Starting phenix.real_space_refine (version: dev) on Wed Feb 22 12:13:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2023/6xzq_10665.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2023/6xzq_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_2023/6xzq_10665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2023/6xzq_10665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2023/6xzq_10665.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/02_2023/6xzq_10665.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 19.09, per 1000 atoms: 0.34 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: 36.00 Conformation dependent library (CDL) restraints added in 3.4 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: 1.50 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: 18.42 Time building geometry restraints manager: 37.84 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: 21486 28.17 - 56.33: 1355 56.33 - 84.50: 155 84.50 - 112.66: 18 112.66 - 140.83: 2 Dihedral angle restraints: 23016 sinusoidal: 11191 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 23013 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 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. 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: 1.610 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: 0.620 Extract box with map and model: 9.040 Check model and map are aligned: 0.620 Process input model: 130.860 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.380 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 15.635 140.830 11207 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 % 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 *********************** 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 : 3.505 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 outliers start: 39 outliers final: 19 residues processed: 366 average time/residue: 1.0105 time to fit residues: 536.3562 Evaluate side-chains 250 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 231 time to evaluate : 3.517 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.6986 time to fit residues: 25.9993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 140 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 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: 3.5788 ------------------------------------------------------------------------------- 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 578 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN C 212 HIS C 283 ASN 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 717 ASN G 30 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 28984 Z= 0.314 Angle : 0.599 7.258 39074 Z= 0.327 Chirality : 0.039 0.181 4319 Planarity : 0.004 0.061 4922 Dihedral : 6.672 121.519 3980 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.93 % 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: -1.41 (0.14), residues: 3462 helix: 0.70 (0.13), residues: 1540 sheet: -2.37 (0.24), residues: 387 loop : -2.30 (0.14), residues: 1535 *********************** 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 265 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 236 time to evaluate : 3.521 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 outliers start: 29 outliers final: 12 residues processed: 260 average time/residue: 0.8928 time to fit residues: 352.2519 Evaluate side-chains 230 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 218 time to evaluate : 3.553 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.7526 time to fit residues: 19.0903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 213 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 312 optimal weight: 10.0000 chunk 107 optimal weight: 0.0000 chunk 252 optimal weight: 4.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- 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 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN F 736 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 28984 Z= 0.284 Angle : 0.550 9.472 39074 Z= 0.296 Chirality : 0.038 0.148 4319 Planarity : 0.004 0.060 4922 Dihedral : 6.259 122.533 3980 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 1.00 % 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: -1.04 (0.14), residues: 3462 helix: 0.95 (0.13), residues: 1540 sheet: -1.89 (0.25), residues: 372 loop : -2.12 (0.14), residues: 1550 *********************** 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 257 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 226 time to evaluate : 3.506 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 outliers start: 31 outliers final: 17 residues processed: 254 average time/residue: 0.8646 time to fit residues: 339.0547 Evaluate side-chains 230 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 213 time to evaluate : 3.537 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 17 average time/residue: 0.6270 time to fit residues: 22.6537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 34 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 334 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 28984 Z= 0.350 Angle : 0.577 5.802 39074 Z= 0.313 Chirality : 0.039 0.173 4319 Planarity : 0.004 0.061 4922 Dihedral : 6.147 123.269 3980 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.93 % 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: 0.75 (0.13), residues: 1547 sheet: -1.76 (0.26), residues: 379 loop : -2.15 (0.14), residues: 1536 *********************** 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 243 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 4.126 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 outliers start: 29 outliers final: 12 residues processed: 239 average time/residue: 0.8785 time to fit residues: 323.2411 Evaluate side-chains 219 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 3.526 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.6071 time to fit residues: 16.9794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 285 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 28984 Z= 0.282 Angle : 0.531 6.955 39074 Z= 0.286 Chirality : 0.038 0.150 4319 Planarity : 0.003 0.057 4922 Dihedral : 6.035 123.763 3980 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.68 % 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: -0.97 (0.14), residues: 3462 helix: 0.89 (0.13), residues: 1553 sheet: -1.69 (0.25), residues: 379 loop : -2.02 (0.14), residues: 1530 *********************** 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 236 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 3.537 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 outliers start: 21 outliers final: 13 residues processed: 231 average time/residue: 0.8807 time to fit residues: 315.6484 Evaluate side-chains 221 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 208 time to evaluate : 3.541 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.6765 time to fit residues: 19.3530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 28984 Z= 0.205 Angle : 0.501 7.270 39074 Z= 0.265 Chirality : 0.037 0.170 4319 Planarity : 0.003 0.050 4922 Dihedral : 5.873 123.924 3980 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.29 % 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: -0.64 (0.14), residues: 3462 helix: 1.21 (0.14), residues: 1547 sheet: -1.60 (0.25), residues: 380 loop : -1.86 (0.15), residues: 1535 *********************** 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 226 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 3.539 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 outliers start: 9 outliers final: 4 residues processed: 225 average time/residue: 0.8950 time to fit residues: 312.8418 Evaluate side-chains 212 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 3.505 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.8790 time to fit residues: 9.9261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 333 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 28984 Z= 0.254 Angle : 0.512 7.623 39074 Z= 0.273 Chirality : 0.037 0.176 4319 Planarity : 0.003 0.048 4922 Dihedral : 5.841 124.280 3980 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.48 % 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: -0.61 (0.14), residues: 3462 helix: 1.22 (0.14), residues: 1540 sheet: -1.57 (0.25), residues: 380 loop : -1.84 (0.15), residues: 1542 *********************** 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 225 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 3.559 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 outliers start: 15 outliers final: 8 residues processed: 222 average time/residue: 0.8358 time to fit residues: 290.1726 Evaluate side-chains 212 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 204 time to evaluate : 3.538 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.7879 time to fit residues: 14.5857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 199 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 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 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 28984 Z= 0.239 Angle : 0.511 8.021 39074 Z= 0.271 Chirality : 0.038 0.183 4319 Planarity : 0.003 0.044 4922 Dihedral : 5.785 124.844 3980 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.19 % 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: -0.50 (0.14), residues: 3462 helix: 1.35 (0.14), residues: 1534 sheet: -1.54 (0.25), residues: 380 loop : -1.79 (0.15), residues: 1548 *********************** 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 212 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 206 time to evaluate : 3.662 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 outliers start: 6 outliers final: 3 residues processed: 211 average time/residue: 0.8374 time to fit residues: 275.1541 Evaluate side-chains 208 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 205 time to evaluate : 3.524 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.9230 time to fit residues: 8.5776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 291 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 309 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 84 ASN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 28984 Z= 0.310 Angle : 0.539 7.708 39074 Z= 0.291 Chirality : 0.038 0.163 4319 Planarity : 0.003 0.048 4922 Dihedral : 5.860 125.147 3980 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.10 % 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: -0.67 (0.14), residues: 3462 helix: 1.13 (0.13), residues: 1540 sheet: -1.51 (0.27), residues: 344 loop : -1.85 (0.14), residues: 1578 *********************** 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 208 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 205 time to evaluate : 4.983 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 outliers start: 3 outliers final: 2 residues processed: 207 average time/residue: 0.8708 time to fit residues: 286.7214 Evaluate side-chains 204 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 3.510 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.1919 time to fit residues: 7.8589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 200 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 344 optimal weight: 0.4980 chunk 317 optimal weight: 8.9990 chunk 274 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 248 GLN ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 28984 Z= 0.143 Angle : 0.486 8.287 39074 Z= 0.252 Chirality : 0.037 0.166 4319 Planarity : 0.003 0.041 4922 Dihedral : 5.630 125.623 3980 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.13 % 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: -0.19 (0.15), residues: 3462 helix: 1.54 (0.14), residues: 1550 sheet: -1.43 (0.27), residues: 356 loop : -1.59 (0.15), residues: 1556 ********************** 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 216 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 3.577 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 outliers start: 4 outliers final: 3 residues processed: 215 average time/residue: 0.8618 time to fit residues: 289.1385 Evaluate side-chains 206 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 3.513 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.9456 time to fit residues: 8.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 84 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.062675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048131 restraints weight = 364939.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.050427 restraints weight = 136864.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.051821 restraints weight = 73685.475| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 28984 Z= 0.171 Angle : 0.489 8.794 39074 Z= 0.254 Chirality : 0.037 0.169 4319 Planarity : 0.003 0.042 4922 Dihedral : 5.563 125.666 3980 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.10 % 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: -0.15 (0.15), residues: 3462 helix: 1.58 (0.14), residues: 1550 sheet: -1.38 (0.27), residues: 352 loop : -1.57 (0.15), residues: 1560 =============================================================================== Job complete usr+sys time: 7588.73 seconds wall clock time: 133 minutes 58.87 seconds (8038.87 seconds total)