Starting phenix.real_space_refine on Wed Mar 20 11:42:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/03_2024/7abr_11707_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/03_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_11707/03_2024/7abr_11707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/03_2024/7abr_11707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/03_2024/7abr_11707_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abr_11707/03_2024/7abr_11707_updated.pdb" } 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 14.15, per 1000 atoms: 0.52 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: 10.84 Conformation dependent library (CDL) restraints added in 5.0 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... running ksdssp... Secondary structure from input PDB file: 168 helices and 20 sheets defined 50.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.66 Creating SS restraints... Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 186 through 196 Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 297 through 305 Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 317 through 323 Processing helix chain 'A' and resid 327 through 332 removed outlier: 4.251A pdb=" N ARG A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 362 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 368 through 380 Processing helix chain 'A' and resid 389 through 407 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.638A pdb=" N VAL A 587 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 608 Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 624 through 634 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 696 Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 718 through 736 Processing helix chain 'A' and resid 745 through 755 Processing helix chain 'A' and resid 764 through 783 Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.617A pdb=" N LYS B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 196 removed outlier: 3.579A pdb=" N ARG B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 296 through 306 Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 317 through 323 Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.569A pdb=" N ILE B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'B' and resid 389 through 407 Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 502 through 508 Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 553 through 562 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 582 through 586 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 624 through 636 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 696 Processing helix chain 'B' and resid 699 through 704 removed outlier: 4.199A pdb=" N ARG B 704 " --> pdb=" O GLU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 737 removed outlier: 4.053A pdb=" N GLU B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 754 removed outlier: 3.651A pdb=" N GLU B 754 " --> pdb=" O LYS B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 782 Processing helix chain 'C' and resid 161 through 166 removed outlier: 4.207A pdb=" N SER C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 244 through 247 No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 306 Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 317 through 322 Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 344 through 362 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 368 through 380 Processing helix chain 'C' and resid 389 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 469 removed outlier: 5.270A pdb=" N SER C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 484 Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'C' and resid 514 through 528 Processing helix chain 'C' and resid 551 through 563 removed outlier: 3.593A pdb=" N ALA C 555 " --> pdb=" O LYS C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 587 removed outlier: 4.073A pdb=" N SER C 584 " --> pdb=" O HIS C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 608 Processing helix chain 'C' and resid 627 through 636 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 696 Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 716 through 737 removed outlier: 3.781A pdb=" N GLU C 736 " --> pdb=" O LYS C 732 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 755 Processing helix chain 'C' and resid 763 through 782 Processing helix chain 'D' and resid 161 through 164 No H-bonds generated for 'chain 'D' and resid 161 through 164' Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 186 through 197 Processing helix chain 'D' and resid 214 through 226 Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 244 through 247 No H-bonds generated for 'chain 'D' and resid 244 through 247' Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 281 through 284 Processing helix chain 'D' and resid 298 through 306 Proline residue: D 302 - end of helix Processing helix chain 'D' and resid 317 through 322 Processing helix chain 'D' and resid 324 through 327 No H-bonds generated for 'chain 'D' and resid 324 through 327' Processing helix chain 'D' and resid 330 through 333 No H-bonds generated for 'chain 'D' and resid 330 through 333' Processing helix chain 'D' and resid 344 through 362 removed outlier: 4.536A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 380 Processing helix chain 'D' and resid 389 through 406 Processing helix chain 'D' and resid 462 through 470 removed outlier: 4.934A pdb=" N SER D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU D 470 " --> pdb=" O GLN D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 494 through 509 removed outlier: 4.077A pdb=" N LEU D 500 " --> pdb=" O THR D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 528 Processing helix chain 'D' and resid 550 through 562 Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 580 through 585 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 601 through 608 Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 624 through 636 removed outlier: 4.027A pdb=" N ASP D 636 " --> pdb=" O GLN D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 666 Processing helix chain 'D' and resid 680 through 696 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 699 through 702 No H-bonds generated for 'chain 'D' and resid 699 through 702' Processing helix chain 'D' and resid 716 through 737 removed outlier: 3.920A pdb=" N GLN D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 754 Processing helix chain 'D' and resid 764 through 772 Processing helix chain 'D' and resid 774 through 782 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 186 through 197 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 215 through 226 Processing helix chain 'E' and resid 244 through 247 No H-bonds generated for 'chain 'E' and resid 244 through 247' Processing helix chain 'E' and resid 256 through 272 removed outlier: 3.544A pdb=" N GLU E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 284 Processing helix chain 'E' and resid 296 through 306 Proline residue: E 302 - end of helix Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 344 through 358 Processing helix chain 'E' and resid 368 through 380 Processing helix chain 'E' and resid 389 through 406 Processing helix chain 'E' and resid 473 through 483 Processing helix chain 'E' and resid 496 through 509 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 514 through 528 Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 574 through 576 No H-bonds generated for 'chain 'E' and resid 574 through 576' Processing helix chain 'E' and resid 581 through 587 removed outlier: 3.712A pdb=" N LEU E 586 " --> pdb=" O THR E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 608 Processing helix chain 'E' and resid 619 through 621 No H-bonds generated for 'chain 'E' and resid 619 through 621' Processing helix chain 'E' and resid 624 through 635 removed outlier: 3.730A pdb=" N VAL E 633 " --> pdb=" O ILE E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 696 Processing helix chain 'E' and resid 699 through 703 Processing helix chain 'E' and resid 717 through 737 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 745 through 754 Processing helix chain 'E' and resid 763 through 772 Processing helix chain 'E' and resid 774 through 783 Processing helix chain 'F' and resid 160 through 166 Processing helix chain 'F' and resid 170 through 176 removed outlier: 4.542A pdb=" N GLU F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 197 Processing helix chain 'F' and resid 214 through 226 Processing helix chain 'F' and resid 257 through 270 Processing helix chain 'F' and resid 281 through 284 No H-bonds generated for 'chain 'F' and resid 281 through 284' Processing helix chain 'F' and resid 297 through 306 Proline residue: F 302 - end of helix Processing helix chain 'F' and resid 317 through 330 removed outlier: 4.328A pdb=" N LYS F 326 " --> pdb=" O LYS F 322 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP F 327 " --> pdb=" O TYR F 323 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 362 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 368 through 381 removed outlier: 3.847A pdb=" N ARG F 380 " --> pdb=" O LYS F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 406 removed outlier: 4.100A pdb=" N ARG F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 484 Processing helix chain 'F' and resid 488 through 495 removed outlier: 4.042A pdb=" N THR F 494 " --> pdb=" O LYS F 490 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU F 495 " --> pdb=" O ILE F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 507 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 514 through 527 Processing helix chain 'F' and resid 551 through 562 Processing helix chain 'F' and resid 582 through 586 Processing helix chain 'F' and resid 602 through 608 Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 624 through 636 Processing helix chain 'F' and resid 683 through 696 removed outlier: 4.376A pdb=" N MET F 690 " --> pdb=" O LYS F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 703 Processing helix chain 'F' and resid 717 through 736 removed outlier: 3.685A pdb=" N LEU F 734 " --> pdb=" O LEU F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 745 through 752 Processing helix chain 'F' and resid 766 through 772 Processing helix chain 'F' and resid 774 through 782 Processing sheet with id= A, first strand: chain 'A' and resid 335 through 338 removed outlier: 3.698A pdb=" N GLY A 208 " --> pdb=" O THR A 315 " (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: 6.767A pdb=" N ARG A 238 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A 277 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET A 240 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP A 279 " --> pdb=" O MET A 240 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A 242 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 707 through 711 Processing sheet with id= C, first strand: chain 'A' and resid 741 through 743 removed outlier: 6.158A pdb=" N ILE A 792 " --> pdb=" O GLU A 742 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 707 through 711 removed outlier: 4.089A pdb=" N GLY B 539 " --> pdb=" O THR B 652 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER B 612 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE B 655 " --> pdb=" O SER B 612 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL B 614 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR B 657 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 616 " --> pdb=" O THR B 657 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 570 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ASP B 617 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE B 572 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 638 through 640 Processing sheet with id= G, first strand: chain 'B' and resid 740 through 743 Processing sheet with id= H, first strand: chain 'C' and resid 204 through 207 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: 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) Processing sheet with id= I, first strand: chain 'C' and resid 707 through 710 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) 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: 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) Processing sheet with id= J, first strand: chain 'C' and resid 638 through 640 Processing sheet with id= K, first strand: chain 'C' and resid 741 through 743 removed outlier: 6.395A pdb=" N ILE C 792 " --> pdb=" O GLU C 742 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 335 through 339 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) 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: 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) Processing sheet with id= M, first strand: chain 'D' and resid 707 through 710 removed outlier: 6.485A pdb=" N LEU D 654 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE D 543 " --> pdb=" O LEU D 654 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET D 656 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 792 through 796 Processing sheet with id= O, first strand: chain 'E' and resid 335 through 338 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: 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) Processing sheet with id= P, first strand: chain 'E' and resid 707 through 711 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) Processing sheet with id= Q, 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= R, first strand: chain 'F' and resid 336 through 338 removed outlier: 6.539A pdb=" N VAL F 205 " --> pdb=" O ILE F 337 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU F 206 " --> pdb=" O CYS F 311 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY F 313 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU F 276 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ALA F 314 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE F 278 " --> pdb=" O ALA F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'F' and resid 707 through 710 removed outlier: 3.856A pdb=" N ILE F 542 " --> pdb=" O GLU F 707 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU F 654 " --> pdb=" O PHE F 541 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N PHE F 543 " --> pdb=" O LEU F 654 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET F 656 " --> pdb=" O PHE F 543 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 740 through 743 1119 hydrogen bonds defined for protein. 3285 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: 8.64 Time building geometry restraints manager: 11.71 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: 634 2.63 - 3.20: 28604 3.20 - 3.77: 42474 3.77 - 4.33: 59537 4.33 - 4.90: 95389 Nonbonded interactions: 226638 Sorted by model distance: nonbonded pdb=" O PHE A 543 " pdb=" OG SER A 658 " model vdw 2.066 2.440 nonbonded pdb=" OE2 GLU C 700 " pdb=" NE ARG C 704 " model vdw 2.084 2.520 nonbonded pdb=" OE1 GLU C 635 " pdb=" NH1 ARG D 763 " model vdw 2.095 2.520 nonbonded pdb=" OG1 THR B 215 " pdb=" O1A ATP A1003 " model vdw 2.102 2.440 nonbonded pdb=" O GLU C 721 " pdb=" OG SER C 724 " model vdw 2.105 2.440 ... (remaining 226633 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.260 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: 6.420 Check model and map are aligned: 0.430 Set scattering table: 0.200 Process input model: 71.090 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.510 ------------------------------------------------------------------------------- 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= 0.691 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 : 3.227 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: 0.4879 time to fit residues: 308.1475 Evaluate side-chains 269 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 258 time to evaluate : 3.272 ------------------------------------------------------------------------------- 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: 2.9990 chunk 258 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 174 optimal weight: 0.4980 chunk 138 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 309 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 A 632 GLN A 682 HIS A 703 ASN A 785 ASN ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 223 GLN B 270 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS C 203 ASN C 227 ASN C 228 ASN C 349 GLN 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 338 GLN E 362 HIS E 501 ASN E 772 HIS F 159 ASN F 228 ASN F 338 GLN F 352 GLN F 513 GLN F 632 GLN F 682 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27542 Z= 0.214 Angle : 0.668 11.592 37181 Z= 0.337 Chirality : 0.044 0.229 4329 Planarity : 0.004 0.050 4789 Dihedral : 9.936 107.161 4035 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.70 % Favored : 93.27 % Rotamer: Outliers : 2.53 % Allowed : 16.28 % Favored : 81.19 % 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: -1.88 (0.14), residues: 3373 helix: -0.65 (0.12), residues: 1817 sheet: -1.58 (0.24), residues: 358 loop : -1.88 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 483 HIS 0.007 0.001 HIS A 282 PHE 0.026 0.002 PHE A 543 TYR 0.018 0.001 TYR F 611 ARG 0.007 0.000 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 426 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 352 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8172 (mmm) cc_final: 0.7969 (mmm) REVERT: A 253 TYR cc_start: 0.7302 (m-80) cc_final: 0.6786 (m-80) REVERT: A 535 LYS cc_start: 0.7440 (mtmm) cc_final: 0.7071 (mmmt) REVERT: A 593 TYR cc_start: 0.7300 (m-80) cc_final: 0.7011 (m-80) REVERT: B 240 MET cc_start: 0.8706 (mmm) cc_final: 0.8074 (mmt) REVERT: B 258 GLU cc_start: 0.8778 (pm20) cc_final: 0.8330 (pm20) REVERT: B 323 TYR cc_start: 0.8208 (p90) cc_final: 0.7329 (p90) REVERT: B 381 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.6719 (p90) REVERT: B 488 VAL cc_start: 0.7266 (m) cc_final: 0.6957 (p) REVERT: C 351 LEU cc_start: 0.9200 (mt) cc_final: 0.8940 (mt) REVERT: C 501 ASN cc_start: 0.6864 (t0) cc_final: 0.6555 (t0) REVERT: C 685 MET cc_start: 0.7305 (mtm) cc_final: 0.6820 (mtm) REVERT: D 553 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7338 (tm-30) REVERT: D 638 ARG cc_start: 0.7439 (ptm-80) cc_final: 0.7178 (ptm-80) REVERT: D 666 LYS cc_start: 0.7207 (tptm) cc_final: 0.6998 (tptp) REVERT: F 304 LEU cc_start: 0.9421 (mt) cc_final: 0.9089 (tt) REVERT: F 308 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7388 (tt0) REVERT: F 319 GLU cc_start: 0.8457 (mp0) cc_final: 0.8114 (mp0) REVERT: F 331 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7298 (tm-30) REVERT: F 726 MET cc_start: 0.9115 (mtp) cc_final: 0.8817 (mtm) outliers start: 74 outliers final: 42 residues processed: 404 average time/residue: 0.3861 time to fit residues: 247.1974 Evaluate side-chains 306 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 263 time to evaluate : 2.999 ------------------------------------------------------------------------------- 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 346 GLU 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 219 GLU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 345 ASP 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 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 311 CYS 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 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain F residue 202 ASN 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 722 ILE Chi-restraints excluded: chain F residue 779 GLU 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: 0.0980 chunk 257 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 335 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2168 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= 0.221 Angle : 0.621 10.872 37181 Z= 0.311 Chirality : 0.043 0.225 4329 Planarity : 0.004 0.045 4789 Dihedral : 9.508 101.851 4028 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.62 % Allowed : 18.87 % Favored : 77.51 % 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: -1.19 (0.14), residues: 3373 helix: -0.05 (0.12), residues: 1804 sheet: -1.33 (0.25), residues: 376 loop : -1.60 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 483 HIS 0.005 0.001 HIS A 282 PHE 0.018 0.001 PHE A 543 TYR 0.018 0.001 TYR D 381 ARG 0.004 0.000 ARG D 667 *********************** 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 410 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 304 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7289 (m-80) cc_final: 0.6818 (m-80) REVERT: A 535 LYS cc_start: 0.7272 (mtmm) cc_final: 0.6918 (mmmt) REVERT: A 593 TYR cc_start: 0.7273 (m-80) cc_final: 0.6994 (m-80) REVERT: B 240 MET cc_start: 0.8621 (mmm) cc_final: 0.8057 (mmt) REVERT: B 381 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.6591 (p90) REVERT: B 488 VAL cc_start: 0.7462 (m) cc_final: 0.7246 (p) REVERT: C 685 MET cc_start: 0.7251 (mtm) cc_final: 0.6860 (mtm) REVERT: D 547 THR cc_start: 0.8360 (m) cc_final: 0.8116 (m) REVERT: D 649 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7806 (p90) REVERT: F 304 LEU cc_start: 0.9377 (mt) cc_final: 0.9083 (tt) REVERT: F 319 GLU cc_start: 0.8355 (mp0) cc_final: 0.7953 (mp0) REVERT: F 331 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7329 (tm-30) outliers start: 106 outliers final: 60 residues processed: 389 average time/residue: 0.3556 time to fit residues: 225.5832 Evaluate side-chains 333 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 271 time to evaluate : 3.096 ------------------------------------------------------------------------------- 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 246 THR Chi-restraints excluded: chain A residue 368 ASP 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 197 SER Chi-restraints excluded: chain B residue 354 LEU 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 243 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 327 ASP 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 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 345 ASP 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 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 494 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 533 ASP Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain F residue 202 ASN 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 351 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 603 THR Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 722 ILE Chi-restraints excluded: chain F residue 779 GLU Chi-restraints excluded: chain F residue 803 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: 0.8980 chunk 161 optimal weight: 0.0050 chunk 34 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 311 optimal weight: 0.0370 chunk 329 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 295 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 overall best weight: 0.5272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 282 HIS ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 27542 Z= 0.165 Angle : 0.591 9.852 37181 Z= 0.294 Chirality : 0.042 0.187 4329 Planarity : 0.003 0.046 4789 Dihedral : 9.037 95.432 4028 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.34 % Allowed : 20.31 % Favored : 76.35 % 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: -0.74 (0.15), residues: 3373 helix: 0.30 (0.12), residues: 1816 sheet: -1.11 (0.25), residues: 373 loop : -1.38 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 483 HIS 0.009 0.001 HIS A 282 PHE 0.015 0.001 PHE A 543 TYR 0.013 0.001 TYR D 381 ARG 0.008 0.000 ARG A 199 *********************** 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 425 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 327 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7273 (m-80) cc_final: 0.6790 (m-80) REVERT: A 535 LYS cc_start: 0.7081 (mtmm) cc_final: 0.6677 (mmmt) REVERT: A 593 TYR cc_start: 0.7252 (m-80) cc_final: 0.6791 (m-80) REVERT: A 596 TYR cc_start: 0.8493 (t80) cc_final: 0.7946 (t80) REVERT: B 381 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.6567 (p90) REVERT: B 488 VAL cc_start: 0.7526 (m) cc_final: 0.7265 (p) REVERT: C 202 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8250 (p0) REVERT: C 598 GLU cc_start: 0.7372 (mp0) cc_final: 0.6967 (pm20) REVERT: C 685 MET cc_start: 0.7294 (mtm) cc_final: 0.6894 (mtm) REVERT: D 649 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7690 (p90) REVERT: E 258 GLU cc_start: 0.7432 (pp20) cc_final: 0.7177 (pp20) REVERT: E 483 TRP cc_start: 0.8532 (t60) cc_final: 0.8252 (t60) REVERT: F 304 LEU cc_start: 0.9359 (mt) cc_final: 0.8990 (tt) REVERT: F 319 GLU cc_start: 0.8410 (mp0) cc_final: 0.8146 (mp0) REVERT: F 320 TYR cc_start: 0.8840 (t80) cc_final: 0.8530 (t80) REVERT: F 331 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7289 (tm-30) REVERT: F 578 MET cc_start: 0.8093 (tpt) cc_final: 0.7666 (tpt) outliers start: 98 outliers final: 60 residues processed: 406 average time/residue: 0.3726 time to fit residues: 243.2485 Evaluate side-chains 339 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 276 time to evaluate : 2.943 ------------------------------------------------------------------------------- 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 368 ASP 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 734 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 484 THR 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 180 ASP Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 327 ASP 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 203 ASN Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 345 ASP 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 E residue 160 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 241 THR 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 392 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 533 ASP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 203 ASN 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 351 LEU Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 722 ILE Chi-restraints excluded: chain F residue 779 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 274 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 245 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 281 optimal weight: 0.6980 chunk 227 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 168 optimal weight: 0.7980 chunk 295 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27542 Z= 0.179 Angle : 0.596 9.757 37181 Z= 0.295 Chirality : 0.042 0.217 4329 Planarity : 0.003 0.048 4789 Dihedral : 8.860 92.952 4026 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.52 % Allowed : 21.33 % Favored : 75.15 % 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: -0.53 (0.15), residues: 3373 helix: 0.46 (0.12), residues: 1819 sheet: -0.95 (0.25), residues: 371 loop : -1.31 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 483 HIS 0.005 0.001 HIS F 581 PHE 0.012 0.001 PHE A 543 TYR 0.014 0.001 TYR E 596 ARG 0.007 0.000 ARG F 695 *********************** 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 405 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 302 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.7284 (m-80) cc_final: 0.6785 (m-80) REVERT: A 535 LYS cc_start: 0.7068 (mtmm) cc_final: 0.6627 (mmmt) REVERT: A 596 TYR cc_start: 0.8496 (t80) cc_final: 0.8255 (t80) REVERT: A 726 MET cc_start: 0.8368 (mpp) cc_final: 0.8030 (mpp) REVERT: B 240 MET cc_start: 0.8693 (mmm) cc_final: 0.8390 (mmt) REVERT: B 381 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.6542 (p90) REVERT: B 488 VAL cc_start: 0.7491 (m) cc_final: 0.7286 (p) REVERT: C 202 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8345 (p0) REVERT: C 685 MET cc_start: 0.7261 (mtm) cc_final: 0.6925 (mtm) REVERT: D 649 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8032 (p90) REVERT: E 258 GLU cc_start: 0.7537 (pp20) cc_final: 0.7313 (pp20) REVERT: E 483 TRP cc_start: 0.8547 (t60) cc_final: 0.8258 (t60) REVERT: F 304 LEU cc_start: 0.9362 (mt) cc_final: 0.9000 (tt) REVERT: F 319 GLU cc_start: 0.8362 (mp0) cc_final: 0.8065 (mp0) REVERT: F 320 TYR cc_start: 0.8809 (t80) cc_final: 0.8533 (t80) REVERT: F 331 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7287 (tm-30) REVERT: F 578 MET cc_start: 0.8134 (tpt) cc_final: 0.7783 (tpt) outliers start: 103 outliers final: 78 residues processed: 386 average time/residue: 0.3596 time to fit residues: 224.7034 Evaluate side-chains 360 residues out of total 2930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 279 time to evaluate : 3.262 ------------------------------------------------------------------------------- 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 368 ASP 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 698 ARG Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 327 ASP 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 202 ASN Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 478 MET 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 697 PHE Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 345 ASP 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 665 LEU Chi-restraints excluded: chain D residue 756 VAL 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 241 THR 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 392 ILE Chi-restraints excluded: chain E residue 474 ASP 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 636 ASP Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 803 VAL Chi-restraints excluded: chain F residue 203 ASN 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 351 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 573 ASP Chi-restraints excluded: chain F residue 611 TYR Chi-restraints excluded: chain F residue 617 ASP Chi-restraints excluded: chain F residue 684 ASP Chi-restraints excluded: chain F residue 779 GLU Chi-restraints excluded: chain F residue 803 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.8333 > 50: distance: 21 - 25: 16.237 distance: 25 - 26: 26.797 distance: 26 - 27: 28.659 distance: 26 - 29: 19.110 distance: 27 - 28: 21.715 distance: 27 - 33: 18.976 distance: 29 - 30: 31.033 distance: 30 - 31: 24.735 distance: 30 - 32: 26.832 distance: 33 - 34: 16.310 distance: 34 - 35: 9.737 distance: 34 - 37: 28.190 distance: 35 - 36: 25.779 distance: 35 - 39: 20.488 distance: 37 - 38: 50.461 distance: 39 - 40: 21.711 distance: 40 - 41: 16.292 distance: 40 - 43: 13.440 distance: 41 - 42: 24.130 distance: 41 - 47: 24.309 distance: 43 - 44: 3.564 distance: 44 - 45: 15.932 distance: 44 - 46: 24.711 distance: 47 - 48: 32.398 distance: 48 - 49: 42.818 distance: 48 - 51: 43.843 distance: 49 - 50: 43.995 distance: 49 - 55: 28.245 distance: 51 - 52: 8.603 distance: 52 - 53: 19.407 distance: 52 - 54: 36.405 distance: 55 - 56: 34.083 distance: 55 - 61: 38.960 distance: 56 - 57: 22.804 distance: 56 - 59: 25.760 distance: 57 - 58: 26.408 distance: 57 - 62: 39.732 distance: 59 - 60: 23.370 distance: 60 - 61: 32.906 distance: 62 - 63: 10.326 distance: 63 - 64: 36.509 distance: 63 - 66: 39.842 distance: 64 - 65: 46.622 distance: 64 - 69: 21.382 distance: 66 - 67: 24.041 distance: 66 - 68: 41.282 distance: 69 - 70: 41.719 distance: 70 - 71: 35.628 distance: 70 - 73: 33.397 distance: 71 - 72: 8.724 distance: 71 - 77: 28.595 distance: 73 - 74: 35.164 distance: 73 - 75: 42.728 distance: 74 - 76: 33.341 distance: 77 - 78: 56.520 distance: 78 - 79: 39.447 distance: 79 - 80: 40.736 distance: 79 - 81: 29.849 distance: 81 - 82: 37.609 distance: 82 - 83: 4.018 distance: 82 - 85: 41.357 distance: 83 - 84: 15.888 distance: 83 - 92: 42.140 distance: 85 - 86: 46.190 distance: 86 - 87: 49.705 distance: 87 - 88: 21.138 distance: 88 - 89: 6.522 distance: 89 - 90: 8.199 distance: 89 - 91: 19.800 distance: 92 - 93: 22.084 distance: 93 - 94: 12.344 distance: 93 - 96: 14.397 distance: 94 - 95: 21.485 distance: 94 - 98: 12.717 distance: 95 - 119: 26.946 distance: 96 - 97: 37.076