Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 22:53:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvl_12605/10_2023/7nvl_12605_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvl_12605/10_2023/7nvl_12605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvl_12605/10_2023/7nvl_12605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvl_12605/10_2023/7nvl_12605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvl_12605/10_2023/7nvl_12605_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvl_12605/10_2023/7nvl_12605_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 402 5.16 5 C 41530 2.51 5 N 11578 2.21 5 O 12855 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 11": "NH1" <-> "NH2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ARG 452": "NH1" <-> "NH2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E ARG 381": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "E ARG 414": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E ARG 478": "NH1" <-> "NH2" Residue "E ARG 480": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 167": "NH1" <-> "NH2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G ARG 260": "NH1" <-> "NH2" Residue "G GLU 280": "OE1" <-> "OE2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G ARG 306": "NH1" <-> "NH2" Residue "G ARG 313": "NH1" <-> "NH2" Residue "G ARG 316": "NH1" <-> "NH2" Residue "G ARG 330": "NH1" <-> "NH2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G ARG 438": "NH1" <-> "NH2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G GLU 473": "OE1" <-> "OE2" Residue "G GLU 476": "OE1" <-> "OE2" Residue "G GLU 497": "OE1" <-> "OE2" Residue "H ARG 37": "NH1" <-> "NH2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H GLU 243": "OE1" <-> "OE2" Residue "H ARG 256": "NH1" <-> "NH2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H GLU 317": "OE1" <-> "OE2" Residue "H ARG 344": "NH1" <-> "NH2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "H ARG 397": "NH1" <-> "NH2" Residue "H ARG 425": "NH1" <-> "NH2" Residue "H GLU 443": "OE1" <-> "OE2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "H GLU 482": "OE1" <-> "OE2" Residue "H GLU 494": "OE1" <-> "OE2" Residue "H ARG 499": "NH1" <-> "NH2" Residue "H ARG 524": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 53": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "Q ARG 31": "NH1" <-> "NH2" Residue "Q ARG 44": "NH1" <-> "NH2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 113": "OE1" <-> "OE2" Residue "Q ARG 120": "NH1" <-> "NH2" Residue "Q GLU 133": "OE1" <-> "OE2" Residue "Q ARG 137": "NH1" <-> "NH2" Residue "Q ARG 155": "NH1" <-> "NH2" Residue "Q ARG 165": "NH1" <-> "NH2" Residue "Q GLU 252": "OE1" <-> "OE2" Residue "Q GLU 263": "OE1" <-> "OE2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q ARG 314": "NH1" <-> "NH2" Residue "Q ARG 322": "NH1" <-> "NH2" Residue "Q GLU 342": "OE1" <-> "OE2" Residue "Q GLU 366": "OE1" <-> "OE2" Residue "Q ARG 404": "NH1" <-> "NH2" Residue "Q ARG 407": "NH1" <-> "NH2" Residue "Q GLU 473": "OE1" <-> "OE2" Residue "Q ARG 520": "NH1" <-> "NH2" Residue "Z ARG 28": "NH1" <-> "NH2" Residue "Z ARG 35": "NH1" <-> "NH2" Residue "Z GLU 112": "OE1" <-> "OE2" Residue "Z GLU 135": "OE1" <-> "OE2" Residue "Z ARG 141": "NH1" <-> "NH2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z ARG 157": "NH1" <-> "NH2" Residue "Z ARG 208": "NH1" <-> "NH2" Residue "Z GLU 226": "OE1" <-> "OE2" Residue "Z GLU 243": "OE1" <-> "OE2" Residue "Z ARG 270": "NH1" <-> "NH2" Residue "Z GLU 276": "OE1" <-> "OE2" Residue "Z ARG 279": "NH1" <-> "NH2" Residue "Z ARG 318": "NH1" <-> "NH2" Residue "Z ARG 323": "NH1" <-> "NH2" Residue "Z ARG 370": "NH1" <-> "NH2" Residue "Z ARG 432": "NH1" <-> "NH2" Residue "Z GLU 469": "OE1" <-> "OE2" Residue "Z GLU 485": "OE1" <-> "OE2" Residue "Z GLU 491": "OE1" <-> "OE2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a GLU 68": "OE1" <-> "OE2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a ARG 145": "NH1" <-> "NH2" Residue "a ARG 185": "NH1" <-> "NH2" Residue "a ARG 189": "NH1" <-> "NH2" Residue "a ARG 203": "NH1" <-> "NH2" Residue "a ARG 228": "NH1" <-> "NH2" Residue "a ARG 264": "NH1" <-> "NH2" Residue "a ARG 314": "NH1" <-> "NH2" Residue "a GLU 341": "OE1" <-> "OE2" Residue "a GLU 354": "OE1" <-> "OE2" Residue "a ARG 355": "NH1" <-> "NH2" Residue "a ARG 370": "NH1" <-> "NH2" Residue "a ARG 443": "NH1" <-> "NH2" Residue "a ARG 480": "NH1" <-> "NH2" Residue "a ARG 496": "NH1" <-> "NH2" Residue "a GLU 505": "OE1" <-> "OE2" Residue "a GLU 519": "OE1" <-> "OE2" Residue "a GLU 536": "OE1" <-> "OE2" Residue "b ARG 20": "NH1" <-> "NH2" Residue "b GLU 94": "OE1" <-> "OE2" Residue "b GLU 197": "OE1" <-> "OE2" Residue "b ARG 255": "NH1" <-> "NH2" Residue "b ARG 257": "NH1" <-> "NH2" Residue "b GLU 280": "OE1" <-> "OE2" Residue "b ARG 281": "NH1" <-> "NH2" Residue "b ARG 388": "NH1" <-> "NH2" Residue "b ARG 405": "NH1" <-> "NH2" Residue "b ARG 427": "NH1" <-> "NH2" Residue "b GLU 437": "OE1" <-> "OE2" Residue "b ARG 444": "NH1" <-> "NH2" Residue "b ARG 481": "NH1" <-> "NH2" Residue "d ARG 27": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 89": "NH1" <-> "NH2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d ARG 153": "NH1" <-> "NH2" Residue "d GLU 156": "OE1" <-> "OE2" Residue "d ARG 206": "NH1" <-> "NH2" Residue "d GLU 222": "OE1" <-> "OE2" Residue "d GLU 225": "OE1" <-> "OE2" Residue "d ARG 274": "NH1" <-> "NH2" Residue "d ARG 277": "NH1" <-> "NH2" Residue "d ARG 280": "NH1" <-> "NH2" Residue "d ARG 306": "NH1" <-> "NH2" Residue "d GLU 329": "OE1" <-> "OE2" Residue "d GLU 334": "OE1" <-> "OE2" Residue "d GLU 364": "OE1" <-> "OE2" Residue "d GLU 429": "OE1" <-> "OE2" Residue "d GLU 431": "OE1" <-> "OE2" Residue "d ARG 452": "NH1" <-> "NH2" Residue "d GLU 459": "OE1" <-> "OE2" Residue "d ARG 483": "NH1" <-> "NH2" Residue "d GLU 524": "OE1" <-> "OE2" Residue "d ARG 527": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e ARG 126": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "e ARG 142": "NH1" <-> "NH2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "e ARG 183": "NH1" <-> "NH2" Residue "e ARG 202": "NH1" <-> "NH2" Residue "e GLU 207": "OE1" <-> "OE2" Residue "e GLU 212": "OE1" <-> "OE2" Residue "e ARG 218": "NH1" <-> "NH2" Residue "e GLU 220": "OE1" <-> "OE2" Residue "e GLU 256": "OE1" <-> "OE2" Residue "e GLU 287": "OE1" <-> "OE2" Residue "e GLU 294": "OE1" <-> "OE2" Residue "e GLU 329": "OE1" <-> "OE2" Residue "e ARG 381": "NH1" <-> "NH2" Residue "e ARG 410": "NH1" <-> "NH2" Residue "e ARG 414": "NH1" <-> "NH2" Residue "e ARG 417": "NH1" <-> "NH2" Residue "e GLU 436": "OE1" <-> "OE2" Residue "e GLU 444": "OE1" <-> "OE2" Residue "e ARG 478": "NH1" <-> "NH2" Residue "e ARG 480": "NH1" <-> "NH2" Residue "g GLU 17": "OE1" <-> "OE2" Residue "g ARG 85": "NH1" <-> "NH2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 167": "NH1" <-> "NH2" Residue "g ARG 190": "NH1" <-> "NH2" Residue "g ARG 216": "NH1" <-> "NH2" Residue "g ARG 228": "NH1" <-> "NH2" Residue "g ARG 230": "NH1" <-> "NH2" Residue "g ARG 260": "NH1" <-> "NH2" Residue "g GLU 280": "OE1" <-> "OE2" Residue "g GLU 293": "OE1" <-> "OE2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "g ARG 313": "NH1" <-> "NH2" Residue "g ARG 316": "NH1" <-> "NH2" Residue "g ARG 330": "NH1" <-> "NH2" Residue "g GLU 337": "OE1" <-> "OE2" Residue "g ARG 339": "NH1" <-> "NH2" Residue "g ARG 438": "NH1" <-> "NH2" Residue "g GLU 445": "OE1" <-> "OE2" Residue "g GLU 473": "OE1" <-> "OE2" Residue "g GLU 476": "OE1" <-> "OE2" Residue "g GLU 497": "OE1" <-> "OE2" Residue "h ARG 37": "NH1" <-> "NH2" Residue "h ARG 43": "NH1" <-> "NH2" Residue "h ARG 53": "NH1" <-> "NH2" Residue "h ARG 123": "NH1" <-> "NH2" Residue "h GLU 150": "OE1" <-> "OE2" Residue "h GLU 243": "OE1" <-> "OE2" Residue "h ARG 256": "NH1" <-> "NH2" Residue "h GLU 261": "OE1" <-> "OE2" Residue "h ARG 306": "NH1" <-> "NH2" Residue "h GLU 317": "OE1" <-> "OE2" Residue "h ARG 344": "NH1" <-> "NH2" Residue "h GLU 386": "OE1" <-> "OE2" Residue "h ARG 397": "NH1" <-> "NH2" Residue "h ARG 425": "NH1" <-> "NH2" Residue "h GLU 443": "OE1" <-> "OE2" Residue "h ARG 467": "NH1" <-> "NH2" Residue "h GLU 482": "OE1" <-> "OE2" Residue "h GLU 494": "OE1" <-> "OE2" Residue "h ARG 499": "NH1" <-> "NH2" Residue "h ARG 524": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n ARG 53": "NH1" <-> "NH2" Residue "n ARG 103": "NH1" <-> "NH2" Residue "q ARG 31": "NH1" <-> "NH2" Residue "q ARG 44": "NH1" <-> "NH2" Residue "q GLU 94": "OE1" <-> "OE2" Residue "q GLU 113": "OE1" <-> "OE2" Residue "q ARG 120": "NH1" <-> "NH2" Residue "q GLU 133": "OE1" <-> "OE2" Residue "q ARG 137": "NH1" <-> "NH2" Residue "q ARG 155": "NH1" <-> "NH2" Residue "q ARG 165": "NH1" <-> "NH2" Residue "q GLU 252": "OE1" <-> "OE2" Residue "q GLU 263": "OE1" <-> "OE2" Residue "q GLU 272": "OE1" <-> "OE2" Residue "q ARG 314": "NH1" <-> "NH2" Residue "q ARG 322": "NH1" <-> "NH2" Residue "q GLU 342": "OE1" <-> "OE2" Residue "q GLU 366": "OE1" <-> "OE2" Residue "q ARG 404": "NH1" <-> "NH2" Residue "q ARG 407": "NH1" <-> "NH2" Residue "q GLU 473": "OE1" <-> "OE2" Residue "q ARG 520": "NH1" <-> "NH2" Residue "z ARG 28": "NH1" <-> "NH2" Residue "z ARG 35": "NH1" <-> "NH2" Residue "z GLU 112": "OE1" <-> "OE2" Residue "z GLU 135": "OE1" <-> "OE2" Residue "z ARG 141": "NH1" <-> "NH2" Residue "z ARG 145": "NH1" <-> "NH2" Residue "z ARG 157": "NH1" <-> "NH2" Residue "z ARG 208": "NH1" <-> "NH2" Residue "z GLU 226": "OE1" <-> "OE2" Residue "z GLU 243": "OE1" <-> "OE2" Residue "z ARG 270": "NH1" <-> "NH2" Residue "z GLU 276": "OE1" <-> "OE2" Residue "z ARG 279": "NH1" <-> "NH2" Residue "z ARG 318": "NH1" <-> "NH2" Residue "z ARG 323": "NH1" <-> "NH2" Residue "z ARG 370": "NH1" <-> "NH2" Residue "z ARG 432": "NH1" <-> "NH2" Residue "z GLU 469": "OE1" <-> "OE2" Residue "z GLU 485": "OE1" <-> "OE2" Residue "z GLU 491": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 66477 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4054 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 14, 'TRANS': 519} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3908 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 14, 'TRANS': 503} Chain: "E" Number of atoms: 4124 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 534, 4116 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 18, 'TRANS': 515} Conformer: "B" Number of residues, atoms: 534, 4116 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 18, 'TRANS': 515} bond proxies already assigned to first conformer: 4156 Chain: "G" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "H" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3996 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 820 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Q" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4054 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 14, 'TRANS': 519} Chain: "b" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "d" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3908 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 14, 'TRANS': 503} Chain: "e" Number of atoms: 4124 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 534, 4116 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 18, 'TRANS': 515} Conformer: "B" Number of residues, atoms: 534, 4116 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 18, 'TRANS': 515} bond proxies already assigned to first conformer: 4156 Chain: "g" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "h" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3996 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "n" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 820 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "q" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 28.54, per 1000 atoms: 0.43 Number of scatterers: 66477 At special positions: 0 Unit cell: (185.5, 172.78, 185.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 402 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12855 8.00 N 11578 7.00 C 41530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.03 Simple disulfide: pdb=" SG CYS n 22 " - pdb=" SG CYS n 95 " distance=2.04 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 Atom "HETATM66056 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66312 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.65 Conformation dependent library (CDL) restraints added in 8.2 seconds 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 312 helices and 112 sheets defined 50.4% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.66 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.593A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 removed outlier: 4.000A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.923A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 143 No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 163 through 179 removed outlier: 3.802A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 281 removed outlier: 4.531A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.644A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.535A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 456 removed outlier: 3.756A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.967A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.875A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 144 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.780A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR B 180 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 189 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.878A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 431 through 454 removed outlier: 3.615A pdb=" N SER B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.670A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'D' and resid 29 through 51 removed outlier: 4.991A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 108 through 126 removed outlier: 4.131A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 180 through 193 Proline residue: D 185 - end of helix removed outlier: 3.892A pdb=" N VAL D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 269 through 293 removed outlier: 3.744A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 333 through 340 Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 Processing helix chain 'D' and resid 447 through 469 removed outlier: 4.075A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'E' and resid 31 through 51 removed outlier: 4.542A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.816A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 151 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.627A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 195 removed outlier: 3.868A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN E 191 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 194 " --> pdb=" O ASN E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 294 Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 439 Processing helix chain 'E' and resid 443 through 465 removed outlier: 3.559A pdb=" N TYR E 446 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE E 458 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 528 Processing helix chain 'G' and resid 20 through 40 removed outlier: 3.773A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N THR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N CYS G 40 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 97 through 114 removed outlier: 3.920A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 140 Processing helix chain 'G' and resid 149 through 160 removed outlier: 3.518A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 183 removed outlier: 3.634A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N SER G 170 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 262 through 285 removed outlier: 4.447A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 306 Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 381 through 403 Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.678A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 455 removed outlier: 4.106A pdb=" N GLU G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL G 446 " --> pdb=" O GLN G 442 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) Proline residue: G 448 - end of helix Processing helix chain 'G' and resid 459 through 471 removed outlier: 3.569A pdb=" N THR G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 19 through 39 removed outlier: 3.777A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 77 through 89 Processing helix chain 'H' and resid 94 through 113 removed outlier: 3.592A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 139 Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 169 through 184 removed outlier: 6.089A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE H 175 " --> pdb=" O LYS H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 260 through 283 Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 3.809A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 3.550A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 469 Processing helix chain 'H' and resid 487 through 490 No H-bonds generated for 'chain 'H' and resid 487 through 490' Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'N' and resid 87 through 89 No H-bonds generated for 'chain 'N' and resid 87 through 89' Processing helix chain 'N' and resid 104 through 106 No H-bonds generated for 'chain 'N' and resid 104 through 106' Processing helix chain 'Q' and resid 11 through 14 No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 24 through 27 No H-bonds generated for 'chain 'Q' and resid 24 through 27' Processing helix chain 'Q' and resid 29 through 46 removed outlier: 4.540A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 158 through 170 removed outlier: 4.636A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER Q 170 " --> pdb=" O THR Q 166 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 189 Processing helix chain 'Q' and resid 199 through 201 No H-bonds generated for 'chain 'Q' and resid 199 through 201' Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 262 through 285 removed outlier: 4.887A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 328 Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.565A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 456 removed outlier: 3.748A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 473 Processing helix chain 'Q' and resid 492 through 495 No H-bonds generated for 'chain 'Q' and resid 492 through 495' Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 7 removed outlier: 3.692A pdb=" N LEU Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 3 through 7' Processing helix chain 'Z' and resid 16 through 37 removed outlier: 3.521A pdb=" N LEU Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN Z 37 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 66 Processing helix chain 'Z' and resid 72 through 88 Processing helix chain 'Z' and resid 92 through 110 removed outlier: 3.864A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 Processing helix chain 'Z' and resid 145 through 159 removed outlier: 4.053A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 4.068A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 190 No H-bonds generated for 'chain 'Z' and resid 188 through 190' Processing helix chain 'Z' and resid 201 through 203 No H-bonds generated for 'chain 'Z' and resid 201 through 203' Processing helix chain 'Z' and resid 253 through 262 Processing helix chain 'Z' and resid 265 through 281 removed outlier: 3.754A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.601A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.203A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 432 through 455 removed outlier: 3.612A pdb=" N LEU Z 445 " --> pdb=" O ASP Z 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix Processing helix chain 'Z' and resid 459 through 473 Processing helix chain 'Z' and resid 489 through 492 No H-bonds generated for 'chain 'Z' and resid 489 through 492' Processing helix chain 'Z' and resid 498 through 517 Processing helix chain 'a' and resid 15 through 35 removed outlier: 3.593A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 removed outlier: 4.000A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.923A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 140 through 143 No H-bonds generated for 'chain 'a' and resid 140 through 143' Processing helix chain 'a' and resid 146 through 156 Processing helix chain 'a' and resid 163 through 179 removed outlier: 3.801A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA a 169 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU a 177 " --> pdb=" O ASP a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 281 removed outlier: 4.530A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 removed outlier: 3.644A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 429 removed outlier: 4.536A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 456 removed outlier: 3.757A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix Processing helix chain 'a' and resid 460 through 476 Processing helix chain 'a' and resid 478 through 485 removed outlier: 3.966A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 118 removed outlier: 3.875A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.780A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR b 180 " --> pdb=" O ASP b 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG b 189 " --> pdb=" O ALA b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 261 through 285 removed outlier: 3.879A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 307 Processing helix chain 'b' and resid 317 through 327 Processing helix chain 'b' and resid 338 through 340 No H-bonds generated for 'chain 'b' and resid 338 through 340' Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 426 Processing helix chain 'b' and resid 431 through 454 removed outlier: 3.616A pdb=" N SER b 438 " --> pdb=" O VAL b 434 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.670A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 51 removed outlier: 4.991A pdb=" N THR d 50 " --> pdb=" O ASP d 46 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER d 51 " --> pdb=" O ALA d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 108 through 126 removed outlier: 4.131A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 151 Processing helix chain 'd' and resid 160 through 171 Processing helix chain 'd' and resid 180 through 193 Proline residue: d 185 - end of helix removed outlier: 3.893A pdb=" N VAL d 191 " --> pdb=" O SER d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 205 through 207 No H-bonds generated for 'chain 'd' and resid 205 through 207' Processing helix chain 'd' and resid 218 through 220 No H-bonds generated for 'chain 'd' and resid 218 through 220' Processing helix chain 'd' and resid 269 through 293 removed outlier: 3.744A pdb=" N ASP d 273 " --> pdb=" O TYR d 269 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 319 Processing helix chain 'd' and resid 333 through 340 Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 417 Processing helix chain 'd' and resid 427 through 442 Processing helix chain 'd' and resid 447 through 469 removed outlier: 4.075A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 503 through 506 No H-bonds generated for 'chain 'd' and resid 503 through 506' Processing helix chain 'd' and resid 512 through 530 Processing helix chain 'e' and resid 31 through 51 removed outlier: 4.542A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER e 51 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 108 through 126 removed outlier: 3.817A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 151 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.627A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.867A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN e 191 " --> pdb=" O ILE e 188 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU e 194 " --> pdb=" O ASN e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 294 Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 439 Processing helix chain 'e' and resid 443 through 465 removed outlier: 3.559A pdb=" N TYR e 446 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU e 456 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE e 458 " --> pdb=" O LEU e 455 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 470 through 483 Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 510 through 528 Processing helix chain 'g' and resid 20 through 40 removed outlier: 3.773A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N CYS g 40 " --> pdb=" O ILE g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 97 through 114 removed outlier: 3.921A pdb=" N HIS g 111 " --> pdb=" O SER g 107 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 140 Processing helix chain 'g' and resid 149 through 160 removed outlier: 3.517A pdb=" N SER g 159 " --> pdb=" O ILE g 155 " (cutoff:3.500A) Processing helix chain 'g' and resid 164 through 183 removed outlier: 3.636A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N SER g 170 " --> pdb=" O ARG g 167 " (cutoff:3.500A) Processing helix chain 'g' and resid 209 through 211 No H-bonds generated for 'chain 'g' and resid 209 through 211' Processing helix chain 'g' and resid 262 through 285 removed outlier: 4.446A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 306 Processing helix chain 'g' and resid 317 through 327 Processing helix chain 'g' and resid 335 through 337 No H-bonds generated for 'chain 'g' and resid 335 through 337' Processing helix chain 'g' and resid 340 through 342 No H-bonds generated for 'chain 'g' and resid 340 through 342' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.678A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 433 through 455 removed outlier: 4.106A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE g 447 " --> pdb=" O ALA g 443 " (cutoff:3.500A) Proline residue: g 448 - end of helix Processing helix chain 'g' and resid 459 through 471 removed outlier: 3.570A pdb=" N THR g 471 " --> pdb=" O ARG g 467 " (cutoff:3.500A) Processing helix chain 'g' and resid 490 through 493 No H-bonds generated for 'chain 'g' and resid 490 through 493' Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 19 through 39 removed outlier: 3.777A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR h 38 " --> pdb=" O GLU h 34 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 77 through 89 Processing helix chain 'h' and resid 94 through 113 removed outlier: 3.592A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 169 through 184 removed outlier: 6.090A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE h 175 " --> pdb=" O LYS h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 260 through 283 Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 3.809A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 3.551A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix Processing helix chain 'h' and resid 457 through 469 Processing helix chain 'h' and resid 487 through 490 No H-bonds generated for 'chain 'h' and resid 487 through 490' Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'n' and resid 87 through 89 No H-bonds generated for 'chain 'n' and resid 87 through 89' Processing helix chain 'n' and resid 104 through 106 No H-bonds generated for 'chain 'n' and resid 104 through 106' Processing helix chain 'q' and resid 11 through 14 No H-bonds generated for 'chain 'q' and resid 11 through 14' Processing helix chain 'q' and resid 24 through 27 No H-bonds generated for 'chain 'q' and resid 24 through 27' Processing helix chain 'q' and resid 29 through 46 removed outlier: 4.540A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 158 through 170 removed outlier: 4.635A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER q 170 " --> pdb=" O THR q 166 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 189 Processing helix chain 'q' and resid 199 through 201 No H-bonds generated for 'chain 'q' and resid 199 through 201' Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 262 through 285 removed outlier: 4.889A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 318 through 328 Processing helix chain 'q' and resid 382 through 404 Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.565A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.749A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE q 448 " --> pdb=" O ALA q 444 " (cutoff:3.500A) Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 460 through 473 Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 3 through 7 removed outlier: 3.692A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 3 through 7' Processing helix chain 'z' and resid 16 through 37 removed outlier: 4.854A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN z 37 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 66 Processing helix chain 'z' and resid 72 through 88 Processing helix chain 'z' and resid 92 through 110 removed outlier: 3.865A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 Processing helix chain 'z' and resid 145 through 159 removed outlier: 4.053A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 4.067A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 253 through 262 Processing helix chain 'z' and resid 265 through 281 removed outlier: 3.754A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.601A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.203A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 428 Proline residue: z 427 - end of helix Processing helix chain 'z' and resid 432 through 455 removed outlier: 3.613A pdb=" N LEU z 445 " --> pdb=" O ASP z 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 517 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= C, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= D, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= E, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= F, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.836A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= H, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.518A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= J, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.143A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= L, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.713A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= N, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= P, first strand: chain 'D' and resid 208 through 212 removed outlier: 6.674A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= R, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.907A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= T, first strand: chain 'D' and resid 491 through 494 Processing sheet with id= U, first strand: chain 'E' and resid 26 through 29 Processing sheet with id= V, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= W, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.810A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= Y, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.850A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU E 251 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE E 301 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N CYS E 302 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 322 " --> pdb=" O CYS E 302 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AA, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AB, first strand: chain 'G' and resid 184 through 186 Processing sheet with id= AC, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.605A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.647A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AF, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AG, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AH, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AI, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AJ, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.536A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 213 through 217 Processing sheet with id= AL, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.786A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AN, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AO, first strand: chain 'N' and resid 2 through 7 Processing sheet with id= AP, first strand: chain 'N' and resid 57 through 59 removed outlier: 3.543A pdb=" N GLU N 46 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR N 52 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ASN N 32 " --> pdb=" O THR N 52 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN N 98 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET N 34 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS N 96 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TRP N 36 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR N 94 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG N 38 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL N 92 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AR, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AS, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.391A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AU, first strand: chain 'Q' and resid 237 through 239 removed outlier: 3.575A pdb=" N CYS Q 347 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.103A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.649A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AY, first strand: chain 'Z' and resid 12 through 14 Processing sheet with id= AZ, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= BA, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.631A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BC, first strand: chain 'Z' and resid 345 through 347 removed outlier: 6.488A pdb=" N GLY Z 288 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU Z 231 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL Z 290 " --> pdb=" O LEU Z 231 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N CYS Z 233 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE Z 292 " --> pdb=" O CYS Z 233 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL Z 311 " --> pdb=" O VAL Z 291 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASN Z 293 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU Z 313 " --> pdb=" O ASN Z 293 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id= BE, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BF, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BG, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BH, first strand: chain 'a' and resid 196 through 199 Processing sheet with id= BI, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BJ, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.835A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BL, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.519A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BN, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.143A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BP, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.713A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BR, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BS, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BT, first strand: chain 'd' and resid 208 through 212 removed outlier: 6.674A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'd' and resid 227 through 229 Processing sheet with id= BV, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.907A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BX, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BY, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= BZ, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= CA, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.810A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CC, first strand: chain 'e' and resid 354 through 356 removed outlier: 6.850A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CE, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CF, first strand: chain 'g' and resid 184 through 186 Processing sheet with id= CG, first strand: chain 'g' and resid 199 through 205 removed outlier: 6.604A pdb=" N CYS g 372 " --> pdb=" O ARG g 200 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLU g 202 " --> pdb=" O CYS g 372 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE g 374 " --> pdb=" O GLU g 202 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE g 204 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU g 376 " --> pdb=" O ILE g 204 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR g 373 " --> pdb=" O LEU g 215 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.647A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CH Processing sheet with id= CI, first strand: chain 'g' and resid 351 through 355 Processing sheet with id= CJ, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CK, first strand: chain 'g' and resid 478 through 480 Processing sheet with id= CL, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CM, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CN, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.536A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'h' and resid 213 through 217 Processing sheet with id= CP, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.786A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CP Processing sheet with id= CQ, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CR, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CS, first strand: chain 'n' and resid 2 through 7 Processing sheet with id= CT, first strand: chain 'n' and resid 57 through 59 removed outlier: 3.543A pdb=" N GLU n 46 " --> pdb=" O ARG n 38 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP n 36 " --> pdb=" O VAL n 48 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER n 50 " --> pdb=" O MET n 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET n 34 " --> pdb=" O SER n 50 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR n 52 " --> pdb=" O ASN n 32 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASN n 32 " --> pdb=" O THR n 52 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN n 98 " --> pdb=" O ASN n 32 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET n 34 " --> pdb=" O LYS n 96 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS n 96 " --> pdb=" O MET n 34 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TRP n 36 " --> pdb=" O TYR n 94 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR n 94 " --> pdb=" O TRP n 36 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG n 38 " --> pdb=" O VAL n 92 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL n 92 " --> pdb=" O ARG n 38 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CV, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CW, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.391A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CY, first strand: chain 'q' and resid 237 through 239 removed outlier: 3.576A pdb=" N CYS q 347 " --> pdb=" O ALA q 237 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.103A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.649A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DC, first strand: chain 'z' and resid 12 through 14 Processing sheet with id= DD, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DE, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.631A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DG, first strand: chain 'z' and resid 345 through 347 removed outlier: 6.487A pdb=" N GLY z 288 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU z 231 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL z 290 " --> pdb=" O LEU z 231 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N CYS z 233 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE z 292 " --> pdb=" O CYS z 233 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL z 311 " --> pdb=" O VAL z 291 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN z 293 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU z 313 " --> pdb=" O ASN z 293 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'z' and resid 477 through 479 3423 hydrogen bonds defined for protein. 9243 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: 27.69 Time building geometry restraints manager: 24.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18714 1.33 - 1.45: 9657 1.45 - 1.57: 38096 1.57 - 1.69: 97 1.69 - 1.82: 664 Bond restraints: 67228 Sorted by residual: bond pdb=" N ARG Z 15 " pdb=" CA ARG Z 15 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" CG LEU D 443 " pdb=" CD2 LEU D 443 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.11e+01 bond pdb=" CG LEU d 443 " pdb=" CD2 LEU d 443 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.11e+01 bond pdb=" N ARG z 15 " pdb=" CA ARG z 15 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.17e-02 7.31e+03 1.05e+01 bond pdb=" N VAL E 482 " pdb=" CA VAL E 482 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.49e+00 ... (remaining 67223 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.85: 976 104.85 - 112.90: 38100 112.90 - 120.96: 33088 120.96 - 129.01: 18326 129.01 - 137.07: 298 Bond angle restraints: 90788 Sorted by residual: angle pdb=" CA LYS n 86 " pdb=" CB LYS n 86 " pdb=" CG LYS n 86 " ideal model delta sigma weight residual 114.10 122.79 -8.69 2.00e+00 2.50e-01 1.89e+01 angle pdb=" CA LYS N 86 " pdb=" CB LYS N 86 " pdb=" CG LYS N 86 " ideal model delta sigma weight residual 114.10 122.77 -8.67 2.00e+00 2.50e-01 1.88e+01 angle pdb=" CA ASN N 100 " pdb=" C ASN N 100 " pdb=" N TRP N 101 " ideal model delta sigma weight residual 119.63 116.42 3.21 8.10e-01 1.52e+00 1.57e+01 angle pdb=" CA LEU n 85 " pdb=" CB LEU n 85 " pdb=" CG LEU n 85 " ideal model delta sigma weight residual 116.30 129.52 -13.22 3.50e+00 8.16e-02 1.43e+01 angle pdb=" CA LEU N 85 " pdb=" CB LEU N 85 " pdb=" CG LEU N 85 " ideal model delta sigma weight residual 116.30 129.51 -13.21 3.50e+00 8.16e-02 1.42e+01 ... (remaining 90783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.35: 39903 32.35 - 64.70: 1477 64.70 - 97.05: 128 97.05 - 129.40: 12 129.40 - 161.75: 10 Dihedral angle restraints: 41530 sinusoidal: 16702 harmonic: 24828 Sorted by residual: dihedral pdb=" O1B ADP h 601 " pdb=" O3A ADP h 601 " pdb=" PB ADP h 601 " pdb=" PA ADP h 601 " ideal model delta sinusoidal sigma weight residual -60.00 101.75 -161.75 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O1B ADP H 601 " pdb=" O3A ADP H 601 " pdb=" PB ADP H 601 " pdb=" PA ADP H 601 " ideal model delta sinusoidal sigma weight residual -60.00 101.75 -161.75 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual 300.00 140.46 159.54 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 41527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 8781 0.060 - 0.120: 1742 0.120 - 0.180: 265 0.180 - 0.240: 18 0.240 - 0.300: 6 Chirality restraints: 10812 Sorted by residual: chirality pdb=" CA ARG b 57 " pdb=" N ARG b 57 " pdb=" C ARG b 57 " pdb=" CB ARG b 57 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ARG B 57 " pdb=" N ARG B 57 " pdb=" C ARG B 57 " pdb=" CB ARG B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA GLU E 444 " pdb=" N GLU E 444 " pdb=" C GLU E 444 " pdb=" CB GLU E 444 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 10809 not shown) Planarity restraints: 11578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN H 151 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLN H 151 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN H 151 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG H 152 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN h 151 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C GLN h 151 " 0.059 2.00e-02 2.50e+03 pdb=" O GLN h 151 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG h 152 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER Q 210 " 0.016 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C SER Q 210 " -0.053 2.00e-02 2.50e+03 pdb=" O SER Q 210 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY Q 211 " 0.018 2.00e-02 2.50e+03 ... (remaining 11575 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 469 2.51 - 3.11: 50309 3.11 - 3.71: 106551 3.71 - 4.30: 162928 4.30 - 4.90: 265302 Nonbonded interactions: 585559 Sorted by model distance: nonbonded pdb="MG MG q 602 " pdb=" F3 AF3 q 603 " model vdw 1.915 2.120 nonbonded pdb="MG MG Q 602 " pdb=" F3 AF3 Q 603 " model vdw 1.915 2.120 nonbonded pdb="MG MG e 602 " pdb=" F2 AF3 e 603 " model vdw 1.944 2.120 nonbonded pdb="MG MG E 602 " pdb=" F2 AF3 E 603 " model vdw 1.945 2.120 nonbonded pdb="MG MG d 602 " pdb=" F2 AF3 d 603 " model vdw 1.950 2.120 ... (remaining 585554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 3 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 3 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 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: 0.070 Extract box with map and model: 15.710 Check model and map are aligned: 0.780 Set scattering table: 0.500 Process input model: 146.490 Find NCS groups from input model: 6.060 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 0.110 67228 Z= 0.309 Angle : 0.783 13.221 90788 Z= 0.414 Chirality : 0.049 0.300 10812 Planarity : 0.004 0.063 11578 Dihedral : 16.488 161.751 25448 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.56 % Allowed : 15.71 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.08), residues: 8584 helix: -0.60 (0.07), residues: 4472 sheet: -1.29 (0.14), residues: 1138 loop : -2.34 (0.09), residues: 2974 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1384 time to evaluate : 6.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 40 residues processed: 1475 average time/residue: 1.7898 time to fit residues: 3311.5812 Evaluate side-chains 961 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 921 time to evaluate : 5.996 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 36 residues processed: 4 average time/residue: 1.1915 time to fit residues: 14.6062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 721 optimal weight: 10.0000 chunk 647 optimal weight: 0.6980 chunk 359 optimal weight: 6.9990 chunk 221 optimal weight: 0.6980 chunk 436 optimal weight: 0.6980 chunk 345 optimal weight: 0.8980 chunk 669 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 407 optimal weight: 6.9990 chunk 498 optimal weight: 4.9990 chunk 775 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 56 ASN A 103 ASN A 113 HIS A 223 GLN A 251 GLN A 276 GLN A 472 ASN A 475 GLN A 477 ASN B 65 ASN B 122 HIS B 148 HIS B 228 GLN ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 294 GLN B 381 GLN B 464 GLN B 502 GLN D 32 GLN D 62 GLN D 72 ASN D 138 GLN D 235 ASN D 262 ASN D 263 GLN D 271 GLN D 366 ASN D 482 ASN E 22 GLN E 86 GLN E 139 GLN E 445 GLN E 465 ASN E 495 HIS E 503 GLN E 522 GLN G 87 GLN G 116 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 ASN G 269 GLN G 392 GLN G 400 ASN G 504 GLN H 119 GLN H 252 ASN H 272 ASN H 283 HIS H 470 GLN ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN Q 53 ASN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 172 GLN Q 175 ASN Q 198 ASN Q 274 ASN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 GLN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN Z 95 ASN Z 161 HIS Z 294 GLN ** Z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 438 GLN Z 470 HIS a 56 ASN a 103 ASN a 113 HIS a 223 GLN a 251 GLN a 276 GLN a 458 GLN a 472 ASN a 475 GLN a 477 ASN b 65 ASN b 122 HIS b 148 HIS b 228 GLN ** b 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 288 ASN b 294 GLN b 381 GLN b 464 GLN b 502 GLN d 32 GLN d 62 GLN d 72 ASN d 138 GLN d 235 ASN d 262 ASN d 263 GLN d 271 GLN d 366 ASN d 482 ASN e 22 GLN e 86 GLN e 139 GLN e 445 GLN e 465 ASN e 495 HIS e 503 GLN e 504 GLN e 522 GLN g 28 ASN g 116 GLN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 235 ASN g 269 GLN g 392 GLN g 400 ASN g 504 GLN h 119 GLN h 252 ASN h 272 ASN h 283 HIS h 470 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 81 GLN q 53 ASN ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 172 GLN q 175 ASN q 198 ASN q 274 ASN ** q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 95 ASN z 161 HIS z 294 GLN ** z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 438 GLN z 460 GLN z 470 HIS Total number of N/Q/H flips: 126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 67228 Z= 0.183 Angle : 0.595 9.799 90788 Z= 0.295 Chirality : 0.042 0.175 10812 Planarity : 0.004 0.043 11578 Dihedral : 8.116 175.549 9346 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 3.06 % Allowed : 18.42 % Favored : 78.51 % 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: -0.20 (0.09), residues: 8584 helix: 0.92 (0.08), residues: 4474 sheet: -0.85 (0.14), residues: 1146 loop : -1.38 (0.10), residues: 2964 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 999 time to evaluate : 6.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 220 outliers final: 79 residues processed: 1135 average time/residue: 1.6872 time to fit residues: 2429.9684 Evaluate side-chains 971 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 892 time to evaluate : 6.076 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 60 residues processed: 21 average time/residue: 0.8695 time to fit residues: 35.7711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 431 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 645 optimal weight: 2.9990 chunk 528 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 776 optimal weight: 6.9990 chunk 839 optimal weight: 2.9990 chunk 691 optimal weight: 0.6980 chunk 770 optimal weight: 9.9990 chunk 264 optimal weight: 0.0050 chunk 623 optimal weight: 5.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN D 366 ASN D 510 GLN E 55 ASN E 522 GLN G 28 ASN G 226 HIS ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN Z 346 HIS ** Z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 477 ASN b 91 GLN b 288 ASN d 62 GLN d 366 ASN d 510 GLN e 55 ASN e 139 GLN e 522 GLN g 28 ASN g 87 GLN g 226 HIS h 119 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 346 HIS ** z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 67228 Z= 0.221 Angle : 0.589 8.593 90788 Z= 0.292 Chirality : 0.043 0.178 10812 Planarity : 0.004 0.043 11578 Dihedral : 7.952 175.814 9346 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 3.30 % Allowed : 18.88 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.09), residues: 8584 helix: 1.30 (0.08), residues: 4424 sheet: -0.47 (0.14), residues: 1216 loop : -0.84 (0.11), residues: 2944 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 973 time to evaluate : 6.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 237 outliers final: 110 residues processed: 1130 average time/residue: 1.6968 time to fit residues: 2439.5357 Evaluate side-chains 1000 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 890 time to evaluate : 6.116 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 83 residues processed: 28 average time/residue: 0.9928 time to fit residues: 48.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 767 optimal weight: 2.9990 chunk 584 optimal weight: 6.9990 chunk 403 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 370 optimal weight: 10.0000 chunk 521 optimal weight: 0.7980 chunk 779 optimal weight: 9.9990 chunk 825 optimal weight: 7.9990 chunk 407 optimal weight: 9.9990 chunk 738 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN D 32 GLN D 62 GLN D 366 ASN E 522 GLN G 284 GLN G 308 ASN G 396 GLN G 481 ASN ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN Z 346 HIS ** Z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 460 GLN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN a 477 ASN d 32 GLN d 366 ASN e 122 GLN e 435 GLN e 445 GLN e 522 GLN g 308 ASN g 396 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 346 HIS ** z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 67228 Z= 0.273 Angle : 0.612 10.676 90788 Z= 0.304 Chirality : 0.044 0.176 10812 Planarity : 0.004 0.046 11578 Dihedral : 7.916 176.722 9346 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 3.44 % Allowed : 19.04 % Favored : 77.53 % 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: 0.49 (0.09), residues: 8584 helix: 1.23 (0.08), residues: 4446 sheet: -0.33 (0.14), residues: 1220 loop : -0.68 (0.11), residues: 2918 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 905 time to evaluate : 6.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 247 outliers final: 135 residues processed: 1070 average time/residue: 1.6788 time to fit residues: 2294.8064 Evaluate side-chains 998 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 863 time to evaluate : 6.143 Switching outliers to nearest non-outliers outliers start: 135 outliers final: 104 residues processed: 31 average time/residue: 1.0869 time to fit residues: 55.7793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 687 optimal weight: 0.9980 chunk 468 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 614 optimal weight: 5.9990 chunk 340 optimal weight: 4.9990 chunk 704 optimal weight: 5.9990 chunk 570 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 421 optimal weight: 0.9990 chunk 740 optimal weight: 20.0000 chunk 208 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN E 298 ASN E 522 GLN ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 472 GLN Z 8 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN Z 161 HIS Z 346 HIS ** Z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 460 GLN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN d 366 ASN e 298 ASN g 71 GLN g 284 GLN g 390 ASN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 472 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 161 HIS z 346 HIS ** z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 67228 Z= 0.270 Angle : 0.609 9.943 90788 Z= 0.303 Chirality : 0.044 0.178 10812 Planarity : 0.004 0.048 11578 Dihedral : 7.883 177.278 9346 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 3.16 % Allowed : 19.55 % Favored : 77.29 % 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: 0.53 (0.09), residues: 8584 helix: 1.21 (0.08), residues: 4446 sheet: -0.27 (0.15), residues: 1200 loop : -0.57 (0.11), residues: 2938 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 888 time to evaluate : 6.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 136 residues processed: 1044 average time/residue: 1.6574 time to fit residues: 2216.5659 Evaluate side-chains 982 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 846 time to evaluate : 6.473 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 109 residues processed: 27 average time/residue: 0.9972 time to fit residues: 47.4294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 277 optimal weight: 4.9990 chunk 743 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 484 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 826 optimal weight: 4.9990 chunk 685 optimal weight: 2.9990 chunk 382 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 433 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN D 366 ASN D 394 ASN E 298 ASN G 87 GLN G 390 ASN G 481 ASN ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 472 GLN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN Z 161 HIS Z 346 HIS ** Z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 460 GLN a 20 GLN d 32 GLN d 366 ASN d 394 ASN e 298 ASN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 481 ASN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 472 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 161 HIS z 346 HIS ** z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 460 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 67228 Z= 0.333 Angle : 0.644 9.251 90788 Z= 0.322 Chirality : 0.045 0.187 10812 Planarity : 0.004 0.050 11578 Dihedral : 8.044 178.325 9346 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 3.13 % Allowed : 19.34 % Favored : 77.53 % 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: 0.47 (0.09), residues: 8584 helix: 1.08 (0.08), residues: 4436 sheet: -0.16 (0.15), residues: 1172 loop : -0.53 (0.11), residues: 2976 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 877 time to evaluate : 6.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 225 outliers final: 151 residues processed: 1044 average time/residue: 1.6989 time to fit residues: 2264.9857 Evaluate side-chains 988 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 837 time to evaluate : 6.103 Switching outliers to nearest non-outliers outliers start: 151 outliers final: 123 residues processed: 28 average time/residue: 1.0906 time to fit residues: 52.2065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 470 optimal weight: 5.9990 chunk 603 optimal weight: 6.9990 chunk 467 optimal weight: 0.0040 chunk 695 optimal weight: 2.9990 chunk 461 optimal weight: 7.9990 chunk 823 optimal weight: 3.9990 chunk 515 optimal weight: 0.8980 chunk 501 optimal weight: 0.9990 chunk 380 optimal weight: 10.0000 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN D 32 GLN D 285 ASN D 366 ASN D 394 ASN E 298 ASN G 284 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 ASN ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS Q 422 GLN Q 472 GLN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN Z 346 HIS ** Z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 460 GLN Z 497 ASN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 265 GLN d 285 ASN d 366 ASN d 394 ASN e 298 ASN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 481 ASN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 365 HIS q 472 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 346 HIS ** z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 460 GLN z 497 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 67228 Z= 0.187 Angle : 0.562 9.839 90788 Z= 0.278 Chirality : 0.041 0.179 10812 Planarity : 0.004 0.046 11578 Dihedral : 7.725 176.355 9346 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.51 % Favored : 97.47 % Rotamer: Outliers : 2.69 % Allowed : 19.86 % Favored : 77.46 % 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: 0.78 (0.09), residues: 8584 helix: 1.38 (0.08), residues: 4422 sheet: -0.15 (0.15), residues: 1196 loop : -0.39 (0.11), residues: 2966 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 873 time to evaluate : 6.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 193 outliers final: 131 residues processed: 1026 average time/residue: 1.6558 time to fit residues: 2183.1387 Evaluate side-chains 959 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 828 time to evaluate : 6.276 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 118 residues processed: 14 average time/residue: 0.8246 time to fit residues: 26.3862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 491 optimal weight: 0.0170 chunk 247 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 523 optimal weight: 1.9990 chunk 560 optimal weight: 10.0000 chunk 406 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 646 optimal weight: 1.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN D 366 ASN D 394 ASN E 139 GLN E 298 ASN G 71 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 472 GLN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN Z 346 HIS ** Z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 460 GLN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 394 ASN e 298 ASN g 71 GLN g 284 GLN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 472 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 346 HIS ** z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 460 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 67228 Z= 0.192 Angle : 0.562 8.171 90788 Z= 0.278 Chirality : 0.042 0.175 10812 Planarity : 0.004 0.045 11578 Dihedral : 7.619 176.385 9346 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.66 % Favored : 97.32 % Rotamer: Outliers : 2.71 % Allowed : 20.15 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.09), residues: 8584 helix: 1.45 (0.08), residues: 4426 sheet: -0.12 (0.15), residues: 1222 loop : -0.31 (0.11), residues: 2936 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 857 time to evaluate : 6.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 195 outliers final: 137 residues processed: 1008 average time/residue: 1.6820 time to fit residues: 2172.2464 Evaluate side-chains 963 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 826 time to evaluate : 6.017 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 121 residues processed: 17 average time/residue: 0.8792 time to fit residues: 30.7528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 748 optimal weight: 1.9990 chunk 788 optimal weight: 6.9990 chunk 719 optimal weight: 3.9990 chunk 767 optimal weight: 0.7980 chunk 461 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 602 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 693 optimal weight: 9.9990 chunk 725 optimal weight: 0.9990 chunk 764 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN D 366 ASN D 394 ASN E 139 GLN E 278 GLN E 298 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 GLN ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 472 GLN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN Z 346 HIS ** Z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 460 GLN a 20 GLN d 394 ASN e 278 GLN e 298 ASN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 472 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 346 HIS ** z 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 67228 Z= 0.227 Angle : 0.584 11.705 90788 Z= 0.289 Chirality : 0.042 0.207 10812 Planarity : 0.004 0.046 11578 Dihedral : 7.671 177.631 9346 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.34 % Rotamer: Outliers : 2.31 % Allowed : 20.48 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.82 (0.09), residues: 8584 helix: 1.37 (0.08), residues: 4452 sheet: -0.07 (0.15), residues: 1206 loop : -0.36 (0.11), residues: 2926 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 826 time to evaluate : 6.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 132 residues processed: 963 average time/residue: 1.7179 time to fit residues: 2122.9503 Evaluate side-chains 937 residues out of total 7192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 805 time to evaluate : 6.010 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 120 residues processed: 13 average time/residue: 1.0343 time to fit residues: 27.5759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0533 > 50: distance: 75 - 78: 35.488 distance: 78 - 79: 55.663 distance: 79 - 80: 39.537 distance: 80 - 81: 4.495 distance: 82 - 83: 38.752 distance: 86 - 87: 40.375 distance: 86 - 89: 57.675 distance: 87 - 88: 41.202 distance: 87 - 90: 39.659 distance: 90 - 91: 56.252 distance: 91 - 92: 5.198 distance: 91 - 94: 41.635 distance: 92 - 93: 3.321 distance: 92 - 98: 5.393 distance: 94 - 95: 43.205 distance: 95 - 96: 48.340 distance: 95 - 97: 50.220 distance: 98 - 99: 38.820 distance: 98 - 104: 55.646 distance: 99 - 100: 56.886 distance: 99 - 102: 40.791 distance: 100 - 105: 40.004 distance: 102 - 103: 39.529 distance: 103 - 104: 41.397 distance: 106 - 109: 24.142 distance: 107 - 108: 39.007 distance: 107 - 116: 28.822 distance: 109 - 110: 17.224 distance: 110 - 111: 39.510 distance: 111 - 112: 39.486 distance: 113 - 114: 51.105 distance: 116 - 117: 30.930 distance: 117 - 118: 42.539 distance: 118 - 119: 46.529 distance: 118 - 124: 33.425 distance: 120 - 121: 38.895 distance: 121 - 123: 41.893 distance: 124 - 125: 17.261 distance: 125 - 126: 48.421 distance: 125 - 128: 50.161 distance: 126 - 127: 39.985 distance: 126 - 131: 35.736 distance: 128 - 129: 43.600 distance: 128 - 130: 41.804 distance: 131 - 132: 40.996 distance: 131 - 137: 33.326 distance: 132 - 133: 58.023 distance: 132 - 135: 38.571 distance: 133 - 134: 55.777 distance: 133 - 138: 56.183 distance: 135 - 136: 27.270 distance: 136 - 137: 46.875 distance: 138 - 139: 40.504 distance: 138 - 144: 56.227 distance: 139 - 142: 40.891 distance: 142 - 143: 39.567 distance: 143 - 144: 39.646 distance: 145 - 146: 39.990 distance: 146 - 147: 57.372 distance: 146 - 149: 39.328 distance: 147 - 152: 34.211 distance: 149 - 151: 22.883