or name CA or name C or name O or name CB )) or resid 594)) selection = (chain 'D' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 throu \ gh 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 41 or (resid 42 through 43 and (name N or name CA or name C or name O or name \ CB )) or resid 44 through 45 or (resid 46 through 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 50 or (resid 51 and (name N o \ r name CA or name C or name O or name CB )) or resid 52 through 55 or (resid 56 \ through 58 and (name N or name CA or name C or name O or name CB )) or resid 59 \ through 64 or (resid 65 through 67 and (name N or name CA or name C or name O or \ name CB )) or resid 68 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 75 or (resid 76 through 77 and (nam \ e N or name CA or name C or name O or name CB )) or resid 78 or (resid 79 throug \ h 81 and (name N or name CA or name C or name O or name CB )) or resid 82 throug \ h 85 or (resid 86 through 91 and (name N or name CA or name C or name O or name \ CB )) or resid 92 through 94 or (resid 95 through 97 and (name N or name CA or n \ ame C or name O or name CB )) or resid 98 or (resid 99 and (name N or name CA or \ name C or name O or name CB )) or resid 100 or (resid 101 and (name N or name C \ A or name C or name O or name CB )) or resid 102 or (resid 103 through 104 and ( \ name N or name CA or name C or name O or name CB )) or resid 105 or (resid 106 t \ hrough 107 and (name N or name CA or name C or name O or name CB )) or resid 108 \ through 110 or (resid 111 and (name N or name CA or name C or name O or name CB \ )) or resid 112 through 114 or (resid 115 and (name N or name CA or name C or n \ ame O or name CB )) or resid 116 through 117 or (resid 118 and (name N or name C \ A or name C or name O or name CB )) or resid 119 through 127 or (resid 128 and ( \ name N or name CA or name C or name O or name CB )) or resid 129 through 131 or \ (resid 132 through 133 and (name N or name CA or name C or name O or name CB )) \ or resid 134 through 136 or (resid 137 and (name N or name CA or name C or name \ O or name CB )) or resid 138 or (resid 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 or (resid 147 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 or (resid 149 and (name \ N or name CA or name C or name O or name CB )) or resid 150 or (resid 151 throu \ gh 152 and (name N or name CA or name C or name O or name CB )) or resid 153 thr \ ough 154 or (resid 155 through 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 or (resid 164 through 165 and (name N o \ r name CA or name C or name O or name CB )) or resid 166 through 168 or (resid 1 \ 69 through 172 and (name N or name CA or name C or name O or name CB )) or resid \ 173 or (resid 174 and (name N or name CA or name C or name O or name CB )) or r \ esid 175 through 176 or (resid 177 and (name N or name CA or name C or name O or \ name CB )) or resid 178 or (resid 179 and (name N or name CA or name C or name \ O or name CB )) or resid 180 through 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 192 or (resid 193 and (name \ N or name CA or name C or name O or name CB )) or resid 194 through 195 or (res \ id 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thr \ ough 199 or (resid 200 and (name N or name CA or name C or name O or name CB )) \ or resid 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 or (resid 204 and (name N or name CA or name C or name O or nam \ e CB )) or resid 205 through 211 or (resid 212 and (name N or name CA or name C \ or name O or name CB )) or resid 213 through 230 or (resid 231 and (name N or na \ me CA or name C or name O or name CB )) or resid 232 through 240 or (resid 241 a \ nd (name N or name CA or name C or name O or name CB )) or resid 242 through 245 \ or (resid 246 and (name N or name CA or name C or name O or name CB )) or resid \ 247 through 249 or (resid 250 and (name N or name CA or name C or name O or nam \ e CB )) or resid 251 through 254 or (resid 255 through 257 and (name N or name C \ A or name C or name O or name CB )) or resid 258 through 260 or (resid 261 throu \ gh 262 and (name N or name CA or name C or name O or name CB )) or resid 263 thr \ ough 264 or (resid 265 and (name N or name CA or name C or name O or name CB )) \ or resid 266 through 267 or (resid 268 through 269 and (name N or name CA or nam \ e C or name O or name CB )) or resid 270 or (resid 271 and (name N or name CA or \ name C or name O or name CB )) or resid 272 through 274 or (resid 275 through 2 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 278 or (res \ id 279 and (name N or name CA or name C or name O or name CB )) or resid 280 thr \ ough 284 or (resid 285 and (name N or name CA or name C or name O or name CB )) \ or resid 286 through 291 or (resid 292 and (name N or name CA or name C or name \ O or name CB )) or resid 293 through 296 or (resid 297 through 298 and (name N o \ r name CA or name C or name O or name CB )) or resid 299 through 312 or (resid 3 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 314 or (res \ id 315 and (name N or name CA or name C or name O or name CB )) or resid 316 or \ (resid 317 through 320 and (name N or name CA or name C or name O or name CB )) \ or resid 321 through 325 or (resid 326 and (name N or name CA or name C or name \ O or name CB )) or resid 327 or (resid 328 and (name N or name CA or name C or n \ ame O or name CB )) or resid 329 through 337 or (resid 338 and (name N or name C \ A or name C or name O or name CB )) or resid 339 or (resid 340 and (name N or na \ me CA or name C or name O or name CB )) or resid 341 through 343 or (resid 344 a \ nd (name N or name CA or name C or name O or name CB )) or resid 345 through 350 \ or (resid 351 and (name N or name CA or name C or name O or name CB )) or resid \ 352 through 355 or (resid 356 and (name N or name CA or name C or name O or nam \ e CB )) or resid 357 through 361 or (resid 362 through 366 and (name N or name C \ A or name C or name O or name CB )) or resid 367 through 368 or (resid 369 and ( \ name N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 a \ nd (name N or name CA or name C or name O or name CB )) or resid 372 through 374 \ or (resid 375 through 376 and (name N or name CA or name C or name O or name CB \ )) or resid 377 through 390 or (resid 391 and (name N or name CA or name C or n \ ame O or name CB )) or resid 392 through 393 or (resid 394 through 395 and (name \ N or name CA or name C or name O or name CB )) or resid 396 or (resid 397 and ( \ name N or name CA or name C or name O or name CB )) or resid 398 through 402 or \ (resid 403 and (name N or name CA or name C or name O or name CB )) or resid 404 \ through 412 or (resid 413 and (name N or name CA or name C or name O or name CB \ )) or resid 414 or (resid 415 and (name N or name CA or name C or name O or nam \ e CB )) or resid 416 or (resid 417 and (name N or name CA or name C or name O or \ name CB )) or resid 418 through 424 or (resid 425 through 426 and (name N or na \ me CA or name C or name O or name CB )) or resid 427 through 429 or (resid 430 a \ nd (name N or name CA or name C or name O or name CB )) or resid 431 through 439 \ or (resid 440 and (name N or name CA or name C or name O or name CB )) or resid \ 441 through 444 or (resid 445 and (name N or name CA or name C or name O or nam \ e CB )) or resid 446 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 451 or (resid 452 through 453 and ( \ name N or name CA or name C or name O or name CB )) or resid 454 through 462 or \ (resid 463 and (name N or name CA or name C or name O or name CB )) or resid 464 \ through 468 or (resid 469 and (name N or name CA or name C or name O or name CB \ )) or resid 470 through 473 or (resid 474 through 477 and (name N or name CA or \ name C or name O or name CB )) or resid 478 through 485 or (resid 486 through 4 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 488 through \ 489 or (resid 490 and (name N or name CA or name C or name O or name CB )) or r \ esid 491 or (resid 492 through 496 and (name N or name CA or name C or name O or \ name CB )) or resid 497 through 498 or (resid 499 and (name N or name CA or nam \ e C or name O or name CB )) or resid 500 through 501 or (resid 502 through 504 a \ nd (name N or name CA or name C or name O or name CB )) or resid 505 or (resid 5 \ 06 through 508 and (name N or name CA or name C or name O or name CB )) or resid \ 509 through 510 or (resid 511 through 512 and (name N or name CA or name C or n \ ame O or name CB )) or resid 513 through 520 or (resid 521 through 522 and (name \ N or name CA or name C or name O or name CB )) or resid 523 through 524 or (res \ id 525 and (name N or name CA or name C or name O or name CB )) or resid 526 thr \ ough 527 or (resid 528 through 532 and (name N or name CA or name C or name O or \ name CB )) or resid 533 or (resid 534 and (name N or name CA or name C or name \ O or name CB )) or resid 535 through 536 or (resid 537 and (name N or name CA or \ name C or name O or name CB )) or resid 538 or (resid 539 through 541 and (name \ N or name CA or name C or name O or name CB )) or resid 542 through 544 or (res \ id 545 and (name N or name CA or name C or name O or name CB )) or resid 546 thr \ ough 547 or (resid 548 and (name N or name CA or name C or name O or name CB )) \ or resid 549 through 551 or (resid 552 and (name N or name CA or name C or name \ O or name CB )) or resid 553 through 557 or (resid 558 through 560 and (name N o \ r name CA or name C or name O or name CB )) or resid 561 through 562 or (resid 5 \ 63 and (name N or name CA or name C or name O or name CB )) or resid 564 through \ 569 or (resid 570 through 572 and (name N or name CA or name C or name O or nam \ e CB )) or resid 573 through 575 or (resid 576 and (name N or name CA or name C \ or name O or name CB )) or resid 577 or (resid 578 and (name N or name CA or nam \ e C or name O or name CB )) or resid 579 through 581 or (resid 582 through 584 a \ nd (name N or name CA or name C or name O or name CB )) or resid 585 through 590 \ or (resid 591 through 593 and (name N or name CA or name C or name O or name CB \ )) or resid 594)) selection = (chain 'E' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 12 or (resid 13 through 29 and (name N \ or name CA or name C or name O or name CB )) or resid 30 through 31 or (resid 3 \ 2 through 33 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 4 through 36 or (resid 37 and (name N or name CA or name C or name O or name CB \ )) or resid 38 through 41 or (resid 42 through 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 52 or (resid 53 and (name N or na \ me CA or name C or name O or name CB )) or resid 54 through 55 or (resid 56 thro \ ugh 58 and (name N or name CA or name C or name O or name CB )) or resid 59 thro \ ugh 71 or (resid 72 and (name N or name CA or name C or name O or name CB )) or \ resid 73 through 76 or (resid 77 and (name N or name CA or name C or name O or n \ ame CB )) or resid 78 through 79 or (resid 80 through 81 and (name N or name CA \ or name C or name O or name CB )) or resid 82 through 84 or (resid 85 through 91 \ and (name N or name CA or name C or name O or name CB )) or resid 92 through 95 \ or (resid 96 through 97 and (name N or name CA or name C or name O or name CB ) \ ) or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ )) or resid 100 or (resid 101 and (name N or name CA or name C or name O or nam \ e CB )) or resid 102 or (resid 103 through 104 and (name N or name CA or name C \ or name O or name CB )) or resid 105 through 114 or (resid 115 and (name N or na \ me CA or name C or name O or name CB )) or resid 116 through 117 or (resid 118 a \ nd (name N or name CA or name C or name O or name CB )) or resid 119 through 131 \ or (resid 132 through 133 and (name N or name CA or name C or name O or name CB \ )) or resid 134 through 136 or (resid 137 and (name N or name CA or name C or n \ ame O or name CB )) or resid 138 or (resid 139 and (name N or name CA or name C \ or name O or name CB )) or resid 140 or (resid 141 and (name N or name CA or nam \ e C or name O or name CB )) or resid 142 through 148 or (resid 149 and (name N o \ r name CA or name C or name O or name CB )) or resid 150 or (resid 151 through 1 \ 52 and (name N or name CA or name C or name O or name CB )) or resid 153 through \ 154 or (resid 155 through 157 and (name N or name CA or name C or name O or nam \ e CB )) or resid 158 through 161 or (resid 162 and (name N or name CA or name C \ or name O or name CB )) or resid 163 through 169 or (resid 170 through 172 and ( \ name N or name CA or name C or name O or name CB )) or resid 173 or (resid 174 a \ nd (name N or name CA or name C or name O or name CB )) or resid 175 through 176 \ or (resid 177 and (name N or name CA or name C or name O or name CB )) or resid \ 178 or (resid 179 and (name N or name CA or name C or name O or name CB )) or r \ esid 180 through 195 or (resid 196 and (name N or name CA or name C or name O or \ name CB )) or resid 197 through 201 or (resid 202 and (name N or name CA or nam \ e C or name O or name CB )) or resid 203 through 211 or (resid 212 and (name N o \ r name CA or name C or name O or name CB )) or resid 213 through 230 or (resid 2 \ 31 and (name N or name CA or name C or name O or name CB )) or resid 232 through \ 233 or (resid 234 through 238 and (name N or name CA or name C or name O or nam \ e CB )) or resid 239 through 245 or (resid 246 and (name N or name CA or name C \ or name O or name CB )) or resid 247 through 249 or (resid 250 and (name N or na \ me CA or name C or name O or name CB )) or resid 251 through 256 or (resid 257 a \ nd (name N or name CA or name C or name O or name CB )) or resid 258 or (resid 2 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 267 or (resid 268 through 269 and (name N or name CA or name C or name O or nam \ e CB )) or resid 270 through 278 or (resid 279 and (name N or name CA or name C \ or name O or name CB )) or resid 280 through 310 or (resid 311 and (name N or na \ me CA or name C or name O or name CB )) or resid 312 through 319 or (resid 320 a \ nd (name N or name CA or name C or name O or name CB )) or resid 321 through 327 \ or (resid 328 and (name N or name CA or name C or name O or name CB )) or resid \ 329 through 337 or (resid 338 and (name N or name CA or name C or name O or nam \ e CB )) or resid 339 or (resid 340 and (name N or name CA or name C or name O or \ name CB )) or resid 341 through 350 or (resid 351 and (name N or name CA or nam \ e C or name O or name CB )) or resid 352 through 355 or (resid 356 and (name N o \ r name CA or name C or name O or name CB )) or resid 357 through 361 or (resid 3 \ 62 through 366 and (name N or name CA or name C or name O or name CB )) or resid \ 367 through 368 or (resid 369 and (name N or name CA or name C or name O or nam \ e CB )) or resid 370 or (resid 371 and (name N or name CA or name C or name O or \ name CB )) or resid 372 through 390 or (resid 391 and (name N or name CA or nam \ e C or name O or name CB )) or resid 392 through 393 or (resid 394 through 395 a \ nd (name N or name CA or name C or name O or name CB )) or resid 396 through 402 \ or (resid 403 and (name N or name CA or name C or name O or name CB )) or resid \ 404 through 412 or (resid 413 and (name N or name CA or name C or name O or nam \ e CB )) or resid 414 or (resid 415 and (name N or name CA or name C or name O or \ name CB )) or resid 416 or (resid 417 and (name N or name CA or name C or name \ O or name CB )) or resid 418 through 424 or (resid 425 through 426 and (name N o \ r name CA or name C or name O or name CB )) or resid 427 through 439 or (resid 4 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 441 or (res \ id 442 and (name N or name CA or name C or name O or name CB )) or resid 443 thr \ ough 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) \ or resid 446 through 447 or (resid 448 and (name N or name CA or name C or name \ O or name CB )) or resid 449 through 451 or (resid 452 through 453 and (name N o \ r name CA or name C or name O or name CB )) or resid 454 through 462 or (resid 4 \ 63 and (name N or name CA or name C or name O or name CB )) or resid 464 through \ 471 or (resid 472 and (name N or name CA or name C or name O or name CB )) or r \ esid 473 through 474 or (resid 475 through 477 and (name N or name CA or name C \ or name O or name CB )) or resid 478 through 485 or (resid 486 through 487 and ( \ name N or name CA or name C or name O or name CB )) or resid 488 or (resid 489 t \ hrough 490 and (name N or name CA or name C or name O or name CB )) or resid 491 \ or (resid 492 through 496 and (name N or name CA or name C or name O or name CB \ )) or resid 497 through 498 or (resid 499 and (name N or name CA or name C or n \ ame O or name CB )) or resid 500 through 501 or (resid 502 through 504 and (name \ N or name CA or name C or name O or name CB )) or resid 505 through 506 or (res \ id 507 through 508 and (name N or name CA or name C or name O or name CB )) or r \ esid 509 through 520 or (resid 521 through 522 and (name N or name CA or name C \ or name O or name CB )) or resid 523 through 524 or (resid 525 and (name N or na \ me CA or name C or name O or name CB )) or resid 526 through 527 or (resid 528 t \ hrough 532 and (name N or name CA or name C or name O or name CB )) or resid 533 \ or (resid 534 and (name N or name CA or name C or name O or name CB )) or resid \ 535 through 536 or (resid 537 and (name N or name CA or name C or name O or nam \ e CB )) or resid 538 or (resid 539 through 541 and (name N or name CA or name C \ or name O or name CB )) or resid 542 through 544 or (resid 545 and (name N or na \ me CA or name C or name O or name CB )) or resid 546 through 551 or (resid 552 a \ nd (name N or name CA or name C or name O or name CB )) or resid 553 through 557 \ or (resid 558 through 560 and (name N or name CA or name C or name O or name CB \ )) or resid 561 through 562 or (resid 563 and (name N or name CA or name C or n \ ame O or name CB )) or resid 564 through 569 or (resid 570 through 572 and (name \ N or name CA or name C or name O or name CB )) or resid 573 through 575 or (res \ id 576 and (name N or name CA or name C or name O or name CB )) or resid 577 thr \ ough 581 or (resid 582 through 584 and (name N or name CA or name C or name O or \ name CB )) or resid 585 through 591 or (resid 592 through 593 and (name N or na \ me CA or name C or name O or name CB )) or resid 594)) selection = (chain 'F' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 13 or (resid 14 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 31 or (resid 32 through 3 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 34 through 3 \ 5 or (resid 36 through 37 and (name N or name CA or name C or name O or name CB \ )) or resid 38 through 45 or (resid 46 through 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 50 or (resid 51 and (name N or na \ me CA or name C or name O or name CB )) or resid 52 or (resid 53 and (name N or \ name CA or name C or name O or name CB )) or resid 54 through 64 or (resid 65 th \ rough 67 and (name N or name CA or name C or name O or name CB )) or resid 68 th \ rough 75 or (resid 76 through 77 and (name N or name CA or name C or name O or n \ ame CB )) or resid 78 or (resid 79 through 81 and (name N or name CA or name C o \ r name O or name CB )) or resid 82 through 85 or (resid 86 through 91 and (name \ N or name CA or name C or name O or name CB )) or resid 92 through 103 or (resid \ 104 and (name N or name CA or name C or name O or name CB )) or resid 105 or (r \ esid 106 through 107 and (name N or name CA or name C or name O or name CB )) or \ resid 108 through 110 or (resid 111 and (name N or name CA or name C or name O \ or name CB )) or resid 112 through 127 or (resid 128 and (name N or name CA or n \ ame C or name O or name CB )) or resid 129 through 132 or (resid 133 and (name N \ or name CA or name C or name O or name CB )) or resid 134 through 138 or (resid \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 or (r \ esid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 t \ hrough 146 or (resid 147 and (name N or name CA or name C or name O or name CB ) \ ) or resid 148 or (resid 149 and (name N or name CA or name C or name O or name \ CB )) or resid 150 through 163 or (resid 164 through 165 and (name N or name CA \ or name C or name O or name CB )) or resid 166 through 169 or (resid 170 through \ 172 and (name N or name CA or name C or name O or name CB )) or resid 173 throu \ gh 176 or (resid 177 and (name N or name CA or name C or name O or name CB )) or \ resid 178 or (resid 179 and (name N or name CA or name C or name O or name CB ) \ ) or resid 180 through 189 or (resid 190 and (name N or name CA or name C or nam \ e O or name CB )) or resid 191 through 195 or (resid 196 and (name N or name CA \ or name C or name O or name CB )) or resid 197 through 201 or (resid 202 and (na \ me N or name CA or name C or name O or name CB )) or resid 203 or (resid 204 and \ (name N or name CA or name C or name O or name CB )) or resid 205 through 233 o \ r (resid 234 through 238 and (name N or name CA or name C or name O or name CB ) \ ) or resid 239 or (resid 240 through 241 and (name N or name CA or name C or nam \ e O or name CB )) or resid 242 through 245 or (resid 246 and (name N or name CA \ or name C or name O or name CB )) or resid 247 through 254 or (resid 255 through \ 257 and (name N or name CA or name C or name O or name CB )) or resid 258 or (r \ esid 259 and (name N or name CA or name C or name O or name CB )) or resid 260 o \ r (resid 261 through 262 and (name N or name CA or name C or name O or name CB ) \ ) or resid 263 through 264 or (resid 265 and (name N or name CA or name C or nam \ e O or name CB )) or resid 266 through 274 or (resid 275 through 277 and (name N \ or name CA or name C or name O or name CB )) or resid 278 through 284 or (resid \ 285 and (name N or name CA or name C or name O or name CB )) or resid 286 throu \ gh 291 or (resid 292 and (name N or name CA or name C or name O or name CB )) or \ resid 293 through 296 or (resid 297 through 298 and (name N or name CA or name \ C or name O or name CB )) or resid 299 through 310 or (resid 311 and (name N or \ name CA or name C or name O or name CB )) or resid 312 or (resid 313 and (name N \ or name CA or name C or name O or name CB )) or resid 314 through 318 or (resid \ 319 through 320 and (name N or name CA or name C or name O or name CB )) or res \ id 321 through 343 or (resid 344 and (name N or name CA or name C or name O or n \ ame CB )) or resid 345 through 362 or (resid 363 through 366 and (name N or name \ CA or name C or name O or name CB )) or resid 367 through 368 or (resid 369 and \ (name N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 \ and (name N or name CA or name C or name O or name CB )) or resid 372 through 3 \ 74 or (resid 375 through 376 and (name N or name CA or name C or name O or name \ CB )) or resid 377 through 412 or (resid 413 and (name N or name CA or name C or \ name O or name CB )) or resid 414 through 429 or (resid 430 and (name N or name \ CA or name C or name O or name CB )) or resid 431 through 441 or (resid 442 and \ (name N or name CA or name C or name O or name CB )) or resid 443 through 447 o \ r (resid 448 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 49 through 468 or (resid 469 and (name N or name CA or name C or name O or name \ CB )) or resid 470 through 471 or (resid 472 and (name N or name CA or name C or \ name O or name CB )) or resid 473 or (resid 474 through 477 and (name N or name \ CA or name C or name O or name CB )) or resid 478 through 495 or (resid 496 and \ (name N or name CA or name C or name O or name CB )) or resid 497 through 498 o \ r (resid 499 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 00 through 502 or (resid 503 through 504 and (name N or name CA or name C or nam \ e O or name CB )) or resid 505 or (resid 506 through 508 and (name N or name CA \ or name C or name O or name CB )) or resid 509 through 510 or (resid 511 through \ 512 and (name N or name CA or name C or name O or name CB )) or resid 513 throu \ gh 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) or \ resid 523 through 529 or (resid 530 through 532 and (name N or name CA or name \ C or name O or name CB )) or resid 533 or (resid 534 and (name N or name CA or n \ ame C or name O or name CB )) or resid 535 through 540 or (resid 541 and (name N \ or name CA or name C or name O or name CB )) or resid 542 through 547 or (resid \ 548 and (name N or name CA or name C or name O or name CB )) or resid 549 throu \ gh 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) or \ resid 579 through 592 or (resid 593 and (name N or name CA or name C or name O \ or name CB )) or resid 594)) } 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: 6.100 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: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 65.260 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.230 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: 0.010 Load rotamer database and sin/cos tables:5.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 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 : 0.002 0.026 28752 Z= 0.161 Angle : 0.632 12.494 38971 Z= 0.396 Chirality : 0.040 0.223 4600 Planarity : 0.003 0.047 5115 Dihedral : 10.713 82.693 10718 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Rotamer: Outliers : 0.38 % Allowed : 3.36 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.29 (0.12), residues: 3729 helix: -2.40 (0.11), residues: 1372 sheet: -2.19 (0.20), residues: 581 loop : -1.86 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 46 HIS 0.007 0.001 HIS F 446 PHE 0.010 0.001 PHE F 186 TYR 0.010 0.001 TYR F 679 ARG 0.004 0.000 ARG F 536 Details of bonding type rmsd hydrogen bonds : bond 0.26265 ( 1055) hydrogen bonds : angle 8.40538 ( 3045) covalent geometry : bond 0.00248 (28752) covalent geometry : angle 0.63239 (38971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 387 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 MET cc_start: 0.6212 (ptp) cc_final: 0.5986 (ptp) REVERT: D 263 SER cc_start: 0.8042 (t) cc_final: 0.7827 (p) REVERT: D 445 ARG cc_start: 0.8107 (mmt180) cc_final: 0.7865 (mmt180) REVERT: C 154 TYR cc_start: 0.6976 (p90) cc_final: 0.6473 (p90) REVERT: C 203 PHE cc_start: 0.8622 (p90) cc_final: 0.8261 (p90) REVERT: B 163 CYS cc_start: 0.6493 (t) cc_final: 0.5377 (m) REVERT: B 207 ILE cc_start: 0.7920 (pt) cc_final: 0.7684 (mm) REVERT: E 335 LYS cc_start: 0.0878 (OUTLIER) cc_final: -0.0805 (pttp) REVERT: E 555 ARG cc_start: 0.6746 (ttt90) cc_final: 0.6329 (ttp80) REVERT: F 411 GLU cc_start: 0.5665 (tp30) cc_final: 0.5086 (mm-30) REVERT: F 535 MET cc_start: 0.7501 (ttt) cc_final: 0.7245 (ttm) REVERT: F 626 ILE cc_start: 0.5619 (mm) cc_final: 0.5396 (mt) REVERT: A 134 GLU cc_start: 0.5841 (tt0) cc_final: 0.5632 (pm20) REVERT: A 209 LEU cc_start: 0.6273 (mm) cc_final: 0.5938 (mt) REVERT: A 285 ASP cc_start: 0.6641 (t0) cc_final: 0.6369 (m-30) REVERT: A 464 ASP cc_start: 0.8112 (m-30) cc_final: 0.7809 (m-30) REVERT: A 468 LEU cc_start: 0.8394 (tp) cc_final: 0.8153 (tp) REVERT: A 470 LEU cc_start: 0.7348 (mt) cc_final: 0.6895 (pt) REVERT: A 589 GLU cc_start: 0.6857 (pt0) cc_final: 0.6600 (mm-30) REVERT: A 591 MET cc_start: 0.6915 (ttp) cc_final: 0.6194 (ttp) outliers start: 11 outliers final: 2 residues processed: 395 average time/residue: 0.5185 time to fit residues: 298.1617 Evaluate side-chains 221 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain F residue 213 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 0.5980 chunk 283 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 293 optimal weight: 0.1980 chunk 113 optimal weight: 0.7980 chunk 178 optimal weight: 0.0970 chunk 218 optimal weight: 0.7980 chunk 339 optimal weight: 0.0050 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN D 484 HIS C 76 GLN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 HIS C 484 HIS C 556 GLN B 249 HIS B 412 GLN E 63 ASN E 151 GLN E 248 ASN E 413 GLN F 62 ASN F 98 ASN F 252 GLN F 567 HIS F 618 ASN F 649 GLN A 112 HIS A 452 GLN A 484 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.145260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.118204 restraints weight = 68181.568| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.09 r_work: 0.3653 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28752 Z= 0.129 Angle : 0.565 7.541 38971 Z= 0.293 Chirality : 0.042 0.220 4600 Planarity : 0.004 0.051 5115 Dihedral : 4.067 49.749 4041 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 0.87 % Allowed : 8.04 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.13), residues: 3729 helix: -0.87 (0.12), residues: 1449 sheet: -1.89 (0.20), residues: 582 loop : -1.43 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 46 HIS 0.007 0.001 HIS E 484 PHE 0.025 0.001 PHE D 203 TYR 0.013 0.001 TYR F 679 ARG 0.006 0.000 ARG F 569 Details of bonding type rmsd hydrogen bonds : bond 0.05155 ( 1055) hydrogen bonds : angle 5.61285 ( 3045) covalent geometry : bond 0.00275 (28752) covalent geometry : angle 0.56504 (38971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 MET cc_start: 0.6582 (ptp) cc_final: 0.6172 (ptp) REVERT: D 270 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7377 (mp) REVERT: C 154 TYR cc_start: 0.7372 (p90) cc_final: 0.6929 (p90) REVERT: C 203 PHE cc_start: 0.8524 (p90) cc_final: 0.8110 (p90) REVERT: C 445 ARG cc_start: 0.7317 (mtp85) cc_final: 0.7008 (tmt170) REVERT: B 163 CYS cc_start: 0.5576 (t) cc_final: 0.4152 (m) REVERT: B 535 MET cc_start: 0.8121 (mmm) cc_final: 0.7226 (mmp) REVERT: E 412 GLN cc_start: 0.7394 (tt0) cc_final: 0.7076 (mp10) REVERT: E 483 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7163 (mt-10) REVERT: F 1 MET cc_start: 0.6706 (mmm) cc_final: 0.6497 (mmm) REVERT: F 621 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7146 (tm-30) REVERT: F 623 LEU cc_start: 0.6801 (mt) cc_final: 0.6488 (tt) REVERT: F 626 ILE cc_start: 0.5432 (mm) cc_final: 0.5183 (mt) REVERT: A 209 LEU cc_start: 0.6197 (mm) cc_final: 0.5881 (mt) REVERT: A 285 ASP cc_start: 0.7247 (t0) cc_final: 0.6922 (m-30) REVERT: A 502 TYR cc_start: 0.7217 (m-80) cc_final: 0.6958 (m-80) outliers start: 25 outliers final: 10 residues processed: 259 average time/residue: 0.4749 time to fit residues: 188.4675 Evaluate side-chains 211 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain A residue 132 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 124 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 363 optimal weight: 0.0370 chunk 250 optimal weight: 9.9990 chunk 206 optimal weight: 0.0010 chunk 163 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 268 optimal weight: 10.0000 chunk 322 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 overall best weight: 0.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 484 HIS D 602 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN B 437 ASN B 484 HIS F 567 HIS A 112 HIS ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.143632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.116437 restraints weight = 67126.125| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.84 r_work: 0.3655 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28752 Z= 0.126 Angle : 0.544 14.835 38971 Z= 0.275 Chirality : 0.042 0.151 4600 Planarity : 0.004 0.058 5115 Dihedral : 3.922 38.270 4036 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.25 % Allowed : 9.12 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.13), residues: 3729 helix: -0.08 (0.13), residues: 1453 sheet: -1.55 (0.21), residues: 571 loop : -1.26 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 46 HIS 0.004 0.001 HIS F 446 PHE 0.030 0.002 PHE D 96 TYR 0.021 0.001 TYR F 341 ARG 0.007 0.001 ARG C 442 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 1055) hydrogen bonds : angle 5.02661 ( 3045) covalent geometry : bond 0.00293 (28752) covalent geometry : angle 0.54389 (38971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 270 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7508 (mp) REVERT: C 154 TYR cc_start: 0.7262 (p90) cc_final: 0.6924 (p90) REVERT: C 203 PHE cc_start: 0.8460 (p90) cc_final: 0.7970 (p90) REVERT: C 445 ARG cc_start: 0.7255 (mtp85) cc_final: 0.6996 (tmt170) REVERT: B 163 CYS cc_start: 0.6090 (t) cc_final: 0.4546 (m) REVERT: B 266 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7197 (t0) REVERT: B 445 ARG cc_start: 0.7874 (tpp-160) cc_final: 0.7657 (mtp180) REVERT: B 535 MET cc_start: 0.7824 (mmm) cc_final: 0.7098 (mmp) REVERT: E 499 LYS cc_start: 0.4542 (tptp) cc_final: 0.3926 (mptt) REVERT: E 592 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.5803 (mpp) REVERT: F 623 LEU cc_start: 0.6737 (mt) cc_final: 0.6486 (tt) REVERT: A 209 LEU cc_start: 0.6175 (mm) cc_final: 0.5913 (mt) REVERT: A 285 ASP cc_start: 0.7221 (t0) cc_final: 0.6890 (m-30) outliers start: 36 outliers final: 18 residues processed: 250 average time/residue: 0.4481 time to fit residues: 175.0277 Evaluate side-chains 210 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain E residue 592 MET Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 422 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 177 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 363 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 284 optimal weight: 0.0170 chunk 103 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 484 HIS D 663 ASN C 76 GLN C 446 HIS B 517 HIS E 248 ASN F 567 HIS ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.141962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.113757 restraints weight = 67375.961| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.24 r_work: 0.3584 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28752 Z= 0.131 Angle : 0.533 11.795 38971 Z= 0.269 Chirality : 0.042 0.139 4600 Planarity : 0.004 0.053 5115 Dihedral : 3.922 39.463 4036 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 1.94 % Allowed : 10.44 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.13), residues: 3729 helix: 0.31 (0.14), residues: 1454 sheet: -1.32 (0.21), residues: 569 loop : -1.16 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 375 HIS 0.004 0.001 HIS D 324 PHE 0.027 0.002 PHE D 203 TYR 0.018 0.001 TYR F 341 ARG 0.005 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 1055) hydrogen bonds : angle 4.79085 ( 3045) covalent geometry : bond 0.00311 (28752) covalent geometry : angle 0.53267 (38971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6753 (ptt) cc_final: 0.6028 (pmm) REVERT: D 147 MET cc_start: 0.6820 (ptp) cc_final: 0.6488 (ptp) REVERT: D 225 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8570 (t) REVERT: D 270 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7474 (mp) REVERT: C 154 TYR cc_start: 0.7410 (p90) cc_final: 0.7094 (p90) REVERT: C 445 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7045 (tmt170) REVERT: C 552 ILE cc_start: 0.8255 (mm) cc_final: 0.7992 (mp) REVERT: B 163 CYS cc_start: 0.6207 (t) cc_final: 0.4578 (m) REVERT: B 333 VAL cc_start: 0.6851 (t) cc_final: 0.6610 (t) REVERT: B 445 ARG cc_start: 0.7956 (tpp-160) cc_final: 0.7386 (mtp180) REVERT: B 535 MET cc_start: 0.7888 (mmm) cc_final: 0.7283 (mmp) REVERT: E 483 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6972 (mp0) REVERT: E 499 LYS cc_start: 0.4594 (tptp) cc_final: 0.3958 (mptt) REVERT: F 411 GLU cc_start: 0.4386 (tp30) cc_final: 0.4143 (mm-30) REVERT: A 209 LEU cc_start: 0.6259 (mm) cc_final: 0.5997 (mt) REVERT: A 285 ASP cc_start: 0.7392 (t0) cc_final: 0.6993 (m-30) REVERT: A 454 ASP cc_start: 0.6564 (p0) cc_final: 0.5873 (t0) outliers start: 56 outliers final: 26 residues processed: 265 average time/residue: 0.4280 time to fit residues: 178.3366 Evaluate side-chains 227 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 422 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 20 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 288 optimal weight: 6.9990 chunk 355 optimal weight: 0.7980 chunk 234 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 484 HIS E 189 GLN ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.141434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.112593 restraints weight = 67291.817| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.89 r_work: 0.3578 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28752 Z= 0.136 Angle : 0.538 12.838 38971 Z= 0.271 Chirality : 0.042 0.142 4600 Planarity : 0.004 0.060 5115 Dihedral : 3.927 39.293 4036 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 1.70 % Allowed : 11.89 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.13), residues: 3729 helix: 0.55 (0.14), residues: 1451 sheet: -1.31 (0.21), residues: 584 loop : -1.08 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.007 0.001 HIS C 324 PHE 0.028 0.002 PHE D 203 TYR 0.017 0.001 TYR F 341 ARG 0.006 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 1055) hydrogen bonds : angle 4.67290 ( 3045) covalent geometry : bond 0.00325 (28752) covalent geometry : angle 0.53822 (38971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6877 (ptt) cc_final: 0.6267 (pmm) REVERT: D 147 MET cc_start: 0.6884 (ptp) cc_final: 0.6443 (ptp) REVERT: D 225 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8577 (t) REVERT: C 445 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7127 (tmt170) REVERT: B 163 CYS cc_start: 0.6387 (t) cc_final: 0.4751 (m) REVERT: B 445 ARG cc_start: 0.7957 (tpp-160) cc_final: 0.7493 (mtp180) REVERT: B 535 MET cc_start: 0.7854 (mmm) cc_final: 0.7333 (mmp) REVERT: B 603 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5730 (tp) REVERT: E 499 LYS cc_start: 0.4853 (tptp) cc_final: 0.4140 (mptt) REVERT: F 626 ILE cc_start: 0.5057 (mm) cc_final: 0.4550 (mt) REVERT: A 209 LEU cc_start: 0.6270 (mm) cc_final: 0.6022 (mt) REVERT: A 285 ASP cc_start: 0.7391 (t0) cc_final: 0.6955 (m-30) REVERT: A 440 PHE cc_start: 0.5650 (m-80) cc_final: 0.5186 (m-80) REVERT: A 454 ASP cc_start: 0.6336 (p0) cc_final: 0.5790 (t0) outliers start: 49 outliers final: 29 residues processed: 252 average time/residue: 0.4364 time to fit residues: 172.3069 Evaluate side-chains 224 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 16 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 225 optimal weight: 0.0000 chunk 337 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN D 484 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.138435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.109593 restraints weight = 66830.989| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.99 r_work: 0.3522 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 28752 Z= 0.236 Angle : 0.639 12.156 38971 Z= 0.319 Chirality : 0.045 0.162 4600 Planarity : 0.005 0.074 5115 Dihedral : 4.285 40.393 4036 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 2.18 % Allowed : 12.52 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.13), residues: 3729 helix: 0.49 (0.14), residues: 1456 sheet: -1.43 (0.21), residues: 587 loop : -1.21 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 375 HIS 0.008 0.001 HIS C 324 PHE 0.029 0.002 PHE D 203 TYR 0.019 0.002 TYR F 341 ARG 0.008 0.001 ARG C 320 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 1055) hydrogen bonds : angle 4.81605 ( 3045) covalent geometry : bond 0.00591 (28752) covalent geometry : angle 0.63865 (38971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6783 (ptt) cc_final: 0.6383 (pmm) REVERT: D 147 MET cc_start: 0.6884 (ptp) cc_final: 0.6423 (ptp) REVERT: D 225 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8703 (p) REVERT: C 140 CYS cc_start: 0.6254 (m) cc_final: 0.5968 (m) REVERT: C 445 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7303 (tmt170) REVERT: B 163 CYS cc_start: 0.6709 (t) cc_final: 0.5069 (m) REVERT: B 445 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7670 (mtp180) REVERT: B 535 MET cc_start: 0.8000 (mmm) cc_final: 0.7437 (mmp) REVERT: F 645 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7394 (pt0) REVERT: A 209 LEU cc_start: 0.6689 (mm) cc_final: 0.6409 (mt) REVERT: A 440 PHE cc_start: 0.6157 (m-80) cc_final: 0.5849 (m-80) REVERT: A 454 ASP cc_start: 0.6340 (p0) cc_final: 0.6000 (t0) outliers start: 63 outliers final: 40 residues processed: 257 average time/residue: 0.4296 time to fit residues: 172.8862 Evaluate side-chains 232 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 375 TRP Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 588 ILE Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 147 optimal weight: 3.9990 chunk 314 optimal weight: 20.0000 chunk 243 optimal weight: 1.9990 chunk 316 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 chunk 238 optimal weight: 0.1980 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 484 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.136707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.107258 restraints weight = 66256.587| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.18 r_work: 0.3513 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28752 Z= 0.157 Angle : 0.567 11.121 38971 Z= 0.284 Chirality : 0.042 0.144 4600 Planarity : 0.004 0.049 5115 Dihedral : 4.147 38.827 4036 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 1.70 % Allowed : 13.45 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.14), residues: 3729 helix: 0.63 (0.14), residues: 1455 sheet: -1.33 (0.22), residues: 568 loop : -1.09 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 375 HIS 0.005 0.001 HIS C 324 PHE 0.027 0.002 PHE D 203 TYR 0.024 0.001 TYR F 341 ARG 0.004 0.000 ARG C 320 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 1055) hydrogen bonds : angle 4.67700 ( 3045) covalent geometry : bond 0.00385 (28752) covalent geometry : angle 0.56729 (38971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6817 (ptt) cc_final: 0.6247 (pmm) REVERT: D 147 MET cc_start: 0.6866 (ptp) cc_final: 0.6398 (ptp) REVERT: C 140 CYS cc_start: 0.6378 (m) cc_final: 0.6081 (m) REVERT: C 255 LYS cc_start: 0.7903 (tppt) cc_final: 0.7536 (mmtp) REVERT: C 445 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7290 (tmt170) REVERT: B 163 CYS cc_start: 0.6683 (t) cc_final: 0.5028 (m) REVERT: B 445 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7698 (mtp180) REVERT: B 535 MET cc_start: 0.7999 (mmm) cc_final: 0.7527 (mmp) REVERT: B 603 LEU cc_start: 0.6368 (tt) cc_final: 0.6096 (tp) REVERT: E 483 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7000 (mp0) REVERT: F 305 LEU cc_start: 0.6333 (pp) cc_final: 0.5859 (mt) REVERT: F 623 LEU cc_start: 0.6079 (tt) cc_final: 0.5871 (mt) REVERT: A 209 LEU cc_start: 0.6705 (mm) cc_final: 0.6412 (mt) REVERT: A 440 PHE cc_start: 0.6237 (m-80) cc_final: 0.5877 (m-80) REVERT: A 447 LYS cc_start: 0.7992 (tppt) cc_final: 0.7572 (mmmt) outliers start: 49 outliers final: 38 residues processed: 245 average time/residue: 0.5315 time to fit residues: 210.0340 Evaluate side-chains 232 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 4.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 174 optimal weight: 0.8980 chunk 270 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 352 optimal weight: 2.9990 chunk 227 optimal weight: 0.0870 chunk 89 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN D 484 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.140334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.110427 restraints weight = 67720.695| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.21 r_work: 0.3547 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28752 Z= 0.112 Angle : 0.532 10.964 38971 Z= 0.267 Chirality : 0.041 0.149 4600 Planarity : 0.004 0.049 5115 Dihedral : 3.956 38.302 4036 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 1.42 % Allowed : 14.08 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.14), residues: 3729 helix: 0.78 (0.14), residues: 1460 sheet: -1.28 (0.21), residues: 592 loop : -0.96 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 375 HIS 0.002 0.001 HIS B 48 PHE 0.025 0.001 PHE D 203 TYR 0.027 0.001 TYR F 341 ARG 0.004 0.000 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 1055) hydrogen bonds : angle 4.52647 ( 3045) covalent geometry : bond 0.00263 (28752) covalent geometry : angle 0.53205 (38971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6853 (ptt) cc_final: 0.6038 (pmm) REVERT: D 147 MET cc_start: 0.6872 (ptp) cc_final: 0.6419 (ptp) REVERT: C 140 CYS cc_start: 0.6489 (m) cc_final: 0.6169 (m) REVERT: C 255 LYS cc_start: 0.7884 (tppt) cc_final: 0.7582 (mmtp) REVERT: C 445 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7332 (tmt170) REVERT: B 535 MET cc_start: 0.7890 (mmm) cc_final: 0.7449 (mmp) REVERT: B 603 LEU cc_start: 0.6309 (tt) cc_final: 0.6007 (tp) REVERT: E 224 VAL cc_start: 0.6625 (OUTLIER) cc_final: 0.6395 (m) REVERT: E 273 LEU cc_start: 0.7184 (mt) cc_final: 0.6951 (tp) REVERT: E 483 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6916 (mp0) REVERT: F 305 LEU cc_start: 0.6083 (pp) cc_final: 0.5858 (mt) REVERT: F 645 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: A 209 LEU cc_start: 0.6698 (mm) cc_final: 0.6426 (mt) REVERT: A 447 LYS cc_start: 0.8030 (tppt) cc_final: 0.7534 (mmmt) outliers start: 41 outliers final: 29 residues processed: 232 average time/residue: 0.4656 time to fit residues: 169.9859 Evaluate side-chains 218 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 132 optimal weight: 0.0020 chunk 322 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 330 optimal weight: 0.2980 chunk 145 optimal weight: 0.0010 chunk 102 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 484 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.136966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.107202 restraints weight = 66823.433| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.11 r_work: 0.3519 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28752 Z= 0.143 Angle : 0.556 10.710 38971 Z= 0.278 Chirality : 0.042 0.142 4600 Planarity : 0.004 0.050 5115 Dihedral : 4.017 38.935 4036 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 1.56 % Allowed : 14.04 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.14), residues: 3729 helix: 0.82 (0.14), residues: 1457 sheet: -1.28 (0.21), residues: 598 loop : -0.96 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 375 HIS 0.004 0.001 HIS C 324 PHE 0.038 0.002 PHE B 52 TYR 0.032 0.001 TYR F 341 ARG 0.005 0.000 ARG C 320 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 1055) hydrogen bonds : angle 4.55164 ( 3045) covalent geometry : bond 0.00348 (28752) covalent geometry : angle 0.55556 (38971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6750 (ptt) cc_final: 0.6192 (pmm) REVERT: D 147 MET cc_start: 0.6933 (ptp) cc_final: 0.6459 (ptp) REVERT: D 225 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8464 (t) REVERT: C 140 CYS cc_start: 0.6371 (m) cc_final: 0.6102 (m) REVERT: C 255 LYS cc_start: 0.7941 (tppt) cc_final: 0.7591 (mmtp) REVERT: C 445 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7388 (tmt170) REVERT: B 149 ARG cc_start: 0.6748 (mtt180) cc_final: 0.6520 (mtt90) REVERT: B 445 ARG cc_start: 0.7893 (tpp-160) cc_final: 0.7520 (mtp180) REVERT: B 535 MET cc_start: 0.7909 (mmm) cc_final: 0.7458 (mmp) REVERT: B 603 LEU cc_start: 0.6457 (tt) cc_final: 0.6173 (tp) REVERT: E 224 VAL cc_start: 0.6664 (OUTLIER) cc_final: 0.6454 (m) REVERT: E 483 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7003 (mp0) REVERT: F 645 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7463 (pt0) REVERT: A 209 LEU cc_start: 0.6744 (mm) cc_final: 0.6448 (mt) REVERT: A 440 PHE cc_start: 0.6218 (m-80) cc_final: 0.5672 (m-80) REVERT: A 447 LYS cc_start: 0.7981 (tppt) cc_final: 0.7514 (mmmt) outliers start: 45 outliers final: 36 residues processed: 233 average time/residue: 0.4266 time to fit residues: 157.1143 Evaluate side-chains 230 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 30 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 312 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 138 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 484 HIS B 50 ASN B 93 HIS ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.139687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.110981 restraints weight = 66664.742| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.82 r_work: 0.3517 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28752 Z= 0.187 Angle : 0.600 11.376 38971 Z= 0.301 Chirality : 0.043 0.164 4600 Planarity : 0.005 0.065 5115 Dihedral : 4.212 39.732 4036 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 1.60 % Allowed : 14.18 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.14), residues: 3729 helix: 0.74 (0.14), residues: 1456 sheet: -1.33 (0.21), residues: 589 loop : -1.04 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 375 HIS 0.006 0.001 HIS C 324 PHE 0.024 0.002 PHE D 203 TYR 0.032 0.002 TYR F 341 ARG 0.008 0.001 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 1055) hydrogen bonds : angle 4.61800 ( 3045) covalent geometry : bond 0.00463 (28752) covalent geometry : angle 0.60049 (38971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7458 Ramachandran restraints generated. 3729 Oldfield, 0 Emsley, 3729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6775 (ptt) cc_final: 0.6251 (pmm) REVERT: D 147 MET cc_start: 0.6926 (ptp) cc_final: 0.6459 (ptp) REVERT: D 225 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8456 (t) REVERT: C 140 CYS cc_start: 0.6275 (m) cc_final: 0.6060 (m) REVERT: C 255 LYS cc_start: 0.7887 (tppt) cc_final: 0.7548 (mmtp) REVERT: C 445 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7662 (mtp180) REVERT: B 445 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7528 (mtp180) REVERT: B 535 MET cc_start: 0.7915 (mmm) cc_final: 0.7432 (mmp) REVERT: B 603 LEU cc_start: 0.6742 (tt) cc_final: 0.6469 (tp) REVERT: F 623 LEU cc_start: 0.6593 (pp) cc_final: 0.5734 (tt) REVERT: F 645 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7408 (pt0) REVERT: A 209 LEU cc_start: 0.6743 (mm) cc_final: 0.6517 (mt) REVERT: A 440 PHE cc_start: 0.6349 (m-80) cc_final: 0.5842 (m-80) outliers start: 46 outliers final: 41 residues processed: 230 average time/residue: 0.4313 time to fit residues: 159.4872 Evaluate side-chains 226 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 588 ILE Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 62 optimal weight: 20.0000 chunk 18 optimal weight: 0.0970 chunk 282 optimal weight: 7.9990 chunk 163 optimal weight: 0.5980 chunk 372 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 106 optimal weight: 0.0570 chunk 228 optimal weight: 0.4980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 484 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.137425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.108408 restraints weight = 66083.423| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.09 r_work: 0.3550 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28752 Z= 0.107 Angle : 0.537 15.194 38971 Z= 0.269 Chirality : 0.041 0.171 4600 Planarity : 0.004 0.070 5115 Dihedral : 3.982 37.899 4036 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 1.35 % Allowed : 14.56 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.14), residues: 3729 helix: 0.89 (0.14), residues: 1461 sheet: -1.20 (0.21), residues: 580 loop : -0.92 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 375 HIS 0.009 0.001 HIS C 446 PHE 0.023 0.001 PHE D 203 TYR 0.037 0.001 TYR F 341 ARG 0.005 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 1055) hydrogen bonds : angle 4.45998 ( 3045) covalent geometry : bond 0.00249 (28752) covalent geometry : angle 0.53677 (38971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14360.05 seconds wall clock time: 251 minutes 2.86 seconds (15062.86 seconds total)