Starting phenix.real_space_refine on Tue Feb 13 21:46:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2024/6xzq_10665.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2024/6xzq_10665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2024/6xzq_10665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2024/6xzq_10665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2024/6xzq_10665.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2024/6xzq_10665.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 S 212 5.16 5 C 17983 2.51 5 N 4850 2.21 5 O 5345 1.98 5 H 28480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 195": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 299": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A ARG 468": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 552": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 568": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 383": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 523": "OD1" <-> "OD2" Residue "B ASP 566": "OD1" <-> "OD2" Residue "B ARG 624": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 663": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 665": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B ASP 690": "OD1" <-> "OD2" Residue "B PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 738": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "C ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C ASP 265": "OD1" <-> "OD2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C ASP 315": "OD1" <-> "OD2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C ASP 434": "OD1" <-> "OD2" Residue "C ARG 441": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ASP 559": "OD1" <-> "OD2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C ARG 611": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 656": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 692": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 700": "OE1" <-> "OE2" Residue "C ASP 703": "OD1" <-> "OD2" Residue "C PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 195": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 299": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 302": "OD1" <-> "OD2" Residue "D ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D ASP 392": "OD1" <-> "OD2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D ASP 408": "OD1" <-> "OD2" Residue "D GLU 410": "OE1" <-> "OE2" Residue "D TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 468": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D GLU 480": "OE1" <-> "OE2" Residue "D ASP 498": "OD1" <-> "OD2" Residue "D ASP 499": "OD1" <-> "OD2" Residue "D ARG 552": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 568": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 595": "OE1" <-> "OE2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "D ASP 636": "OD1" <-> "OD2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 654": "OE1" <-> "OE2" Residue "D PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 672": "OE1" <-> "OE2" Residue "D GLU 675": "OE1" <-> "OE2" Residue "D GLU 676": "OE1" <-> "OE2" Residue "E ASP 48": "OD1" <-> "OD2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E ASP 212": "OD1" <-> "OD2" Residue "E ASP 217": "OD1" <-> "OD2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ASP 298": "OD1" <-> "OD2" Residue "E TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 383": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 400": "OD1" <-> "OD2" Residue "E PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 446": "OD1" <-> "OD2" Residue "E ASP 447": "OD1" <-> "OD2" Residue "E GLU 492": "OE1" <-> "OE2" Residue "F GLU 560": "OE1" <-> "OE2" Residue "F ASP 579": "OD1" <-> "OD2" Residue "F ASP 590": "OD1" <-> "OD2" Residue "F GLU 599": "OE1" <-> "OE2" Residue "F ARG 611": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 656": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 680": "OD1" <-> "OD2" Residue "F TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 692": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 699": "OD1" <-> "OD2" Residue "F GLU 710": "OE1" <-> "OE2" Residue "F GLU 716": "OE1" <-> "OE2" Residue "F ASP 728": "OD1" <-> "OD2" Residue "F ASP 731": "OD1" <-> "OD2" Residue "F PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G ASP 119": "OD1" <-> "OD2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ASP 157": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 56888 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 617 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 14} Chain breaks: 1 Chain: "A" Number of atoms: 11269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 11269 Classifications: {'peptide': 696} Link IDs: {'PTRANS': 32, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 11188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 11188 Classifications: {'peptide': 698} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 672} Chain breaks: 4 Chain: "C" Number of atoms: 12385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 12385 Classifications: {'peptide': 772} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 743} Chain: "D" Number of atoms: 8550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8550 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 27, 'TRANS': 497} Chain: "E" Number of atoms: 7239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 7239 Classifications: {'peptide': 448} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 433} Chain breaks: 3 Chain: "F" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3101 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "G" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2539 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Time building chain proxies: 17.73, per 1000 atoms: 0.31 Number of scatterers: 56888 At special positions: 0 Unit cell: (121.52, 154.07, 176.855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 212 16.00 P 18 15.00 O 5345 8.00 N 4850 7.00 C 17983 6.00 H 28480 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.09 Conformation dependent library (CDL) restraints added in 4.6 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 37 sheets defined 48.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.675A pdb=" N ILE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.738A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.857A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.782A pdb=" N LYS A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 309 through 327 removed outlier: 4.050A pdb=" N TYR A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 409 through 427 Processing helix chain 'A' and resid 430 through 452 removed outlier: 3.630A pdb=" N LEU A 451 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 569 through 588 removed outlier: 3.667A pdb=" N ARG A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 617 through 634 removed outlier: 5.091A pdb=" N ARG A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 666 through 677 removed outlier: 3.707A pdb=" N LEU A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 700 removed outlier: 3.808A pdb=" N LYS A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.771A pdb=" N MET B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 removed outlier: 4.530A pdb=" N SER B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 86 through 102 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.955A pdb=" N HIS B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.707A pdb=" N ASP B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.753A pdb=" N LEU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 removed outlier: 4.132A pdb=" N LYS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.719A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.631A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 3.771A pdb=" N LYS B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.951A pdb=" N THR B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 425 " --> pdb=" O GLY B 421 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.533A pdb=" N LYS B 433 " --> pdb=" O ASP B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.531A pdb=" N TRP B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 519 through 538 removed outlier: 4.102A pdb=" N PHE B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.653A pdb=" N ILE B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS B 582 " --> pdb=" O ASN B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.878A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 675 through 696 removed outlier: 4.007A pdb=" N MET B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 681 " --> pdb=" O ALA B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 728 removed outlier: 3.546A pdb=" N ILE B 728 " --> pdb=" O MET B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 754 removed outlier: 3.557A pdb=" N ARG B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.774A pdb=" N THR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 removed outlier: 3.786A pdb=" N SER C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.910A pdb=" N ASN C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.923A pdb=" N ASP C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.850A pdb=" N VAL C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 259 through 277 removed outlier: 3.858A pdb=" N LYS C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 306 through 313 Processing helix chain 'C' and resid 317 through 328 removed outlier: 3.593A pdb=" N LEU C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 417 Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.979A pdb=" N LYS C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 3.947A pdb=" N SER C 436 " --> pdb=" O MET C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.580A pdb=" N SER C 456 " --> pdb=" O TRP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 467 removed outlier: 3.580A pdb=" N LEU C 460 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.881A pdb=" N ASP C 535 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 536 " --> pdb=" O ILE C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 536' Processing helix chain 'C' and resid 558 through 574 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 590 through 595 removed outlier: 4.153A pdb=" N LEU C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 595' Processing helix chain 'C' and resid 597 through 604 Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 611 through 630 removed outlier: 3.801A pdb=" N SER C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 641 Processing helix chain 'C' and resid 642 through 644 No H-bonds generated for 'chain 'C' and resid 642 through 644' Processing helix chain 'C' and resid 705 through 709 removed outlier: 3.936A pdb=" N LEU C 708 " --> pdb=" O SER C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 732 removed outlier: 3.507A pdb=" N ILE C 730 " --> pdb=" O GLN C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 771 removed outlier: 4.031A pdb=" N ASP C 762 " --> pdb=" O ALA C 758 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 771 " --> pdb=" O VAL C 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 219 through 233 Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.957A pdb=" N SER D 280 " --> pdb=" O PRO D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 292 removed outlier: 3.700A pdb=" N LYS D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 309 through 326 removed outlier: 3.727A pdb=" N TYR D 313 " --> pdb=" O TYR D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 356 through 364 removed outlier: 3.638A pdb=" N ILE D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 390 Processing helix chain 'D' and resid 409 through 427 Processing helix chain 'D' and resid 429 through 452 removed outlier: 3.671A pdb=" N ARG D 433 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 565 Processing helix chain 'D' and resid 568 through 589 removed outlier: 3.692A pdb=" N ILE D 572 " --> pdb=" O ARG D 568 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 585 " --> pdb=" O ILE D 581 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER D 586 " --> pdb=" O CYS D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 601 Processing helix chain 'D' and resid 617 through 635 removed outlier: 4.595A pdb=" N ARG D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL D 623 " --> pdb=" O GLU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.875A pdb=" N LYS D 647 " --> pdb=" O CYS D 643 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS D 648 " --> pdb=" O ASN D 644 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE D 649 " --> pdb=" O GLU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 677 removed outlier: 3.603A pdb=" N LEU D 670 " --> pdb=" O ASN D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 700 removed outlier: 4.030A pdb=" N LYS D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 13 through 18 removed outlier: 3.942A pdb=" N LEU E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 22 Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.694A pdb=" N SER E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 102 removed outlier: 3.590A pdb=" N LEU E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.791A pdb=" N LYS E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 141 through 158 removed outlier: 3.591A pdb=" N ALA E 145 " --> pdb=" O PRO E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 178 removed outlier: 3.536A pdb=" N ASP E 177 " --> pdb=" O ILE E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 224 Processing helix chain 'E' and resid 250 through 268 removed outlier: 4.388A pdb=" N LYS E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 268 " --> pdb=" O ILE E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 295 Processing helix chain 'E' and resid 316 through 329 removed outlier: 3.669A pdb=" N TYR E 320 " --> pdb=" O GLN E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 341 through 348 Processing helix chain 'E' and resid 374 through 378 Processing helix chain 'E' and resid 383 through 389 Processing helix chain 'E' and resid 390 through 395 removed outlier: 4.438A pdb=" N LYS E 395 " --> pdb=" O GLU E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 426 Processing helix chain 'E' and resid 429 through 436 removed outlier: 3.720A pdb=" N LYS E 433 " --> pdb=" O ASP E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 473 Processing helix chain 'F' and resid 560 through 575 removed outlier: 4.033A pdb=" N LEU F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 589 Processing helix chain 'F' and resid 591 through 596 Processing helix chain 'F' and resid 597 through 604 removed outlier: 3.564A pdb=" N LYS F 601 " --> pdb=" O LEU F 597 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 607 No H-bonds generated for 'chain 'F' and resid 605 through 607' Processing helix chain 'F' and resid 611 through 630 Processing helix chain 'F' and resid 633 through 641 Processing helix chain 'F' and resid 642 through 644 No H-bonds generated for 'chain 'F' and resid 642 through 644' Processing helix chain 'F' and resid 726 through 732 removed outlier: 3.841A pdb=" N ILE F 730 " --> pdb=" O GLN F 727 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'G' and resid 82 through 87 Processing helix chain 'G' and resid 106 through 112 Processing helix chain 'G' and resid 123 through 128 Processing helix chain 'G' and resid 130 through 139 removed outlier: 3.762A pdb=" N ASN G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 removed outlier: 3.513A pdb=" N VAL A 62 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.753A pdb=" N ALA B 454 " --> pdb=" O PHE B 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.569A pdb=" N PHE A 271 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS A 551 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 removed outlier: 3.545A pdb=" N ILE A 331 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 456 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 457 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA A 463 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU A 484 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER A 465 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP A 482 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 350 removed outlier: 3.733A pdb=" N GLU B 367 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 369 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA7, first strand: chain 'A' and resid 611 through 616 removed outlier: 6.275A pdb=" N GLU A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 607 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 605 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 615 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 3.690A pdb=" N ARG B 138 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.556A pdb=" N ILE B 214 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AB4, first strand: chain 'B' and resid 491 through 492 removed outlier: 3.773A pdb=" N PHE B 491 " --> pdb=" O PHE B 498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 61 through 63 Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 142 removed outlier: 6.429A pdb=" N TRP C 137 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN C 252 " --> pdb=" O TRP C 137 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU C 139 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 153 Processing sheet with id=AB8, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AB9, first strand: chain 'C' and resid 335 through 336 removed outlier: 3.555A pdb=" N LEU C 342 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU C 374 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 397 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP C 395 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR C 497 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 396 " --> pdb=" O THR C 497 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 352 through 357 Processing sheet with id=AC2, first strand: chain 'C' and resid 469 through 471 Processing sheet with id=AC3, first strand: chain 'C' and resid 657 through 658 Processing sheet with id=AC4, first strand: chain 'C' and resid 683 through 685 Processing sheet with id=AC5, first strand: chain 'C' and resid 713 through 714 removed outlier: 3.609A pdb=" N SER C 746 " --> pdb=" O VAL C 742 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.309A pdb=" N ILE D 461 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE D 487 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL D 459 " --> pdb=" O ILE D 487 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL D 489 " --> pdb=" O LYS D 457 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS D 457 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 274 removed outlier: 7.572A pdb=" N PHE D 485 " --> pdb=" O PHE D 509 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 366 through 367 Processing sheet with id=AC9, first strand: chain 'D' and resid 395 through 396 Processing sheet with id=AD1, first strand: chain 'D' and resid 529 through 536 Processing sheet with id=AD2, first strand: chain 'D' and resid 612 through 616 removed outlier: 6.617A pdb=" N ILE D 613 " --> pdb=" O ILE D 605 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU E 2 " --> pdb=" O LYS D 607 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 54 through 58 removed outlier: 4.404A pdb=" N VAL E 54 " --> pdb=" O LYS E 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AD5, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AD6, first strand: chain 'E' and resid 225 through 226 removed outlier: 7.068A pdb=" N ILE E 226 " --> pdb=" O LYS E 352 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 438 through 443 removed outlier: 3.592A pdb=" N ALA E 454 " --> pdb=" O PHE E 300 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 684 through 686 Processing sheet with id=AD9, first strand: chain 'F' and resid 712 through 714 Processing sheet with id=AE1, first strand: chain 'G' and resid 92 through 94 1273 hydrogen bonds defined for protein. 3531 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: 18.14 Time building geometry restraints manager: 34.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 28406 1.00 - 1.20: 74 1.20 - 1.41: 11506 1.41 - 1.61: 17127 1.61 - 1.81: 351 Bond restraints: 57464 Sorted by residual: bond pdb=" ND2 ASN C 103 " pdb="HD22 ASN C 103 " ideal model delta sigma weight residual 0.860 0.798 0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" NE2 GLN A 627 " pdb="HE22 GLN A 627 " ideal model delta sigma weight residual 0.860 0.803 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" NE2 GLN B 554 " pdb="HE22 GLN B 554 " ideal model delta sigma weight residual 0.860 0.804 0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" ND2 ASN A 318 " pdb="HD22 ASN A 318 " ideal model delta sigma weight residual 0.860 0.805 0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" NE2 GLN D 367 " pdb="HE22 GLN D 367 " ideal model delta sigma weight residual 0.860 0.808 0.052 2.00e-02 2.50e+03 6.74e+00 ... (remaining 57459 not shown) Histogram of bond angle deviations from ideal: 92.50 - 103.82: 501 103.82 - 115.14: 74004 115.14 - 126.46: 29203 126.46 - 137.78: 434 137.78 - 149.10: 2 Bond angle restraints: 104144 Sorted by residual: angle pdb=" CD GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE22 GLN B 130 " ideal model delta sigma weight residual 120.00 149.10 -29.10 3.00e+00 1.11e-01 9.41e+01 angle pdb="HE21 GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE22 GLN B 130 " ideal model delta sigma weight residual 120.00 92.50 27.50 3.00e+00 1.11e-01 8.40e+01 angle pdb=" CG ASN A 318 " pdb=" ND2 ASN A 318 " pdb="HD22 ASN A 318 " ideal model delta sigma weight residual 120.00 145.67 -25.67 3.00e+00 1.11e-01 7.32e+01 angle pdb="HD21 ASN A 318 " pdb=" ND2 ASN A 318 " pdb="HD22 ASN A 318 " ideal model delta sigma weight residual 120.00 95.68 24.32 3.00e+00 1.11e-01 6.57e+01 angle pdb=" CD GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE21 GLN B 130 " ideal model delta sigma weight residual 120.00 96.50 23.50 3.00e+00 1.11e-01 6.14e+01 ... (remaining 104139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.17: 24921 28.17 - 56.33: 1699 56.33 - 84.50: 222 84.50 - 112.66: 18 112.66 - 140.83: 2 Dihedral angle restraints: 26862 sinusoidal: 15037 harmonic: 11825 Sorted by residual: dihedral pdb=" C4' U I 38 " pdb=" C3' U I 38 " pdb=" C2' U I 38 " pdb=" C1' U I 38 " ideal model delta sinusoidal sigma weight residual -35.00 30.50 -65.50 1 8.00e+00 1.56e-02 8.78e+01 dihedral pdb=" C5' U I 38 " pdb=" C4' U I 38 " pdb=" C3' U I 38 " pdb=" O3' U I 38 " ideal model delta sinusoidal sigma weight residual 147.00 87.57 59.43 1 8.00e+00 1.56e-02 7.37e+01 dihedral pdb=" O4' U I 38 " pdb=" C4' U I 38 " pdb=" C3' U I 38 " pdb=" C2' U I 38 " ideal model delta sinusoidal sigma weight residual 24.00 -33.52 57.52 1 8.00e+00 1.56e-02 6.95e+01 ... (remaining 26859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2803 0.034 - 0.068: 1090 0.068 - 0.102: 318 0.102 - 0.136: 95 0.136 - 0.170: 13 Chirality restraints: 4319 Sorted by residual: chirality pdb=" CA PRO B 488 " pdb=" N PRO B 488 " pdb=" C PRO B 488 " pdb=" CB PRO B 488 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" C1' C I 37 " pdb=" O4' C I 37 " pdb=" C2' C I 37 " pdb=" N1 C I 37 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CB THR A 554 " pdb=" CA THR A 554 " pdb=" OG1 THR A 554 " pdb=" CG2 THR A 554 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 4316 not shown) Planarity restraints: 8275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 103 " -0.070 2.00e-02 2.50e+03 9.65e-02 1.40e+02 pdb=" CG ASN C 103 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 103 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 103 " 0.155 2.00e-02 2.50e+03 pdb="HD21 ASN C 103 " 0.022 2.00e-02 2.50e+03 pdb="HD22 ASN C 103 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 554 " 0.070 2.00e-02 2.50e+03 9.46e-02 1.34e+02 pdb=" CD GLN B 554 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN B 554 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN B 554 " -0.152 2.00e-02 2.50e+03 pdb="HE21 GLN B 554 " -0.021 2.00e-02 2.50e+03 pdb="HE22 GLN B 554 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 627 " 0.067 2.00e-02 2.50e+03 9.28e-02 1.29e+02 pdb=" CD GLN A 627 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN A 627 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 627 " -0.151 2.00e-02 2.50e+03 pdb="HE21 GLN A 627 " -0.022 2.00e-02 2.50e+03 pdb="HE22 GLN A 627 " 0.149 2.00e-02 2.50e+03 ... (remaining 8272 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 3282 2.17 - 2.78: 111740 2.78 - 3.39: 154867 3.39 - 3.99: 196707 3.99 - 4.60: 312020 Nonbonded interactions: 778616 Sorted by model distance: nonbonded pdb=" OE1 GLU E 385 " pdb=" H GLU E 385 " model vdw 1.567 1.850 nonbonded pdb=" HE ARG E 383 " pdb=" OE2 GLU E 385 " model vdw 1.611 1.850 nonbonded pdb=" OP2 G I 5 " pdb=" H22 G I 5 " model vdw 1.612 1.850 nonbonded pdb=" O LYS B 255 " pdb=" HG1 THR B 259 " model vdw 1.612 1.850 nonbonded pdb=" OD1 ASP G 149 " pdb=" H ARG G 150 " model vdw 1.622 1.850 ... (remaining 778611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.220 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: 0.610 Extract box with map and model: 7.350 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 128.730 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.005 0.047 28984 Z= 0.303 Angle : 0.643 6.263 39074 Z= 0.362 Chirality : 0.041 0.170 4319 Planarity : 0.006 0.062 4922 Dihedral : 15.894 140.830 11267 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.26 % Allowed : 13.07 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.13), residues: 3462 helix: -0.17 (0.13), residues: 1519 sheet: -3.19 (0.23), residues: 378 loop : -2.71 (0.13), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 398 HIS 0.006 0.001 HIS B 606 PHE 0.026 0.002 PHE A 378 TYR 0.024 0.002 TYR B 6 ARG 0.007 0.001 ARG F 620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 332 time to evaluate : 3.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7475 (t) REVERT: E 108 HIS cc_start: 0.8485 (t70) cc_final: 0.8123 (t70) REVERT: E 172 MET cc_start: 0.8993 (mmp) cc_final: 0.8295 (mmm) REVERT: E 410 MET cc_start: 0.8718 (pmm) cc_final: 0.8489 (pmm) REVERT: F 717 ASN cc_start: 0.8221 (m110) cc_final: 0.7323 (m110) REVERT: F 736 GLN cc_start: 0.7726 (tt0) cc_final: 0.6318 (tt0) outliers start: 39 outliers final: 19 residues processed: 366 average time/residue: 1.0054 time to fit residues: 533.8171 Evaluate side-chains 252 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 568 ARG Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 319 GLN A 615 GLN B 147 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 505 ASN B 578 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN C 202 ASN C 212 HIS C 631 HIS C 766 ASN D 231 GLN D 248 GLN D 319 GLN D 496 ASN D 561 ASN E 62 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN F 610 ASN ** F 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 28984 Z= 0.356 Angle : 0.614 7.079 39074 Z= 0.337 Chirality : 0.040 0.183 4319 Planarity : 0.004 0.063 4922 Dihedral : 8.705 120.783 4081 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.42 % Allowed : 14.35 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3462 helix: 0.57 (0.13), residues: 1548 sheet: -2.45 (0.25), residues: 367 loop : -2.37 (0.14), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 439 HIS 0.010 0.001 HIS G 8 PHE 0.013 0.001 PHE B 556 TYR 0.021 0.002 TYR A 502 ARG 0.014 0.001 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 233 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 703 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: D 248 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.6230 (pp30) REVERT: E 108 HIS cc_start: 0.8312 (t70) cc_final: 0.7950 (t70) REVERT: E 408 MET cc_start: 0.6551 (mmm) cc_final: 0.5989 (mmm) REVERT: E 410 MET cc_start: 0.8885 (pmm) cc_final: 0.8672 (pmm) REVERT: E 478 MET cc_start: 0.6627 (tpt) cc_final: 0.6285 (tpt) outliers start: 44 outliers final: 23 residues processed: 271 average time/residue: 0.8577 time to fit residues: 352.7884 Evaluate side-chains 242 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 280 optimal weight: 0.3980 chunk 312 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN F 717 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28984 Z= 0.292 Angle : 0.553 9.469 39074 Z= 0.300 Chirality : 0.038 0.148 4319 Planarity : 0.004 0.062 4922 Dihedral : 8.282 122.433 4061 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.22 % Allowed : 14.74 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3462 helix: 0.88 (0.13), residues: 1540 sheet: -1.95 (0.25), residues: 372 loop : -2.14 (0.14), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 439 HIS 0.010 0.001 HIS C 212 PHE 0.012 0.001 PHE D 246 TYR 0.015 0.001 TYR A 502 ARG 0.006 0.000 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 228 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7620 (m-10) cc_final: 0.5814 (m-10) REVERT: C 703 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: E 108 HIS cc_start: 0.8295 (t70) cc_final: 0.7918 (t70) REVERT: E 328 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.7863 (t) REVERT: E 478 MET cc_start: 0.6845 (tpt) cc_final: 0.6555 (tpt) REVERT: F 744 GLN cc_start: 0.7999 (tp40) cc_final: 0.7730 (tp-100) outliers start: 38 outliers final: 24 residues processed: 261 average time/residue: 0.8342 time to fit residues: 334.7150 Evaluate side-chains 243 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 315 optimal weight: 6.9990 chunk 334 optimal weight: 0.0010 chunk 165 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN A 561 ASN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 GLN E 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 28984 Z= 0.363 Angle : 0.575 6.036 39074 Z= 0.314 Chirality : 0.039 0.148 4319 Planarity : 0.004 0.063 4922 Dihedral : 8.167 123.201 4054 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.64 % Allowed : 14.77 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3462 helix: 0.73 (0.13), residues: 1540 sheet: -1.80 (0.26), residues: 379 loop : -2.11 (0.14), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 439 HIS 0.010 0.001 HIS G 8 PHE 0.011 0.001 PHE C 386 TYR 0.016 0.001 TYR G 131 ARG 0.005 0.001 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 216 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 108 HIS cc_start: 0.8111 (t70) cc_final: 0.7676 (t70) REVERT: E 172 MET cc_start: 0.8943 (mmm) cc_final: 0.8720 (mmm) REVERT: E 328 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.7756 (t) outliers start: 51 outliers final: 31 residues processed: 264 average time/residue: 0.8442 time to fit residues: 344.4113 Evaluate side-chains 241 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 209 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 285 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28984 Z= 0.153 Angle : 0.483 6.201 39074 Z= 0.256 Chirality : 0.037 0.155 4319 Planarity : 0.003 0.054 4922 Dihedral : 7.976 123.669 4052 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.00 % Allowed : 15.35 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3462 helix: 1.19 (0.14), residues: 1546 sheet: -1.58 (0.25), residues: 383 loop : -1.83 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 311 HIS 0.009 0.001 HIS G 8 PHE 0.010 0.001 PHE B 692 TYR 0.014 0.001 TYR F 645 ARG 0.003 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 MET cc_start: 0.6416 (ttm) cc_final: 0.5000 (ttm) REVERT: C 703 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: E 97 MET cc_start: 0.9075 (tmm) cc_final: 0.8800 (tmm) REVERT: E 108 HIS cc_start: 0.8215 (t70) cc_final: 0.7845 (t70) REVERT: E 328 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.7660 (t) outliers start: 31 outliers final: 22 residues processed: 246 average time/residue: 0.8362 time to fit residues: 318.2673 Evaluate side-chains 235 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain F residue 631 HIS Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 689 GLN F 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 28984 Z= 0.426 Angle : 0.604 7.823 39074 Z= 0.330 Chirality : 0.039 0.165 4319 Planarity : 0.004 0.062 4922 Dihedral : 8.129 123.792 4051 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.67 % Allowed : 15.77 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3462 helix: 0.65 (0.13), residues: 1554 sheet: -1.74 (0.25), residues: 381 loop : -2.11 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 439 HIS 0.010 0.001 HIS G 8 PHE 0.013 0.002 PHE E 68 TYR 0.016 0.002 TYR G 131 ARG 0.004 0.001 ARG F 608 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 212 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 MET cc_start: 0.8511 (tpt) cc_final: 0.8305 (tpt) REVERT: D 689 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: E 108 HIS cc_start: 0.8022 (t70) cc_final: 0.7604 (t70) outliers start: 52 outliers final: 39 residues processed: 257 average time/residue: 0.8124 time to fit residues: 326.5862 Evaluate side-chains 247 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 689 GLN Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain F residue 631 HIS Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28984 Z= 0.260 Angle : 0.522 7.026 39074 Z= 0.281 Chirality : 0.038 0.150 4319 Planarity : 0.003 0.050 4922 Dihedral : 8.060 124.458 4051 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.29 % Allowed : 16.35 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3462 helix: 0.90 (0.13), residues: 1554 sheet: -1.68 (0.25), residues: 380 loop : -2.00 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 311 HIS 0.010 0.001 HIS G 8 PHE 0.011 0.001 PHE C 386 TYR 0.014 0.001 TYR F 645 ARG 0.003 0.000 ARG F 608 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 MET cc_start: 0.8602 (tpt) cc_final: 0.8263 (tpt) REVERT: D 612 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7686 (mp) REVERT: E 108 HIS cc_start: 0.7930 (t70) cc_final: 0.7563 (t70) outliers start: 40 outliers final: 33 residues processed: 246 average time/residue: 0.8019 time to fit residues: 309.9975 Evaluate side-chains 238 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 204 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain F residue 631 HIS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28984 Z= 0.170 Angle : 0.487 7.460 39074 Z= 0.257 Chirality : 0.037 0.206 4319 Planarity : 0.003 0.044 4922 Dihedral : 7.911 124.575 4051 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.13 % Allowed : 16.35 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3462 helix: 1.37 (0.14), residues: 1542 sheet: -1.50 (0.25), residues: 380 loop : -1.75 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 311 HIS 0.007 0.001 HIS G 8 PHE 0.010 0.001 PHE B 692 TYR 0.013 0.001 TYR F 645 ARG 0.006 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 MET cc_start: 0.6545 (ttm) cc_final: 0.5923 (ttt) REVERT: A 575 MET cc_start: 0.8574 (tpt) cc_final: 0.8370 (tpt) REVERT: C 703 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: D 612 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7734 (mp) outliers start: 35 outliers final: 25 residues processed: 239 average time/residue: 0.8225 time to fit residues: 312.6518 Evaluate side-chains 230 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 10.0000 chunk 319 optimal weight: 0.6980 chunk 291 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 187 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28984 Z= 0.287 Angle : 0.530 9.265 39074 Z= 0.284 Chirality : 0.038 0.165 4319 Planarity : 0.003 0.046 4922 Dihedral : 7.965 124.791 4051 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.26 % Allowed : 16.41 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3462 helix: 1.22 (0.14), residues: 1536 sheet: -1.55 (0.26), residues: 383 loop : -1.81 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 439 HIS 0.007 0.001 HIS E 108 PHE 0.012 0.001 PHE B 692 TYR 0.013 0.001 TYR A 502 ARG 0.007 0.000 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 MET cc_start: 0.6608 (ttm) cc_final: 0.5480 (ttm) REVERT: A 575 MET cc_start: 0.8634 (tpt) cc_final: 0.8235 (tpt) REVERT: D 612 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7751 (mp) outliers start: 39 outliers final: 34 residues processed: 238 average time/residue: 0.8137 time to fit residues: 307.5991 Evaluate side-chains 235 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain F residue 631 HIS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 5.9990 chunk 328 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 344 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN B 84 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28984 Z= 0.232 Angle : 0.507 8.394 39074 Z= 0.270 Chirality : 0.037 0.169 4319 Planarity : 0.003 0.048 4922 Dihedral : 7.924 125.377 4051 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.13 % Allowed : 16.64 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3462 helix: 1.31 (0.14), residues: 1541 sheet: -1.51 (0.26), residues: 383 loop : -1.74 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 311 HIS 0.009 0.001 HIS E 108 PHE 0.010 0.001 PHE B 692 TYR 0.012 0.001 TYR F 645 ARG 0.006 0.000 ARG G 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 MET cc_start: 0.6614 (ttm) cc_final: 0.5495 (ttm) REVERT: A 575 MET cc_start: 0.8609 (tpt) cc_final: 0.8218 (tpt) REVERT: C 703 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7389 (m-30) REVERT: D 612 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7725 (mp) REVERT: E 280 LYS cc_start: 0.6969 (ttpt) cc_final: 0.6468 (ttpp) REVERT: F 580 ASN cc_start: 0.8853 (t0) cc_final: 0.8622 (p0) outliers start: 35 outliers final: 31 residues processed: 237 average time/residue: 0.8249 time to fit residues: 308.8192 Evaluate side-chains 232 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 6.9990 chunk 292 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 689 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.061686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.047175 restraints weight = 367913.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049398 restraints weight = 139016.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.050785 restraints weight = 75694.332| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28984 Z= 0.267 Angle : 0.523 10.511 39074 Z= 0.280 Chirality : 0.038 0.173 4319 Planarity : 0.003 0.049 4922 Dihedral : 7.922 125.746 4050 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.22 % Allowed : 16.64 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3462 helix: 1.22 (0.13), residues: 1543 sheet: -1.53 (0.26), residues: 383 loop : -1.75 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 439 HIS 0.005 0.001 HIS G 8 PHE 0.030 0.001 PHE E 106 TYR 0.012 0.001 TYR F 645 ARG 0.006 0.000 ARG G 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8066.34 seconds wall clock time: 142 minutes 4.44 seconds (8524.44 seconds total)