Starting phenix.real_space_refine on Fri Dec 8 23:22:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ell_31184/12_2023/7ell_31184_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ell_31184/12_2023/7ell_31184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ell_31184/12_2023/7ell_31184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ell_31184/12_2023/7ell_31184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ell_31184/12_2023/7ell_31184_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ell_31184/12_2023/7ell_31184_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 242 5.16 5 C 38469 2.51 5 N 10040 2.21 5 O 11833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 16": "OD1" <-> "OD2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 54": "OE1" <-> "OE2" Residue "a ARG 64": "NH1" <-> "NH2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 98": "OE1" <-> "OE2" Residue "a PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 115": "OE1" <-> "OE2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a GLU 123": "OE1" <-> "OE2" Residue "a PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 139": "OD1" <-> "OD2" Residue "a ASP 176": "OD1" <-> "OD2" Residue "a GLU 189": "OE1" <-> "OE2" Residue "a ASP 220": "OD1" <-> "OD2" Residue "a ARG 231": "NH1" <-> "NH2" Residue "a TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 280": "OE1" <-> "OE2" Residue "a GLU 299": "OE1" <-> "OE2" Residue "a ASP 320": "OD1" <-> "OD2" Residue "a ARG 324": "NH1" <-> "NH2" Residue "a ARG 327": "NH1" <-> "NH2" Residue "a GLU 330": "OE1" <-> "OE2" Residue "a ARG 335": "NH1" <-> "NH2" Residue "a ARG 362": "NH1" <-> "NH2" Residue "a ARG 377": "NH1" <-> "NH2" Residue "a GLU 389": "OE1" <-> "OE2" Residue "a ASP 393": "OD1" <-> "OD2" Residue "a PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 512": "OE1" <-> "OE2" Residue "a TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 560": "OE1" <-> "OE2" Residue "a ARG 584": "NH1" <-> "NH2" Residue "a PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 53": "OD1" <-> "OD2" Residue "b GLU 54": "OE1" <-> "OE2" Residue "b ARG 65": "NH1" <-> "NH2" Residue "b GLU 89": "OE1" <-> "OE2" Residue "b GLU 98": "OE1" <-> "OE2" Residue "b PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "b GLU 123": "OE1" <-> "OE2" Residue "b ASP 126": "OD1" <-> "OD2" Residue "b TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 145": "OD1" <-> "OD2" Residue "b TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 207": "OE1" <-> "OE2" Residue "b ASP 221": "OD1" <-> "OD2" Residue "b GLU 297": "OE1" <-> "OE2" Residue "b PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 324": "NH1" <-> "NH2" Residue "b GLU 330": "OE1" <-> "OE2" Residue "b ARG 335": "NH1" <-> "NH2" Residue "b ARG 377": "NH1" <-> "NH2" Residue "b PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 381": "OD1" <-> "OD2" Residue "b GLU 389": "OE1" <-> "OE2" Residue "b ASP 393": "OD1" <-> "OD2" Residue "b PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 411": "OE1" <-> "OE2" Residue "b TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 433": "OE1" <-> "OE2" Residue "b GLU 455": "OE1" <-> "OE2" Residue "b ASP 461": "OD1" <-> "OD2" Residue "b GLU 463": "OE1" <-> "OE2" Residue "b TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 502": "OE1" <-> "OE2" Residue "b GLU 512": "OE1" <-> "OE2" Residue "b ARG 584": "NH1" <-> "NH2" Residue "b ARG 598": "NH1" <-> "NH2" Residue "b PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 606": "OD1" <-> "OD2" Residue "b PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 65": "NH1" <-> "NH2" Residue "c GLU 73": "OE1" <-> "OE2" Residue "c GLU 89": "OE1" <-> "OE2" Residue "c PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 189": "OE1" <-> "OE2" Residue "c ASP 221": "OD1" <-> "OD2" Residue "c GLU 235": "OE1" <-> "OE2" Residue "c GLU 280": "OE1" <-> "OE2" Residue "c GLU 287": "OE1" <-> "OE2" Residue "c TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 324": "NH1" <-> "NH2" Residue "c ARG 327": "NH1" <-> "NH2" Residue "c GLU 330": "OE1" <-> "OE2" Residue "c ARG 335": "NH1" <-> "NH2" Residue "c PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 377": "NH1" <-> "NH2" Residue "c GLU 389": "OE1" <-> "OE2" Residue "c ASP 393": "OD1" <-> "OD2" Residue "c GLU 411": "OE1" <-> "OE2" Residue "c TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 433": "OE1" <-> "OE2" Residue "c GLU 463": "OE1" <-> "OE2" Residue "c TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 512": "OE1" <-> "OE2" Residue "c ASP 554": "OD1" <-> "OD2" Residue "c ASP 559": "OD1" <-> "OD2" Residue "c ARG 584": "NH1" <-> "NH2" Residue "c PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 606": "OD1" <-> "OD2" Residue "c ASP 666": "OD1" <-> "OD2" Residue "c PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 64": "NH1" <-> "NH2" Residue "d ARG 65": "NH1" <-> "NH2" Residue "d TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "d ARG 122": "NH1" <-> "NH2" Residue "d PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 189": "OE1" <-> "OE2" Residue "d GLU 207": "OE1" <-> "OE2" Residue "d ASP 221": "OD1" <-> "OD2" Residue "d ASP 225": "OD1" <-> "OD2" Residue "d TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 281": "OE1" <-> "OE2" Residue "d GLU 297": "OE1" <-> "OE2" Residue "d GLU 299": "OE1" <-> "OE2" Residue "d ARG 324": "NH1" <-> "NH2" Residue "d ARG 335": "NH1" <-> "NH2" Residue "d ARG 362": "NH1" <-> "NH2" Residue "d ARG 377": "NH1" <-> "NH2" Residue "d PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 381": "OD1" <-> "OD2" Residue "d GLU 389": "OE1" <-> "OE2" Residue "d ASP 393": "OD1" <-> "OD2" Residue "d PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 525": "OE1" <-> "OE2" Residue "d ASP 553": "OD1" <-> "OD2" Residue "d ASP 559": "OD1" <-> "OD2" Residue "d TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 584": "NH1" <-> "NH2" Residue "d GLU 655": "OE1" <-> "OE2" Residue "d PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 666": "OD1" <-> "OD2" Residue "d PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 65": "NH1" <-> "NH2" Residue "e GLU 89": "OE1" <-> "OE2" Residue "e GLU 98": "OE1" <-> "OE2" Residue "e PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 119": "OE1" <-> "OE2" Residue "e TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 145": "OD1" <-> "OD2" Residue "e TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 186": "OE1" <-> "OE2" Residue "e GLU 189": "OE1" <-> "OE2" Residue "e ASP 226": "OD1" <-> "OD2" Residue "e GLU 235": "OE1" <-> "OE2" Residue "e TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 324": "NH1" <-> "NH2" Residue "e GLU 330": "OE1" <-> "OE2" Residue "e ARG 335": "NH1" <-> "NH2" Residue "e PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 377": "NH1" <-> "NH2" Residue "e ASP 381": "OD1" <-> "OD2" Residue "e GLU 389": "OE1" <-> "OE2" Residue "e PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 455": "OE1" <-> "OE2" Residue "e GLU 463": "OE1" <-> "OE2" Residue "e PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 512": "OE1" <-> "OE2" Residue "e TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 525": "OE1" <-> "OE2" Residue "e ASP 554": "OD1" <-> "OD2" Residue "e TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 584": "NH1" <-> "NH2" Residue "e PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 598": "NH1" <-> "NH2" Residue "e PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 65": "NH1" <-> "NH2" Residue "f GLU 89": "OE1" <-> "OE2" Residue "f PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 115": "OE1" <-> "OE2" Residue "f PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 126": "OD1" <-> "OD2" Residue "f TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 176": "OD1" <-> "OD2" Residue "f ASP 220": "OD1" <-> "OD2" Residue "f ASP 291": "OD1" <-> "OD2" Residue "f GLU 299": "OE1" <-> "OE2" Residue "f ASP 320": "OD1" <-> "OD2" Residue "f ARG 324": "NH1" <-> "NH2" Residue "f ARG 335": "NH1" <-> "NH2" Residue "f ASP 371": "OD1" <-> "OD2" Residue "f ARG 377": "NH1" <-> "NH2" Residue "f ASP 381": "OD1" <-> "OD2" Residue "f TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 541": "OD1" <-> "OD2" Residue "f TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 584": "NH1" <-> "NH2" Residue "f GLU 655": "OE1" <-> "OE2" Residue "f PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 64": "NH1" <-> "NH2" Residue "g ARG 65": "NH1" <-> "NH2" Residue "g GLU 73": "OE1" <-> "OE2" Residue "g GLU 89": "OE1" <-> "OE2" Residue "g PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 115": "OE1" <-> "OE2" Residue "g PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 122": "NH1" <-> "NH2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 145": "OD1" <-> "OD2" Residue "g PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 207": "OE1" <-> "OE2" Residue "g ASP 220": "OD1" <-> "OD2" Residue "g ASP 225": "OD1" <-> "OD2" Residue "g TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 260": "OE1" <-> "OE2" Residue "g GLU 280": "OE1" <-> "OE2" Residue "g GLU 287": "OE1" <-> "OE2" Residue "g GLU 299": "OE1" <-> "OE2" Residue "g ASP 320": "OD1" <-> "OD2" Residue "g ARG 324": "NH1" <-> "NH2" Residue "g ARG 327": "NH1" <-> "NH2" Residue "g ASP 329": "OD1" <-> "OD2" Residue "g ARG 335": "NH1" <-> "NH2" Residue "g ARG 362": "NH1" <-> "NH2" Residue "g ARG 377": "NH1" <-> "NH2" Residue "g PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 502": "OE1" <-> "OE2" Residue "g GLU 512": "OE1" <-> "OE2" Residue "g TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 554": "OD1" <-> "OD2" Residue "g GLU 560": "OE1" <-> "OE2" Residue "g GLU 578": "OE1" <-> "OE2" Residue "g ARG 584": "NH1" <-> "NH2" Residue "g PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 65": "NH1" <-> "NH2" Residue "h GLU 73": "OE1" <-> "OE2" Residue "h PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 115": "OE1" <-> "OE2" Residue "h PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 145": "OD1" <-> "OD2" Residue "h TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 191": "OD1" <-> "OD2" Residue "h ASP 221": "OD1" <-> "OD2" Residue "h GLU 254": "OE1" <-> "OE2" Residue "h GLU 260": "OE1" <-> "OE2" Residue "h PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 324": "NH1" <-> "NH2" Residue "h ARG 335": "NH1" <-> "NH2" Residue "h ARG 377": "NH1" <-> "NH2" Residue "h TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 433": "OE1" <-> "OE2" Residue "h GLU 455": "OE1" <-> "OE2" Residue "h TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 502": "OE1" <-> "OE2" Residue "h TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 525": "OE1" <-> "OE2" Residue "h TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 578": "OE1" <-> "OE2" Residue "h ARG 584": "NH1" <-> "NH2" Residue "h ARG 598": "NH1" <-> "NH2" Residue "h PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 666": "OD1" <-> "OD2" Residue "h PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 65": "NH1" <-> "NH2" Residue "i GLU 119": "OE1" <-> "OE2" Residue "i GLU 123": "OE1" <-> "OE2" Residue "i PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 251": "OD1" <-> "OD2" Residue "i GLU 281": "OE1" <-> "OE2" Residue "i ASP 320": "OD1" <-> "OD2" Residue "i TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 324": "NH1" <-> "NH2" Residue "i ARG 335": "NH1" <-> "NH2" Residue "i ARG 377": "NH1" <-> "NH2" Residue "i PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 411": "OE1" <-> "OE2" Residue "i TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 474": "OD1" <-> "OD2" Residue "i GLU 548": "OE1" <-> "OE2" Residue "i ASP 559": "OD1" <-> "OD2" Residue "i TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 584": "NH1" <-> "NH2" Residue "i ASP 620": "OD1" <-> "OD2" Residue "i PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ASP 97": "OD1" <-> "OD2" Residue "j GLU 98": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "j GLU 119": "OE1" <-> "OE2" Residue "j TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 186": "OE1" <-> "OE2" Residue "j GLU 254": "OE1" <-> "OE2" Residue "j GLU 287": "OE1" <-> "OE2" Residue "j GLU 299": "OE1" <-> "OE2" Residue "j TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 324": "NH1" <-> "NH2" Residue "j ARG 335": "NH1" <-> "NH2" Residue "j PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 377": "NH1" <-> "NH2" Residue "j PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 433": "OE1" <-> "OE2" Residue "j PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 584": "NH1" <-> "NH2" Residue "j ARG 598": "NH1" <-> "NH2" Residue "j PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 29": "OD1" <-> "OD2" Residue "K GLU 41": "OE1" <-> "OE2" Residue "K PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 184": "OD1" <-> "OD2" Residue "K PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "K PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 258": "OE1" <-> "OE2" Residue "K PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 294": "OE1" <-> "OE2" Residue "K PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 362": "OD1" <-> "OD2" Residue "K TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 408": "OD1" <-> "OD2" Residue "K GLU 409": "OE1" <-> "OE2" Residue "K TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 462": "OD1" <-> "OD2" Residue "K TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 486": "OD1" <-> "OD2" Residue "K TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 498": "OD1" <-> "OD2" Residue "K TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 531": "OE1" <-> "OE2" Residue "K PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 682": "OE1" <-> "OE2" Residue "K ASP 699": "OD1" <-> "OD2" Residue "K GLU 707": "OE1" <-> "OE2" Residue "K PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 776": "OD1" <-> "OD2" Residue "K TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 821": "OD1" <-> "OD2" Residue "K ASP 850": "OD1" <-> "OD2" Residue "K GLU 869": "OE1" <-> "OE2" Residue "K ASP 875": "OD1" <-> "OD2" Residue "K TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 964": "OD1" <-> "OD2" Residue "K TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1022": "OD1" <-> "OD2" Residue "K PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1056": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1081": "OD1" <-> "OD2" Residue "K GLU 1086": "OE1" <-> "OE2" Residue "K ASP 1135": "OD1" <-> "OD2" Residue "K TYR 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1169": "OD1" <-> "OD2" Residue "K PHE 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1191": "OD1" <-> "OD2" Residue "K TYR 1193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 1205": "OD1" <-> "OD2" Residue "K PHE 1208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1284": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 60584 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 282 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "a" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4662 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 42, 'TRANS': 567} Chain breaks: 1 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "b" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "c" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "d" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "e" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "F" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "f" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "G" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "g" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "H" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "h" Number of atoms: 4761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 623, 4756 Classifications: {'peptide': 623} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 577} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 623, 4756 Classifications: {'peptide': 623} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 577} Chain breaks: 1 bond proxies already assigned to first conformer: 4849 Chain: "I" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 222 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 3, 'TRANS': 28} Chain: "i" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "J" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 229 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "j" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4820 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "K" Number of atoms: 10115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1283, 10115 Classifications: {'peptide': 1283} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 73, 'TRANS': 1206} Chain breaks: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA h 62 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA h 62 " occ=0.50 Time building chain proxies: 25.73, per 1000 atoms: 0.42 Number of scatterers: 60584 At special positions: 0 Unit cell: (292.11, 166.92, 247.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 242 16.00 O 11833 8.00 N 10040 7.00 C 38469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.50 Conformation dependent library (CDL) restraints added in 9.5 seconds 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 273 helices and 91 sheets defined 34.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.06 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 38 through 41 No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'a' and resid 105 through 128 removed outlier: 3.509A pdb=" N ALA a 117 " --> pdb=" O LYS a 113 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU a 118 " --> pdb=" O ALA a 114 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU a 119 " --> pdb=" O GLU a 115 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE a 120 " --> pdb=" O MET a 116 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN a 121 " --> pdb=" O ALA a 117 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG a 122 " --> pdb=" O LEU a 118 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU a 123 " --> pdb=" O GLU a 119 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE a 124 " --> pdb=" O PHE a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 137 through 140 No H-bonds generated for 'chain 'a' and resid 137 through 140' Processing helix chain 'a' and resid 152 through 157 removed outlier: 5.626A pdb=" N ASN a 157 " --> pdb=" O ARG a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 186 removed outlier: 3.784A pdb=" N LEU a 185 " --> pdb=" O ALA a 181 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU a 186 " --> pdb=" O LEU a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 197 Processing helix chain 'a' and resid 212 through 222 removed outlier: 3.730A pdb=" N ASP a 221 " --> pdb=" O LYS a 217 " (cutoff:3.500A) Processing helix chain 'a' and resid 228 through 230 No H-bonds generated for 'chain 'a' and resid 228 through 230' Processing helix chain 'a' and resid 233 through 243 removed outlier: 3.685A pdb=" N ARG a 243 " --> pdb=" O ALA a 239 " (cutoff:3.500A) Processing helix chain 'a' and resid 264 through 268 Processing helix chain 'a' and resid 279 through 295 Processing helix chain 'a' and resid 298 through 301 No H-bonds generated for 'chain 'a' and resid 298 through 301' Processing helix chain 'a' and resid 309 through 312 No H-bonds generated for 'chain 'a' and resid 309 through 312' Processing helix chain 'a' and resid 323 through 325 No H-bonds generated for 'chain 'a' and resid 323 through 325' Processing helix chain 'a' and resid 410 through 412 No H-bonds generated for 'chain 'a' and resid 410 through 412' Processing helix chain 'a' and resid 417 through 419 No H-bonds generated for 'chain 'a' and resid 417 through 419' Processing helix chain 'a' and resid 454 through 457 No H-bonds generated for 'chain 'a' and resid 454 through 457' Processing helix chain 'a' and resid 480 through 482 No H-bonds generated for 'chain 'a' and resid 480 through 482' Processing helix chain 'a' and resid 524 through 528 Processing helix chain 'a' and resid 535 through 553 Processing helix chain 'a' and resid 566 through 576 Processing helix chain 'a' and resid 589 through 605 Processing helix chain 'a' and resid 607 through 610 Processing helix chain 'a' and resid 621 through 636 removed outlier: 3.932A pdb=" N LYS a 632 " --> pdb=" O ALA a 628 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR a 633 " --> pdb=" O GLN a 629 " (cutoff:3.500A) Processing helix chain 'a' and resid 644 through 671 Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'b' and resid 60 through 62 No H-bonds generated for 'chain 'b' and resid 60 through 62' Processing helix chain 'b' and resid 72 through 74 No H-bonds generated for 'chain 'b' and resid 72 through 74' Processing helix chain 'b' and resid 105 through 128 removed outlier: 3.964A pdb=" N THR b 109 " --> pdb=" O GLU b 105 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN b 110 " --> pdb=" O HIS b 106 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU b 115 " --> pdb=" O PHE b 111 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA b 117 " --> pdb=" O LYS b 113 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU b 118 " --> pdb=" O ALA b 114 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU b 119 " --> pdb=" O GLU b 115 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE b 120 " --> pdb=" O MET b 116 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN b 121 " --> pdb=" O ALA b 117 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU b 123 " --> pdb=" O GLU b 119 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE b 124 " --> pdb=" O PHE b 120 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS b 127 " --> pdb=" O GLU b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 137 through 139 No H-bonds generated for 'chain 'b' and resid 137 through 139' Processing helix chain 'b' and resid 152 through 156 Processing helix chain 'b' and resid 168 through 197 removed outlier: 3.926A pdb=" N ALA b 181 " --> pdb=" O SER b 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS b 183 " --> pdb=" O GLN b 179 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS b 187 " --> pdb=" O LYS b 183 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP b 188 " --> pdb=" O ALA b 184 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE b 190 " --> pdb=" O GLU b 186 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR b 197 " --> pdb=" O ARG b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 212 through 222 removed outlier: 3.839A pdb=" N LYS b 217 " --> pdb=" O GLN b 213 " (cutoff:3.500A) Processing helix chain 'b' and resid 228 through 230 No H-bonds generated for 'chain 'b' and resid 228 through 230' Processing helix chain 'b' and resid 233 through 242 Processing helix chain 'b' and resid 279 through 296 removed outlier: 3.911A pdb=" N SER b 283 " --> pdb=" O LEU b 279 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS b 284 " --> pdb=" O GLU b 280 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA b 289 " --> pdb=" O LEU b 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET b 290 " --> pdb=" O THR b 286 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU b 292 " --> pdb=" O GLN b 288 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR b 294 " --> pdb=" O MET b 290 " (cutoff:3.500A) Processing helix chain 'b' and resid 300 through 302 No H-bonds generated for 'chain 'b' and resid 300 through 302' Processing helix chain 'b' and resid 309 through 312 No H-bonds generated for 'chain 'b' and resid 309 through 312' Processing helix chain 'b' and resid 410 through 412 No H-bonds generated for 'chain 'b' and resid 410 through 412' Processing helix chain 'b' and resid 416 through 418 No H-bonds generated for 'chain 'b' and resid 416 through 418' Processing helix chain 'b' and resid 454 through 457 No H-bonds generated for 'chain 'b' and resid 454 through 457' Processing helix chain 'b' and resid 524 through 529 removed outlier: 3.561A pdb=" N ASN b 528 " --> pdb=" O PRO b 524 " (cutoff:3.500A) Processing helix chain 'b' and resid 535 through 553 removed outlier: 3.933A pdb=" N LYS b 545 " --> pdb=" O ASP b 541 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE b 546 " --> pdb=" O ARG b 542 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS b 551 " --> pdb=" O ALA b 547 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP b 553 " --> pdb=" O ALA b 549 " (cutoff:3.500A) Processing helix chain 'b' and resid 566 through 577 removed outlier: 3.833A pdb=" N GLN b 571 " --> pdb=" O PRO b 567 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU b 577 " --> pdb=" O ALA b 573 " (cutoff:3.500A) Processing helix chain 'b' and resid 589 through 605 Processing helix chain 'b' and resid 607 through 611 Processing helix chain 'b' and resid 621 through 637 removed outlier: 3.628A pdb=" N GLN b 629 " --> pdb=" O ILE b 625 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL b 631 " --> pdb=" O LEU b 627 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS b 632 " --> pdb=" O ALA b 628 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR b 633 " --> pdb=" O GLN b 629 " (cutoff:3.500A) Processing helix chain 'b' and resid 644 through 671 removed outlier: 3.691A pdb=" N VAL b 668 " --> pdb=" O PHE b 664 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER b 669 " --> pdb=" O LEU b 665 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA b 670 " --> pdb=" O ASP b 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'c' and resid 72 through 74 No H-bonds generated for 'chain 'c' and resid 72 through 74' Processing helix chain 'c' and resid 105 through 128 removed outlier: 3.913A pdb=" N LYS c 113 " --> pdb=" O THR c 109 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU c 115 " --> pdb=" O PHE c 111 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET c 116 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA c 117 " --> pdb=" O LYS c 113 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU c 118 " --> pdb=" O ALA c 114 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN c 121 " --> pdb=" O ALA c 117 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU c 123 " --> pdb=" O GLU c 119 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE c 124 " --> pdb=" O PHE c 120 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU c 125 " --> pdb=" O ASN c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 137 through 139 No H-bonds generated for 'chain 'c' and resid 137 through 139' Processing helix chain 'c' and resid 152 through 155 No H-bonds generated for 'chain 'c' and resid 152 through 155' Processing helix chain 'c' and resid 168 through 184 removed outlier: 3.709A pdb=" N ALA c 181 " --> pdb=" O SER c 177 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 196 removed outlier: 3.709A pdb=" N ILE c 190 " --> pdb=" O GLU c 186 " (cutoff:3.500A) Processing helix chain 'c' and resid 212 through 222 removed outlier: 3.768A pdb=" N ASP c 221 " --> pdb=" O LYS c 217 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 228 through 231 No H-bonds generated for 'chain 'c' and resid 228 through 231' Processing helix chain 'c' and resid 233 through 243 removed outlier: 3.825A pdb=" N LEU c 240 " --> pdb=" O ALA c 236 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA c 241 " --> pdb=" O ALA c 237 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 270 removed outlier: 3.638A pdb=" N SER c 268 " --> pdb=" O ALA c 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA c 269 " --> pdb=" O VAL c 265 " (cutoff:3.500A) Processing helix chain 'c' and resid 279 through 282 No H-bonds generated for 'chain 'c' and resid 279 through 282' Processing helix chain 'c' and resid 284 through 296 removed outlier: 4.439A pdb=" N ALA c 289 " --> pdb=" O LEU c 285 " (cutoff:3.500A) Processing helix chain 'c' and resid 298 through 301 No H-bonds generated for 'chain 'c' and resid 298 through 301' Processing helix chain 'c' and resid 309 through 312 No H-bonds generated for 'chain 'c' and resid 309 through 312' Processing helix chain 'c' and resid 454 through 457 No H-bonds generated for 'chain 'c' and resid 454 through 457' Processing helix chain 'c' and resid 515 through 518 Processing helix chain 'c' and resid 524 through 528 removed outlier: 3.523A pdb=" N ASN c 528 " --> pdb=" O PRO c 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 524 through 528' Processing helix chain 'c' and resid 535 through 553 removed outlier: 3.730A pdb=" N ARG c 542 " --> pdb=" O CYS c 538 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE c 546 " --> pdb=" O ARG c 542 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA c 547 " --> pdb=" O ALA c 543 " (cutoff:3.500A) Processing helix chain 'c' and resid 566 through 577 removed outlier: 4.227A pdb=" N ALA c 573 " --> pdb=" O GLN c 569 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE c 574 " --> pdb=" O GLY c 570 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER c 575 " --> pdb=" O GLN c 571 " (cutoff:3.500A) Processing helix chain 'c' and resid 589 through 605 removed outlier: 3.953A pdb=" N LYS c 594 " --> pdb=" O GLY c 590 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA c 596 " --> pdb=" O LEU c 592 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN c 601 " --> pdb=" O SER c 597 " (cutoff:3.500A) Processing helix chain 'c' and resid 607 through 609 No H-bonds generated for 'chain 'c' and resid 607 through 609' Processing helix chain 'c' and resid 621 through 636 removed outlier: 4.331A pdb=" N LYS c 632 " --> pdb=" O ALA c 628 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR c 633 " --> pdb=" O GLN c 629 " (cutoff:3.500A) Processing helix chain 'c' and resid 644 through 671 removed outlier: 4.328A pdb=" N VAL c 648 " --> pdb=" O VAL c 644 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER c 649 " --> pdb=" O LYS c 645 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER c 656 " --> pdb=" O SER c 652 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS c 667 " --> pdb=" O GLY c 663 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS c 671 " --> pdb=" O LYS c 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 41 No H-bonds generated for 'chain 'D' and resid 38 through 41' Processing helix chain 'd' and resid 105 through 128 removed outlier: 3.740A pdb=" N LYS d 113 " --> pdb=" O THR d 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU d 115 " --> pdb=" O PHE d 111 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET d 116 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU d 118 " --> pdb=" O ALA d 114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE d 120 " --> pdb=" O MET d 116 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN d 121 " --> pdb=" O ALA d 117 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG d 122 " --> pdb=" O LEU d 118 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE d 124 " --> pdb=" O PHE d 120 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS d 127 " --> pdb=" O GLU d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 140 No H-bonds generated for 'chain 'd' and resid 137 through 140' Processing helix chain 'd' and resid 152 through 157 removed outlier: 5.362A pdb=" N ASN d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 168 through 185 removed outlier: 4.081A pdb=" N ALA d 184 " --> pdb=" O ALA d 180 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU d 185 " --> pdb=" O ALA d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 197 Processing helix chain 'd' and resid 212 through 222 Processing helix chain 'd' and resid 228 through 231 No H-bonds generated for 'chain 'd' and resid 228 through 231' Processing helix chain 'd' and resid 233 through 243 removed outlier: 3.621A pdb=" N ARG d 243 " --> pdb=" O ALA d 239 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 270 removed outlier: 4.011A pdb=" N ALA d 269 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU d 270 " --> pdb=" O ALA d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 279 through 296 removed outlier: 3.739A pdb=" N THR d 286 " --> pdb=" O LYS d 282 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU d 287 " --> pdb=" O SER d 283 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 301 No H-bonds generated for 'chain 'd' and resid 298 through 301' Processing helix chain 'd' and resid 309 through 312 No H-bonds generated for 'chain 'd' and resid 309 through 312' Processing helix chain 'd' and resid 410 through 412 No H-bonds generated for 'chain 'd' and resid 410 through 412' Processing helix chain 'd' and resid 416 through 419 Processing helix chain 'd' and resid 524 through 529 Processing helix chain 'd' and resid 535 through 553 removed outlier: 3.746A pdb=" N ILE d 546 " --> pdb=" O ARG d 542 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA d 549 " --> pdb=" O LYS d 545 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS d 551 " --> pdb=" O ALA d 547 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE d 552 " --> pdb=" O GLU d 548 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP d 553 " --> pdb=" O ALA d 549 " (cutoff:3.500A) Processing helix chain 'd' and resid 566 through 577 removed outlier: 3.944A pdb=" N GLN d 571 " --> pdb=" O PRO d 567 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE d 574 " --> pdb=" O GLY d 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU d 577 " --> pdb=" O ALA d 573 " (cutoff:3.500A) Processing helix chain 'd' and resid 589 through 605 removed outlier: 3.528A pdb=" N LYS d 594 " --> pdb=" O GLY d 590 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY d 605 " --> pdb=" O GLN d 601 " (cutoff:3.500A) Processing helix chain 'd' and resid 607 through 611 Processing helix chain 'd' and resid 621 through 636 removed outlier: 4.419A pdb=" N LYS d 632 " --> pdb=" O ALA d 628 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR d 633 " --> pdb=" O GLN d 629 " (cutoff:3.500A) Processing helix chain 'd' and resid 644 through 671 removed outlier: 4.045A pdb=" N VAL d 648 " --> pdb=" O VAL d 644 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA d 670 " --> pdb=" O ASP d 666 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS d 671 " --> pdb=" O LYS d 667 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 74 No H-bonds generated for 'chain 'e' and resid 72 through 74' Processing helix chain 'e' and resid 105 through 128 removed outlier: 3.730A pdb=" N THR e 109 " --> pdb=" O GLU e 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA e 117 " --> pdb=" O LYS e 113 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU e 119 " --> pdb=" O GLU e 115 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE e 120 " --> pdb=" O MET e 116 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN e 121 " --> pdb=" O ALA e 117 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG e 122 " --> pdb=" O LEU e 118 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE e 124 " --> pdb=" O PHE e 120 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS e 127 " --> pdb=" O GLU e 123 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET e 128 " --> pdb=" O PHE e 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 137 through 140 Processing helix chain 'e' and resid 152 through 156 Processing helix chain 'e' and resid 168 through 198 removed outlier: 4.261A pdb=" N ALA e 184 " --> pdb=" O ALA e 180 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU e 185 " --> pdb=" O ALA e 181 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU e 186 " --> pdb=" O LEU e 182 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS e 187 " --> pdb=" O LYS e 183 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP e 188 " --> pdb=" O ALA e 184 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE e 190 " --> pdb=" O GLU e 186 " (cutoff:3.500A) Processing helix chain 'e' and resid 212 through 221 removed outlier: 3.891A pdb=" N LYS e 217 " --> pdb=" O GLN e 213 " (cutoff:3.500A) Processing helix chain 'e' and resid 233 through 243 Processing helix chain 'e' and resid 262 through 270 removed outlier: 4.656A pdb=" N VAL e 265 " --> pdb=" O VAL e 262 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA e 267 " --> pdb=" O ALA e 264 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER e 268 " --> pdb=" O VAL e 265 " (cutoff:3.500A) Processing helix chain 'e' and resid 279 through 296 removed outlier: 3.525A pdb=" N GLN e 288 " --> pdb=" O LYS e 284 " (cutoff:3.500A) Processing helix chain 'e' and resid 298 through 302 Processing helix chain 'e' and resid 309 through 312 No H-bonds generated for 'chain 'e' and resid 309 through 312' Processing helix chain 'e' and resid 410 through 412 No H-bonds generated for 'chain 'e' and resid 410 through 412' Processing helix chain 'e' and resid 416 through 418 No H-bonds generated for 'chain 'e' and resid 416 through 418' Processing helix chain 'e' and resid 454 through 457 No H-bonds generated for 'chain 'e' and resid 454 through 457' Processing helix chain 'e' and resid 515 through 518 Processing helix chain 'e' and resid 524 through 528 removed outlier: 4.164A pdb=" N ASN e 528 " --> pdb=" O PRO e 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 524 through 528' Processing helix chain 'e' and resid 535 through 553 removed outlier: 3.577A pdb=" N ARG e 542 " --> pdb=" O CYS e 538 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS e 545 " --> pdb=" O ASP e 541 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE e 546 " --> pdb=" O ARG e 542 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE e 552 " --> pdb=" O GLU e 548 " (cutoff:3.500A) Processing helix chain 'e' and resid 566 through 577 removed outlier: 3.873A pdb=" N GLY e 570 " --> pdb=" O PRO e 567 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU e 572 " --> pdb=" O GLN e 569 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA e 573 " --> pdb=" O GLY e 570 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE e 574 " --> pdb=" O GLN e 571 " (cutoff:3.500A) Processing helix chain 'e' and resid 589 through 605 Processing helix chain 'e' and resid 607 through 609 No H-bonds generated for 'chain 'e' and resid 607 through 609' Processing helix chain 'e' and resid 621 through 636 removed outlier: 3.594A pdb=" N GLN e 629 " --> pdb=" O ILE e 625 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS e 632 " --> pdb=" O ALA e 628 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR e 633 " --> pdb=" O GLN e 629 " (cutoff:3.500A) Processing helix chain 'e' and resid 644 through 671 removed outlier: 3.624A pdb=" N LEU e 651 " --> pdb=" O ALA e 647 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER e 652 " --> pdb=" O VAL e 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'f' and resid 82 through 84 No H-bonds generated for 'chain 'f' and resid 82 through 84' Processing helix chain 'f' and resid 105 through 128 removed outlier: 3.795A pdb=" N ALA f 117 " --> pdb=" O LYS f 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU f 118 " --> pdb=" O ALA f 114 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASN f 121 " --> pdb=" O ALA f 117 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG f 122 " --> pdb=" O LEU f 118 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU f 123 " --> pdb=" O GLU f 119 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE f 124 " --> pdb=" O PHE f 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 140 Processing helix chain 'f' and resid 154 through 157 No H-bonds generated for 'chain 'f' and resid 154 through 157' Processing helix chain 'f' and resid 168 through 186 removed outlier: 3.653A pdb=" N VAL f 175 " --> pdb=" O GLN f 171 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA f 181 " --> pdb=" O SER f 177 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU f 186 " --> pdb=" O LEU f 182 " (cutoff:3.500A) Processing helix chain 'f' and resid 188 through 198 removed outlier: 3.667A pdb=" N ALA f 195 " --> pdb=" O ASP f 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 212 through 220 Processing helix chain 'f' and resid 228 through 231 No H-bonds generated for 'chain 'f' and resid 228 through 231' Processing helix chain 'f' and resid 233 through 243 removed outlier: 3.942A pdb=" N ARG f 243 " --> pdb=" O ALA f 239 " (cutoff:3.500A) Processing helix chain 'f' and resid 264 through 270 removed outlier: 3.668A pdb=" N LEU f 270 " --> pdb=" O ALA f 266 " (cutoff:3.500A) Processing helix chain 'f' and resid 279 through 296 removed outlier: 3.567A pdb=" N LEU f 285 " --> pdb=" O GLU f 281 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU f 287 " --> pdb=" O SER f 283 " (cutoff:3.500A) Processing helix chain 'f' and resid 298 through 301 No H-bonds generated for 'chain 'f' and resid 298 through 301' Processing helix chain 'f' and resid 309 through 312 No H-bonds generated for 'chain 'f' and resid 309 through 312' Processing helix chain 'f' and resid 323 through 325 No H-bonds generated for 'chain 'f' and resid 323 through 325' Processing helix chain 'f' and resid 410 through 412 No H-bonds generated for 'chain 'f' and resid 410 through 412' Processing helix chain 'f' and resid 454 through 457 No H-bonds generated for 'chain 'f' and resid 454 through 457' Processing helix chain 'f' and resid 515 through 518 Processing helix chain 'f' and resid 526 through 529 No H-bonds generated for 'chain 'f' and resid 526 through 529' Processing helix chain 'f' and resid 535 through 553 removed outlier: 4.578A pdb=" N LYS f 545 " --> pdb=" O ASP f 541 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE f 546 " --> pdb=" O ARG f 542 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS f 551 " --> pdb=" O ALA f 547 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE f 552 " --> pdb=" O GLU f 548 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP f 553 " --> pdb=" O ALA f 549 " (cutoff:3.500A) Processing helix chain 'f' and resid 566 through 577 removed outlier: 3.686A pdb=" N GLN f 571 " --> pdb=" O PRO f 567 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA f 573 " --> pdb=" O GLN f 569 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE f 574 " --> pdb=" O GLY f 570 " (cutoff:3.500A) Processing helix chain 'f' and resid 589 through 605 removed outlier: 3.527A pdb=" N LYS f 594 " --> pdb=" O GLY f 590 " (cutoff:3.500A) Processing helix chain 'f' and resid 607 through 609 No H-bonds generated for 'chain 'f' and resid 607 through 609' Processing helix chain 'f' and resid 621 through 636 removed outlier: 4.391A pdb=" N LYS f 632 " --> pdb=" O ALA f 628 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR f 633 " --> pdb=" O GLN f 629 " (cutoff:3.500A) Processing helix chain 'f' and resid 644 through 671 removed outlier: 3.572A pdb=" N VAL f 648 " --> pdb=" O VAL f 644 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER f 656 " --> pdb=" O SER f 652 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL f 668 " --> pdb=" O PHE f 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 26 No H-bonds generated for 'chain 'G' and resid 24 through 26' Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'g' and resid 105 through 128 removed outlier: 3.737A pdb=" N ASN g 110 " --> pdb=" O HIS g 106 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS g 113 " --> pdb=" O THR g 109 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU g 115 " --> pdb=" O PHE g 111 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET g 116 " --> pdb=" O THR g 112 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA g 117 " --> pdb=" O LYS g 113 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU g 118 " --> pdb=" O ALA g 114 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN g 121 " --> pdb=" O ALA g 117 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU g 123 " --> pdb=" O GLU g 119 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE g 124 " --> pdb=" O PHE g 120 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS g 127 " --> pdb=" O GLU g 123 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 140 Processing helix chain 'g' and resid 152 through 157 removed outlier: 5.492A pdb=" N ASN g 157 " --> pdb=" O ARG g 153 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 197 removed outlier: 3.786A pdb=" N ALA g 181 " --> pdb=" O SER g 177 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYS g 187 " --> pdb=" O LYS g 183 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N TRP g 188 " --> pdb=" O ALA g 184 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE g 190 " --> pdb=" O GLU g 186 " (cutoff:3.500A) Processing helix chain 'g' and resid 212 through 222 removed outlier: 3.570A pdb=" N LYS g 217 " --> pdb=" O GLN g 213 " (cutoff:3.500A) Processing helix chain 'g' and resid 228 through 231 No H-bonds generated for 'chain 'g' and resid 228 through 231' Processing helix chain 'g' and resid 233 through 241 Processing helix chain 'g' and resid 264 through 270 removed outlier: 3.686A pdb=" N ALA g 269 " --> pdb=" O VAL g 265 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU g 270 " --> pdb=" O ALA g 266 " (cutoff:3.500A) Processing helix chain 'g' and resid 279 through 296 removed outlier: 3.681A pdb=" N GLU g 287 " --> pdb=" O SER g 283 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL g 293 " --> pdb=" O ALA g 289 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 301 No H-bonds generated for 'chain 'g' and resid 298 through 301' Processing helix chain 'g' and resid 309 through 312 No H-bonds generated for 'chain 'g' and resid 309 through 312' Processing helix chain 'g' and resid 410 through 412 No H-bonds generated for 'chain 'g' and resid 410 through 412' Processing helix chain 'g' and resid 417 through 419 No H-bonds generated for 'chain 'g' and resid 417 through 419' Processing helix chain 'g' and resid 454 through 457 No H-bonds generated for 'chain 'g' and resid 454 through 457' Processing helix chain 'g' and resid 524 through 528 Processing helix chain 'g' and resid 535 through 553 removed outlier: 3.562A pdb=" N ASP g 541 " --> pdb=" O ARG g 537 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE g 546 " --> pdb=" O ARG g 542 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA g 547 " --> pdb=" O ALA g 543 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU g 548 " --> pdb=" O SER g 544 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP g 553 " --> pdb=" O ALA g 549 " (cutoff:3.500A) Processing helix chain 'g' and resid 566 through 577 removed outlier: 4.064A pdb=" N ILE g 574 " --> pdb=" O GLY g 570 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU g 577 " --> pdb=" O ALA g 573 " (cutoff:3.500A) Processing helix chain 'g' and resid 589 through 605 removed outlier: 3.535A pdb=" N SER g 593 " --> pdb=" O LYS g 589 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS g 594 " --> pdb=" O GLY g 590 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE g 604 " --> pdb=" O MET g 600 " (cutoff:3.500A) Processing helix chain 'g' and resid 608 through 610 No H-bonds generated for 'chain 'g' and resid 608 through 610' Processing helix chain 'g' and resid 621 through 637 removed outlier: 4.497A pdb=" N LYS g 632 " --> pdb=" O ALA g 628 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR g 633 " --> pdb=" O GLN g 629 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR g 637 " --> pdb=" O THR g 633 " (cutoff:3.500A) Processing helix chain 'g' and resid 644 through 671 removed outlier: 3.531A pdb=" N GLU g 655 " --> pdb=" O LEU g 651 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER g 656 " --> pdb=" O SER g 652 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE g 657 " --> pdb=" O SER g 653 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA g 670 " --> pdb=" O ASP g 666 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 41 No H-bonds generated for 'chain 'H' and resid 38 through 41' Processing helix chain 'h' and resid 105 through 128 removed outlier: 3.535A pdb=" N ASN h 110 " --> pdb=" O HIS h 106 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR h 112 " --> pdb=" O ILE h 108 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS h 113 " --> pdb=" O THR h 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU h 118 " --> pdb=" O ALA h 114 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU h 119 " --> pdb=" O GLU h 115 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE h 120 " --> pdb=" O MET h 116 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASN h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLU h 123 " --> pdb=" O GLU h 119 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE h 124 " --> pdb=" O PHE h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 137 through 140 No H-bonds generated for 'chain 'h' and resid 137 through 140' Processing helix chain 'h' and resid 152 through 155 No H-bonds generated for 'chain 'h' and resid 152 through 155' Processing helix chain 'h' and resid 168 through 198 removed outlier: 3.610A pdb=" N ALA h 181 " --> pdb=" O SER h 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA h 184 " --> pdb=" O ALA h 180 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU h 186 " --> pdb=" O LEU h 182 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS h 187 " --> pdb=" O LYS h 183 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP h 188 " --> pdb=" O ALA h 184 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE h 190 " --> pdb=" O GLU h 186 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU h 192 " --> pdb=" O TRP h 188 " (cutoff:3.500A) Processing helix chain 'h' and resid 212 through 222 removed outlier: 3.950A pdb=" N LYS h 217 " --> pdb=" O GLN h 213 " (cutoff:3.500A) Processing helix chain 'h' and resid 228 through 230 No H-bonds generated for 'chain 'h' and resid 228 through 230' Processing helix chain 'h' and resid 233 through 243 removed outlier: 3.656A pdb=" N ALA h 241 " --> pdb=" O ALA h 237 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS h 242 " --> pdb=" O VAL h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 266 through 270 removed outlier: 3.664A pdb=" N LEU h 270 " --> pdb=" O ALA h 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 266 through 270' Processing helix chain 'h' and resid 279 through 295 removed outlier: 3.531A pdb=" N THR h 294 " --> pdb=" O MET h 290 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 302 No H-bonds generated for 'chain 'h' and resid 300 through 302' Processing helix chain 'h' and resid 309 through 312 No H-bonds generated for 'chain 'h' and resid 309 through 312' Processing helix chain 'h' and resid 410 through 412 No H-bonds generated for 'chain 'h' and resid 410 through 412' Processing helix chain 'h' and resid 416 through 419 removed outlier: 3.771A pdb=" N ILE h 419 " --> pdb=" O ALA h 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 416 through 419' Processing helix chain 'h' and resid 515 through 518 removed outlier: 3.556A pdb=" N LEU h 518 " --> pdb=" O PRO h 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 515 through 518' Processing helix chain 'h' and resid 524 through 528 removed outlier: 4.559A pdb=" N ASN h 528 " --> pdb=" O PRO h 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 524 through 528' Processing helix chain 'h' and resid 535 through 553 removed outlier: 3.933A pdb=" N LYS h 545 " --> pdb=" O ASP h 541 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE h 546 " --> pdb=" O ARG h 542 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP h 553 " --> pdb=" O ALA h 549 " (cutoff:3.500A) Processing helix chain 'h' and resid 566 through 577 removed outlier: 4.070A pdb=" N GLN h 571 " --> pdb=" O PRO h 567 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU h 577 " --> pdb=" O ALA h 573 " (cutoff:3.500A) Processing helix chain 'h' and resid 589 through 605 removed outlier: 3.569A pdb=" N LYS h 594 " --> pdb=" O GLY h 590 " (cutoff:3.500A) Processing helix chain 'h' and resid 607 through 611 Processing helix chain 'h' and resid 621 through 637 removed outlier: 4.141A pdb=" N LYS h 632 " --> pdb=" O ALA h 628 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR h 633 " --> pdb=" O GLN h 629 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR h 637 " --> pdb=" O THR h 633 " (cutoff:3.500A) Processing helix chain 'h' and resid 644 through 671 removed outlier: 4.004A pdb=" N VAL h 648 " --> pdb=" O VAL h 644 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER h 649 " --> pdb=" O LYS h 645 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE h 657 " --> pdb=" O SER h 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS h 667 " --> pdb=" O GLY h 663 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL h 668 " --> pdb=" O PHE h 664 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER h 669 " --> pdb=" O LEU h 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 26 No H-bonds generated for 'chain 'I' and resid 24 through 26' Processing helix chain 'I' and resid 38 through 41 No H-bonds generated for 'chain 'I' and resid 38 through 41' Processing helix chain 'i' and resid 82 through 84 No H-bonds generated for 'chain 'i' and resid 82 through 84' Processing helix chain 'i' and resid 105 through 119 removed outlier: 3.764A pdb=" N LYS i 113 " --> pdb=" O THR i 109 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU i 115 " --> pdb=" O PHE i 111 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET i 116 " --> pdb=" O THR i 112 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA i 117 " --> pdb=" O LYS i 113 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU i 119 " --> pdb=" O GLU i 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 122 through 128 removed outlier: 3.596A pdb=" N LYS i 127 " --> pdb=" O GLU i 123 " (cutoff:3.500A) Processing helix chain 'i' and resid 137 through 140 No H-bonds generated for 'chain 'i' and resid 137 through 140' Processing helix chain 'i' and resid 152 through 157 removed outlier: 4.779A pdb=" N ASN i 157 " --> pdb=" O ARG i 153 " (cutoff:3.500A) Processing helix chain 'i' and resid 168 through 184 removed outlier: 3.602A pdb=" N ASP i 176 " --> pdb=" O THR i 172 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER i 177 " --> pdb=" O MET i 173 " (cutoff:3.500A) Processing helix chain 'i' and resid 186 through 198 Processing helix chain 'i' and resid 212 through 220 Processing helix chain 'i' and resid 228 through 231 No H-bonds generated for 'chain 'i' and resid 228 through 231' Processing helix chain 'i' and resid 233 through 243 removed outlier: 3.535A pdb=" N VAL i 238 " --> pdb=" O LYS i 234 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG i 243 " --> pdb=" O ALA i 239 " (cutoff:3.500A) Processing helix chain 'i' and resid 264 through 269 removed outlier: 3.510A pdb=" N SER i 268 " --> pdb=" O ALA i 264 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA i 269 " --> pdb=" O VAL i 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 264 through 269' Processing helix chain 'i' and resid 279 through 295 removed outlier: 4.293A pdb=" N THR i 286 " --> pdb=" O LYS i 282 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA i 295 " --> pdb=" O ASP i 291 " (cutoff:3.500A) Processing helix chain 'i' and resid 298 through 301 No H-bonds generated for 'chain 'i' and resid 298 through 301' Processing helix chain 'i' and resid 309 through 312 No H-bonds generated for 'chain 'i' and resid 309 through 312' Processing helix chain 'i' and resid 323 through 325 No H-bonds generated for 'chain 'i' and resid 323 through 325' Processing helix chain 'i' and resid 410 through 412 No H-bonds generated for 'chain 'i' and resid 410 through 412' Processing helix chain 'i' and resid 454 through 457 No H-bonds generated for 'chain 'i' and resid 454 through 457' Processing helix chain 'i' and resid 515 through 518 Processing helix chain 'i' and resid 524 through 529 removed outlier: 3.846A pdb=" N THR i 529 " --> pdb=" O GLU i 525 " (cutoff:3.500A) Processing helix chain 'i' and resid 535 through 553 removed outlier: 3.814A pdb=" N ASP i 541 " --> pdb=" O ARG i 537 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG i 542 " --> pdb=" O CYS i 538 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE i 546 " --> pdb=" O ARG i 542 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA i 547 " --> pdb=" O ALA i 543 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU i 548 " --> pdb=" O SER i 544 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA i 549 " --> pdb=" O LYS i 545 " (cutoff:3.500A) Processing helix chain 'i' and resid 566 through 577 removed outlier: 4.112A pdb=" N SER i 575 " --> pdb=" O GLN i 571 " (cutoff:3.500A) Processing helix chain 'i' and resid 589 through 605 removed outlier: 3.896A pdb=" N LYS i 594 " --> pdb=" O GLY i 590 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA i 596 " --> pdb=" O LEU i 592 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA i 602 " --> pdb=" O ARG i 598 " (cutoff:3.500A) Processing helix chain 'i' and resid 607 through 610 Processing helix chain 'i' and resid 621 through 637 removed outlier: 3.896A pdb=" N GLY i 630 " --> pdb=" O ALA i 626 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS i 632 " --> pdb=" O ALA i 628 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU i 635 " --> pdb=" O VAL i 631 " (cutoff:3.500A) Processing helix chain 'i' and resid 644 through 670 removed outlier: 3.781A pdb=" N LEU i 651 " --> pdb=" O ALA i 647 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER i 652 " --> pdb=" O VAL i 648 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE i 657 " --> pdb=" O SER i 653 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA i 670 " --> pdb=" O ASP i 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 26 No H-bonds generated for 'chain 'J' and resid 24 through 26' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'j' and resid 72 through 74 No H-bonds generated for 'chain 'j' and resid 72 through 74' Processing helix chain 'j' and resid 105 through 128 removed outlier: 3.507A pdb=" N THR j 109 " --> pdb=" O GLU j 105 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU j 115 " --> pdb=" O PHE j 111 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET j 116 " --> pdb=" O THR j 112 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA j 117 " --> pdb=" O LYS j 113 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU j 118 " --> pdb=" O ALA j 114 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE j 120 " --> pdb=" O MET j 116 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG j 122 " --> pdb=" O LEU j 118 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU j 123 " --> pdb=" O GLU j 119 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE j 124 " --> pdb=" O PHE j 120 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS j 127 " --> pdb=" O GLU j 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 137 through 140 No H-bonds generated for 'chain 'j' and resid 137 through 140' Processing helix chain 'j' and resid 152 through 155 No H-bonds generated for 'chain 'j' and resid 152 through 155' Processing helix chain 'j' and resid 168 through 184 removed outlier: 3.576A pdb=" N VAL j 175 " --> pdb=" O GLN j 171 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA j 181 " --> pdb=" O SER j 177 " (cutoff:3.500A) Processing helix chain 'j' and resid 186 through 198 removed outlier: 3.516A pdb=" N THR j 197 " --> pdb=" O ARG j 193 " (cutoff:3.500A) Processing helix chain 'j' and resid 212 through 222 removed outlier: 4.017A pdb=" N LYS j 217 " --> pdb=" O GLN j 213 " (cutoff:3.500A) Processing helix chain 'j' and resid 228 through 231 No H-bonds generated for 'chain 'j' and resid 228 through 231' Processing helix chain 'j' and resid 233 through 243 removed outlier: 3.887A pdb=" N ARG j 243 " --> pdb=" O ALA j 239 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 270 removed outlier: 3.663A pdb=" N ALA j 269 " --> pdb=" O VAL j 265 " (cutoff:3.500A) Processing helix chain 'j' and resid 279 through 296 removed outlier: 4.001A pdb=" N THR j 286 " --> pdb=" O LYS j 282 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN j 288 " --> pdb=" O LYS j 284 " (cutoff:3.500A) Processing helix chain 'j' and resid 298 through 300 No H-bonds generated for 'chain 'j' and resid 298 through 300' Processing helix chain 'j' and resid 309 through 312 No H-bonds generated for 'chain 'j' and resid 309 through 312' Processing helix chain 'j' and resid 410 through 412 No H-bonds generated for 'chain 'j' and resid 410 through 412' Processing helix chain 'j' and resid 416 through 418 No H-bonds generated for 'chain 'j' and resid 416 through 418' Processing helix chain 'j' and resid 454 through 457 No H-bonds generated for 'chain 'j' and resid 454 through 457' Processing helix chain 'j' and resid 480 through 482 No H-bonds generated for 'chain 'j' and resid 480 through 482' Processing helix chain 'j' and resid 524 through 528 removed outlier: 3.729A pdb=" N ASN j 528 " --> pdb=" O PRO j 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 524 through 528' Processing helix chain 'j' and resid 535 through 553 removed outlier: 3.661A pdb=" N ASP j 541 " --> pdb=" O ARG j 537 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG j 542 " --> pdb=" O CYS j 538 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE j 546 " --> pdb=" O ARG j 542 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA j 547 " --> pdb=" O ALA j 543 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS j 551 " --> pdb=" O ALA j 547 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE j 552 " --> pdb=" O GLU j 548 " (cutoff:3.500A) Processing helix chain 'j' and resid 563 through 576 Proline residue: j 567 - end of helix removed outlier: 3.769A pdb=" N GLN j 571 " --> pdb=" O PRO j 567 " (cutoff:3.500A) Processing helix chain 'j' and resid 589 through 605 removed outlier: 3.558A pdb=" N SER j 593 " --> pdb=" O LYS j 589 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN j 601 " --> pdb=" O SER j 597 " (cutoff:3.500A) Processing helix chain 'j' and resid 607 through 609 No H-bonds generated for 'chain 'j' and resid 607 through 609' Processing helix chain 'j' and resid 621 through 636 removed outlier: 4.056A pdb=" N LYS j 632 " --> pdb=" O ALA j 628 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR j 633 " --> pdb=" O GLN j 629 " (cutoff:3.500A) Processing helix chain 'j' and resid 644 through 671 removed outlier: 3.513A pdb=" N VAL j 648 " --> pdb=" O VAL j 644 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS j 650 " --> pdb=" O THR j 646 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU j 651 " --> pdb=" O ALA j 647 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER j 652 " --> pdb=" O VAL j 648 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS j 667 " --> pdb=" O GLY j 663 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 35 removed outlier: 3.581A pdb=" N ASP K 35 " --> pdb=" O CYS K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 73 No H-bonds generated for 'chain 'K' and resid 70 through 73' Processing helix chain 'K' and resid 79 through 100 removed outlier: 3.734A pdb=" N ARG K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG K 99 " --> pdb=" O TYR K 95 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE K 100 " --> pdb=" O GLU K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 124 Processing helix chain 'K' and resid 133 through 135 No H-bonds generated for 'chain 'K' and resid 133 through 135' Processing helix chain 'K' and resid 204 through 213 removed outlier: 3.953A pdb=" N THR K 213 " --> pdb=" O ARG K 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 268 removed outlier: 3.745A pdb=" N VAL K 268 " --> pdb=" O PHE K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 291 No H-bonds generated for 'chain 'K' and resid 289 through 291' Processing helix chain 'K' and resid 297 through 309 Processing helix chain 'K' and resid 324 through 334 Processing helix chain 'K' and resid 361 through 364 No H-bonds generated for 'chain 'K' and resid 361 through 364' Processing helix chain 'K' and resid 407 through 417 removed outlier: 3.636A pdb=" N ASP K 411 " --> pdb=" O MET K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 450 through 452 No H-bonds generated for 'chain 'K' and resid 450 through 452' Processing helix chain 'K' and resid 463 through 474 Processing helix chain 'K' and resid 481 through 495 removed outlier: 4.090A pdb=" N GLN K 495 " --> pdb=" O LYS K 491 " (cutoff:3.500A) Processing helix chain 'K' and resid 530 through 534 Processing helix chain 'K' and resid 589 through 605 Processing helix chain 'K' and resid 621 through 630 Processing helix chain 'K' and resid 632 through 634 No H-bonds generated for 'chain 'K' and resid 632 through 634' Processing helix chain 'K' and resid 668 through 690 removed outlier: 4.431A pdb=" N TYR K 681 " --> pdb=" O HIS K 677 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN K 690 " --> pdb=" O THR K 686 " (cutoff:3.500A) Processing helix chain 'K' and resid 724 through 734 removed outlier: 3.703A pdb=" N SER K 728 " --> pdb=" O ARG K 724 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU K 730 " --> pdb=" O GLY K 726 " (cutoff:3.500A) Processing helix chain 'K' and resid 760 through 768 removed outlier: 3.622A pdb=" N LYS K 766 " --> pdb=" O SER K 762 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER K 767 " --> pdb=" O ALA K 763 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG K 768 " --> pdb=" O ARG K 764 " (cutoff:3.500A) Processing helix chain 'K' and resid 777 through 781 removed outlier: 4.032A pdb=" N GLU K 781 " --> pdb=" O ARG K 778 " (cutoff:3.500A) Processing helix chain 'K' and resid 803 through 817 removed outlier: 3.975A pdb=" N GLU K 814 " --> pdb=" O MET K 810 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL K 815 " --> pdb=" O TYR K 811 " (cutoff:3.500A) Processing helix chain 'K' and resid 835 through 838 Processing helix chain 'K' and resid 892 through 898 Processing helix chain 'K' and resid 903 through 915 Processing helix chain 'K' and resid 963 through 973 removed outlier: 3.582A pdb=" N LYS K 968 " --> pdb=" O ASP K 964 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE K 969 " --> pdb=" O ALA K 965 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA K 973 " --> pdb=" O ILE K 969 " (cutoff:3.500A) Processing helix chain 'K' and resid 989 through 997 removed outlier: 4.015A pdb=" N LEU K 995 " --> pdb=" O ARG K 992 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU K 996 " --> pdb=" O LEU K 993 " (cutoff:3.500A) Processing helix chain 'K' and resid 1003 through 1015 removed outlier: 4.101A pdb=" N TYR K1015 " --> pdb=" O LEU K1011 " (cutoff:3.500A) Processing helix chain 'K' and resid 1190 through 1193 Processing helix chain 'K' and resid 1217 through 1219 No H-bonds generated for 'chain 'K' and resid 1217 through 1219' Processing sheet with id= A, first strand: chain 'a' and resid 147 through 149 Processing sheet with id= B, first strand: chain 'a' and resid 100 through 102 Processing sheet with id= C, first strand: chain 'a' and resid 306 through 308 Processing sheet with id= D, first strand: chain 'a' and resid 319 through 322 Processing sheet with id= E, first strand: chain 'a' and resid 334 through 336 removed outlier: 3.626A pdb=" N ARG a 335 " --> pdb=" O VAL a 367 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'a' and resid 344 through 350 Processing sheet with id= G, first strand: chain 'a' and resid 465 through 472 removed outlier: 4.007A pdb=" N ASN a 426 " --> pdb=" O PHE a 401 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL a 403 " --> pdb=" O VAL a 424 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL a 424 " --> pdb=" O VAL a 403 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLN a 405 " --> pdb=" O ALA a 422 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA a 422 " --> pdb=" O GLN a 405 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'a' and resid 432 through 434 Processing sheet with id= I, first strand: chain 'a' and resid 503 through 505 removed outlier: 4.454A pdb=" N VAL a 503 " --> pdb=" O VAL a 510 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'b' and resid 147 through 149 removed outlier: 3.775A pdb=" N TYR b 147 " --> pdb=" O TRP b 48 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'b' and resid 100 through 102 Processing sheet with id= L, first strand: chain 'b' and resid 319 through 322 Processing sheet with id= M, first strand: chain 'b' and resid 334 through 336 Processing sheet with id= N, first strand: chain 'b' and resid 348 through 350 Processing sheet with id= O, first strand: chain 'b' and resid 465 through 473 removed outlier: 3.936A pdb=" N LYS b 398 " --> pdb=" O ILE b 473 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL b 399 " --> pdb=" O VAL b 428 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN b 426 " --> pdb=" O PHE b 401 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL b 403 " --> pdb=" O VAL b 424 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL b 424 " --> pdb=" O VAL b 403 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLN b 405 " --> pdb=" O ALA b 422 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA b 422 " --> pdb=" O GLN b 405 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'b' and resid 432 through 434 Processing sheet with id= Q, first strand: chain 'c' and resid 147 through 149 Processing sheet with id= R, first strand: chain 'c' and resid 100 through 103 removed outlier: 3.531A pdb=" N VAL c 103 " --> pdb=" O PRO c 164 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'c' and resid 319 through 321 removed outlier: 3.691A pdb=" N LEU c 492 " --> pdb=" O ASP c 381 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'c' and resid 334 through 336 Processing sheet with id= U, first strand: chain 'c' and resid 345 through 348 removed outlier: 3.586A pdb=" N PHE c 345 " --> pdb=" O LEU c 361 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'c' and resid 466 through 473 removed outlier: 3.523A pdb=" N THR c 471 " --> pdb=" O GLY c 400 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS c 398 " --> pdb=" O ILE c 473 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN c 426 " --> pdb=" O PHE c 401 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL c 403 " --> pdb=" O VAL c 424 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL c 424 " --> pdb=" O VAL c 403 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN c 405 " --> pdb=" O ALA c 422 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA c 422 " --> pdb=" O GLN c 405 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'c' and resid 432 through 434 Processing sheet with id= X, first strand: chain 'c' and resid 503 through 505 removed outlier: 4.685A pdb=" N VAL c 503 " --> pdb=" O VAL c 510 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'd' and resid 147 through 149 removed outlier: 3.833A pdb=" N TYR d 147 " --> pdb=" O TRP d 48 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'd' and resid 142 through 144 Processing sheet with id= AA, first strand: chain 'd' and resid 319 through 321 Processing sheet with id= AB, first strand: chain 'd' and resid 334 through 336 Processing sheet with id= AC, first strand: chain 'd' and resid 344 through 350 removed outlier: 3.515A pdb=" N ILE d 347 " --> pdb=" O LEU d 359 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU d 359 " --> pdb=" O ILE d 347 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'd' and resid 465 through 473 removed outlier: 3.505A pdb=" N THR d 471 " --> pdb=" O GLY d 400 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS d 398 " --> pdb=" O ILE d 473 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN d 426 " --> pdb=" O PHE d 401 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL d 403 " --> pdb=" O VAL d 424 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL d 424 " --> pdb=" O VAL d 403 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN d 405 " --> pdb=" O ALA d 422 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA d 422 " --> pdb=" O GLN d 405 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'd' and resid 432 through 434 Processing sheet with id= AF, first strand: chain 'd' and resid 503 through 505 removed outlier: 4.459A pdb=" N VAL d 503 " --> pdb=" O VAL d 510 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'e' and resid 100 through 102 Processing sheet with id= AH, first strand: chain 'e' and resid 319 through 322 Processing sheet with id= AI, first strand: chain 'e' and resid 334 through 336 Processing sheet with id= AJ, first strand: chain 'e' and resid 345 through 349 removed outlier: 3.713A pdb=" N PHE e 345 " --> pdb=" O LEU e 361 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'e' and resid 465 through 472 removed outlier: 3.543A pdb=" N SER e 406 " --> pdb=" O ASN e 465 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR e 471 " --> pdb=" O GLY e 400 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY e 400 " --> pdb=" O THR e 471 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL e 399 " --> pdb=" O VAL e 428 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN e 426 " --> pdb=" O PHE e 401 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL e 403 " --> pdb=" O VAL e 424 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL e 424 " --> pdb=" O VAL e 403 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN e 405 " --> pdb=" O ALA e 422 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ALA e 422 " --> pdb=" O GLN e 405 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'e' and resid 432 through 434 Processing sheet with id= AM, first strand: chain 'f' and resid 147 through 149 removed outlier: 3.552A pdb=" N TYR f 147 " --> pdb=" O TRP f 48 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'f' and resid 100 through 102 removed outlier: 3.508A pdb=" N THR f 142 " --> pdb=" O VAL f 165 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'f' and resid 319 through 321 Processing sheet with id= AP, first strand: chain 'f' and resid 334 through 336 Processing sheet with id= AQ, first strand: chain 'f' and resid 345 through 350 Processing sheet with id= AR, first strand: chain 'f' and resid 465 through 473 removed outlier: 3.676A pdb=" N THR f 471 " --> pdb=" O GLY f 400 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY f 400 " --> pdb=" O THR f 471 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS f 398 " --> pdb=" O ILE f 473 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN f 426 " --> pdb=" O PHE f 401 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL f 403 " --> pdb=" O VAL f 424 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL f 424 " --> pdb=" O VAL f 403 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLN f 405 " --> pdb=" O ALA f 422 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA f 422 " --> pdb=" O GLN f 405 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'f' and resid 432 through 434 Processing sheet with id= AT, first strand: chain 'g' and resid 46 through 48 removed outlier: 3.768A pdb=" N TYR g 147 " --> pdb=" O TRP g 48 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'g' and resid 142 through 144 Processing sheet with id= AV, first strand: chain 'g' and resid 306 through 308 Processing sheet with id= AW, first strand: chain 'g' and resid 319 through 322 Processing sheet with id= AX, first strand: chain 'g' and resid 334 through 336 Processing sheet with id= AY, first strand: chain 'g' and resid 345 through 350 Processing sheet with id= AZ, first strand: chain 'g' and resid 465 through 473 removed outlier: 3.847A pdb=" N THR g 471 " --> pdb=" O GLY g 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS g 398 " --> pdb=" O ILE g 473 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL g 399 " --> pdb=" O VAL g 428 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN g 426 " --> pdb=" O PHE g 401 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL g 403 " --> pdb=" O VAL g 424 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL g 424 " --> pdb=" O VAL g 403 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN g 405 " --> pdb=" O ALA g 422 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA g 422 " --> pdb=" O GLN g 405 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 503 through 505 removed outlier: 4.297A pdb=" N VAL g 503 " --> pdb=" O VAL g 510 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA g 508 " --> pdb=" O VAL g 505 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'h' and resid 147 through 149 removed outlier: 4.105A pdb=" N TYR h 147 " --> pdb=" O TRP h 48 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'h' and resid 142 through 144 Processing sheet with id= BD, first strand: chain 'h' and resid 319 through 321 Processing sheet with id= BE, first strand: chain 'h' and resid 334 through 336 Processing sheet with id= BF, first strand: chain 'h' and resid 345 through 349 removed outlier: 3.607A pdb=" N PHE h 345 " --> pdb=" O LEU h 361 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'h' and resid 465 through 470 removed outlier: 4.079A pdb=" N VAL h 399 " --> pdb=" O VAL h 428 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL h 428 " --> pdb=" O VAL h 399 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN h 426 " --> pdb=" O PHE h 401 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL h 403 " --> pdb=" O VAL h 424 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL h 424 " --> pdb=" O VAL h 403 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLN h 405 " --> pdb=" O ALA h 422 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA h 422 " --> pdb=" O GLN h 405 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'h' and resid 432 through 434 Processing sheet with id= BI, first strand: chain 'h' and resid 503 through 505 removed outlier: 4.300A pdb=" N VAL h 503 " --> pdb=" O VAL h 510 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'i' and resid 147 through 149 removed outlier: 3.754A pdb=" N TYR i 147 " --> pdb=" O TRP i 48 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'i' and resid 319 through 321 removed outlier: 3.538A pdb=" N LEU i 492 " --> pdb=" O ASP i 381 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'i' and resid 334 through 336 Processing sheet with id= BM, first strand: chain 'i' and resid 344 through 347 Processing sheet with id= BN, first strand: chain 'i' and resid 470 through 473 removed outlier: 4.238A pdb=" N ASN i 426 " --> pdb=" O PHE i 401 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL i 403 " --> pdb=" O VAL i 424 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL i 424 " --> pdb=" O VAL i 403 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLN i 405 " --> pdb=" O ALA i 422 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA i 422 " --> pdb=" O GLN i 405 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'i' and resid 432 through 434 Processing sheet with id= BP, first strand: chain 'i' and resid 503 through 505 removed outlier: 4.429A pdb=" N VAL i 503 " --> pdb=" O VAL i 510 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'j' and resid 46 through 48 removed outlier: 4.020A pdb=" N TYR j 147 " --> pdb=" O TRP j 48 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'j' and resid 100 through 102 Processing sheet with id= BS, first strand: chain 'j' and resid 319 through 321 Processing sheet with id= BT, first strand: chain 'j' and resid 334 through 336 Processing sheet with id= BU, first strand: chain 'j' and resid 465 through 473 removed outlier: 3.923A pdb=" N LYS j 398 " --> pdb=" O ILE j 473 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN j 426 " --> pdb=" O PHE j 401 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL j 403 " --> pdb=" O VAL j 424 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL j 424 " --> pdb=" O VAL j 403 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLN j 405 " --> pdb=" O ALA j 422 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA j 422 " --> pdb=" O GLN j 405 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'j' and resid 432 through 434 Processing sheet with id= BW, first strand: chain 'j' and resid 503 through 505 removed outlier: 4.003A pdb=" N VAL j 503 " --> pdb=" O VAL j 510 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'K' and resid 172 through 174 removed outlier: 7.049A pdb=" N LEU K 46 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL K 57 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS K 44 " --> pdb=" O VAL K 57 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'K' and resid 157 through 159 Processing sheet with id= BZ, first strand: chain 'K' and resid 351 through 353 removed outlier: 3.544A pdb=" N ILE K 353 " --> pdb=" O VAL K 370 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'K' and resid 394 through 396 removed outlier: 4.392A pdb=" N LYS K 739 " --> pdb=" O TRP K 396 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY K 705 " --> pdb=" O ARG K 758 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'K' and resid 435 through 440 removed outlier: 3.800A pdb=" N LEU K 435 " --> pdb=" O PHE K 644 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER K 637 " --> pdb=" O PHE K 656 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS K 615 " --> pdb=" O SER K 576 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'K' and resid 825 through 827 removed outlier: 5.859A pdb=" N ILE K 885 " --> pdb=" O LEU K 826 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL K 921 " --> pdb=" O VAL K 886 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N CYS K 888 " --> pdb=" O VAL K 921 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU K 923 " --> pdb=" O CYS K 888 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'K' and resid 846 through 850 removed outlier: 3.912A pdb=" N ASP K 850 " --> pdb=" O LEU K 868 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'K' and resid 941 through 943 removed outlier: 3.720A pdb=" N ARG K 948 " --> pdb=" O ASP K 943 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'K' and resid 1039 through 1044 removed outlier: 3.595A pdb=" N GLU K1086 " --> pdb=" O ASP K1081 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'K' and resid 1052 through 1056 Processing sheet with id= CH, first strand: chain 'K' and resid 1127 through 1129 removed outlier: 3.685A pdb=" N THR K1127 " --> pdb=" O THR K1146 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'K' and resid 1162 through 1165 Processing sheet with id= CJ, first strand: chain 'K' and resid 1228 through 1231 Processing sheet with id= CK, first strand: chain 'K' and resid 1239 through 1241 removed outlier: 4.136A pdb=" N ALA K1239 " --> pdb=" O THR K1287 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR K1287 " --> pdb=" O ALA K1239 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'K' and resid 220 through 222 removed outlier: 3.563A pdb=" N TRP K 287 " --> pdb=" O VAL K 220 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL K 222 " --> pdb=" O LEU K 285 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU K 285 " --> pdb=" O VAL K 222 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'K' and resid 399 through 405 removed outlier: 4.681A pdb=" N GLN K 399 " --> pdb=" O ASP K 776 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU K 774 " --> pdb=" O THR K 401 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP K 403 " --> pdb=" O LEU K 772 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU K 772 " --> pdb=" O ASP K 403 " (cutoff:3.500A) 1853 hydrogen bonds defined for protein. 5193 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: 22.80 Time building geometry restraints manager: 21.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19736 1.34 - 1.46: 10180 1.46 - 1.58: 31511 1.58 - 1.69: 1 1.69 - 1.81: 439 Bond restraints: 61867 Sorted by residual: bond pdb=" N PRO c 344 " pdb=" CD PRO c 344 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" N LEU f 359 " pdb=" CA LEU f 359 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N PRO i 344 " pdb=" CD PRO i 344 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 9.18e+00 bond pdb=" N PRO f 344 " pdb=" CD PRO f 344 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.19e+00 bond pdb=" N ILE d 328 " pdb=" CA ILE d 328 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.00e+00 ... (remaining 61862 not shown) Histogram of bond angle deviations from ideal: 97.39 - 105.28: 1863 105.28 - 113.16: 35158 113.16 - 121.05: 29840 121.05 - 128.93: 17253 128.93 - 136.81: 347 Bond angle restraints: 84461 Sorted by residual: angle pdb=" CA PRO c 344 " pdb=" N PRO c 344 " pdb=" CD PRO c 344 " ideal model delta sigma weight residual 112.00 99.93 12.07 1.40e+00 5.10e-01 7.44e+01 angle pdb=" CA PRO i 344 " pdb=" N PRO i 344 " pdb=" CD PRO i 344 " ideal model delta sigma weight residual 112.00 100.00 12.00 1.40e+00 5.10e-01 7.35e+01 angle pdb=" CA PRO g 344 " pdb=" N PRO g 344 " pdb=" CD PRO g 344 " ideal model delta sigma weight residual 112.00 100.02 11.98 1.40e+00 5.10e-01 7.32e+01 angle pdb=" CA PRO j 344 " pdb=" N PRO j 344 " pdb=" CD PRO j 344 " ideal model delta sigma weight residual 112.00 100.17 11.83 1.40e+00 5.10e-01 7.14e+01 angle pdb=" C ILE b 337 " pdb=" N PRO b 338 " pdb=" CA PRO b 338 " ideal model delta sigma weight residual 119.84 130.38 -10.54 1.25e+00 6.40e-01 7.11e+01 ... (remaining 84456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 34040 17.95 - 35.90: 2986 35.90 - 53.85: 521 53.85 - 71.80: 134 71.80 - 89.75: 84 Dihedral angle restraints: 37765 sinusoidal: 14616 harmonic: 23149 Sorted by residual: dihedral pdb=" CA ALA c 374 " pdb=" C ALA c 374 " pdb=" N PRO c 375 " pdb=" CA PRO c 375 " ideal model delta harmonic sigma weight residual -180.00 -143.56 -36.44 0 5.00e+00 4.00e-02 5.31e+01 dihedral pdb=" CA ALA f 374 " pdb=" C ALA f 374 " pdb=" N PRO f 375 " pdb=" CA PRO f 375 " ideal model delta harmonic sigma weight residual 180.00 -146.07 -33.93 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA ALA i 374 " pdb=" C ALA i 374 " pdb=" N PRO i 375 " pdb=" CA PRO i 375 " ideal model delta harmonic sigma weight residual -180.00 -148.30 -31.70 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 37762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 8789 0.083 - 0.166: 1088 0.166 - 0.248: 37 0.248 - 0.331: 9 0.331 - 0.414: 1 Chirality restraints: 9924 Sorted by residual: chirality pdb=" CG LEU j 359 " pdb=" CB LEU j 359 " pdb=" CD1 LEU j 359 " pdb=" CD2 LEU j 359 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CA TRP K 5 " pdb=" N TRP K 5 " pdb=" C TRP K 5 " pdb=" CB TRP K 5 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE d 76 " pdb=" CA ILE d 76 " pdb=" CG1 ILE d 76 " pdb=" CG2 ILE d 76 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 9921 not shown) Planarity restraints: 10909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR f 343 " 0.145 5.00e-02 4.00e+02 2.06e-01 6.78e+01 pdb=" N PRO f 344 " -0.354 5.00e-02 4.00e+02 pdb=" CA PRO f 344 " 0.126 5.00e-02 4.00e+02 pdb=" CD PRO f 344 " 0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR i 343 " -0.144 5.00e-02 4.00e+02 2.03e-01 6.62e+01 pdb=" N PRO i 344 " 0.350 5.00e-02 4.00e+02 pdb=" CA PRO i 344 " -0.124 5.00e-02 4.00e+02 pdb=" CD PRO i 344 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR c 343 " 0.139 5.00e-02 4.00e+02 1.98e-01 6.27e+01 pdb=" N PRO c 344 " -0.341 5.00e-02 4.00e+02 pdb=" CA PRO c 344 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO c 344 " 0.087 5.00e-02 4.00e+02 ... (remaining 10906 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 9 1.92 - 2.67: 1665 2.67 - 3.41: 92133 3.41 - 4.16: 144730 4.16 - 4.90: 255877 Nonbonded interactions: 494414 Sorted by model distance: nonbonded pdb=" NZ LYS a 127 " pdb=" CD2 HIS K 585 " model vdw 1.176 3.340 nonbonded pdb=" O VAL g 323 " pdb=" CD1 LEU g 326 " model vdw 1.342 3.460 nonbonded pdb=" OD2 ASP a 225 " pdb=" NE2 HIS K 625 " model vdw 1.411 2.520 nonbonded pdb=" CB ALA A 4 " pdb=" N ASP K 587 " model vdw 1.801 3.540 nonbonded pdb=" CG2 THR d 325 " pdb=" OG1 THR f 445 " model vdw 1.808 3.460 ... (remaining 494409 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 'B' and resid 11 through 42) selection = (chain 'C' and resid 11 through 42) selection = (chain 'D' and resid 11 through 42) selection = (chain 'E' and resid 11 through 42) selection = (chain 'F' and resid 11 through 42) selection = (chain 'G' and resid 11 through 42) selection = (chain 'H' and resid 11 through 42) selection = chain 'I' selection = (chain 'J' and resid 11 through 42) } ncs_group { reference = (chain 'a' and (resid 43 through 61 or resid 63 through 675)) selection = (chain 'b' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'c' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'd' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'e' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'f' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'g' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'h' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'i' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) selection = (chain 'j' and (resid 43 through 61 or resid 63 through 71 or resid 95 through 6 \ 75)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.850 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: 0.050 Extract box with map and model: 42.280 Check model and map are aligned: 0.670 Set scattering table: 0.430 Process input model: 131.580 Find NCS groups from input model: 3.480 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 : 0.006 0.093 61867 Z= 0.404 Angle : 0.862 21.432 84461 Z= 0.473 Chirality : 0.052 0.414 9924 Planarity : 0.008 0.206 10909 Dihedral : 14.827 89.751 22743 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.92 % Favored : 90.85 % Rotamer: Outliers : 0.62 % Allowed : 0.74 % Favored : 98.63 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.91 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.09), residues: 7872 helix: -1.08 (0.10), residues: 2492 sheet: -1.69 (0.15), residues: 1040 loop : -1.52 (0.09), residues: 4340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP K 624 HIS 0.009 0.002 HIS f 106 PHE 0.027 0.002 PHE g 603 TYR 0.031 0.002 TYR d 143 ARG 0.011 0.001 ARG K 738 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1462 time to evaluate : 5.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 15 residues processed: 1486 average time/residue: 0.5871 time to fit residues: 1467.5385 Evaluate side-chains 902 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 887 time to evaluate : 5.366 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6245 time to fit residues: 22.7156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 0.9990 chunk 595 optimal weight: 9.9990 chunk 330 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 401 optimal weight: 0.0670 chunk 318 optimal weight: 5.9990 chunk 616 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 374 optimal weight: 8.9990 chunk 458 optimal weight: 5.9990 chunk 713 optimal weight: 6.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 121 ASN ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 GLN ** a 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 613 GLN b 288 GLN ** c 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 288 GLN ** c 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 564 ASN D 42 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 GLN d 322 ASN ** d 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 358 HIS e 372 GLN e 429 GLN e 564 ASN e 623 ASN f 571 GLN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 659 ASN h 110 ASN h 213 GLN h 288 GLN h 623 ASN ** i 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 576 GLN i 658 GLN j 110 ASN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN K 229 ASN ** K 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 419 GLN ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS K1245 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 61867 Z= 0.228 Angle : 0.697 17.464 84461 Z= 0.356 Chirality : 0.047 0.310 9924 Planarity : 0.007 0.170 10909 Dihedral : 5.648 57.657 8526 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.83 % Rotamer: Outliers : 1.80 % Allowed : 11.55 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.09), residues: 7872 helix: 0.08 (0.10), residues: 2582 sheet: -1.34 (0.15), residues: 1169 loop : -1.15 (0.10), residues: 4121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 624 HIS 0.006 0.001 HIS K 625 PHE 0.022 0.001 PHE h 404 TYR 0.024 0.001 TYR d 95 ARG 0.009 0.001 ARG K 757 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1078 time to evaluate : 5.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 60 residues processed: 1131 average time/residue: 0.5596 time to fit residues: 1099.7458 Evaluate side-chains 933 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 873 time to evaluate : 5.257 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4362 time to fit residues: 56.8290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 396 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 594 optimal weight: 0.7980 chunk 486 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 715 optimal weight: 8.9990 chunk 772 optimal weight: 10.0000 chunk 636 optimal weight: 20.0000 chunk 709 optimal weight: 7.9990 chunk 243 optimal weight: 30.0000 chunk 573 optimal weight: 20.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 202 ASN d 248 GLN d 342 ASN ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 196 GLN ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 622 ASN g 196 GLN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 GLN h 346 GLN i 179 GLN i 458 ASN i 623 ASN ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN K 58 GLN ** K 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 229 ASN ** K 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 61867 Z= 0.255 Angle : 0.647 13.268 84461 Z= 0.329 Chirality : 0.046 0.212 9924 Planarity : 0.006 0.152 10909 Dihedral : 5.244 57.940 8526 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.94 % Rotamer: Outliers : 1.47 % Allowed : 14.65 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.10), residues: 7872 helix: 0.64 (0.10), residues: 2583 sheet: -1.37 (0.14), residues: 1247 loop : -0.89 (0.10), residues: 4042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 624 HIS 0.008 0.001 HIS f 106 PHE 0.030 0.001 PHE K 188 TYR 0.029 0.001 TYR e 137 ARG 0.009 0.000 ARG K 757 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 899 time to evaluate : 5.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 38 residues processed: 960 average time/residue: 0.5514 time to fit residues: 921.0489 Evaluate side-chains 855 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 817 time to evaluate : 5.819 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.5098 time to fit residues: 42.2500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 1.9990 chunk 537 optimal weight: 9.9990 chunk 371 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 341 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 chunk 717 optimal weight: 9.9990 chunk 759 optimal weight: 20.0000 chunk 374 optimal weight: 10.0000 chunk 680 optimal weight: 8.9990 chunk 204 optimal weight: 0.0370 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 ASN ** c 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 622 ASN ** g 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN j 196 GLN ** j 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 ASN ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1058 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 61867 Z= 0.244 Angle : 0.625 12.799 84461 Z= 0.316 Chirality : 0.045 0.257 9924 Planarity : 0.005 0.137 10909 Dihedral : 5.073 59.773 8526 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.50 % Rotamer: Outliers : 1.53 % Allowed : 16.75 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.18 % 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 (0.10), residues: 7872 helix: 0.92 (0.11), residues: 2587 sheet: -1.23 (0.14), residues: 1265 loop : -0.77 (0.10), residues: 4020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 624 HIS 0.007 0.001 HIS f 106 PHE 0.017 0.001 PHE K 79 TYR 0.020 0.001 TYR d 95 ARG 0.009 0.000 ARG f 636 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 891 time to evaluate : 5.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 46 residues processed: 950 average time/residue: 0.5714 time to fit residues: 948.3457 Evaluate side-chains 843 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 797 time to evaluate : 5.412 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.4555 time to fit residues: 46.7443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 632 optimal weight: 30.0000 chunk 431 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 565 optimal weight: 4.9990 chunk 313 optimal weight: 30.0000 chunk 648 optimal weight: 5.9990 chunk 525 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 387 optimal weight: 20.0000 chunk 681 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 overall best weight: 12.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 288 GLN a 613 GLN ** b 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 GLN ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 202 ASN ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 623 ASN f 622 ASN ** g 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 121 ASN i 429 GLN i 458 ASN i 576 GLN j 196 GLN ** j 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 GLN ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 61867 Z= 0.458 Angle : 0.727 11.719 84461 Z= 0.370 Chirality : 0.047 0.226 9924 Planarity : 0.005 0.067 10909 Dihedral : 5.341 59.944 8526 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 2.08 % Allowed : 17.95 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.36 % 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 (0.10), residues: 7872 helix: 0.88 (0.10), residues: 2605 sheet: -1.44 (0.14), residues: 1269 loop : -0.69 (0.10), residues: 3998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 624 HIS 0.011 0.002 HIS h 106 PHE 0.018 0.002 PHE K 188 TYR 0.025 0.002 TYR i 95 ARG 0.010 0.001 ARG K 757 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 793 time to evaluate : 5.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 140 outliers final: 75 residues processed: 891 average time/residue: 0.5608 time to fit residues: 869.6836 Evaluate side-chains 802 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 727 time to evaluate : 5.360 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.4361 time to fit residues: 69.6656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 255 optimal weight: 10.0000 chunk 684 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 446 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 760 optimal weight: 5.9990 chunk 631 optimal weight: 5.9990 chunk 352 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 399 optimal weight: 0.4980 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 110 ASN ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 222 GLN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 458 ASN ** i 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN j 405 GLN ** K 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 61867 Z= 0.267 Angle : 0.653 12.111 84461 Z= 0.329 Chirality : 0.046 0.256 9924 Planarity : 0.005 0.061 10909 Dihedral : 5.136 59.224 8526 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 1.41 % Allowed : 19.02 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % 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: -0.27 (0.10), residues: 7872 helix: 1.09 (0.11), residues: 2585 sheet: -1.25 (0.14), residues: 1283 loop : -0.59 (0.10), residues: 4004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 624 HIS 0.008 0.001 HIS f 106 PHE 0.015 0.001 PHE K 79 TYR 0.020 0.001 TYR i 95 ARG 0.010 0.000 ARG K 757 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 830 time to evaluate : 5.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 42 residues processed: 893 average time/residue: 0.5548 time to fit residues: 865.8750 Evaluate side-chains 822 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 780 time to evaluate : 5.344 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4331 time to fit residues: 42.0738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 733 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 433 optimal weight: 20.0000 chunk 555 optimal weight: 0.0670 chunk 430 optimal weight: 40.0000 chunk 640 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 chunk 757 optimal weight: 10.0000 chunk 474 optimal weight: 3.9990 chunk 461 optimal weight: 10.0000 chunk 349 optimal weight: 20.0000 overall best weight: 5.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 GLN b 179 GLN ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 202 ASN ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN ** g 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 421 GLN h 458 ASN j 196 GLN ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 61867 Z= 0.247 Angle : 0.657 12.677 84461 Z= 0.330 Chirality : 0.045 0.264 9924 Planarity : 0.005 0.061 10909 Dihedral : 5.046 58.954 8526 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 1.17 % Allowed : 19.76 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % 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: -0.17 (0.10), residues: 7872 helix: 1.13 (0.10), residues: 2615 sheet: -1.25 (0.14), residues: 1274 loop : -0.48 (0.10), residues: 3983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 624 HIS 0.006 0.001 HIS h 106 PHE 0.014 0.001 PHE K 79 TYR 0.031 0.001 TYR g 95 ARG 0.009 0.000 ARG K 757 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 836 time to evaluate : 5.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 35 residues processed: 884 average time/residue: 0.5685 time to fit residues: 868.9568 Evaluate side-chains 819 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 784 time to evaluate : 5.421 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4715 time to fit residues: 37.8442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 468 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 481 optimal weight: 2.9990 chunk 516 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 595 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 GLN ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 564 ASN ** d 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN ** g 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 456 GLN j 213 GLN ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 61867 Z= 0.254 Angle : 0.662 13.143 84461 Z= 0.332 Chirality : 0.045 0.273 9924 Planarity : 0.005 0.061 10909 Dihedral : 5.021 59.855 8526 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 0.82 % Allowed : 20.58 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.18 % 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: -0.10 (0.10), residues: 7872 helix: 1.18 (0.11), residues: 2598 sheet: -1.10 (0.14), residues: 1216 loop : -0.49 (0.10), residues: 4058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 624 HIS 0.007 0.001 HIS h 106 PHE 0.020 0.001 PHE J 20 TYR 0.027 0.001 TYR g 95 ARG 0.011 0.000 ARG c 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 804 time to evaluate : 5.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 24 residues processed: 830 average time/residue: 0.5978 time to fit residues: 865.4458 Evaluate side-chains 789 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 765 time to evaluate : 5.385 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5164 time to fit residues: 30.6712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 689 optimal weight: 1.9990 chunk 725 optimal weight: 9.9990 chunk 662 optimal weight: 6.9990 chunk 705 optimal weight: 20.0000 chunk 424 optimal weight: 0.6980 chunk 307 optimal weight: 0.0970 chunk 554 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 637 optimal weight: 20.0000 chunk 667 optimal weight: 20.0000 chunk 703 optimal weight: 9.9990 overall best weight: 3.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 106 HIS ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 623 ASN ** g 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 213 GLN ** g 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 322 ASN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 456 GLN i 465 ASN j 348 GLN j 451 ASN ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 61867 Z= 0.216 Angle : 0.671 13.306 84461 Z= 0.335 Chirality : 0.045 0.268 9924 Planarity : 0.005 0.060 10909 Dihedral : 4.974 59.055 8526 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 0.58 % Allowed : 21.25 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.18 % Twisted General : 0.01 % 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: -0.04 (0.10), residues: 7872 helix: 1.22 (0.11), residues: 2612 sheet: -1.06 (0.14), residues: 1266 loop : -0.44 (0.10), residues: 3994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 624 HIS 0.008 0.001 HIS b 106 PHE 0.021 0.001 PHE K 188 TYR 0.023 0.001 TYR g 95 ARG 0.010 0.000 ARG c 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 822 time to evaluate : 5.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 844 average time/residue: 0.5799 time to fit residues: 859.2001 Evaluate side-chains 792 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 773 time to evaluate : 5.359 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4508 time to fit residues: 23.2836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 463 optimal weight: 5.9990 chunk 746 optimal weight: 0.8980 chunk 455 optimal weight: 20.0000 chunk 354 optimal weight: 0.9980 chunk 518 optimal weight: 5.9990 chunk 783 optimal weight: 5.9990 chunk 720 optimal weight: 5.9990 chunk 623 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 481 optimal weight: 5.9990 chunk 382 optimal weight: 9.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 171 GLN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 322 ASN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 348 GLN j 358 HIS ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 61867 Z= 0.222 Angle : 0.683 13.000 84461 Z= 0.341 Chirality : 0.046 0.369 9924 Planarity : 0.005 0.059 10909 Dihedral : 4.938 58.761 8526 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.44 % Rotamer: Outliers : 0.19 % Allowed : 21.83 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.36 % 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: -0.01 (0.10), residues: 7872 helix: 1.22 (0.11), residues: 2620 sheet: -1.02 (0.14), residues: 1291 loop : -0.41 (0.10), residues: 3961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP K 624 HIS 0.010 0.001 HIS g 106 PHE 0.023 0.001 PHE K 188 TYR 0.028 0.001 TYR K 178 ARG 0.009 0.000 ARG c 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15744 Ramachandran restraints generated. 7872 Oldfield, 0 Emsley, 7872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 791 time to evaluate : 5.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 796 average time/residue: 0.5746 time to fit residues: 800.2295 Evaluate side-chains 777 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 770 time to evaluate : 5.463 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4725 time to fit residues: 15.2201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 495 optimal weight: 20.0000 chunk 664 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 574 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 624 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 641 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 322 ASN ** g 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.044174 restraints weight = 259152.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.045746 restraints weight = 130097.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.046823 restraints weight = 81731.601| |-----------------------------------------------------------------------------| r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 61867 Z= 0.299 Angle : 0.700 12.823 84461 Z= 0.351 Chirality : 0.046 0.284 9924 Planarity : 0.005 0.061 10909 Dihedral : 5.028 58.208 8526 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.78 % Favored : 95.17 % Rotamer: Outliers : 0.34 % Allowed : 22.00 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.03 % Twisted Proline : 0.36 % 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: -0.02 (0.10), residues: 7872 helix: 1.25 (0.11), residues: 2613 sheet: -1.07 (0.14), residues: 1274 loop : -0.43 (0.10), residues: 3985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP K 624 HIS 0.016 0.002 HIS g 106 PHE 0.026 0.001 PHE K 188 TYR 0.026 0.001 TYR K 178 ARG 0.009 0.000 ARG c 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14802.35 seconds wall clock time: 261 minutes 11.04 seconds (15671.04 seconds total)