Starting phenix.real_space_refine on Fri Aug 9 22:01:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/08_2024/7abr_11707.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/08_2024/7abr_11707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/08_2024/7abr_11707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/08_2024/7abr_11707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/08_2024/7abr_11707.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/08_2024/7abr_11707.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 78 5.16 5 C 16898 2.51 5 N 4861 2.21 5 O 5343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 169": "OD1" <-> "OD2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ASP 625": "OD1" <-> "OD2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A ARG 638": "NH1" <-> "NH2" Residue "A PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A ASP 757": "OD1" <-> "OD2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A ARG 776": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 565": "OD1" <-> "OD2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "B TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 608": "NH1" <-> "NH2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B ARG 638": "NH1" <-> "NH2" Residue "B ASP 648": "OD1" <-> "OD2" Residue "B ARG 650": "NH1" <-> "NH2" Residue "B ASP 684": "OD1" <-> "OD2" Residue "B PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B GLU 721": "OE1" <-> "OE2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B GLU 742": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B GLU 779": "OE1" <-> "OE2" Residue "B GLU 797": "OE1" <-> "OE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ARG 536": "NH1" <-> "NH2" Residue "C ASP 565": "OD1" <-> "OD2" Residue "C ARG 571": "NH1" <-> "NH2" Residue "C TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 597": "OD1" <-> "OD2" Residue "C GLU 604": "OE1" <-> "OE2" Residue "C GLU 692": "OE1" <-> "OE2" Residue "C PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 698": "NH1" <-> "NH2" Residue "C ASP 706": "OD1" <-> "OD2" Residue "C GLU 707": "OE1" <-> "OE2" Residue "C GLU 742": "OE1" <-> "OE2" Residue "C TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 774": "OE1" <-> "OE2" Residue "C GLU 779": "OE1" <-> "OE2" Residue "C ASP 795": "OD1" <-> "OD2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 219": "OE1" <-> "OE2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "D ASP 243": "OD1" <-> "OD2" Residue "D TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 266": "OD1" <-> "OD2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "D TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D ARG 380": "NH1" <-> "NH2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 389": "OD1" <-> "OD2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D ARG 536": "NH1" <-> "NH2" Residue "D ASP 565": "OD1" <-> "OD2" Residue "D ASP 573": "OD1" <-> "OD2" Residue "D TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 579": "OE1" <-> "OE2" Residue "D ARG 585": "NH1" <-> "NH2" Residue "D TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 597": "OD1" <-> "OD2" Residue "D GLU 635": "OE1" <-> "OE2" Residue "D ASP 636": "OD1" <-> "OD2" Residue "D ASP 648": "OD1" <-> "OD2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 650": "NH1" <-> "NH2" Residue "D GLU 664": "OE1" <-> "OE2" Residue "D ASP 687": "OD1" <-> "OD2" Residue "D PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 742": "OE1" <-> "OE2" Residue "D TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 763": "NH1" <-> "NH2" Residue "D ASP 795": "OD1" <-> "OD2" Residue "D ASP 798": "OD1" <-> "OD2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 219": "OE1" <-> "OE2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "E TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 333": "NH1" <-> "NH2" Residue "E PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E ARG 380": "NH1" <-> "NH2" Residue "E PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E ASP 396": "OD1" <-> "OD2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ASP 474": "OD1" <-> "OD2" Residue "E GLU 503": "OE1" <-> "OE2" Residue "E ASP 514": "OD1" <-> "OD2" Residue "E ARG 525": "NH1" <-> "NH2" Residue "E ARG 536": "NH1" <-> "NH2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 556": "NH1" <-> "NH2" Residue "E PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 567": "OE1" <-> "OE2" Residue "E ARG 571": "NH1" <-> "NH2" Residue "E ASP 573": "OD1" <-> "OD2" Residue "E TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 585": "NH1" <-> "NH2" Residue "E GLU 598": "OE1" <-> "OE2" Residue "E GLU 604": "OE1" <-> "OE2" Residue "E ARG 607": "NH1" <-> "NH2" Residue "E GLU 620": "OE1" <-> "OE2" Residue "E ARG 645": "NH1" <-> "NH2" Residue "E ASP 648": "OD1" <-> "OD2" Residue "E GLU 664": "OE1" <-> "OE2" Residue "E ASP 687": "OD1" <-> "OD2" Residue "E GLU 700": "OE1" <-> "OE2" Residue "E GLU 707": "OE1" <-> "OE2" Residue "E GLU 715": "OE1" <-> "OE2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E ASP 745": "OD1" <-> "OD2" Residue "E GLU 754": "OE1" <-> "OE2" Residue "E GLU 759": "OE1" <-> "OE2" Residue "E TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 774": "OE1" <-> "OE2" Residue "E GLU 779": "OE1" <-> "OE2" Residue "E GLU 797": "OE1" <-> "OE2" Residue "E ASP 798": "OD1" <-> "OD2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "F ASP 180": "OD1" <-> "OD2" Residue "F ASP 236": "OD1" <-> "OD2" Residue "F ASP 243": "OD1" <-> "OD2" Residue "F ARG 269": "NH1" <-> "NH2" Residue "F PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F ASP 295": "OD1" <-> "OD2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F GLU 308": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F GLU 331": "OE1" <-> "OE2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 384": "OD1" <-> "OD2" Residue "F PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ARG 405": "NH1" <-> "NH2" Residue "F ASP 475": "OD1" <-> "OD2" Residue "F GLU 495": "OE1" <-> "OE2" Residue "F ARG 525": "NH1" <-> "NH2" Residue "F ARG 526": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 565": "OD1" <-> "OD2" Residue "F GLU 566": "OE1" <-> "OE2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F GLU 576": "OE1" <-> "OE2" Residue "F TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 579": "OE1" <-> "OE2" Residue "F GLU 604": "OE1" <-> "OE2" Residue "F GLU 620": "OE1" <-> "OE2" Residue "F ASP 684": "OD1" <-> "OD2" Residue "F PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 707": "OE1" <-> "OE2" Residue "F GLU 715": "OE1" <-> "OE2" Residue "F GLU 721": "OE1" <-> "OE2" Residue "F GLU 754": "OE1" <-> "OE2" Residue "F ARG 763": "NH1" <-> "NH2" Residue "F ARG 766": "NH1" <-> "NH2" Residue "F ARG 767": "NH1" <-> "NH2" Residue "F ASP 775": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27209 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4482 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 554} Chain breaks: 2 Chain: "B" Number of atoms: 4488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4488 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 554} Chain breaks: 2 Chain: "C" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4513 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 558} Chain breaks: 2 Chain: "D" Number of atoms: 4582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4582 Classifications: {'peptide': 586} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 566} Chain breaks: 2 Chain: "E" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4476 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 551} Chain breaks: 3 Chain: "F" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4213 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 518} Chain breaks: 6 Chain: "S" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'ATP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.61, per 1000 atoms: 0.50 Number of scatterers: 27209 At special positions: 0 Unit cell: (116.38, 149.178, 151.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 29 15.00 O 5343 8.00 N 4861 7.00 C 16898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.70 Conformation dependent library (CDL) restraints added in 4.6 seconds 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6444 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 24 sheets defined 58.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.564A pdb=" N GLU A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 197 Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.759A pdb=" N ALA A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 306 Proline residue: A 302 - end of helix removed outlier: 3.882A pdb=" N ARG A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 323 Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.620A pdb=" N LEU A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 363 removed outlier: 3.522A pdb=" N LEU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.635A pdb=" N ILE A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 408 Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 513 through 529 Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.567A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.697A pdb=" N LYS A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 623 through 635 removed outlier: 4.068A pdb=" N PHE A 627 " --> pdb=" O HIS A 623 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 628 " --> pdb=" O PRO A 624 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 698 through 705 removed outlier: 3.747A pdb=" N ILE A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 737 Processing helix chain 'A' and resid 744 through 756 removed outlier: 3.651A pdb=" N VAL A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 784 removed outlier: 4.261A pdb=" N ARG A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 167 removed outlier: 3.600A pdb=" N ASP B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.617A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.579A pdb=" N ARG B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 212 removed outlier: 3.810A pdb=" N VAL B 212 " --> pdb=" O GLU B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 209 through 212' Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'B' and resid 256 through 271 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 295 through 307 Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.569A pdb=" N ILE B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 4.032A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 381 Processing helix chain 'B' and resid 388 through 408 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'B' and resid 501 through 508 Processing helix chain 'B' and resid 513 through 529 Processing helix chain 'B' and resid 552 through 563 removed outlier: 3.509A pdb=" N ARG B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 580 removed outlier: 4.541A pdb=" N GLU B 579 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 580 " --> pdb=" O TYR B 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 576 through 580' Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.665A pdb=" N LYS B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 623 through 637 removed outlier: 4.064A pdb=" N PHE B 627 " --> pdb=" O HIS B 623 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN B 632 " --> pdb=" O ASN B 628 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 680 through 697 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.654A pdb=" N ILE B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 735 Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 744 through 755 removed outlier: 3.651A pdb=" N GLU B 754 " --> pdb=" O LYS B 750 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 783 removed outlier: 3.650A pdb=" N ARG B 766 " --> pdb=" O ALA B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 removed outlier: 4.207A pdb=" N SER C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 213 through 227 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 256 through 272 Processing helix chain 'C' and resid 281 through 285 removed outlier: 3.522A pdb=" N ILE C 285 " --> pdb=" O HIS C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 316 through 323 Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 343 through 363 removed outlier: 4.434A pdb=" N ARG C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 381 Processing helix chain 'C' and resid 388 through 407 removed outlier: 3.618A pdb=" N PHE C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.576A pdb=" N ILE C 476 " --> pdb=" O THR C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 510 Processing helix chain 'C' and resid 513 through 529 Processing helix chain 'C' and resid 550 through 564 removed outlier: 3.593A pdb=" N ALA C 555 " --> pdb=" O LYS C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 582 through 588 removed outlier: 4.334A pdb=" N LEU C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 609 removed outlier: 3.746A pdb=" N LYS C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 removed outlier: 4.070A pdb=" N LEU C 630 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 636 " --> pdb=" O GLN C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 697 Processing helix chain 'C' and resid 698 through 704 removed outlier: 3.760A pdb=" N ARG C 704 " --> pdb=" O GLU C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 736 removed outlier: 3.781A pdb=" N GLU C 736 " --> pdb=" O LYS C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 756 removed outlier: 3.755A pdb=" N VAL C 756 " --> pdb=" O ALA C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 783 removed outlier: 3.786A pdb=" N ARG C 766 " --> pdb=" O ALA C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 185 through 196 Processing helix chain 'D' and resid 213 through 227 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 256 through 271 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 300 through 307 removed outlier: 3.581A pdb=" N LEU D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 343 through 363 removed outlier: 4.536A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 381 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.529A pdb=" N ILE D 476 " --> pdb=" O THR D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 510 removed outlier: 4.077A pdb=" N LEU D 500 " --> pdb=" O THR D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 529 removed outlier: 3.584A pdb=" N VAL D 517 " --> pdb=" O GLN D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 563 Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 579 through 586 removed outlier: 3.637A pdb=" N THR D 583 " --> pdb=" O LYS D 580 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER D 584 " --> pdb=" O HIS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 609 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 623 through 637 removed outlier: 3.911A pdb=" N PHE D 627 " --> pdb=" O HIS D 623 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP D 636 " --> pdb=" O GLN D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 667 Processing helix chain 'D' and resid 680 through 697 removed outlier: 4.170A pdb=" N MET D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY D 691 " --> pdb=" O ASP D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 703 Processing helix chain 'D' and resid 715 through 736 Processing helix chain 'D' and resid 744 through 755 Processing helix chain 'D' and resid 763 through 773 Processing helix chain 'D' and resid 773 through 783 Processing helix chain 'E' and resid 170 through 176 removed outlier: 4.050A pdb=" N GLU E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 197 Processing helix chain 'E' and resid 209 through 213 removed outlier: 4.109A pdb=" N GLY E 213 " --> pdb=" O PRO E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 255 through 270 removed outlier: 3.544A pdb=" N GLU E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 285 removed outlier: 4.045A pdb=" N ILE E 285 " --> pdb=" O HIS E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 307 Proline residue: E 302 - end of helix Processing helix chain 'E' and resid 316 through 325 Processing helix chain 'E' and resid 343 through 359 Processing helix chain 'E' and resid 367 through 381 Processing helix chain 'E' and resid 388 through 407 removed outlier: 4.053A pdb=" N PHE E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 495 through 510 removed outlier: 4.805A pdb=" N GLU E 503 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN E 504 " --> pdb=" O LEU E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 529 removed outlier: 3.882A pdb=" N VAL E 517 " --> pdb=" O GLN E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 563 Processing helix chain 'E' and resid 575 through 577 No H-bonds generated for 'chain 'E' and resid 575 through 577' Processing helix chain 'E' and resid 580 through 582 No H-bonds generated for 'chain 'E' and resid 580 through 582' Processing helix chain 'E' and resid 583 through 588 removed outlier: 4.101A pdb=" N VAL E 587 " --> pdb=" O THR E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 609 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 623 through 636 removed outlier: 3.861A pdb=" N PHE E 627 " --> pdb=" O HIS E 623 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL E 633 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP E 636 " --> pdb=" O GLN E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 697 Processing helix chain 'E' and resid 698 through 704 removed outlier: 3.553A pdb=" N ILE E 702 " --> pdb=" O ARG E 698 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG E 704 " --> pdb=" O GLU E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 737 removed outlier: 4.044A pdb=" N THR E 720 " --> pdb=" O LYS E 716 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU E 721 " --> pdb=" O LYS E 717 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU E 736 " --> pdb=" O LYS E 732 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 755 Processing helix chain 'E' and resid 762 through 773 removed outlier: 4.020A pdb=" N ARG E 766 " --> pdb=" O ALA E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 773 through 784 Processing helix chain 'F' and resid 160 through 167 Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.671A pdb=" N ILE F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 198 Processing helix chain 'F' and resid 213 through 227 Processing helix chain 'F' and resid 256 through 271 Processing helix chain 'F' and resid 280 through 285 Processing helix chain 'F' and resid 296 through 307 Proline residue: F 302 - end of helix Processing helix chain 'F' and resid 316 through 325 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 345 through 363 removed outlier: 3.749A pdb=" N GLN F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP F 356 " --> pdb=" O GLN F 352 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG F 357 " --> pdb=" O GLY F 353 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR F 358 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 382 removed outlier: 3.847A pdb=" N ARG F 380 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 382 " --> pdb=" O SER F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 407 removed outlier: 4.100A pdb=" N ARG F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 487 through 493 Processing helix chain 'F' and resid 494 through 496 No H-bonds generated for 'chain 'F' and resid 494 through 496' Processing helix chain 'F' and resid 497 through 508 removed outlier: 3.737A pdb=" N ASN F 501 " --> pdb=" O ASP F 497 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU F 503 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN F 504 " --> pdb=" O LEU F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 528 Processing helix chain 'F' and resid 550 through 563 Processing helix chain 'F' and resid 581 through 586 Processing helix chain 'F' and resid 601 through 609 Processing helix chain 'F' and resid 619 through 622 Processing helix chain 'F' and resid 623 through 637 Processing helix chain 'F' and resid 683 through 697 removed outlier: 4.376A pdb=" N MET F 690 " --> pdb=" O LYS F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 698 through 704 removed outlier: 3.884A pdb=" N ILE F 702 " --> pdb=" O ARG F 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 716 through 737 removed outlier: 3.727A pdb=" N THR F 720 " --> pdb=" O LYS F 716 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 734 " --> pdb=" O LEU F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 753 Processing helix chain 'F' and resid 765 through 773 Processing helix chain 'F' and resid 773 through 783 removed outlier: 3.588A pdb=" N ARG F 783 " --> pdb=" O GLU F 779 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 169 removed outlier: 3.575A pdb=" N MET A 240 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ILE A 312 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 276 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA A 314 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE A 278 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR A 316 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 208 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.330A pdb=" N SER A 365 " --> pdb=" O VAL A 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 569 through 573 removed outlier: 5.592A pdb=" N ILE A 570 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP A 617 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 572 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLY A 539 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N MET A 656 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 541 " --> pdb=" O MET A 656 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 741 through 743 removed outlier: 3.508A pdb=" N LEU A 794 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 169 removed outlier: 3.772A pdb=" N ARG B 168 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARG B 238 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B 277 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET B 240 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP B 279 " --> pdb=" O MET B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 204 through 205 Processing sheet with id=AA7, first strand: chain 'B' and resid 570 through 573 removed outlier: 6.578A pdb=" N SER B 540 " --> pdb=" O GLU B 707 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE B 709 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE B 542 " --> pdb=" O ILE B 709 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 638 through 640 Processing sheet with id=AA9, first strand: chain 'B' and resid 740 through 743 Processing sheet with id=AB1, first strand: chain 'C' and resid 238 through 242 removed outlier: 6.372A pdb=" N ARG C 238 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE C 277 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N MET C 240 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASP C 279 " --> pdb=" O MET C 240 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU C 242 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN C 310 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 314 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR C 315 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU C 206 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 570 through 573 removed outlier: 6.803A pdb=" N ILE C 570 " --> pdb=" O LEU C 615 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP C 617 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE C 572 " --> pdb=" O ASP C 617 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL C 614 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR C 657 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU C 616 " --> pdb=" O THR C 657 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 707 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 542 " --> pdb=" O GLU C 707 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 638 through 640 Processing sheet with id=AB4, first strand: chain 'C' and resid 741 through 743 removed outlier: 6.922A pdb=" N GLU C 742 " --> pdb=" O LEU C 794 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 169 removed outlier: 6.357A pdb=" N ARG D 238 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE D 277 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N MET D 240 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP D 279 " --> pdb=" O MET D 240 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU D 242 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE D 312 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 276 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA D 314 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE D 278 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N THR D 316 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR D 315 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 208 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 570 through 573 removed outlier: 6.507A pdb=" N VAL D 614 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR D 657 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 616 " --> pdb=" O THR D 657 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE D 541 " --> pdb=" O MET D 656 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER D 658 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE D 543 " --> pdb=" O SER D 658 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER D 540 " --> pdb=" O GLU D 707 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE D 709 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE D 542 " --> pdb=" O ILE D 709 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 639 through 640 Processing sheet with id=AB8, first strand: chain 'D' and resid 792 through 796 Processing sheet with id=AB9, first strand: chain 'E' and resid 168 through 169 removed outlier: 5.591A pdb=" N ARG E 238 " --> pdb=" O ILE E 275 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE E 277 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N MET E 240 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP E 279 " --> pdb=" O MET E 240 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE E 312 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU E 276 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ALA E 314 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE E 278 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR E 315 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU E 206 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 570 through 573 removed outlier: 6.447A pdb=" N ILE E 570 " --> pdb=" O LEU E 615 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP E 617 " --> pdb=" O ILE E 570 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 572 " --> pdb=" O ASP E 617 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 614 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR E 657 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU E 616 " --> pdb=" O THR E 657 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER E 540 " --> pdb=" O GLU E 707 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE E 709 " --> pdb=" O SER E 540 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE E 542 " --> pdb=" O ILE E 709 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 740 through 743 removed outlier: 3.707A pdb=" N LEU E 794 " --> pdb=" O GLU E 742 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 276 through 279 Processing sheet with id=AC4, first strand: chain 'F' and resid 365 through 366 removed outlier: 7.101A pdb=" N SER F 365 " --> pdb=" O VAL F 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 569 through 573 removed outlier: 6.329A pdb=" N ILE F 570 " --> pdb=" O LEU F 615 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP F 617 " --> pdb=" O ILE F 570 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE F 572 " --> pdb=" O ASP F 617 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 614 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR F 657 " --> pdb=" O VAL F 614 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 616 " --> pdb=" O THR F 657 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE F 542 " --> pdb=" O GLU F 707 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 740 through 743 removed outlier: 6.264A pdb=" N SER F 740 " --> pdb=" O ILE F 792 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 794 " --> pdb=" O SER F 740 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU F 742 " --> pdb=" O LEU F 794 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL F 796 " --> pdb=" O GLU F 742 " (cutoff:3.500A) 1325 hydrogen bonds defined for protein. 3852 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: 8.98 Time building geometry restraints manager: 11.68 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: 9239 1.34 - 1.45: 3324 1.45 - 1.57: 14782 1.57 - 1.69: 47 1.69 - 1.81: 150 Bond restraints: 27542 Sorted by residual: bond pdb=" C4 ATP E1001 " pdb=" C5 ATP E1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" C4 ATP A1003 " pdb=" C5 ATP A1003 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C4 ATP D1003 " pdb=" C5 ATP D1003 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" C4 ATP C1002 " pdb=" C5 ATP C1002 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.19e+01 bond pdb=" C4 ATP D1002 " pdb=" N9 ATP D1002 " ideal model delta sigma weight residual 1.374 1.311 0.063 1.00e-02 1.00e+04 4.02e+01 ... (remaining 27537 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.91: 550 105.91 - 113.49: 16403 113.49 - 121.08: 13395 121.08 - 128.67: 6690 128.67 - 136.25: 143 Bond angle restraints: 37181 Sorted by residual: angle pdb=" PB ATP C1002 " pdb=" O3B ATP C1002 " pdb=" PG ATP C1002 " ideal model delta sigma weight residual 139.87 112.15 27.72 1.00e+00 1.00e+00 7.68e+02 angle pdb=" PB ATP E1001 " pdb=" O3B ATP E1001 " pdb=" PG ATP E1001 " ideal model delta sigma weight residual 139.87 112.86 27.01 1.00e+00 1.00e+00 7.29e+02 angle pdb=" PB ATP A1003 " pdb=" O3B ATP A1003 " pdb=" PG ATP A1003 " ideal model delta sigma weight residual 139.87 116.82 23.05 1.00e+00 1.00e+00 5.31e+02 angle pdb=" PA ATP C1002 " pdb=" O3A ATP C1002 " pdb=" PB ATP C1002 " ideal model delta sigma weight residual 136.83 113.85 22.98 1.00e+00 1.00e+00 5.28e+02 angle pdb=" PA ATP E1001 " pdb=" O3A ATP E1001 " pdb=" PB ATP E1001 " ideal model delta sigma weight residual 136.83 114.23 22.60 1.00e+00 1.00e+00 5.11e+02 ... (remaining 37176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 15740 21.81 - 43.61: 1319 43.61 - 65.42: 133 65.42 - 87.23: 40 87.23 - 109.04: 3 Dihedral angle restraints: 17235 sinusoidal: 7314 harmonic: 9921 Sorted by residual: dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 49.04 -109.04 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" CA ASP A 327 " pdb=" C ASP A 327 " pdb=" N ALA A 328 " pdb=" CA ALA A 328 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA TYR B 323 " pdb=" C TYR B 323 " pdb=" N ILE B 324 " pdb=" CA ILE B 324 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 17232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2715 0.043 - 0.085: 1210 0.085 - 0.128: 331 0.128 - 0.170: 61 0.170 - 0.213: 12 Chirality restraints: 4329 Sorted by residual: chirality pdb=" C3' ADP B 901 " pdb=" C2' ADP B 901 " pdb=" C4' ADP B 901 " pdb=" O3' ADP B 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE D 274 " pdb=" CA ILE D 274 " pdb=" CG1 ILE D 274 " pdb=" CG2 ILE D 274 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE C 274 " pdb=" CA ILE C 274 " pdb=" CG1 ILE C 274 " pdb=" CG2 ILE C 274 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 4326 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 590 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO B 591 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 590 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO A 591 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 770 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C GLN C 770 " 0.039 2.00e-02 2.50e+03 pdb=" O GLN C 770 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS C 771 " -0.013 2.00e-02 2.50e+03 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 615 2.63 - 3.20: 28457 3.20 - 3.77: 42258 3.77 - 4.33: 59168 4.33 - 4.90: 95316 Nonbonded interactions: 225814 Sorted by model distance: nonbonded pdb=" O PHE A 543 " pdb=" OG SER A 658 " model vdw 2.066 3.040 nonbonded pdb=" OE2 GLU C 700 " pdb=" NE ARG C 704 " model vdw 2.084 3.120 nonbonded pdb=" OE1 GLU C 635 " pdb=" NH1 ARG D 763 " model vdw 2.095 3.120 nonbonded pdb=" OG1 THR B 215 " pdb=" O1A ATP A1003 " model vdw 2.102 3.040 nonbonded pdb=" O GLU C 721 " pdb=" OG SER C 724 " model vdw 2.105 3.040 ... (remaining 225809 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 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'B' and (resid 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'C' and (resid 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'D' and (resid 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'E' and (resid 159 through 247 or resid 255 through 285 or resid 295 thro \ ugh 407 or resid 469 through 588 or resid 600 through 660 or resid 683 through 7 \ 55 or resid 762 through 806)) selection = (chain 'F' and (resid 159 through 660 or resid 683 through 806)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 67.400 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.110 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.011 0.108 27542 Z= 0.689 Angle : 1.090 27.715 37181 Z= 0.712 Chirality : 0.050 0.213 4329 Planarity : 0.005 0.063 4789 Dihedral : 15.373 109.037 10791 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.64 % Favored : 90.13 % Rotamer: Outliers : 0.51 % Allowed : 11.60 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -3.56 (0.12), residues: 3373 helix: -2.07 (0.10), residues: 1783 sheet: -2.12 (0.23), residues: 385 loop : -2.61 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 483 HIS 0.008 0.002 HIS A 507 PHE 0.032 0.003 PHE D 649 TYR 0.033 0.003 TYR F 611 ARG 0.011 0.001 ARG C 733 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 423 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8603 (mmm) cc_final: 0.8217 (mmm) REVERT: A 246 THR cc_start: 0.8722 (p) cc_final: 0.8340 (p) REVERT: A 535 LYS cc_start: 0.7818 (mtmm) cc_final: 0.7409 (mmmt) REVERT: A 593 TYR cc_start: 0.7493 (m-80) cc_final: 0.7226 (m-80) REVERT: B 240 MET cc_start: 0.8703 (mmm) cc_final: 0.7972 (mmt) REVERT: B 381 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7302 (p90) REVERT: B 617 ASP cc_start: 0.7698 (t70) cc_final: 0.7498 (t70) REVERT: C 501 ASN cc_start: 0.7025 (t0) cc_final: 0.6758 (t0) REVERT: C 502 MET cc_start: 0.8633 (tmm) cc_final: 0.8352 (tmm) REVERT: C 705 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 666 LYS cc_start: 0.7278 (tptm) cc_final: 0.7029 (tptp) REVERT: D 781 LEU cc_start: 0.8972 (tp) cc_final: 0.8639 (tt) REVERT: E 381 TYR cc_start: 0.8716 (m-80) cc_final: 0.8491 (m-80) REVERT: E 397 GLU cc_start: 0.7953 (tt0) cc_final: 0.7732 (tt0) REVERT: E 472 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8579 (p) REVERT: E 474 ASP cc_start: 0.7722 (p0) cc_final: 0.7506 (p0) REVERT: E 573 ASP cc_start: 0.8138 (m-30) cc_final: 0.7882 (m-30) REVERT: F 242 LEU cc_start: 0.8296 (pt) cc_final: 0.7936 (pp) REVERT: F 269 ARG cc_start: 0.8654 (tpp80) cc_final: 0.8385 (tmm-80) REVERT: F 308 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7241 (tt0) REVERT: F 331 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 15 outliers final: 8 residues processed: 435 average time/residue: 0.4802 time to fit residues: 303.3397 Evaluate side-chains 269 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 258 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 705 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 202 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 287 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 267 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 309 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 682 HIS A 703 ASN A 785 ASN A 787 HIS B 203 ASN B 223 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS C 203 ASN C 227 ASN C 228 ASN C 352 GLN C 501 ASN C 513 GLN C 581 HIS C 787 HIS D 228 ASN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS E 501 ASN E 772 HIS F 159 ASN F 228 ASN F 338 GLN F 352 GLN ** F 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN F 682 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27542 Z= 0.221 Angle : 0.706 12.244 37181 Z= 0.361 Chirality : 0.045 0.199 4329 Planarity : 0.005 0.050 4789 Dihedral : 10.005 105.727 4035 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.22 % Allowed : 15.43 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.87 (0.14), residues: 3373 helix: -0.60 (0.11), residues: 1835 sheet: -1.72 (0.24), residues: 365 loop : -1.92 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 483 HIS 0.006 0.001 HIS A 282 PHE 0.022 0.001 PHE A 543 TYR 0.017 0.001 TYR F 611 ARG 0.006 0.001 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 358 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7335 (m-80) cc_final: 0.6819 (m-80) REVERT: A 535 LYS cc_start: 0.7443 (mtmm) cc_final: 0.7087 (mmmt) REVERT: A 593 TYR cc_start: 0.7293 (m-80) cc_final: 0.6951 (m-80) REVERT: A 734 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7904 (mm) REVERT: B 240 MET cc_start: 0.8683 (mmm) cc_final: 0.8215 (mmt) REVERT: B 323 TYR cc_start: 0.8199 (p90) cc_final: 0.7417 (p90) REVERT: B 381 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.6766 (p90) REVERT: B 488 VAL cc_start: 0.7276 (m) cc_final: 0.6900 (p) REVERT: C 351 LEU cc_start: 0.9212 (mt) cc_final: 0.8950 (mt) REVERT: C 393 ASP cc_start: 0.7310 (t0) cc_final: 0.6893 (t0) REVERT: C 501 ASN cc_start: 0.6844 (t0) cc_final: 0.6552 (t0) REVERT: C 685 MET cc_start: 0.7341 (mtm) cc_final: 0.6861 (mtm) REVERT: E 258 GLU cc_start: 0.7381 (pp20) cc_final: 0.7117 (pp20) REVERT: E 295 ASP cc_start: 0.6452 (m-30) cc_final: 0.6131 (m-30) REVERT: E 298 ASN cc_start: 0.8259 (m110) cc_final: 0.8048 (m110) REVERT: E 571 ARG cc_start: 0.8262 (ttt-90) cc_final: 0.7956 (ttt-90) REVERT: F 242 LEU cc_start: 0.8233 (pt) cc_final: 0.7526 (pp) REVERT: F 269 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8381 (tmm-80) REVERT: F 320 TYR cc_start: 0.8589 (t80) cc_final: 0.8346 (t80) REVERT: F 331 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7338 (tm-30) REVERT: F 624 PRO cc_start: 0.7617 (Cg_exo) cc_final: 0.7329 (Cg_endo) REVERT: F 726 MET cc_start: 0.9119 (mtp) cc_final: 0.8815 (mtm) outliers start: 65 outliers final: 34 residues processed: 406 average time/residue: 0.3937 time to fit residues: 249.7634 Evaluate side-chains 308 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 272 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 787 HIS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 722 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 172 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 310 optimal weight: 0.6980 chunk 335 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 HIS ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 GLN F 581 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27542 Z= 0.264 Angle : 0.670 11.413 37181 Z= 0.339 Chirality : 0.044 0.222 4329 Planarity : 0.004 0.045 4789 Dihedral : 9.706 102.926 4027 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.80 % Allowed : 18.19 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.32 (0.14), residues: 3373 helix: -0.11 (0.12), residues: 1838 sheet: -1.60 (0.24), residues: 365 loop : -1.70 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 483 HIS 0.010 0.001 HIS B 772 PHE 0.014 0.001 PHE A 543 TYR 0.019 0.002 TYR D 381 ARG 0.012 0.000 ARG C 571 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 305 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8260 (mmm) cc_final: 0.7875 (mmm) REVERT: A 253 TYR cc_start: 0.7363 (m-80) cc_final: 0.6869 (m-80) REVERT: A 535 LYS cc_start: 0.7377 (mtmm) cc_final: 0.7006 (mmmt) REVERT: A 593 TYR cc_start: 0.7291 (m-80) cc_final: 0.7001 (m-80) REVERT: A 734 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7894 (tp) REVERT: B 354 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8846 (tt) REVERT: B 381 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.6636 (p90) REVERT: B 488 VAL cc_start: 0.7390 (m) cc_final: 0.7075 (p) REVERT: C 351 LEU cc_start: 0.9258 (mt) cc_final: 0.9056 (mt) REVERT: C 393 ASP cc_start: 0.7270 (t0) cc_final: 0.6970 (t0) REVERT: C 685 MET cc_start: 0.7277 (mtm) cc_final: 0.6891 (mtm) REVERT: D 649 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7614 (p90) REVERT: E 295 ASP cc_start: 0.6428 (m-30) cc_final: 0.6176 (m-30) REVERT: E 298 ASN cc_start: 0.8198 (m110) cc_final: 0.7476 (m110) REVERT: E 483 TRP cc_start: 0.8570 (t60) cc_final: 0.8269 (t60) REVERT: E 571 ARG cc_start: 0.8241 (ttt-90) cc_final: 0.7853 (ttt-90) REVERT: F 269 ARG cc_start: 0.8633 (tpp80) cc_final: 0.8256 (tmm-80) REVERT: F 304 LEU cc_start: 0.9345 (mt) cc_final: 0.9070 (tt) REVERT: F 331 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7237 (tm-30) REVERT: F 578 MET cc_start: 0.7942 (tpt) cc_final: 0.7398 (tpt) outliers start: 82 outliers final: 47 residues processed: 365 average time/residue: 0.3560 time to fit residues: 210.5640 Evaluate side-chains 323 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 272 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 581 HIS Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 722 ILE Chi-restraints excluded: chain F residue 723 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 306 optimal weight: 9.9990 chunk 233 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 311 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 581 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27542 Z= 0.209 Angle : 0.641 10.458 37181 Z= 0.323 Chirality : 0.044 0.191 4329 Planarity : 0.004 0.047 4789 Dihedral : 9.376 98.301 4027 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.14 % Allowed : 19.25 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.94 (0.14), residues: 3373 helix: 0.21 (0.12), residues: 1837 sheet: -1.49 (0.24), residues: 363 loop : -1.56 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 483 HIS 0.010 0.001 HIS F 581 PHE 0.013 0.001 PHE A 543 TYR 0.014 0.001 TYR D 381 ARG 0.006 0.000 ARG C 571 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 315 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7408 (m-80) cc_final: 0.6917 (m-80) REVERT: A 535 LYS cc_start: 0.7181 (mtmm) cc_final: 0.6826 (mmmt) REVERT: A 593 TYR cc_start: 0.7278 (m-80) cc_final: 0.6997 (m-80) REVERT: B 381 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.6624 (p90) REVERT: B 488 VAL cc_start: 0.7550 (m) cc_final: 0.7270 (p) REVERT: C 316 THR cc_start: 0.8732 (m) cc_final: 0.8515 (p) REVERT: C 319 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: C 393 ASP cc_start: 0.7226 (t0) cc_final: 0.6959 (t0) REVERT: C 598 GLU cc_start: 0.7301 (mp0) cc_final: 0.7012 (pm20) REVERT: C 685 MET cc_start: 0.7312 (mtm) cc_final: 0.6954 (mtm) REVERT: D 649 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7635 (p90) REVERT: E 483 TRP cc_start: 0.8568 (t60) cc_final: 0.8264 (t60) REVERT: F 269 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8256 (tmm-80) REVERT: F 304 LEU cc_start: 0.9381 (mt) cc_final: 0.9089 (tt) REVERT: F 326 LYS cc_start: 0.6604 (mttt) cc_final: 0.5871 (mttp) REVERT: F 331 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7311 (tm-30) REVERT: F 578 MET cc_start: 0.7817 (tpt) cc_final: 0.7238 (tpt) outliers start: 92 outliers final: 52 residues processed: 387 average time/residue: 0.3724 time to fit residues: 233.5798 Evaluate side-chains 333 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 278 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 640 THR Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 722 ILE Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 274 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 245 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 281 optimal weight: 6.9990 chunk 227 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN B 632 GLN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN E 298 ASN ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27542 Z= 0.184 Angle : 0.631 10.850 37181 Z= 0.316 Chirality : 0.043 0.191 4329 Planarity : 0.004 0.049 4789 Dihedral : 9.053 94.558 4027 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.97 % Allowed : 20.38 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.66 (0.15), residues: 3373 helix: 0.41 (0.12), residues: 1840 sheet: -1.34 (0.25), residues: 367 loop : -1.37 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 483 HIS 0.007 0.001 HIS A 282 PHE 0.011 0.001 PHE B 697 TYR 0.015 0.001 TYR D 381 ARG 0.007 0.000 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 321 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7372 (m-80) cc_final: 0.6876 (m-80) REVERT: A 535 LYS cc_start: 0.7148 (mtmm) cc_final: 0.6755 (mmmt) REVERT: A 593 TYR cc_start: 0.7226 (m-80) cc_final: 0.6965 (m-80) REVERT: B 240 MET cc_start: 0.8654 (mmm) cc_final: 0.8395 (mmt) REVERT: B 381 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.6427 (p90) REVERT: B 488 VAL cc_start: 0.7516 (m) cc_final: 0.7273 (p) REVERT: B 705 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8866 (mm) REVERT: C 166 LEU cc_start: 0.9051 (mt) cc_final: 0.8685 (mp) REVERT: C 393 ASP cc_start: 0.7296 (t0) cc_final: 0.7018 (t0) REVERT: C 685 MET cc_start: 0.7285 (mtm) cc_final: 0.6934 (mtm) REVERT: D 649 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7860 (p90) REVERT: E 483 TRP cc_start: 0.8526 (t60) cc_final: 0.8280 (t60) REVERT: E 700 GLU cc_start: 0.7528 (mp0) cc_final: 0.7290 (mp0) REVERT: F 266 ASP cc_start: 0.7991 (m-30) cc_final: 0.7530 (m-30) REVERT: F 269 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8240 (tmm-80) REVERT: F 304 LEU cc_start: 0.9342 (mt) cc_final: 0.9049 (tt) REVERT: F 326 LYS cc_start: 0.6657 (mttt) cc_final: 0.5946 (mttp) REVERT: F 331 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7340 (tm-30) REVERT: F 578 MET cc_start: 0.7857 (tpt) cc_final: 0.7356 (tpt) outliers start: 87 outliers final: 55 residues processed: 388 average time/residue: 0.3607 time to fit residues: 227.3138 Evaluate side-chains 338 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 280 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 722 ILE Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 110 optimal weight: 0.9980 chunk 296 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 193 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 329 optimal weight: 0.7980 chunk 273 optimal weight: 0.4980 chunk 152 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 703 ASN D 628 ASN ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 785 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27542 Z= 0.173 Angle : 0.628 11.021 37181 Z= 0.314 Chirality : 0.043 0.228 4329 Planarity : 0.004 0.048 4789 Dihedral : 8.779 91.604 4024 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 2.97 % Allowed : 21.60 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.45 (0.15), residues: 3373 helix: 0.56 (0.12), residues: 1841 sheet: -1.21 (0.25), residues: 368 loop : -1.26 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 483 HIS 0.007 0.001 HIS D 718 PHE 0.011 0.001 PHE B 697 TYR 0.015 0.001 TYR E 596 ARG 0.007 0.000 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 307 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7379 (m-80) cc_final: 0.6856 (m-10) REVERT: A 335 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: A 535 LYS cc_start: 0.7063 (mtmm) cc_final: 0.6598 (mmmt) REVERT: A 593 TYR cc_start: 0.7222 (m-80) cc_final: 0.7006 (m-80) REVERT: B 240 MET cc_start: 0.8689 (mmm) cc_final: 0.8442 (mmt) REVERT: B 381 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.6454 (p90) REVERT: B 488 VAL cc_start: 0.7481 (m) cc_final: 0.7255 (p) REVERT: C 166 LEU cc_start: 0.9029 (mt) cc_final: 0.8681 (mp) REVERT: C 393 ASP cc_start: 0.7306 (t0) cc_final: 0.7007 (t0) REVERT: C 598 GLU cc_start: 0.7166 (mp0) cc_final: 0.6816 (pm20) REVERT: C 685 MET cc_start: 0.7249 (mtm) cc_final: 0.6881 (mtm) REVERT: D 649 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7871 (p90) REVERT: E 483 TRP cc_start: 0.8476 (t60) cc_final: 0.8164 (t60) REVERT: E 571 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.8007 (ttt-90) REVERT: F 304 LEU cc_start: 0.9309 (mt) cc_final: 0.9051 (tt) REVERT: F 331 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7322 (tm-30) REVERT: F 578 MET cc_start: 0.7782 (tpt) cc_final: 0.7409 (tpt) outliers start: 87 outliers final: 54 residues processed: 369 average time/residue: 0.3727 time to fit residues: 220.1734 Evaluate side-chains 323 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 266 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 318 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 328 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN F 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27542 Z= 0.210 Angle : 0.634 10.435 37181 Z= 0.316 Chirality : 0.043 0.299 4329 Planarity : 0.004 0.048 4789 Dihedral : 8.718 90.886 4024 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.07 % Allowed : 22.12 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.29 (0.15), residues: 3373 helix: 0.66 (0.12), residues: 1837 sheet: -1.11 (0.25), residues: 371 loop : -1.14 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 483 HIS 0.009 0.001 HIS A 282 PHE 0.012 0.001 PHE B 697 TYR 0.016 0.001 TYR E 596 ARG 0.007 0.000 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 287 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8220 (mmm) cc_final: 0.7974 (mmm) REVERT: A 253 TYR cc_start: 0.7423 (m-80) cc_final: 0.6848 (m-10) REVERT: A 265 MET cc_start: 0.8061 (mmp) cc_final: 0.7678 (mmm) REVERT: A 335 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: A 535 LYS cc_start: 0.7012 (mtmm) cc_final: 0.6526 (mmmt) REVERT: A 593 TYR cc_start: 0.7330 (m-80) cc_final: 0.6870 (m-80) REVERT: B 240 MET cc_start: 0.8743 (mmm) cc_final: 0.8493 (mmt) REVERT: B 381 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.6568 (p90) REVERT: B 488 VAL cc_start: 0.7544 (m) cc_final: 0.7283 (p) REVERT: C 166 LEU cc_start: 0.9039 (mt) cc_final: 0.8674 (mp) REVERT: C 393 ASP cc_start: 0.7294 (t0) cc_final: 0.7018 (t0) REVERT: C 685 MET cc_start: 0.7252 (mtm) cc_final: 0.6884 (mtm) REVERT: C 798 ASP cc_start: 0.7132 (p0) cc_final: 0.6865 (p0) REVERT: D 649 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7885 (p90) REVERT: E 483 TRP cc_start: 0.8588 (t60) cc_final: 0.8264 (t60) REVERT: F 304 LEU cc_start: 0.9311 (mt) cc_final: 0.9066 (tt) REVERT: F 326 LYS cc_start: 0.6484 (pttt) cc_final: 0.5866 (pttm) REVERT: F 331 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7303 (tm-30) REVERT: F 578 MET cc_start: 0.7782 (tpt) cc_final: 0.7431 (tpt) outliers start: 90 outliers final: 72 residues processed: 355 average time/residue: 0.3556 time to fit residues: 206.6839 Evaluate side-chains 342 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 267 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 407 PHE Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 203 optimal weight: 0.3980 chunk 131 optimal weight: 0.5980 chunk 196 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 208 optimal weight: 0.0370 chunk 223 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27542 Z= 0.174 Angle : 0.633 11.913 37181 Z= 0.315 Chirality : 0.043 0.224 4329 Planarity : 0.004 0.048 4789 Dihedral : 8.585 88.444 4024 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.97 % Allowed : 22.25 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.21 (0.15), residues: 3373 helix: 0.68 (0.12), residues: 1848 sheet: -0.99 (0.26), residues: 360 loop : -1.07 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 483 HIS 0.011 0.001 HIS A 282 PHE 0.022 0.001 PHE B 386 TYR 0.018 0.001 TYR E 596 ARG 0.007 0.000 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 294 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7316 (m-80) cc_final: 0.6764 (m-10) REVERT: A 265 MET cc_start: 0.8020 (mmp) cc_final: 0.7646 (mmm) REVERT: A 323 TYR cc_start: 0.8320 (m-80) cc_final: 0.8060 (m-10) REVERT: A 335 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: A 535 LYS cc_start: 0.6953 (mtmm) cc_final: 0.6466 (mmmt) REVERT: A 726 MET cc_start: 0.8362 (mpp) cc_final: 0.8155 (pmm) REVERT: B 240 MET cc_start: 0.8707 (mmm) cc_final: 0.8452 (mmt) REVERT: B 381 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.6507 (p90) REVERT: B 488 VAL cc_start: 0.7478 (m) cc_final: 0.7273 (p) REVERT: C 166 LEU cc_start: 0.9004 (mt) cc_final: 0.8607 (mp) REVERT: C 393 ASP cc_start: 0.7263 (t0) cc_final: 0.6950 (t0) REVERT: C 598 GLU cc_start: 0.7156 (mp0) cc_final: 0.6783 (pm20) REVERT: C 685 MET cc_start: 0.7389 (mtm) cc_final: 0.6781 (mtm) REVERT: D 649 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7759 (p90) REVERT: E 483 TRP cc_start: 0.8537 (t60) cc_final: 0.8233 (t60) REVERT: F 304 LEU cc_start: 0.9277 (mt) cc_final: 0.9050 (tt) REVERT: F 326 LYS cc_start: 0.6605 (pttt) cc_final: 0.6059 (pttm) REVERT: F 331 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7287 (tm-30) REVERT: F 578 MET cc_start: 0.7694 (tpt) cc_final: 0.7372 (tpt) REVERT: F 726 MET cc_start: 0.9012 (mtp) cc_final: 0.8762 (mtm) outliers start: 87 outliers final: 68 residues processed: 360 average time/residue: 0.3757 time to fit residues: 221.3500 Evaluate side-chains 337 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 266 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 649 PHE Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 407 PHE Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 298 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 240 optimal weight: 0.0670 chunk 93 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 289 optimal weight: 0.7980 chunk 305 optimal weight: 6.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.003 0.051 27542 Z= 0.193 Angle : 0.640 11.932 37181 Z= 0.318 Chirality : 0.043 0.210 4329 Planarity : 0.004 0.048 4789 Dihedral : 8.542 87.542 4024 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.70 % Allowed : 22.56 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.16 (0.15), residues: 3373 helix: 0.70 (0.12), residues: 1864 sheet: -0.90 (0.26), residues: 365 loop : -1.03 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 483 HIS 0.013 0.001 HIS A 282 PHE 0.013 0.001 PHE B 386 TYR 0.023 0.001 TYR E 596 ARG 0.008 0.000 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 276 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7335 (m-80) cc_final: 0.6767 (m-10) REVERT: A 265 MET cc_start: 0.8056 (mmp) cc_final: 0.7672 (mmm) REVERT: A 335 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: A 535 LYS cc_start: 0.6985 (mtmm) cc_final: 0.6492 (mmmt) REVERT: B 240 MET cc_start: 0.8714 (mmm) cc_final: 0.8460 (mmt) REVERT: B 381 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.6399 (p90) REVERT: B 488 VAL cc_start: 0.7511 (m) cc_final: 0.7243 (p) REVERT: C 166 LEU cc_start: 0.8983 (mt) cc_final: 0.8603 (mp) REVERT: C 393 ASP cc_start: 0.7293 (t0) cc_final: 0.6999 (t0) REVERT: C 685 MET cc_start: 0.7388 (mtm) cc_final: 0.6772 (mtm) REVERT: E 483 TRP cc_start: 0.8574 (t60) cc_final: 0.8277 (t60) REVERT: F 304 LEU cc_start: 0.9285 (mt) cc_final: 0.9055 (tt) REVERT: F 326 LYS cc_start: 0.6602 (pttt) cc_final: 0.6071 (pttm) REVERT: F 331 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7176 (tm-30) REVERT: F 573 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8150 (p0) REVERT: F 726 MET cc_start: 0.9010 (mtp) cc_final: 0.8770 (mtm) outliers start: 79 outliers final: 68 residues processed: 337 average time/residue: 0.3615 time to fit residues: 200.5422 Evaluate side-chains 338 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 267 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 407 PHE Chi-restraints excluded: chain F residue 573 ASP Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 201 optimal weight: 6.9990 chunk 323 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 312 optimal weight: 6.9990 chunk 270 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 208 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27542 Z= 0.209 Angle : 0.655 12.424 37181 Z= 0.324 Chirality : 0.043 0.192 4329 Planarity : 0.004 0.048 4789 Dihedral : 8.552 86.621 4024 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.59 % Allowed : 22.90 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.12 (0.15), residues: 3373 helix: 0.74 (0.12), residues: 1851 sheet: -0.88 (0.26), residues: 371 loop : -1.02 (0.20), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 483 HIS 0.016 0.001 HIS A 282 PHE 0.023 0.001 PHE B 386 TYR 0.018 0.001 TYR E 596 ARG 0.009 0.000 ARG E 571 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6746 Ramachandran restraints generated. 3373 Oldfield, 0 Emsley, 3373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 281 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7323 (m-80) cc_final: 0.6732 (m-10) REVERT: A 265 MET cc_start: 0.8072 (mmp) cc_final: 0.7683 (mmm) REVERT: A 335 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8224 (mp10) REVERT: A 535 LYS cc_start: 0.7022 (mtmm) cc_final: 0.6523 (mmmt) REVERT: B 240 MET cc_start: 0.8728 (mmm) cc_final: 0.8470 (mmt) REVERT: B 381 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.6498 (p90) REVERT: B 488 VAL cc_start: 0.7517 (m) cc_final: 0.7268 (p) REVERT: C 166 LEU cc_start: 0.8971 (mt) cc_final: 0.8581 (mp) REVERT: C 393 ASP cc_start: 0.7313 (t0) cc_final: 0.7030 (t0) REVERT: C 598 GLU cc_start: 0.7150 (mp0) cc_final: 0.6783 (pm20) REVERT: C 685 MET cc_start: 0.7349 (mtm) cc_final: 0.6748 (mtm) REVERT: E 483 TRP cc_start: 0.8615 (t60) cc_final: 0.8320 (t60) REVERT: F 304 LEU cc_start: 0.9277 (mt) cc_final: 0.9047 (tt) REVERT: F 326 LYS cc_start: 0.6733 (pttt) cc_final: 0.6208 (pttm) REVERT: F 331 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7189 (tm-30) REVERT: F 573 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8061 (p0) REVERT: F 578 MET cc_start: 0.7459 (tpt) cc_final: 0.7135 (mmm) REVERT: F 685 MET cc_start: 0.2753 (mmm) cc_final: 0.2292 (mmt) REVERT: F 726 MET cc_start: 0.9015 (mtp) cc_final: 0.8766 (mtm) outliers start: 76 outliers final: 66 residues processed: 339 average time/residue: 0.3709 time to fit residues: 204.4526 Evaluate side-chains 333 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 264 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 407 PHE Chi-restraints excluded: chain F residue 573 ASP Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 214 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 270 optimal weight: 0.0470 chunk 113 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN B 791 HIS D 228 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.107204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.086796 restraints weight = 65954.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.088926 restraints weight = 37926.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.090370 restraints weight = 25478.005| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3551 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: