Starting phenix.real_space_refine on Fri Feb 23 03:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbp_27297/02_2024/8dbp_27297_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbp_27297/02_2024/8dbp_27297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbp_27297/02_2024/8dbp_27297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbp_27297/02_2024/8dbp_27297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbp_27297/02_2024/8dbp_27297_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbp_27297/02_2024/8dbp_27297_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 178 5.16 5 C 23265 2.51 5 N 6256 2.21 5 O 6902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ASP 7": "OD1" <-> "OD2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "J ASP 7": "OD1" <-> "OD2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 61": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 44": "OD1" <-> "OD2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ASP 61": "OD1" <-> "OD2" Residue "M TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 44": "OD1" <-> "OD2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 44": "OD1" <-> "OD2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 61": "OD1" <-> "OD2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q ASP 61": "OD1" <-> "OD2" Residue "R ASP 7": "OD1" <-> "OD2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ASP 61": "OD1" <-> "OD2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 7": "OD1" <-> "OD2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 458": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ASP 458": "OD1" <-> "OD2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 200": "OD1" <-> "OD2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D ASP 302": "OD1" <-> "OD2" Residue "D ASP 305": "OD1" <-> "OD2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E ASP 236": "OD1" <-> "OD2" Residue "E TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 338": "OD1" <-> "OD2" Residue "E ASP 355": "OD1" <-> "OD2" Residue "E ASP 372": "OD1" <-> "OD2" Residue "E ASP 386": "OD1" <-> "OD2" Residue "E PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 422": "OD1" <-> "OD2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E GLU 454": "OE1" <-> "OE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F ASP 188": "OD1" <-> "OD2" Residue "F PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 242": "OD1" <-> "OD2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F ASP 316": "OD1" <-> "OD2" Residue "F TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F GLU 384": "OE1" <-> "OE2" Residue "F PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "G GLU 278": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "W PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 36": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W ASP 160": "OD1" <-> "OD2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ASP 55": "OD1" <-> "OD2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X GLU 108": "OE1" <-> "OE2" Residue "X GLU 112": "OE1" <-> "OE2" Residue "X ARG 113": "NH1" <-> "NH2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "X GLU 142": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y ASP 55": "OD1" <-> "OD2" Residue "Y GLU 71": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y GLU 110": "OE1" <-> "OE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y ASP 141": "OD1" <-> "OD2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 196": "OE1" <-> "OE2" Residue "a TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36622 Number of models: 1 Model: "" Number of chains: 28 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "L" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "M" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "N" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "O" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "P" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "Q" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "R" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "S" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3863 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "H" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.19, per 1000 atoms: 0.50 Number of scatterers: 36622 At special positions: 0 Unit cell: (182.351, 224.432, 137.033, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 16 15.00 Mg 5 11.99 O 6902 8.00 N 6256 7.00 C 23265 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=0, symmetry=0 Time building additional restraints: 14.02 Conformation dependent library (CDL) restraints added in 6.8 seconds 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 175 helices and 25 sheets defined 56.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.74 Creating SS restraints... Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.701A pdb=" N MET I 11 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA I 14 " --> pdb=" O MET I 11 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET I 16 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET I 17 " --> pdb=" O ALA I 14 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY I 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU I 19 " --> pdb=" O MET I 16 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA I 24 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE I 26 " --> pdb=" O GLY I 23 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE I 28 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE I 30 " --> pdb=" O GLY I 27 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS I 34 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU I 37 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 Proline residue: I 47 - end of helix removed outlier: 3.712A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE I 53 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.804A pdb=" N VAL I 68 " --> pdb=" O MET I 65 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL I 74 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 Processing helix chain 'J' and resid 43 through 76 removed outlier: 3.747A pdb=" N ILE J 46 " --> pdb=" O PRO J 43 " (cutoff:3.500A) Proline residue: J 47 - end of helix removed outlier: 3.969A pdb=" N PHE J 54 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET J 57 " --> pdb=" O PHE J 54 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY J 58 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP J 61 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE J 63 " --> pdb=" O VAL J 60 " (cutoff:3.500A) Proline residue: J 64 - end of helix removed outlier: 3.742A pdb=" N LEU J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU J 72 " --> pdb=" O GLY J 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL J 74 " --> pdb=" O GLY J 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 41 Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.746A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.189A pdb=" N THR L 51 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.629A pdb=" N VAL L 68 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL L 74 " --> pdb=" O GLY L 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.880A pdb=" N LEU M 9 " --> pdb=" O MET M 6 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET M 11 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA M 12 " --> pdb=" O LEU M 9 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL M 15 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET M 17 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU M 19 " --> pdb=" O MET M 16 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA M 21 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY M 23 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA M 24 " --> pdb=" O ALA M 21 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE M 26 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY M 27 " --> pdb=" O ALA M 24 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE M 28 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE M 30 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU M 31 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS M 34 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 4.021A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 5 through 41 removed outlier: 3.607A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.627A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA N 62 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 5 through 41 Processing helix chain 'O' and resid 43 through 76 Proline residue: O 47 - end of helix removed outlier: 3.764A pdb=" N PHE O 54 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE O 55 " --> pdb=" O GLN O 52 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL O 56 " --> pdb=" O PHE O 53 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP O 61 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE O 63 " --> pdb=" O VAL O 60 " (cutoff:3.500A) Proline residue: O 64 - end of helix removed outlier: 3.976A pdb=" N VAL O 68 " --> pdb=" O MET O 65 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR O 73 " --> pdb=" O LEU O 70 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL O 74 " --> pdb=" O GLY O 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 41 removed outlier: 3.583A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG P 41 " --> pdb=" O GLU P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 76 Proline residue: P 47 - end of helix removed outlier: 3.503A pdb=" N ARG P 50 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET P 57 " --> pdb=" O PHE P 54 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP P 61 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE P 63 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.717A pdb=" N VAL P 68 " --> pdb=" O MET P 65 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU P 70 " --> pdb=" O ALA P 67 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL P 74 " --> pdb=" O GLY P 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 39 Processing helix chain 'Q' and resid 46 through 60 removed outlier: 3.888A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 76 removed outlier: 3.583A pdb=" N GLY Q 69 " --> pdb=" O MET Q 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.593A pdb=" N TYR R 10 " --> pdb=" O MET R 6 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET R 11 " --> pdb=" O ASP R 7 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA R 14 " --> pdb=" O TYR R 10 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA R 25 " --> pdb=" O ALA R 21 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 76 Proline residue: R 47 - end of helix removed outlier: 3.696A pdb=" N THR R 51 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 4.006A pdb=" N LEU R 70 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU R 72 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 74 " --> pdb=" O GLY R 71 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE R 76 " --> pdb=" O TYR R 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 41 removed outlier: 3.580A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA S 13 " --> pdb=" O TYR S 10 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET S 16 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET S 17 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU S 19 " --> pdb=" O MET S 16 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE S 22 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY S 23 " --> pdb=" O ALA S 20 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE S 26 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE S 28 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE S 30 " --> pdb=" O GLY S 27 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY S 32 " --> pdb=" O GLY S 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU S 37 " --> pdb=" O LYS S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.806A pdb=" N ARG S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR S 51 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN S 52 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.855A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.814A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.623A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 404 removed outlier: 4.075A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.875A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.824A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.559A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 297 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 384 through 407 removed outlier: 6.341A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.579A pdb=" N GLY B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.670A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.735A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 291 through 300 removed outlier: 3.583A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 409 removed outlier: 3.515A pdb=" N LEU C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 removed outlier: 4.014A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 455 through 458 removed outlier: 4.441A pdb=" N ASP C 458 " --> pdb=" O TYR C 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 455 through 458' Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.125A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 468 " --> pdb=" O GLY C 465 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL C 475 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 168 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.644A pdb=" N SER D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 232 removed outlier: 4.070A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 271 through 279 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.899A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 377 Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 384 through 400 Processing helix chain 'D' and resid 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.531A pdb=" N GLU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 169 removed outlier: 3.524A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 232 removed outlier: 4.399A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 255 removed outlier: 3.528A pdb=" N LEU E 249 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA E 250 " --> pdb=" O TYR E 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 253 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.665A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 314 removed outlier: 4.227A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N HIS E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 removed outlier: 3.639A pdb=" N LEU E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 351 through 377 removed outlier: 4.640A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 386 through 399 Processing helix chain 'E' and resid 420 through 432 Processing helix chain 'E' and resid 440 through 443 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 116 through 118 No H-bonds generated for 'chain 'F' and resid 116 through 118' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 155 through 170 removed outlier: 3.676A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 5.181A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 258 removed outlier: 3.961A pdb=" N LEU F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 271 through 281 removed outlier: 4.351A pdb=" N ARG F 281 " --> pdb=" O VAL F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 306 through 314 removed outlier: 4.234A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 346 through 377 removed outlier: 5.607A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLU F 352 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS F 353 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 399 removed outlier: 3.507A pdb=" N VAL F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 411 Processing helix chain 'F' and resid 420 through 431 Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.591A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 90 through 107 Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 5.183A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 211 through 280 removed outlier: 3.833A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 Processing helix chain 'W' and resid 7 through 20 Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.582A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.601A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU W 46 " --> pdb=" O GLN W 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 Processing helix chain 'W' and resid 72 through 82 Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 3.946A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 131 Processing helix chain 'W' and resid 144 through 146 No H-bonds generated for 'chain 'W' and resid 144 through 146' Processing helix chain 'W' and resid 163 through 168 Processing helix chain 'X' and resid 5 through 22 removed outlier: 4.230A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE X 12 " --> pdb=" O GLY X 9 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE X 14 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL X 15 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU X 19 " --> pdb=" O LEU X 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET X 22 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 3.533A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG X 49 " --> pdb=" O ALA X 45 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS X 52 " --> pdb=" O GLU X 48 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU X 54 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 155 Processing helix chain 'Y' and resid 4 through 24 removed outlier: 3.620A pdb=" N GLY Y 9 " --> pdb=" O THR Y 6 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN Y 10 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA Y 11 " --> pdb=" O LEU Y 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE Y 12 " --> pdb=" O GLY Y 9 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA Y 13 " --> pdb=" O GLN Y 10 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE Y 17 " --> pdb=" O PHE Y 14 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE Y 20 " --> pdb=" O PHE Y 17 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET Y 22 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS Y 23 " --> pdb=" O PHE Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 139 removed outlier: 4.089A pdb=" N GLU Y 39 " --> pdb=" O LYS Y 35 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE Y 40 " --> pdb=" O ARG Y 36 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS Y 100 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 144 through 155 Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.591A pdb=" N HIS a 14 " --> pdb=" O ASP a 10 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 64 removed outlier: 3.826A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.916A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 3.536A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 131 Processing helix chain 'a' and resid 143 through 145 No H-bonds generated for 'chain 'a' and resid 143 through 145' Processing helix chain 'a' and resid 147 through 180 removed outlier: 7.414A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS a 176 " --> pdb=" O GLY a 172 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 227 removed outlier: 3.585A pdb=" N ILE a 189 " --> pdb=" O TRP a 186 " (cutoff:3.500A) Proline residue: a 190 - end of helix removed outlier: 3.672A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY a 197 " --> pdb=" O ILE a 194 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL a 198 " --> pdb=" O LEU a 195 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER a 199 " --> pdb=" O GLU a 196 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU a 201 " --> pdb=" O VAL a 198 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER a 202 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 4.110A pdb=" N LEU a 209 " --> pdb=" O SER a 206 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG a 210 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU a 211 " --> pdb=" O GLY a 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY a 213 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN a 214 " --> pdb=" O LEU a 211 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR a 216 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA a 217 " --> pdb=" O ASN a 214 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY a 218 " --> pdb=" O MET a 215 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU a 220 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA a 226 " --> pdb=" O ILE a 223 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 3.704A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.862A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA a 267 " --> pdb=" O TYR a 263 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.375A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.759A pdb=" N GLY A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.301A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 224 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.582A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.422A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.625A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N VAL B 224 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 327 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.517A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.516A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.400A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE C 222 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL C 224 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP C 255 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILE C 194 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE C 198 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 351 through 355 Processing sheet with id= M, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.551A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= O, first strand: chain 'D' and resid 317 through 319 removed outlier: 8.514A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 3 through 9 removed outlier: 6.699A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.632A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 317 through 320 removed outlier: 8.029A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY E 149 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 296 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 3 through 9 removed outlier: 6.601A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 76 through 78 Processing sheet with id= U, first strand: chain 'F' and resid 317 through 321 removed outlier: 8.373A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 181 through 188 removed outlier: 6.832A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 45 removed outlier: 3.597A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 23 through 26 Processing sheet with id= Y, first strand: chain 'W' and resid 135 through 142 1945 hydrogen bonds defined for protein. 5043 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: 13.10 Time building geometry restraints manager: 15.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10676 1.33 - 1.45: 4797 1.45 - 1.57: 21324 1.57 - 1.69: 26 1.69 - 1.81: 356 Bond restraints: 37179 Sorted by residual: bond pdb=" C4 ATP E 500 " pdb=" C5 ATP E 500 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.21e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.20e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C5 ATP E 500 " pdb=" N7 ATP E 500 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.70e+01 ... (remaining 37174 not shown) Histogram of bond angle deviations from ideal: 95.23 - 103.45: 351 103.45 - 111.67: 16242 111.67 - 119.88: 16728 119.88 - 128.10: 16781 128.10 - 136.32: 220 Bond angle restraints: 50322 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.49 23.38 1.00e+00 1.00e+00 5.47e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.48 22.39 1.00e+00 1.00e+00 5.01e+02 angle pdb=" PB ATP E 500 " pdb=" O3B ATP E 500 " pdb=" PG ATP E 500 " ideal model delta sigma weight residual 139.87 119.42 20.45 1.00e+00 1.00e+00 4.18e+02 angle pdb=" PA ATP E 500 " pdb=" O3A ATP E 500 " pdb=" PB ATP E 500 " ideal model delta sigma weight residual 136.83 116.90 19.93 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 117.51 19.32 1.00e+00 1.00e+00 3.73e+02 ... (remaining 50317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.14: 21926 31.14 - 62.28: 583 62.28 - 93.41: 87 93.41 - 124.55: 2 124.55 - 155.69: 1 Dihedral angle restraints: 22599 sinusoidal: 8967 harmonic: 13632 Sorted by residual: dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 144.31 155.69 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 -179.15 119.15 1 2.00e+01 2.50e-03 3.57e+01 dihedral pdb=" C5' ADP D 500 " pdb=" O5' ADP D 500 " pdb=" PA ADP D 500 " pdb=" O2A ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 52.77 -112.77 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 22596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4904 0.084 - 0.168: 873 0.168 - 0.251: 61 0.251 - 0.335: 11 0.335 - 0.419: 3 Chirality restraints: 5852 Sorted by residual: chirality pdb=" CA ASP Y 53 " pdb=" N ASP Y 53 " pdb=" C ASP Y 53 " pdb=" CB ASP Y 53 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB VAL a 29 " pdb=" CA VAL a 29 " pdb=" CG1 VAL a 29 " pdb=" CG2 VAL a 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ASP C 262 " pdb=" N ASP C 262 " pdb=" C ASP C 262 " pdb=" CB ASP C 262 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 5849 not shown) Planarity restraints: 6491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 164 " -0.169 9.50e-02 1.11e+02 9.29e-02 3.96e+01 pdb=" NE ARG C 164 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG C 164 " -0.102 2.00e-02 2.50e+03 pdb=" NH1 ARG C 164 " 0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG C 164 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 41 " -0.133 9.50e-02 1.11e+02 7.69e-02 3.15e+01 pdb=" NE ARG M 41 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG M 41 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG M 41 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG M 41 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 52 " 0.128 9.50e-02 1.11e+02 7.36e-02 2.84e+01 pdb=" NE ARG F 52 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG F 52 " 0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG F 52 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG F 52 " -0.025 2.00e-02 2.50e+03 ... (remaining 6488 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 20 2.35 - 2.99: 19393 2.99 - 3.63: 54400 3.63 - 4.26: 84311 4.26 - 4.90: 142298 Nonbonded interactions: 300422 Sorted by model distance: nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.714 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 1.719 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.774 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.801 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.888 2.170 ... (remaining 300417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 513 or resid 600 thr \ ough 601)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 513 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.650 Check model and map are aligned: 0.540 Set scattering table: 0.360 Process input model: 93.530 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.360 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: 0.020 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.010 0.085 37179 Z= 0.659 Angle : 1.204 23.378 50322 Z= 0.768 Chirality : 0.062 0.419 5852 Planarity : 0.008 0.101 6491 Dihedral : 14.622 155.690 13881 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.38 % Favored : 97.52 % Rotamer: Outliers : 1.39 % Allowed : 7.29 % Favored : 91.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 4756 helix: -0.72 (0.09), residues: 2561 sheet: -0.20 (0.20), residues: 545 loop : -0.69 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP G 203 HIS 0.017 0.003 HIS W 21 PHE 0.037 0.004 PHE G 125 TYR 0.052 0.008 TYR E 435 ARG 0.104 0.013 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 489 time to evaluate : 4.018 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: I 37 GLU cc_start: 0.6790 (tt0) cc_final: 0.6575 (mt-10) REVERT: I 66 ILE cc_start: 0.7263 (mt) cc_final: 0.6929 (mt) REVERT: J 75 MET cc_start: 0.6058 (tmm) cc_final: 0.5845 (tmm) REVERT: L 8 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6164 (mp) REVERT: L 65 MET cc_start: 0.6493 (mmt) cc_final: 0.6232 (mmm) REVERT: L 68 VAL cc_start: 0.4683 (t) cc_final: 0.4116 (m) REVERT: M 17 MET cc_start: 0.6990 (mmm) cc_final: 0.6746 (tmm) REVERT: M 28 ILE cc_start: 0.6855 (mt) cc_final: 0.6578 (mm) REVERT: M 41 ARG cc_start: 0.6601 (mtm110) cc_final: 0.6268 (ptp-170) REVERT: N 54 PHE cc_start: 0.7763 (m-80) cc_final: 0.7363 (t80) REVERT: O 17 MET cc_start: 0.0147 (mpp) cc_final: -0.0756 (mmt) REVERT: O 54 PHE cc_start: 0.5399 (m-80) cc_final: 0.4731 (p90) REVERT: O 57 MET cc_start: 0.4811 (tmm) cc_final: 0.4539 (tpp) REVERT: P 16 MET cc_start: 0.6137 (ttp) cc_final: 0.5898 (tmm) REVERT: P 17 MET cc_start: 0.6271 (tmm) cc_final: 0.5862 (tpt) REVERT: P 37 GLU cc_start: 0.8980 (tt0) cc_final: 0.8201 (tt0) REVERT: P 54 PHE cc_start: 0.6767 (m-10) cc_final: 0.6134 (t80) REVERT: Q 17 MET cc_start: 0.4685 (mmm) cc_final: 0.2324 (tpp) REVERT: Q 37 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6529 (mm-30) REVERT: Q 68 VAL cc_start: 0.7502 (m) cc_final: 0.7171 (p) REVERT: R 6 MET cc_start: 0.4386 (ptt) cc_final: 0.4164 (tmm) REVERT: A 48 MET cc_start: 0.8579 (ptp) cc_final: 0.8374 (ptp) REVERT: A 52 MET cc_start: 0.7713 (mtp) cc_final: 0.7503 (mtp) REVERT: B 48 MET cc_start: 0.7847 (ptp) cc_final: 0.7625 (ptm) REVERT: C 262 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: E 56 MET cc_start: 0.9314 (mmp) cc_final: 0.9075 (mmt) REVERT: F 56 MET cc_start: 0.9172 (mmm) cc_final: 0.8955 (mmt) REVERT: F 88 MET cc_start: 0.8519 (mtm) cc_final: 0.8246 (mtp) REVERT: G 48 MET cc_start: 0.9021 (ttm) cc_final: 0.8705 (ttp) REVERT: H 25 VAL cc_start: 0.7854 (t) cc_final: 0.7474 (m) REVERT: H 29 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7321 (mt-10) REVERT: X 22 MET cc_start: 0.6152 (ttm) cc_final: 0.5867 (tpt) outliers start: 53 outliers final: 11 residues processed: 535 average time/residue: 0.5476 time to fit residues: 458.3960 Evaluate side-chains 293 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 280 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain Y residue 42 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 397 optimal weight: 6.9990 chunk 356 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 369 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 GLN J 3 ASN M 52 GLN N 5 ASN O 52 GLN P 52 GLN R 52 GLN S 52 GLN A 42 HIS A 65 ASN A 344 ASN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 GLN B 20 ASN B 42 HIS B 58 ASN B 147 GLN B 186 GLN B 484 GLN C 420 GLN C 511 GLN D 361 GLN D 397 GLN F 32 GLN F 365 GLN G 57 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN H 56 HIS H 58 HIS H 75 ASN W 71 ASN a 181 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 37179 Z= 0.257 Angle : 0.659 9.029 50322 Z= 0.346 Chirality : 0.043 0.227 5852 Planarity : 0.005 0.052 6491 Dihedral : 7.753 144.291 5329 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.32 % Favored : 98.65 % Rotamer: Outliers : 1.97 % Allowed : 10.47 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.12), residues: 4756 helix: 0.82 (0.10), residues: 2531 sheet: 0.27 (0.21), residues: 538 loop : -0.35 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP G 203 HIS 0.011 0.001 HIS H 56 PHE 0.025 0.002 PHE C 406 TYR 0.039 0.002 TYR a 263 ARG 0.007 0.001 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 318 time to evaluate : 4.668 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: J 44 ASP cc_start: 0.7931 (p0) cc_final: 0.7325 (p0) REVERT: L 8 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.5940 (mp) REVERT: L 68 VAL cc_start: 0.4157 (t) cc_final: 0.3803 (m) REVERT: M 6 MET cc_start: 0.1438 (OUTLIER) cc_final: 0.1208 (mmm) REVERT: M 16 MET cc_start: 0.5925 (ptm) cc_final: 0.5696 (ptm) REVERT: N 54 PHE cc_start: 0.7707 (m-80) cc_final: 0.7261 (t80) REVERT: O 17 MET cc_start: 0.0048 (mpp) cc_final: -0.0696 (mmt) REVERT: O 54 PHE cc_start: 0.6100 (m-80) cc_final: 0.5479 (p90) REVERT: O 57 MET cc_start: 0.5174 (tmm) cc_final: 0.4770 (tpp) REVERT: P 17 MET cc_start: 0.6167 (tmm) cc_final: 0.5869 (tpt) REVERT: P 54 PHE cc_start: 0.6297 (m-10) cc_final: 0.5982 (t80) REVERT: Q 37 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6871 (mm-30) REVERT: R 6 MET cc_start: 0.4350 (ptt) cc_final: 0.3064 (tpp) REVERT: S 65 MET cc_start: 0.3005 (mtt) cc_final: 0.2556 (mmm) REVERT: A 52 MET cc_start: 0.7764 (mtp) cc_final: 0.7545 (mtp) REVERT: A 95 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8832 (tp) REVERT: B 48 MET cc_start: 0.7823 (ptp) cc_final: 0.7508 (ptm) REVERT: B 439 MET cc_start: 0.8859 (ptp) cc_final: 0.8533 (mtm) REVERT: C 262 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: F 56 MET cc_start: 0.9100 (mmm) cc_final: 0.8836 (mmt) REVERT: F 387 LYS cc_start: 0.5306 (OUTLIER) cc_final: 0.5095 (mptt) REVERT: F 431 MET cc_start: 0.8347 (mmm) cc_final: 0.8130 (mmm) REVERT: F 458 LYS cc_start: 0.8095 (tmtt) cc_final: 0.7673 (mtmm) REVERT: G 116 MET cc_start: 0.9012 (mmm) cc_final: 0.8710 (mmm) REVERT: G 155 MET cc_start: 0.9147 (mmt) cc_final: 0.8887 (mmt) REVERT: X 22 MET cc_start: 0.6317 (ttm) cc_final: 0.5994 (tpt) REVERT: X 82 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8482 (tpp-160) REVERT: Y 96 GLN cc_start: 0.9258 (tm-30) cc_final: 0.9043 (mp10) REVERT: a 89 SER cc_start: 0.8410 (m) cc_final: 0.8179 (p) outliers start: 75 outliers final: 23 residues processed: 377 average time/residue: 0.4584 time to fit residues: 291.0373 Evaluate side-chains 295 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 266 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 6 MET Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain Q residue 42 GLN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 82 ARG Chi-restraints excluded: chain Y residue 114 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 237 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 355 optimal weight: 0.2980 chunk 291 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 428 optimal weight: 0.0020 chunk 462 optimal weight: 0.8980 chunk 381 optimal weight: 4.9990 chunk 424 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 343 optimal weight: 5.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN H 58 HIS X 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37179 Z= 0.167 Angle : 0.585 9.690 50322 Z= 0.301 Chirality : 0.041 0.197 5852 Planarity : 0.004 0.053 6491 Dihedral : 7.092 138.557 5321 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.49 % Favored : 98.49 % Rotamer: Outliers : 1.60 % Allowed : 10.97 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 4756 helix: 1.19 (0.10), residues: 2533 sheet: 0.34 (0.21), residues: 550 loop : -0.26 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 203 HIS 0.004 0.001 HIS A 123 PHE 0.023 0.001 PHE C 406 TYR 0.023 0.001 TYR a 263 ARG 0.007 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 302 time to evaluate : 4.564 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: I 57 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.5951 (ptt) REVERT: L 6 MET cc_start: 0.4844 (pmm) cc_final: 0.4376 (tmm) REVERT: L 68 VAL cc_start: 0.4258 (t) cc_final: 0.3979 (m) REVERT: N 54 PHE cc_start: 0.7852 (m-80) cc_final: 0.7383 (t80) REVERT: O 17 MET cc_start: 0.0013 (mpp) cc_final: -0.0733 (mmt) REVERT: O 54 PHE cc_start: 0.5890 (m-80) cc_final: 0.5347 (p90) REVERT: O 57 MET cc_start: 0.5028 (tmm) cc_final: 0.4823 (tpp) REVERT: P 11 MET cc_start: 0.7116 (tpt) cc_final: 0.6345 (tmm) REVERT: P 54 PHE cc_start: 0.6464 (m-10) cc_final: 0.6221 (t80) REVERT: Q 22 ILE cc_start: 0.7102 (mt) cc_final: 0.6641 (mt) REVERT: Q 42 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: Q 57 MET cc_start: 0.5970 (ttp) cc_final: 0.5712 (mtt) REVERT: R 6 MET cc_start: 0.4340 (ptt) cc_final: 0.3907 (tmm) REVERT: S 65 MET cc_start: 0.3000 (mtt) cc_final: 0.2695 (mmm) REVERT: B 48 MET cc_start: 0.7612 (ptp) cc_final: 0.7295 (ptm) REVERT: F 56 MET cc_start: 0.9114 (mmm) cc_final: 0.8845 (mmt) REVERT: F 254 VAL cc_start: 0.8564 (t) cc_final: 0.8286 (p) REVERT: G 116 MET cc_start: 0.8986 (mmm) cc_final: 0.8715 (mmm) REVERT: H 29 GLU cc_start: 0.7841 (mm-30) cc_final: 0.6821 (mp0) REVERT: H 70 GLU cc_start: 0.8504 (mp0) cc_final: 0.7847 (tp30) REVERT: X 22 MET cc_start: 0.6399 (ttm) cc_final: 0.6023 (tpt) REVERT: X 49 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7479 (ptt-90) REVERT: X 85 GLN cc_start: 0.8989 (mt0) cc_final: 0.8744 (mt0) REVERT: a 93 MET cc_start: 0.8041 (mpp) cc_final: 0.6273 (tpp) REVERT: a 120 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5166 (mm) REVERT: a 245 HIS cc_start: 0.0904 (OUTLIER) cc_final: 0.0410 (t70) REVERT: a 257 MET cc_start: 0.9163 (tmm) cc_final: 0.8869 (ppp) outliers start: 61 outliers final: 24 residues processed: 350 average time/residue: 0.4652 time to fit residues: 274.2964 Evaluate side-chains 290 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 262 time to evaluate : 4.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 42 GLN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 114 LYS Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 245 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 423 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 430 optimal weight: 30.0000 chunk 455 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 407 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS B 27 ASN B 42 HIS C 399 GLN D 7 GLN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 37179 Z= 0.219 Angle : 0.575 12.064 50322 Z= 0.294 Chirality : 0.041 0.209 5852 Planarity : 0.004 0.052 6491 Dihedral : 6.742 132.190 5315 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.72 % Favored : 98.25 % Rotamer: Outliers : 1.89 % Allowed : 11.34 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.12), residues: 4756 helix: 1.34 (0.10), residues: 2547 sheet: 0.47 (0.21), residues: 551 loop : -0.22 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 203 HIS 0.040 0.001 HIS B 42 PHE 0.023 0.001 PHE C 406 TYR 0.018 0.001 TYR a 263 ARG 0.005 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 278 time to evaluate : 4.330 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: I 57 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.5753 (ptt) REVERT: L 6 MET cc_start: 0.4374 (pmm) cc_final: 0.4081 (tmm) REVERT: L 68 VAL cc_start: 0.4517 (t) cc_final: 0.4192 (m) REVERT: N 54 PHE cc_start: 0.7863 (m-80) cc_final: 0.7363 (t80) REVERT: O 17 MET cc_start: 0.0032 (mpp) cc_final: -0.0680 (tpt) REVERT: O 54 PHE cc_start: 0.6046 (m-80) cc_final: 0.5438 (p90) REVERT: O 57 MET cc_start: 0.5105 (tmm) cc_final: 0.4701 (tpp) REVERT: P 11 MET cc_start: 0.7279 (tpt) cc_final: 0.6683 (tmm) REVERT: P 54 PHE cc_start: 0.6482 (m-10) cc_final: 0.6178 (t80) REVERT: Q 42 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: R 6 MET cc_start: 0.4463 (ptt) cc_final: 0.3933 (tmm) REVERT: S 65 MET cc_start: 0.2956 (mtt) cc_final: 0.2640 (mmm) REVERT: B 48 MET cc_start: 0.7838 (ptp) cc_final: 0.7535 (ptm) REVERT: C 262 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: F 56 MET cc_start: 0.9046 (mmm) cc_final: 0.8751 (mmt) REVERT: F 254 VAL cc_start: 0.8672 (t) cc_final: 0.8414 (p) REVERT: F 458 LYS cc_start: 0.7797 (tmtt) cc_final: 0.7262 (mtmm) REVERT: G 116 MET cc_start: 0.9017 (mmm) cc_final: 0.8729 (mmm) REVERT: H 29 GLU cc_start: 0.7833 (mm-30) cc_final: 0.6781 (mp0) REVERT: H 70 GLU cc_start: 0.8510 (mp0) cc_final: 0.7919 (tp30) REVERT: X 22 MET cc_start: 0.6464 (ttm) cc_final: 0.6102 (tpt) REVERT: X 49 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7609 (ptt-90) REVERT: X 82 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8578 (tpp-160) REVERT: a 120 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.5422 (mm) REVERT: a 245 HIS cc_start: 0.0606 (OUTLIER) cc_final: 0.0184 (t70) outliers start: 72 outliers final: 40 residues processed: 332 average time/residue: 0.4643 time to fit residues: 263.8862 Evaluate side-chains 302 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 42 GLN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 82 ARG Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 114 LYS Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 118 MET Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 245 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 379 optimal weight: 0.2980 chunk 258 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 338 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 388 optimal weight: 30.0000 chunk 314 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 232 optimal weight: 3.9990 chunk 408 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 42 HIS ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37179 Z= 0.272 Angle : 0.595 12.509 50322 Z= 0.302 Chirality : 0.041 0.181 5852 Planarity : 0.004 0.051 6491 Dihedral : 6.554 110.755 5315 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.79 % Rotamer: Outliers : 2.24 % Allowed : 11.97 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.12), residues: 4756 helix: 1.44 (0.10), residues: 2522 sheet: 0.44 (0.21), residues: 555 loop : -0.36 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 203 HIS 0.005 0.001 HIS B 42 PHE 0.025 0.001 PHE Q 53 TYR 0.013 0.001 TYR F 247 ARG 0.012 0.000 ARG X 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 274 time to evaluate : 4.138 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: I 57 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5734 (ptt) REVERT: L 6 MET cc_start: 0.4336 (pmm) cc_final: 0.3989 (tmm) REVERT: L 68 VAL cc_start: 0.4890 (t) cc_final: 0.4574 (m) REVERT: N 54 PHE cc_start: 0.7849 (m-10) cc_final: 0.7348 (t80) REVERT: O 17 MET cc_start: -0.0540 (mpp) cc_final: -0.1136 (tpt) REVERT: O 57 MET cc_start: 0.5116 (tmm) cc_final: 0.4726 (tpp) REVERT: P 11 MET cc_start: 0.7310 (tpt) cc_final: 0.6737 (tmm) REVERT: P 54 PHE cc_start: 0.6672 (m-10) cc_final: 0.6348 (t80) REVERT: P 61 ASP cc_start: 0.4153 (m-30) cc_final: 0.3883 (p0) REVERT: P 65 MET cc_start: 0.5531 (mmt) cc_final: 0.5189 (ppp) REVERT: R 6 MET cc_start: 0.4547 (ptt) cc_final: 0.4005 (tmm) REVERT: R 16 MET cc_start: 0.1351 (ttp) cc_final: 0.0933 (tmm) REVERT: S 65 MET cc_start: 0.2904 (mtt) cc_final: 0.2622 (mmm) REVERT: A 483 MET cc_start: 0.8603 (mmm) cc_final: 0.8395 (mmm) REVERT: B 48 MET cc_start: 0.8076 (ptp) cc_final: 0.7835 (ptm) REVERT: C 262 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: D 160 MET cc_start: 0.8821 (mtm) cc_final: 0.8618 (mtm) REVERT: D 438 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8416 (pp) REVERT: E 380 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8792 (p0) REVERT: F 56 MET cc_start: 0.8994 (mmm) cc_final: 0.8696 (mmt) REVERT: F 193 MET cc_start: 0.8577 (mmm) cc_final: 0.8335 (mmm) REVERT: F 254 VAL cc_start: 0.8769 (t) cc_final: 0.8555 (p) REVERT: F 364 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9185 (mm) REVERT: F 379 MET cc_start: 0.7995 (tpt) cc_final: 0.7733 (mmm) REVERT: F 445 MET cc_start: 0.8630 (tpp) cc_final: 0.8364 (tpp) REVERT: G 116 MET cc_start: 0.8975 (mmm) cc_final: 0.8661 (mmm) REVERT: H 29 GLU cc_start: 0.7886 (mm-30) cc_final: 0.6847 (mp0) REVERT: H 70 GLU cc_start: 0.8473 (mp0) cc_final: 0.7868 (tp30) REVERT: X 49 ARG cc_start: 0.8316 (tpp80) cc_final: 0.7736 (ptt-90) REVERT: X 83 ARG cc_start: 0.8614 (ttt-90) cc_final: 0.8372 (mtp180) REVERT: X 85 GLN cc_start: 0.8929 (mt0) cc_final: 0.8652 (mt0) REVERT: a 93 MET cc_start: 0.8023 (mpp) cc_final: 0.6191 (tpp) REVERT: a 245 HIS cc_start: 0.1195 (OUTLIER) cc_final: 0.0958 (t-90) outliers start: 85 outliers final: 55 residues processed: 338 average time/residue: 0.4607 time to fit residues: 264.1275 Evaluate side-chains 320 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 259 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain M residue 6 MET Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 118 MET Chi-restraints excluded: chain a residue 245 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 0.5980 chunk 409 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 455 optimal weight: 9.9990 chunk 378 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 37 optimal weight: 30.0000 chunk 150 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 42 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 42 HIS E 208 GLN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37179 Z= 0.189 Angle : 0.566 12.375 50322 Z= 0.285 Chirality : 0.040 0.176 5852 Planarity : 0.004 0.050 6491 Dihedral : 6.276 92.968 5313 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.87 % Favored : 98.11 % Rotamer: Outliers : 1.92 % Allowed : 13.05 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.12), residues: 4756 helix: 1.53 (0.10), residues: 2539 sheet: 0.54 (0.21), residues: 544 loop : -0.34 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP G 203 HIS 0.024 0.001 HIS B 42 PHE 0.027 0.001 PHE Q 53 TYR 0.014 0.001 TYR a 263 ARG 0.008 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 269 time to evaluate : 4.608 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: L 6 MET cc_start: 0.4325 (pmm) cc_final: 0.4047 (tmm) REVERT: L 68 VAL cc_start: 0.4859 (t) cc_final: 0.4550 (m) REVERT: N 54 PHE cc_start: 0.7833 (m-10) cc_final: 0.7338 (t80) REVERT: O 17 MET cc_start: -0.0437 (mpp) cc_final: -0.1025 (tpt) REVERT: O 57 MET cc_start: 0.5048 (tmm) cc_final: 0.4664 (tpp) REVERT: P 11 MET cc_start: 0.7356 (tpt) cc_final: 0.6864 (tmm) REVERT: P 54 PHE cc_start: 0.6568 (m-10) cc_final: 0.6273 (t80) REVERT: P 61 ASP cc_start: 0.4176 (m-30) cc_final: 0.3891 (p0) REVERT: Q 42 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: R 6 MET cc_start: 0.4362 (ptt) cc_final: 0.3863 (tmm) REVERT: B 48 MET cc_start: 0.8022 (ptp) cc_final: 0.7793 (ptm) REVERT: B 261 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7520 (t0) REVERT: D 438 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8416 (pp) REVERT: E 379 MET cc_start: 0.7549 (tmm) cc_final: 0.7275 (tmm) REVERT: F 56 MET cc_start: 0.8977 (mmm) cc_final: 0.8685 (mmt) REVERT: F 254 VAL cc_start: 0.8750 (t) cc_final: 0.8545 (p) REVERT: F 364 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9179 (mm) REVERT: F 379 MET cc_start: 0.8038 (tpt) cc_final: 0.7717 (mmm) REVERT: F 445 MET cc_start: 0.8603 (tpp) cc_final: 0.8359 (tpp) REVERT: G 48 MET cc_start: 0.8686 (ttm) cc_final: 0.8471 (ttt) REVERT: G 57 HIS cc_start: 0.7976 (m-70) cc_final: 0.7559 (t70) REVERT: G 116 MET cc_start: 0.8826 (mmm) cc_final: 0.8525 (mmm) REVERT: G 243 MET cc_start: 0.8736 (ttp) cc_final: 0.8520 (ttt) REVERT: H 29 GLU cc_start: 0.7902 (mm-30) cc_final: 0.6896 (mp0) REVERT: H 70 GLU cc_start: 0.8458 (mp0) cc_final: 0.7842 (tp30) REVERT: X 49 ARG cc_start: 0.8292 (tpp80) cc_final: 0.7730 (ptt-90) REVERT: X 83 ARG cc_start: 0.8625 (ttt-90) cc_final: 0.8395 (mtp180) REVERT: a 54 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7545 (pp) REVERT: a 93 MET cc_start: 0.7947 (mpp) cc_final: 0.6207 (tpp) outliers start: 73 outliers final: 44 residues processed: 324 average time/residue: 0.4387 time to fit residues: 245.0126 Evaluate side-chains 308 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 259 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 42 GLN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 118 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 439 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 259 optimal weight: 0.9990 chunk 332 optimal weight: 8.9990 chunk 257 optimal weight: 2.9990 chunk 383 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 453 optimal weight: 20.0000 chunk 284 optimal weight: 8.9990 chunk 276 optimal weight: 0.9980 chunk 209 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS E 121 ASN E 368 GLN F 243 ASN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37179 Z= 0.267 Angle : 0.596 13.038 50322 Z= 0.301 Chirality : 0.041 0.194 5852 Planarity : 0.004 0.051 6491 Dihedral : 6.247 91.094 5312 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.29 % Favored : 97.69 % Rotamer: Outliers : 2.05 % Allowed : 13.20 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.12), residues: 4756 helix: 1.58 (0.10), residues: 2509 sheet: 0.50 (0.21), residues: 553 loop : -0.32 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP G 203 HIS 0.020 0.001 HIS H 56 PHE 0.023 0.001 PHE C 406 TYR 0.013 0.001 TYR F 247 ARG 0.005 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 268 time to evaluate : 4.443 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: L 6 MET cc_start: 0.4377 (pmm) cc_final: 0.4062 (tmm) REVERT: L 68 VAL cc_start: 0.5071 (t) cc_final: 0.4751 (m) REVERT: N 54 PHE cc_start: 0.7645 (m-10) cc_final: 0.7174 (t80) REVERT: O 17 MET cc_start: -0.0581 (mpp) cc_final: -0.1260 (tpt) REVERT: O 57 MET cc_start: 0.5106 (tmm) cc_final: 0.4696 (tpp) REVERT: P 11 MET cc_start: 0.7346 (tpt) cc_final: 0.6790 (tmm) REVERT: P 54 PHE cc_start: 0.6625 (m-10) cc_final: 0.6224 (t80) REVERT: P 61 ASP cc_start: 0.4556 (m-30) cc_final: 0.4185 (p0) REVERT: R 6 MET cc_start: 0.4371 (ptt) cc_final: 0.3806 (tmm) REVERT: D 438 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8450 (pp) REVERT: E 380 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8839 (p0) REVERT: F 56 MET cc_start: 0.8961 (mmm) cc_final: 0.8396 (mmp) REVERT: F 243 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8186 (t160) REVERT: F 364 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9171 (mm) REVERT: F 379 MET cc_start: 0.8154 (tpt) cc_final: 0.7872 (mmm) REVERT: G 48 MET cc_start: 0.8764 (ttm) cc_final: 0.8501 (ttt) REVERT: G 57 HIS cc_start: 0.8047 (m-70) cc_final: 0.7557 (t-90) REVERT: G 116 MET cc_start: 0.8878 (mmm) cc_final: 0.8543 (mmm) REVERT: G 155 MET cc_start: 0.9244 (mmt) cc_final: 0.8874 (mmm) REVERT: G 243 MET cc_start: 0.8734 (ttp) cc_final: 0.8513 (ttt) REVERT: H 29 GLU cc_start: 0.7922 (mm-30) cc_final: 0.6906 (mp0) REVERT: H 70 GLU cc_start: 0.8464 (mp0) cc_final: 0.7843 (tp30) REVERT: W 157 MET cc_start: 0.7457 (mmm) cc_final: 0.7135 (mmm) REVERT: X 49 ARG cc_start: 0.8346 (tpp80) cc_final: 0.7780 (ptt-90) REVERT: X 83 ARG cc_start: 0.8673 (ttt-90) cc_final: 0.8448 (mtp180) REVERT: a 54 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7519 (pp) REVERT: a 263 TYR cc_start: 0.8304 (m-10) cc_final: 0.8075 (m-80) outliers start: 78 outliers final: 55 residues processed: 328 average time/residue: 0.4352 time to fit residues: 244.3613 Evaluate side-chains 317 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 257 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 243 ASN Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 44 LEU Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 118 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 280 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 288 optimal weight: 0.4980 chunk 309 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 356 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 42 HIS ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 ASN ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37179 Z= 0.171 Angle : 0.573 12.725 50322 Z= 0.286 Chirality : 0.040 0.195 5852 Planarity : 0.004 0.051 6491 Dihedral : 6.068 89.937 5312 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.55 % Allowed : 13.68 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.12), residues: 4756 helix: 1.67 (0.10), residues: 2511 sheet: 0.59 (0.21), residues: 538 loop : -0.28 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP G 203 HIS 0.023 0.001 HIS B 42 PHE 0.022 0.001 PHE C 406 TYR 0.012 0.001 TYR C 455 ARG 0.006 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 268 time to evaluate : 4.483 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: L 6 MET cc_start: 0.4344 (pmm) cc_final: 0.4048 (tmm) REVERT: L 68 VAL cc_start: 0.5024 (t) cc_final: 0.4704 (m) REVERT: N 54 PHE cc_start: 0.7633 (m-10) cc_final: 0.7168 (t80) REVERT: O 17 MET cc_start: -0.0464 (mpp) cc_final: -0.1198 (tpt) REVERT: O 57 MET cc_start: 0.5345 (tmm) cc_final: 0.4947 (tpp) REVERT: P 11 MET cc_start: 0.7327 (tpt) cc_final: 0.6810 (tmm) REVERT: P 17 MET cc_start: 0.5386 (tpt) cc_final: 0.4577 (ptt) REVERT: P 54 PHE cc_start: 0.6632 (m-10) cc_final: 0.6216 (t80) REVERT: R 6 MET cc_start: 0.4324 (ptt) cc_final: 0.3861 (tmm) REVERT: A 386 MET cc_start: 0.8949 (mmm) cc_final: 0.8722 (mmt) REVERT: B 261 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7547 (t0) REVERT: D 160 MET cc_start: 0.8733 (mtm) cc_final: 0.8517 (mtm) REVERT: D 438 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8400 (pp) REVERT: F 56 MET cc_start: 0.8953 (mmm) cc_final: 0.8670 (mmt) REVERT: F 364 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9070 (mm) REVERT: F 379 MET cc_start: 0.8112 (tpt) cc_final: 0.7887 (mmm) REVERT: F 445 MET cc_start: 0.8383 (tpp) cc_final: 0.8167 (tpp) REVERT: G 25 MET cc_start: 0.8508 (tpp) cc_final: 0.8098 (tpp) REVERT: G 48 MET cc_start: 0.8801 (ttm) cc_final: 0.8540 (ttt) REVERT: G 57 HIS cc_start: 0.8003 (m-70) cc_final: 0.7536 (t70) REVERT: G 116 MET cc_start: 0.8795 (mmm) cc_final: 0.8501 (mmm) REVERT: G 243 MET cc_start: 0.8712 (ttp) cc_final: 0.8480 (ttt) REVERT: H 29 GLU cc_start: 0.7891 (mm-30) cc_final: 0.6900 (mp0) REVERT: H 70 GLU cc_start: 0.8440 (mp0) cc_final: 0.7819 (tp30) REVERT: W 157 MET cc_start: 0.7448 (mmm) cc_final: 0.7222 (mmm) REVERT: X 49 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7779 (ptt-90) REVERT: X 83 ARG cc_start: 0.8668 (ttt-90) cc_final: 0.8426 (mtp180) REVERT: a 54 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7529 (pp) REVERT: a 93 MET cc_start: 0.7741 (mpp) cc_final: 0.5987 (tpp) REVERT: a 263 TYR cc_start: 0.8288 (m-10) cc_final: 0.8063 (m-80) outliers start: 59 outliers final: 45 residues processed: 311 average time/residue: 0.4574 time to fit residues: 245.3829 Evaluate side-chains 307 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 258 time to evaluate : 4.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 80 ASN Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 118 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 412 optimal weight: 0.0010 chunk 434 optimal weight: 7.9990 chunk 396 optimal weight: 20.0000 chunk 423 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 332 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 chunk 400 optimal weight: 1.9990 chunk 421 optimal weight: 8.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN E 121 ASN G 57 HIS ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN Y 80 ASN ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37179 Z= 0.265 Angle : 0.601 14.315 50322 Z= 0.301 Chirality : 0.041 0.190 5852 Planarity : 0.004 0.052 6491 Dihedral : 6.096 90.020 5312 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.68 % Allowed : 13.73 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.12), residues: 4756 helix: 1.67 (0.10), residues: 2513 sheet: 0.55 (0.21), residues: 536 loop : -0.26 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP G 203 HIS 0.004 0.001 HIS W 21 PHE 0.023 0.001 PHE C 406 TYR 0.015 0.001 TYR C 455 ARG 0.004 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 259 time to evaluate : 4.349 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: L 6 MET cc_start: 0.4481 (pmm) cc_final: 0.4165 (tmm) REVERT: L 68 VAL cc_start: 0.5445 (t) cc_final: 0.5138 (m) REVERT: N 54 PHE cc_start: 0.7491 (m-10) cc_final: 0.7065 (t80) REVERT: O 17 MET cc_start: -0.0482 (mpp) cc_final: -0.1205 (tpt) REVERT: O 57 MET cc_start: 0.5355 (tmm) cc_final: 0.4966 (tpp) REVERT: P 11 MET cc_start: 0.7332 (tpt) cc_final: 0.6844 (tmm) REVERT: P 54 PHE cc_start: 0.6485 (m-10) cc_final: 0.6055 (t80) REVERT: R 6 MET cc_start: 0.4323 (ptt) cc_final: 0.3868 (tmm) REVERT: S 16 MET cc_start: 0.4290 (ptt) cc_final: 0.1635 (tmm) REVERT: A 386 MET cc_start: 0.8988 (mmm) cc_final: 0.8768 (mmt) REVERT: B 42 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7192 (t70) REVERT: B 261 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7563 (t0) REVERT: D 438 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8420 (pp) REVERT: E 380 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8847 (p0) REVERT: F 56 MET cc_start: 0.8989 (mmm) cc_final: 0.8366 (mmt) REVERT: F 193 MET cc_start: 0.8569 (mmm) cc_final: 0.8353 (mmm) REVERT: F 364 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9134 (mm) REVERT: F 431 MET cc_start: 0.8439 (mmm) cc_final: 0.8106 (mmm) REVERT: F 445 MET cc_start: 0.8611 (tpp) cc_final: 0.8347 (tpp) REVERT: G 116 MET cc_start: 0.8814 (mmm) cc_final: 0.8508 (mmm) REVERT: H 29 GLU cc_start: 0.7907 (mm-30) cc_final: 0.6895 (mp0) REVERT: H 70 GLU cc_start: 0.8413 (mp0) cc_final: 0.7779 (tp30) REVERT: H 95 MET cc_start: 0.9058 (mtm) cc_final: 0.8834 (mtm) REVERT: X 49 ARG cc_start: 0.8356 (tpp80) cc_final: 0.7822 (ptt-90) REVERT: X 83 ARG cc_start: 0.8685 (ttt-90) cc_final: 0.8406 (mtp180) REVERT: a 54 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7453 (pp) REVERT: a 215 MET cc_start: 0.5201 (mmm) cc_final: 0.3910 (mpp) outliers start: 64 outliers final: 49 residues processed: 308 average time/residue: 0.4452 time to fit residues: 235.4530 Evaluate side-chains 308 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 253 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 118 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 277 optimal weight: 7.9990 chunk 447 optimal weight: 40.0000 chunk 273 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 469 optimal weight: 5.9990 chunk 431 optimal weight: 6.9990 chunk 373 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 288 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 5 ASN P 52 GLN ** S 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN E 121 ASN E 191 HIS E 437 HIS F 243 ASN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 245 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 37179 Z= 0.351 Angle : 0.662 14.623 50322 Z= 0.332 Chirality : 0.042 0.195 5852 Planarity : 0.004 0.054 6491 Dihedral : 6.391 95.038 5312 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.81 % Allowed : 13.78 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.12), residues: 4756 helix: 1.51 (0.10), residues: 2492 sheet: 0.43 (0.21), residues: 550 loop : -0.40 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 203 HIS 0.006 0.001 HIS W 21 PHE 0.024 0.001 PHE C 406 TYR 0.036 0.001 TYR a 263 ARG 0.005 0.001 ARG F 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 256 time to evaluate : 4.175 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: L 6 MET cc_start: 0.4768 (pmm) cc_final: 0.4436 (tmm) REVERT: M 16 MET cc_start: 0.4846 (ptm) cc_final: 0.4413 (tpt) REVERT: N 54 PHE cc_start: 0.7434 (m-10) cc_final: 0.7023 (t80) REVERT: N 75 MET cc_start: 0.5198 (ppp) cc_final: 0.4689 (tpp) REVERT: O 17 MET cc_start: -0.0613 (mpp) cc_final: -0.1559 (tpt) REVERT: O 57 MET cc_start: 0.5256 (tmm) cc_final: 0.4870 (tpp) REVERT: P 11 MET cc_start: 0.7427 (tpt) cc_final: 0.7135 (tmm) REVERT: P 54 PHE cc_start: 0.6531 (m-10) cc_final: 0.6021 (t80) REVERT: R 6 MET cc_start: 0.4396 (ptt) cc_final: 0.3882 (tmm) REVERT: R 75 MET cc_start: 0.5446 (ppp) cc_final: 0.5122 (ppp) REVERT: S 16 MET cc_start: 0.4204 (ptt) cc_final: 0.1916 (mmm) REVERT: A 386 MET cc_start: 0.8996 (mmm) cc_final: 0.8781 (mmt) REVERT: B 42 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.7392 (t70) REVERT: B 261 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7633 (t0) REVERT: D 438 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8488 (pp) REVERT: E 380 ASP cc_start: 0.9222 (OUTLIER) cc_final: 0.8740 (p0) REVERT: F 56 MET cc_start: 0.8909 (mmm) cc_final: 0.8700 (mmt) REVERT: F 243 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8173 (t160) REVERT: F 364 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9145 (mm) REVERT: F 431 MET cc_start: 0.8497 (mmm) cc_final: 0.8132 (mmm) REVERT: G 25 MET cc_start: 0.8530 (tpp) cc_final: 0.7979 (tpp) REVERT: G 57 HIS cc_start: 0.7921 (m170) cc_final: 0.7641 (t-90) REVERT: G 116 MET cc_start: 0.8829 (mmm) cc_final: 0.8531 (mmm) REVERT: H 29 GLU cc_start: 0.7991 (mm-30) cc_final: 0.6969 (mp0) REVERT: H 31 GLU cc_start: 0.7910 (tp30) cc_final: 0.7702 (tp30) REVERT: H 35 TYR cc_start: 0.7981 (m-80) cc_final: 0.7778 (m-80) REVERT: H 70 GLU cc_start: 0.8465 (mp0) cc_final: 0.7733 (tp30) REVERT: X 83 ARG cc_start: 0.8707 (ttt-90) cc_final: 0.8494 (mtp180) REVERT: a 54 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7464 (pp) REVERT: a 215 MET cc_start: 0.5377 (OUTLIER) cc_final: 0.3893 (mpp) outliers start: 69 outliers final: 49 residues processed: 308 average time/residue: 0.4416 time to fit residues: 235.3976 Evaluate side-chains 307 residues out of total 3805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 250 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain R residue 76 PHE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 243 ASN Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 88 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 145 ASN Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain a residue 118 MET Chi-restraints excluded: chain a residue 215 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 296 optimal weight: 0.7980 chunk 398 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 344 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 374 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 384 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 52 GLN ** S 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 HIS F 243 ASN ** G 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 ASN a 245 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.068637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.045304 restraints weight = 189776.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.046471 restraints weight = 86587.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.047187 restraints weight = 53285.495| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 37179 Z= 0.158 Angle : 0.591 14.479 50322 Z= 0.295 Chirality : 0.040 0.198 5852 Planarity : 0.004 0.050 6491 Dihedral : 6.073 89.832 5312 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.29 % Allowed : 14.39 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.12), residues: 4756 helix: 1.65 (0.10), residues: 2520 sheet: 0.50 (0.21), residues: 548 loop : -0.24 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP G 203 HIS 0.010 0.001 HIS B 26 PHE 0.028 0.001 PHE C 406 TYR 0.044 0.001 TYR a 263 ARG 0.012 0.000 ARG X 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7035.29 seconds wall clock time: 128 minutes 58.46 seconds (7738.46 seconds total)