Starting phenix.real_space_refine on Fri Feb 23 06:14:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/02_2024/6oqr_20167_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/02_2024/6oqr_20167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/02_2024/6oqr_20167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/02_2024/6oqr_20167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/02_2024/6oqr_20167_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqr_20167/02_2024/6oqr_20167_neut_updated.pdb" } resolution = 3.1 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= 0.003 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 180 5.16 5 C 23471 2.51 5 N 6314 2.21 5 O 6965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 GLU 54": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 69": "OD1" <-> "OD2" 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 GLU 118": "OE1" <-> "OE2" Residue "W ASP 160": "OD1" <-> "OD2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "W GLU 168": "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 PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 195": "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 PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C GLU 429": "OE1" <-> "OE2" 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 505": "OD1" <-> "OD2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B TYR 248": "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 262": "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 PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 412": "OD1" <-> "OD2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 262": "OD1" <-> "OD2" 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 ARG 376": "NH1" <-> "NH2" 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 GLU 460": "OE1" <-> "OE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X ASP 55": "OD1" <-> "OD2" Residue "X GLU 71": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X GLU 93": "OE1" <-> "OE2" Residue "X GLU 95": "OE1" <-> "OE2" Residue "X GLU 97": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ARG 113": "NH1" <-> "NH2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X ASP 141": "OD1" <-> "OD2" Residue "X GLU 142": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H ARG 129": "NH1" <-> "NH2" 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 GLU 68": "OE1" <-> "OE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 147": "OE1" <-> "OE2" 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 ARG 221": "NH1" <-> "NH2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "G GLU 278": "OE1" <-> "OE2" Residue "F ASP 14": "OD1" <-> "OD2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F ASP 236": "OD1" <-> "OD2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F ASP 372": "OD1" <-> "OD2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "F PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 422": "OD1" <-> "OD2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 302": "OD1" <-> "OD2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 338": "OD1" <-> "OD2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E ASP 380": "OD1" <-> "OD2" Residue "E ASP 386": "OD1" <-> "OD2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 44": "OD1" <-> "OD2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ASP 44": "OD1" <-> "OD2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ASP 44": "OD1" <-> "OD2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y GLU 71": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y GLU 93": "OE1" <-> "OE2" Residue "Y GLU 97": "OE1" <-> "OE2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y GLU 108": "OE1" <-> "OE2" 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 GLU 133": "OE1" <-> "OE2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "a TYR 11": "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 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 146": "OD1" <-> "OD2" Residue "a PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 44": "OD1" <-> "OD2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "S TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 50": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36951 Number of models: 1 Model: "" Number of chains: 28 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: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3851 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 492} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} 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: "F" 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: "E" 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: "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: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} 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: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} 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: "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: "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: "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} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 18.76, per 1000 atoms: 0.51 Number of scatterers: 36951 At special positions: 0 Unit cell: (178.035, 214.721, 135.954, 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 180 16.00 P 16 15.00 Mg 5 11.99 O 6965 8.00 N 6314 7.00 C 23471 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: 15.34 Conformation dependent library (CDL) restraints added in 7.9 seconds 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 181 helices and 26 sheets defined 56.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.79 Creating SS restraints... Processing helix chain 'W' and resid 4 through 20 removed outlier: 3.888A pdb=" N ARG W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.677A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.647A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU W 46 " --> pdb=" O GLN W 42 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 4.158A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 82 removed outlier: 3.580A pdb=" N ILE W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 4.340A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 Processing helix chain 'W' and resid 163 through 173 removed outlier: 4.103A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 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 removed outlier: 3.782A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.026A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.601A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) 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: 3.902A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.959A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) 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 288 through 300 removed outlier: 4.325A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU C 299 " --> 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 removed outlier: 3.954A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) 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 412 removed outlier: 3.777A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 3.509A pdb=" N LYS C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.868A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.548A pdb=" N GLU C 485 " --> pdb=" O PRO C 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.562A pdb=" N ARG B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.571A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) 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 251 Proline residue: B 239 - end of helix removed outlier: 3.504A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 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: 4.550A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 298 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.495A 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 341 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.960A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 3.691A pdb=" N HIS B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.643A pdb=" N VAL B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 458 removed outlier: 3.801A pdb=" N ASP B 458 " --> pdb=" O TYR B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 458' Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.772A pdb=" N GLY B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 468 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 removed outlier: 3.826A pdb=" N GLN B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.507A pdb=" N LEU B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.795A pdb=" N SER A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) 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 removed outlier: 3.667A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 156' Processing helix chain 'A' and resid 175 through 188 removed outlier: 4.132A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.341A 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: 3.774A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 4.016A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) 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: 3.517A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.596A 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 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.557A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.677A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.658A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.873A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.692A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 24 removed outlier: 4.301A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA X 11 " --> pdb=" O LEU X 8 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET X 22 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 4.046A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR X 62 " --> pdb=" O LYS X 58 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU X 65 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU X 97 " --> pdb=" O GLU X 93 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 154 removed outlier: 5.990A pdb=" N ASP X 147 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP X 150 " --> pdb=" O ASP X 147 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL X 153 " --> pdb=" O ASP X 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 removed outlier: 3.732A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 removed outlier: 3.522A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 133 No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.862A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 4.168A 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 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 88 through 107 removed outlier: 4.482A pdb=" N ASN G 91 " --> pdb=" O GLY G 88 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN G 93 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 5.054A 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 197 through 202 removed outlier: 3.639A pdb=" N LYS G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 280 removed outlier: 3.909A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) 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 157 through 167 Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.608A pdb=" N SER F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) 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: 4.972A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 223 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 removed outlier: 3.915A pdb=" N LEU F 249 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA F 250 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.711A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (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 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.763A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 377 removed outlier: 3.599A pdb=" N LYS F 371 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 420 through 432 removed outlier: 3.725A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 449 through 457 removed outlier: 4.086A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) 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 168 removed outlier: 3.625A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 198 through 201 Processing helix chain 'E' and resid 213 through 232 removed outlier: 3.501A pdb=" N ARG E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.808A 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 312 Processing helix chain 'E' and resid 323 through 327 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: 3.756A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (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 384 through 399 removed outlier: 3.567A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.728A pdb=" N GLU E 408 " --> pdb=" O PHE E 405 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL E 409 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 411 " --> pdb=" O GLU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 440 through 443 Processing helix chain 'E' and resid 449 through 458 removed outlier: 4.407A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) 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 169 Processing helix chain 'D' and resid 183 through 195 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: 5.054A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 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 314 removed outlier: 3.792A pdb=" N THR D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 346 through 377 removed outlier: 7.670A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) 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 399 removed outlier: 3.607A pdb=" N LEU D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 411 removed outlier: 3.963A pdb=" N VAL D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 removed outlier: 3.521A pdb=" N GLU D 432 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.829A pdb=" N VAL D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 454 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 removed outlier: 4.441A pdb=" N LEU J 9 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR J 10 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA J 13 " --> pdb=" O TYR J 10 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU J 19 " --> pdb=" O MET J 16 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS J 34 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 75 removed outlier: 4.112A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.501A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA L 14 " --> pdb=" O TYR L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 Proline residue: L 47 - end of helix removed outlier: 3.722A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.511A pdb=" N LEU L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU L 72 " --> pdb=" O GLY L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 5.021A pdb=" N LEU M 9 " --> pdb=" O ASN M 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR M 10 " --> pdb=" O MET M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 3.757A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.910A pdb=" N VAL M 68 " --> pdb=" O MET M 65 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.464A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU N 19 " --> pdb=" O VAL N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.770A pdb=" N THR N 51 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 6 through 41 Processing helix chain 'O' and resid 43 through 62 Proline residue: O 47 - end of helix removed outlier: 3.532A pdb=" N THR O 51 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL O 56 " --> pdb=" O PHE O 53 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET O 57 " --> pdb=" O PHE O 54 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA O 62 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 76 Processing helix chain 'P' and resid 8 through 41 removed outlier: 3.779A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU P 31 " --> pdb=" O GLY P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 77 removed outlier: 4.925A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 4.053A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU P 72 " --> pdb=" O VAL P 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.643A pdb=" N LEU Q 8 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU Q 9 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU Q 19 " --> pdb=" O MET Q 16 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 3.873A pdb=" N GLY Q 58 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.560A pdb=" N LEU Q 70 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR Q 73 " --> pdb=" O LEU Q 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.526A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR R 10 " --> pdb=" O MET R 6 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 59 Proline residue: R 47 - end of helix removed outlier: 3.582A pdb=" N PHE R 54 " --> pdb=" O THR R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 76 Processing helix chain 'Y' and resid 4 through 24 removed outlier: 3.540A pdb=" N LEU Y 16 " --> pdb=" O ILE Y 12 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE Y 20 " --> pdb=" O LEU Y 16 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS Y 21 " --> pdb=" O PHE Y 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 139 removed outlier: 3.862A pdb=" N ALA Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA Y 50 " --> pdb=" O SER Y 46 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP Y 53 " --> pdb=" O ARG Y 49 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU Y 56 " --> pdb=" O LYS Y 52 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN Y 96 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR Y 99 " --> pdb=" O GLU Y 95 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS Y 100 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Y 112 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL Y 124 " --> pdb=" O LEU Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 removed outlier: 3.926A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU Y 155 " --> pdb=" O LYS Y 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.693A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 64 removed outlier: 3.718A pdb=" N LEU a 52 " --> pdb=" O PHE a 48 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU a 57 " --> pdb=" O GLY a 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER a 62 " --> pdb=" O VAL a 58 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 92 removed outlier: 3.951A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 120 Proline residue: a 103 - end of helix removed outlier: 3.748A pdb=" N LEU a 106 " --> pdb=" O ALA a 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 132 Proline residue: a 127 - end of helix 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: 7.620A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix removed outlier: 4.314A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 4.076A pdb=" N ARG a 210 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE a 221 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE a 225 " --> pdb=" O PHE a 222 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA a 226 " --> pdb=" O ILE a 223 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 3.569A pdb=" N GLN a 234 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP a 235 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL a 239 " --> pdb=" O ILE a 236 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.925A pdb=" N ILE a 246 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR a 250 " --> pdb=" O LEU a 247 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN a 252 " --> pdb=" O ILE a 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.855A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA I 20 " --> pdb=" O MET I 16 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU I 37 " --> pdb=" O GLY I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.884A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 3.570A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL I 60 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.764A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE I 76 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 41 removed outlier: 4.905A pdb=" N LEU S 8 " --> pdb=" O LEU S 4 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU S 9 " --> pdb=" O ASN S 5 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR S 10 " --> pdb=" O MET S 6 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 76 removed outlier: 3.558A pdb=" N ILE S 46 " --> pdb=" O PRO S 43 " (cutoff:3.500A) Proline residue: S 47 - end of helix removed outlier: 3.567A pdb=" N THR S 51 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE S 54 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL S 56 " --> pdb=" O PHE S 53 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL S 60 " --> pdb=" O MET S 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE S 63 " --> pdb=" O VAL S 60 " (cutoff:3.500A) Proline residue: S 64 - end of helix removed outlier: 3.998A pdb=" N LEU S 70 " --> pdb=" O ALA S 67 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.783A pdb=" N VAL W 110 " --> pdb=" O ASN W 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.438A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 70 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.349A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ILE C 222 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP C 255 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE C 194 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE C 198 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.551A pdb=" N LEU C 166 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.482A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= H, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.234A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.626A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.534A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= L, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.194A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.563A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.336A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 22 through 26 Processing sheet with id= P, first strand: chain 'G' and resid 181 through 188 removed outlier: 6.710A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.516A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N HIS F 73 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU F 30 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU F 71 " --> pdb=" O GLU F 30 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.729A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 317 through 320 removed outlier: 8.014A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 4 through 9 removed outlier: 6.556A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.462A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR E 173 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE E 240 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL E 175 " --> pdb=" O PHE E 240 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER E 203 " --> pdb=" O PHE E 176 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLY E 178 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL E 205 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.570A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N HIS D 73 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLU D 30 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU D 71 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLN D 32 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N LYS D 69 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.589A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 317 through 321 removed outlier: 8.804A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 175 " --> pdb=" O PHE D 240 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 removed outlier: 3.550A pdb=" N ILE a 41 " --> pdb=" O LEU a 21 " (cutoff:3.500A) 1901 hydrogen bonds defined for protein. 4596 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: 12.96 Time building geometry restraints manager: 16.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6329 1.28 - 1.42: 8549 1.42 - 1.55: 22243 1.55 - 1.68: 25 1.68 - 1.81: 360 Bond restraints: 37506 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.75e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C PRO C 342 " pdb=" O PRO C 342 " ideal model delta sigma weight residual 1.238 1.153 0.085 1.24e-02 6.50e+03 4.68e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.36e+01 ... (remaining 37501 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.80: 848 105.80 - 113.35: 21178 113.35 - 120.90: 18635 120.90 - 128.44: 9886 128.44 - 135.99: 219 Bond angle restraints: 50766 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.08 23.79 1.00e+00 1.00e+00 5.66e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.30e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.61 22.26 1.00e+00 1.00e+00 4.95e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.86 19.97 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 118.52 18.31 1.00e+00 1.00e+00 3.35e+02 ... (remaining 50761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 21932 28.35 - 56.71: 732 56.71 - 85.06: 103 85.06 - 113.42: 13 113.42 - 141.77: 5 Dihedral angle restraints: 22785 sinusoidal: 9007 harmonic: 13778 Sorted by residual: dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 158.22 141.77 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O2A ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PA ADP F 500 " pdb=" PB ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 80.10 -140.09 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 170.76 129.24 1 2.00e+01 2.50e-03 3.92e+01 ... (remaining 22782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5338 0.083 - 0.166: 548 0.166 - 0.249: 24 0.249 - 0.332: 5 0.332 - 0.415: 3 Chirality restraints: 5918 Sorted by residual: chirality pdb=" CA LEU a 178 " pdb=" N LEU a 178 " pdb=" C LEU a 178 " pdb=" CB LEU a 178 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA SER a 202 " pdb=" N SER a 202 " pdb=" C SER a 202 " pdb=" CB SER a 202 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ASP L 7 " pdb=" N ASP L 7 " pdb=" C ASP L 7 " pdb=" CB ASP L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 5915 not shown) Planarity restraints: 6547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ALA D 264 " -0.073 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 414 " -0.017 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ASP B 414 " 0.062 2.00e-02 2.50e+03 pdb=" O ASP B 414 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP B 415 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 338 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C SER C 338 " -0.062 2.00e-02 2.50e+03 pdb=" O SER C 338 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA C 339 " 0.022 2.00e-02 2.50e+03 ... (remaining 6544 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 51 2.38 - 3.01: 23648 3.01 - 3.64: 53165 3.64 - 4.27: 84692 4.27 - 4.90: 143337 Nonbonded interactions: 304893 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.753 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.849 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.851 2.170 nonbonded pdb=" O3 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.851 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.892 2.170 ... (remaining 304888 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 4 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 511 or resid 600 thr \ ough 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 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 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 459 or resid 500)) selection = (chain 'E' and (resid 2 through 459 or resid 500)) selection = (chain 'F' and (resid 2 through 459 or resid 500)) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 11.450 Check model and map are aligned: 0.600 Set scattering table: 0.340 Process input model: 99.590 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 0.112 37506 Z= 0.627 Angle : 0.900 23.786 50766 Z= 0.586 Chirality : 0.051 0.415 5918 Planarity : 0.005 0.055 6547 Dihedral : 14.878 141.774 13971 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.50 % Allowed : 8.09 % Favored : 89.41 % Cbeta Deviations : 0.07 % 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: -2.47 (0.10), residues: 4805 helix: -1.67 (0.09), residues: 2555 sheet: -1.11 (0.19), residues: 545 loop : -1.43 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 39 HIS 0.013 0.002 HIS G 200 PHE 0.020 0.002 PHE a 158 TYR 0.022 0.002 TYR F 297 ARG 0.012 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 773 time to evaluate : 4.638 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: W 119 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8094 (tm-30) REVERT: W 156 ASP cc_start: 0.7916 (p0) cc_final: 0.7196 (p0) REVERT: C 161 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8592 (mtt180) REVERT: C 236 TYR cc_start: 0.9424 (OUTLIER) cc_final: 0.8757 (t80) REVERT: C 386 MET cc_start: 0.9000 (mmm) cc_final: 0.8550 (mmt) REVERT: C 412 ASP cc_start: 0.8058 (t0) cc_final: 0.7838 (t0) REVERT: B 2 GLN cc_start: 0.8004 (pm20) cc_final: 0.7516 (pm20) REVERT: B 422 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6609 (m-30) REVERT: A 86 MET cc_start: 0.8609 (mtt) cc_final: 0.8385 (mtt) REVERT: A 376 ARG cc_start: 0.8379 (mmt90) cc_final: 0.8159 (mmp80) REVERT: A 401 ARG cc_start: 0.8633 (mtp-110) cc_final: 0.8347 (ttm-80) REVERT: X 17 PHE cc_start: 0.7855 (m-10) cc_final: 0.7466 (m-10) REVERT: X 64 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8308 (mm-40) REVERT: H 49 MET cc_start: 0.8858 (mmt) cc_final: 0.8440 (mmm) REVERT: H 72 GLN cc_start: 0.8081 (mt0) cc_final: 0.7689 (mt0) REVERT: H 111 ASP cc_start: 0.8761 (t0) cc_final: 0.8404 (t0) REVERT: G 102 MET cc_start: 0.8953 (ttp) cc_final: 0.8729 (mtp) REVERT: G 201 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7137 (mttm) REVERT: F 281 ARG cc_start: 0.9462 (OUTLIER) cc_final: 0.9251 (ptm160) REVERT: E 88 MET cc_start: 0.9099 (mtm) cc_final: 0.8758 (mtp) REVERT: E 371 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8592 (ttpp) REVERT: D 275 MET cc_start: 0.9212 (tpp) cc_final: 0.8883 (tpp) REVERT: D 381 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8110 (mm-30) REVERT: J 42 GLN cc_start: 0.8732 (mt0) cc_final: 0.8440 (mp10) REVERT: J 57 MET cc_start: 0.9149 (tmm) cc_final: 0.8925 (tmm) REVERT: J 63 ILE cc_start: 0.8253 (mm) cc_final: 0.7977 (mm) REVERT: J 65 MET cc_start: 0.8470 (mmt) cc_final: 0.7939 (ptt) REVERT: J 75 MET cc_start: 0.8616 (ttp) cc_final: 0.7888 (tmm) REVERT: L 10 TYR cc_start: 0.8058 (m-80) cc_final: 0.7842 (m-80) REVERT: L 42 GLN cc_start: 0.7898 (mt0) cc_final: 0.7667 (mt0) REVERT: M 6 MET cc_start: 0.7997 (mtt) cc_final: 0.7197 (tpp) REVERT: M 17 MET cc_start: 0.8349 (mtm) cc_final: 0.7923 (tpp) REVERT: M 42 GLN cc_start: 0.8971 (pt0) cc_final: 0.8488 (pp30) REVERT: O 42 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8102 (mp10) REVERT: O 50 ARG cc_start: 0.8190 (tmm-80) cc_final: 0.7806 (ttp-170) REVERT: O 51 THR cc_start: 0.8853 (m) cc_final: 0.8590 (m) REVERT: P 16 MET cc_start: 0.7980 (mtt) cc_final: 0.7760 (mtp) REVERT: P 17 MET cc_start: 0.8356 (mtm) cc_final: 0.8091 (mtt) REVERT: P 42 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8083 (mm-40) REVERT: P 50 ARG cc_start: 0.8208 (ptt180) cc_final: 0.7697 (ttp-110) REVERT: P 54 PHE cc_start: 0.8664 (m-80) cc_final: 0.8270 (m-80) REVERT: Q 50 ARG cc_start: 0.8762 (ttm110) cc_final: 0.8517 (ptm160) REVERT: Q 57 MET cc_start: 0.8317 (tmm) cc_final: 0.8042 (tmm) REVERT: R 6 MET cc_start: 0.7099 (mmt) cc_final: 0.6558 (mtm) REVERT: R 16 MET cc_start: 0.8172 (mtp) cc_final: 0.7909 (mtp) REVERT: R 34 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8517 (mmtp) REVERT: R 55 ILE cc_start: 0.8710 (mm) cc_final: 0.8448 (mm) REVERT: R 57 MET cc_start: 0.8877 (ttp) cc_final: 0.8439 (tmm) REVERT: R 59 LEU cc_start: 0.9012 (mt) cc_final: 0.8600 (tt) REVERT: R 72 LEU cc_start: 0.8827 (mt) cc_final: 0.8602 (mt) REVERT: Y 42 ASP cc_start: 0.8425 (m-30) cc_final: 0.8224 (m-30) REVERT: Y 64 GLN cc_start: 0.8603 (mp10) cc_final: 0.7969 (mp10) REVERT: Y 80 ASN cc_start: 0.8547 (m-40) cc_final: 0.7810 (t0) REVERT: Y 83 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7745 (ttp80) REVERT: Y 96 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8304 (tm-30) REVERT: Y 133 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: a 10 ASP cc_start: 0.8173 (t0) cc_final: 0.7763 (t0) REVERT: a 33 ASN cc_start: 0.4075 (OUTLIER) cc_final: 0.3807 (p0) REVERT: a 54 LEU cc_start: 0.7601 (mp) cc_final: 0.6893 (tt) REVERT: a 66 LYS cc_start: 0.5681 (mtpt) cc_final: 0.5181 (tttt) REVERT: a 115 MET cc_start: 0.7715 (mtm) cc_final: 0.7490 (mtt) REVERT: a 131 GLU cc_start: 0.8010 (tt0) cc_final: 0.7609 (tp30) REVERT: a 139 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7133 (tp) REVERT: a 153 MET cc_start: 0.8439 (mtp) cc_final: 0.8199 (mtt) REVERT: a 181 GLN cc_start: 0.8533 (mt0) cc_final: 0.8275 (mt0) REVERT: a 241 TRP cc_start: 0.8315 (t-100) cc_final: 0.7999 (t-100) REVERT: I 37 GLU cc_start: 0.7508 (tp30) cc_final: 0.7285 (tp30) REVERT: I 42 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7402 (mp10) REVERT: I 73 TYR cc_start: 0.7194 (t80) cc_final: 0.6815 (t80) REVERT: S 6 MET cc_start: 0.7257 (mmt) cc_final: 0.6889 (mmp) REVERT: S 34 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8253 (mmtm) REVERT: S 65 MET cc_start: 0.8952 (mmt) cc_final: 0.8642 (mtm) outliers start: 96 outliers final: 52 residues processed: 851 average time/residue: 0.5347 time to fit residues: 719.1021 Evaluate side-chains 667 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 607 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 20 GLN Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 0.9990 chunk 358 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 275 optimal weight: 0.4980 chunk 429 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN C 333 GLN C 511 GLN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 423 HIS ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 ASN A 65 ASN A 344 ASN H 14 GLN G 142 ASN G 180 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 353 HIS F 437 HIS J 42 GLN L 5 ASN L 52 GLN M 5 ASN N 3 ASN O 3 ASN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 ASN Q 5 ASN Q 42 GLN Q 52 GLN R 52 GLN a 32 GLN a 76 GLN a 132 HIS ** a 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 5 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37506 Z= 0.196 Angle : 0.611 7.880 50766 Z= 0.320 Chirality : 0.043 0.255 5918 Planarity : 0.005 0.051 6547 Dihedral : 8.621 128.886 5439 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.40 % Allowed : 12.70 % Favored : 84.90 % 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: -0.70 (0.12), residues: 4805 helix: -0.11 (0.10), residues: 2589 sheet: -0.59 (0.20), residues: 534 loop : -0.73 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 231 HIS 0.008 0.001 HIS a 14 PHE 0.018 0.001 PHE P 35 TYR 0.014 0.001 TYR C 236 ARG 0.009 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 676 time to evaluate : 4.440 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: W 12 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8765 (tppt) REVERT: W 119 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: W 156 ASP cc_start: 0.7971 (p0) cc_final: 0.7238 (p0) REVERT: C 161 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8707 (mtt180) REVERT: C 236 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8433 (t80) REVERT: C 386 MET cc_start: 0.8985 (mmm) cc_final: 0.8631 (mmm) REVERT: C 422 ASP cc_start: 0.8162 (m-30) cc_final: 0.7911 (m-30) REVERT: B 414 ASP cc_start: 0.5870 (OUTLIER) cc_final: 0.5336 (m-30) REVERT: A 86 MET cc_start: 0.8547 (mtt) cc_final: 0.8313 (mtt) REVERT: A 181 ASP cc_start: 0.8323 (t0) cc_final: 0.8118 (t0) REVERT: A 236 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8671 (t80) REVERT: A 343 THR cc_start: 0.9579 (OUTLIER) cc_final: 0.9280 (p) REVERT: A 484 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7468 (tm-30) REVERT: X 17 PHE cc_start: 0.8118 (m-10) cc_final: 0.7904 (m-80) REVERT: X 64 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8398 (mm-40) REVERT: X 82 ARG cc_start: 0.8679 (tpp-160) cc_final: 0.8420 (tpp-160) REVERT: X 104 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8890 (pp30) REVERT: X 150 ASP cc_start: 0.8815 (m-30) cc_final: 0.8569 (p0) REVERT: H 55 GLN cc_start: 0.7320 (pt0) cc_final: 0.7054 (pt0) REVERT: H 81 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.6947 (p0) REVERT: H 111 ASP cc_start: 0.8658 (t0) cc_final: 0.8304 (t0) REVERT: G 168 TYR cc_start: 0.9063 (m-80) cc_final: 0.8474 (m-80) REVERT: F 226 MET cc_start: 0.8583 (mtt) cc_final: 0.8246 (mtt) REVERT: E 366 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7856 (mmm160) REVERT: E 371 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8477 (ttpp) REVERT: D 381 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8061 (mm-30) REVERT: J 17 MET cc_start: 0.8310 (mtm) cc_final: 0.7750 (mmm) REVERT: J 42 GLN cc_start: 0.8616 (mt0) cc_final: 0.8273 (mp10) REVERT: J 52 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8251 (mm-40) REVERT: J 57 MET cc_start: 0.8872 (tmm) cc_final: 0.8529 (tmm) REVERT: L 37 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8138 (mt-10) REVERT: L 41 ARG cc_start: 0.9015 (ttm110) cc_final: 0.8409 (ttm-80) REVERT: M 17 MET cc_start: 0.8466 (mtm) cc_final: 0.8262 (mtt) REVERT: M 46 ILE cc_start: 0.9157 (mt) cc_final: 0.8922 (mt) REVERT: N 42 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7765 (mp10) REVERT: O 42 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7581 (mp10) REVERT: P 41 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7527 (ttm-80) REVERT: P 42 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7447 (mp10) REVERT: P 50 ARG cc_start: 0.8167 (ptt180) cc_final: 0.7570 (ttm110) REVERT: P 53 PHE cc_start: 0.8993 (t80) cc_final: 0.8753 (t80) REVERT: P 54 PHE cc_start: 0.8735 (m-80) cc_final: 0.8291 (m-80) REVERT: Q 5 ASN cc_start: 0.4737 (OUTLIER) cc_final: 0.4503 (m-40) REVERT: Q 57 MET cc_start: 0.8241 (tmm) cc_final: 0.8039 (tmm) REVERT: R 6 MET cc_start: 0.7244 (mmt) cc_final: 0.6705 (mtm) REVERT: R 34 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8384 (mmtt) REVERT: R 55 ILE cc_start: 0.8549 (mm) cc_final: 0.8276 (mm) REVERT: R 57 MET cc_start: 0.8725 (ttp) cc_final: 0.8393 (tmm) REVERT: Y 1 MET cc_start: 0.4345 (ptt) cc_final: 0.2523 (mmm) REVERT: Y 37 GLN cc_start: 0.7441 (mt0) cc_final: 0.7068 (mm110) REVERT: Y 51 HIS cc_start: 0.7740 (t70) cc_final: 0.7524 (t-90) REVERT: Y 83 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7689 (ttp80) REVERT: Y 84 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9120 (t) REVERT: Y 96 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8306 (tm-30) REVERT: Y 133 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: a 6 MET cc_start: 0.4922 (mmt) cc_final: 0.4069 (ptt) REVERT: a 54 LEU cc_start: 0.7517 (mp) cc_final: 0.6947 (tt) REVERT: a 56 PHE cc_start: 0.7224 (t80) cc_final: 0.6966 (t80) REVERT: a 66 LYS cc_start: 0.5727 (mtpt) cc_final: 0.5351 (tttt) REVERT: a 131 GLU cc_start: 0.7980 (tt0) cc_final: 0.7691 (tp30) REVERT: a 153 MET cc_start: 0.8465 (mtp) cc_final: 0.8242 (mtt) REVERT: I 52 GLN cc_start: 0.8889 (mm110) cc_final: 0.8521 (mp10) REVERT: I 73 TYR cc_start: 0.7119 (t80) cc_final: 0.6670 (t80) REVERT: S 6 MET cc_start: 0.7328 (mmt) cc_final: 0.6914 (mmp) REVERT: S 34 LYS cc_start: 0.8487 (mmtm) cc_final: 0.8188 (mmtm) outliers start: 92 outliers final: 46 residues processed: 736 average time/residue: 0.4992 time to fit residues: 591.2054 Evaluate side-chains 662 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 606 time to evaluate : 4.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 119 GLN Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 47 PHE Chi-restraints excluded: chain a residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 357 optimal weight: 0.5980 chunk 292 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 464 optimal weight: 10.0000 chunk 383 optimal weight: 10.0000 chunk 426 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 345 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN B 479 HIS A 147 GLN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN G 64 HIS D 73 HIS D 121 ASN M 42 GLN Q 3 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN Y 37 GLN Y 64 GLN I 52 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 37506 Z= 0.335 Angle : 0.610 8.778 50766 Z= 0.317 Chirality : 0.044 0.240 5918 Planarity : 0.005 0.050 6547 Dihedral : 7.909 117.650 5387 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.90 % Allowed : 14.35 % Favored : 82.76 % 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: -0.34 (0.12), residues: 4805 helix: 0.22 (0.10), residues: 2584 sheet: -0.53 (0.20), residues: 544 loop : -0.61 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 39 HIS 0.006 0.001 HIS G 64 PHE 0.025 0.002 PHE Y 14 TYR 0.014 0.001 TYR C 236 ARG 0.009 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 610 time to evaluate : 5.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 119 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: W 156 ASP cc_start: 0.8017 (p0) cc_final: 0.7266 (p0) REVERT: C 161 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8830 (mtt180) REVERT: C 236 TYR cc_start: 0.9394 (OUTLIER) cc_final: 0.8553 (t80) REVERT: C 386 MET cc_start: 0.8946 (mmm) cc_final: 0.8586 (mmm) REVERT: C 402 GLU cc_start: 0.8149 (tp30) cc_final: 0.7777 (tp30) REVERT: B 402 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 49 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: A 52 MET cc_start: 0.9045 (mtp) cc_final: 0.8826 (mtm) REVERT: A 86 MET cc_start: 0.8559 (mtt) cc_final: 0.8317 (mtt) REVERT: A 343 THR cc_start: 0.9628 (OUTLIER) cc_final: 0.9285 (p) REVERT: A 484 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7657 (tm-30) REVERT: X 17 PHE cc_start: 0.8030 (m-10) cc_final: 0.7830 (m-80) REVERT: X 49 ARG cc_start: 0.8690 (ptp-110) cc_final: 0.8479 (ptp-170) REVERT: X 104 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8884 (pp30) REVERT: X 112 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: X 150 ASP cc_start: 0.8854 (m-30) cc_final: 0.8541 (p0) REVERT: H 87 GLN cc_start: 0.7783 (tp40) cc_final: 0.7486 (tp-100) REVERT: H 111 ASP cc_start: 0.8738 (t0) cc_final: 0.8339 (t0) REVERT: G 168 TYR cc_start: 0.9042 (m-80) cc_final: 0.8535 (m-80) REVERT: G 201 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7041 (mppt) REVERT: E 366 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7794 (mmm160) REVERT: E 371 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8464 (ttpp) REVERT: D 381 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8081 (mm-30) REVERT: J 17 MET cc_start: 0.8345 (mtm) cc_final: 0.7637 (mmm) REVERT: J 42 GLN cc_start: 0.8473 (mt0) cc_final: 0.8139 (mp10) REVERT: J 52 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8388 (mm-40) REVERT: J 57 MET cc_start: 0.8818 (tmm) cc_final: 0.8536 (tmm) REVERT: L 17 MET cc_start: 0.8175 (mpp) cc_final: 0.7921 (mmp) REVERT: L 37 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8216 (mt-10) REVERT: L 41 ARG cc_start: 0.9065 (ttm110) cc_final: 0.8499 (ttm-80) REVERT: L 57 MET cc_start: 0.9139 (tmm) cc_final: 0.8708 (tmm) REVERT: L 61 ASP cc_start: 0.8577 (m-30) cc_final: 0.7897 (m-30) REVERT: M 46 ILE cc_start: 0.9143 (mt) cc_final: 0.8860 (mt) REVERT: M 63 ILE cc_start: 0.8960 (mt) cc_final: 0.8698 (mt) REVERT: O 31 LEU cc_start: 0.8665 (tp) cc_final: 0.8424 (mt) REVERT: O 42 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7551 (mp10) REVERT: O 57 MET cc_start: 0.8517 (tmm) cc_final: 0.8132 (ppp) REVERT: P 41 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7625 (ttm-80) REVERT: P 42 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7537 (mp10) REVERT: P 50 ARG cc_start: 0.8117 (ptt180) cc_final: 0.7482 (ttp-110) REVERT: P 54 PHE cc_start: 0.8735 (m-80) cc_final: 0.8214 (m-80) REVERT: Q 50 ARG cc_start: 0.9190 (ttm-80) cc_final: 0.8964 (mtp85) REVERT: Q 57 MET cc_start: 0.8245 (tmm) cc_final: 0.7995 (tmm) REVERT: R 6 MET cc_start: 0.7381 (mmt) cc_final: 0.6895 (mtm) REVERT: R 11 MET cc_start: 0.8714 (tpp) cc_final: 0.8430 (tpp) REVERT: R 55 ILE cc_start: 0.8483 (mm) cc_final: 0.8254 (mm) REVERT: R 57 MET cc_start: 0.8677 (ttp) cc_final: 0.8010 (tmm) REVERT: Y 83 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7766 (ttp80) REVERT: Y 84 SER cc_start: 0.9386 (OUTLIER) cc_final: 0.9119 (t) REVERT: Y 96 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8329 (tm-30) REVERT: a 6 MET cc_start: 0.5142 (mmt) cc_final: 0.4529 (ptt) REVERT: a 54 LEU cc_start: 0.7506 (mp) cc_final: 0.6927 (tt) REVERT: a 56 PHE cc_start: 0.7132 (t80) cc_final: 0.6873 (t80) REVERT: a 66 LYS cc_start: 0.5748 (mtpt) cc_final: 0.5437 (tttt) REVERT: a 131 GLU cc_start: 0.7971 (tt0) cc_final: 0.7682 (tp30) REVERT: a 153 MET cc_start: 0.8449 (mtp) cc_final: 0.8246 (mtt) REVERT: I 42 GLN cc_start: 0.6877 (mp10) cc_final: 0.6414 (mp10) REVERT: I 73 TYR cc_start: 0.7046 (t80) cc_final: 0.6719 (t80) REVERT: S 6 MET cc_start: 0.7324 (mmt) cc_final: 0.6789 (mmp) REVERT: S 7 ASP cc_start: 0.6514 (OUTLIER) cc_final: 0.5790 (m-30) REVERT: S 16 MET cc_start: 0.8898 (mtp) cc_final: 0.8145 (mmt) REVERT: S 34 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8209 (mmtm) REVERT: S 57 MET cc_start: 0.8669 (tmm) cc_final: 0.8327 (tmm) REVERT: S 61 ASP cc_start: 0.8110 (p0) cc_final: 0.7671 (p0) outliers start: 111 outliers final: 67 residues processed: 683 average time/residue: 0.5104 time to fit residues: 562.8143 Evaluate side-chains 659 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 583 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 119 GLN Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 112 GLU Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain S residue 7 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 205 optimal weight: 0.5980 chunk 288 optimal weight: 5.9990 chunk 431 optimal weight: 6.9990 chunk 457 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 409 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN Q 3 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN Y 64 GLN ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37506 Z= 0.251 Angle : 0.568 8.007 50766 Z= 0.294 Chirality : 0.042 0.221 5918 Planarity : 0.004 0.050 6547 Dihedral : 7.529 119.458 5375 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.92 % Allowed : 15.44 % Favored : 81.64 % 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: -0.08 (0.12), residues: 4805 helix: 0.45 (0.10), residues: 2582 sheet: -0.40 (0.22), residues: 522 loop : -0.52 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 39 HIS 0.008 0.001 HIS a 14 PHE 0.028 0.001 PHE Y 14 TYR 0.014 0.001 TYR A 236 ARG 0.008 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 603 time to evaluate : 4.215 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: W 156 ASP cc_start: 0.7875 (p0) cc_final: 0.7143 (p0) REVERT: C 236 TYR cc_start: 0.9373 (OUTLIER) cc_final: 0.8548 (t80) REVERT: C 386 MET cc_start: 0.8937 (mmm) cc_final: 0.8597 (mmm) REVERT: C 402 GLU cc_start: 0.8197 (tp30) cc_final: 0.7813 (tp30) REVERT: B 402 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 49 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: A 52 MET cc_start: 0.9016 (mtp) cc_final: 0.8803 (mtm) REVERT: A 86 MET cc_start: 0.8542 (mtt) cc_final: 0.8291 (mtt) REVERT: A 343 THR cc_start: 0.9621 (OUTLIER) cc_final: 0.9312 (p) REVERT: A 484 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7623 (tm-30) REVERT: X 17 PHE cc_start: 0.8014 (m-10) cc_final: 0.7742 (m-10) REVERT: X 49 ARG cc_start: 0.8664 (ptp-110) cc_final: 0.8461 (ptp-170) REVERT: X 104 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8908 (pp30) REVERT: X 112 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8073 (tp30) REVERT: X 150 ASP cc_start: 0.8841 (m-30) cc_final: 0.8531 (p0) REVERT: H 111 ASP cc_start: 0.8742 (t0) cc_final: 0.8365 (t0) REVERT: G 157 GLN cc_start: 0.8427 (tt0) cc_final: 0.8046 (tt0) REVERT: G 168 TYR cc_start: 0.9019 (m-80) cc_final: 0.8552 (m-80) REVERT: G 201 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7036 (mppt) REVERT: F 385 GLU cc_start: 0.8069 (pm20) cc_final: 0.7753 (pm20) REVERT: E 366 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7709 (mmm160) REVERT: E 371 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8352 (ttpp) REVERT: D 381 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7995 (mm-30) REVERT: J 17 MET cc_start: 0.8344 (mtm) cc_final: 0.7729 (mmm) REVERT: J 42 GLN cc_start: 0.8478 (mt0) cc_final: 0.8164 (mp10) REVERT: J 57 MET cc_start: 0.8824 (tmm) cc_final: 0.8466 (tmm) REVERT: J 65 MET cc_start: 0.8763 (mmm) cc_final: 0.8532 (mmm) REVERT: L 17 MET cc_start: 0.8315 (mpp) cc_final: 0.7919 (mmp) REVERT: L 37 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8206 (mt-10) REVERT: L 57 MET cc_start: 0.9161 (tmm) cc_final: 0.8806 (tmm) REVERT: L 61 ASP cc_start: 0.8540 (m-30) cc_final: 0.7820 (m-30) REVERT: L 65 MET cc_start: 0.8618 (mmm) cc_final: 0.8368 (mmp) REVERT: M 46 ILE cc_start: 0.9133 (mt) cc_final: 0.8836 (mt) REVERT: N 42 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7134 (mp10) REVERT: N 75 MET cc_start: 0.7813 (tmm) cc_final: 0.7569 (tmm) REVERT: N 76 PHE cc_start: 0.8616 (m-10) cc_final: 0.8147 (m-10) REVERT: O 42 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7560 (mp10) REVERT: O 50 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8288 (ttm170) REVERT: O 52 GLN cc_start: 0.8664 (mm110) cc_final: 0.8283 (mp10) REVERT: P 31 LEU cc_start: 0.8178 (tp) cc_final: 0.7750 (tp) REVERT: P 42 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7766 (mp10) REVERT: P 50 ARG cc_start: 0.8114 (ptt180) cc_final: 0.7548 (ptp90) REVERT: P 54 PHE cc_start: 0.8721 (m-80) cc_final: 0.8319 (m-80) REVERT: Q 57 MET cc_start: 0.8252 (tmm) cc_final: 0.7974 (tmm) REVERT: Q 75 MET cc_start: 0.8804 (mmm) cc_final: 0.8380 (mmm) REVERT: R 6 MET cc_start: 0.7353 (mmt) cc_final: 0.6860 (mtm) REVERT: R 11 MET cc_start: 0.8645 (tpp) cc_final: 0.8375 (tpp) REVERT: R 55 ILE cc_start: 0.8459 (mm) cc_final: 0.8232 (mm) REVERT: R 57 MET cc_start: 0.8658 (ttp) cc_final: 0.8017 (tmm) REVERT: Y 1 MET cc_start: 0.4417 (ptt) cc_final: 0.4113 (ptp) REVERT: Y 83 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7743 (ttp80) REVERT: Y 84 SER cc_start: 0.9399 (OUTLIER) cc_final: 0.9131 (t) REVERT: Y 96 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8279 (tm-30) REVERT: a 6 MET cc_start: 0.5235 (mmt) cc_final: 0.4616 (ptt) REVERT: a 54 LEU cc_start: 0.7505 (mp) cc_final: 0.6851 (tt) REVERT: a 56 PHE cc_start: 0.7032 (t80) cc_final: 0.6723 (t80) REVERT: a 66 LYS cc_start: 0.5633 (mtpt) cc_final: 0.5413 (tttt) REVERT: a 131 GLU cc_start: 0.7939 (tt0) cc_final: 0.7663 (tp30) REVERT: a 153 MET cc_start: 0.8440 (mtp) cc_final: 0.8227 (mtt) REVERT: a 215 MET cc_start: 0.8896 (mmm) cc_final: 0.8563 (mmm) REVERT: a 241 TRP cc_start: 0.7693 (t-100) cc_final: 0.6973 (t-100) REVERT: I 42 GLN cc_start: 0.6990 (mp10) cc_final: 0.6302 (mp10) REVERT: I 73 TYR cc_start: 0.6999 (t80) cc_final: 0.6633 (t80) REVERT: S 6 MET cc_start: 0.7203 (mmt) cc_final: 0.6658 (mmp) REVERT: S 7 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.5627 (m-30) REVERT: S 16 MET cc_start: 0.8824 (mtp) cc_final: 0.8167 (mmt) REVERT: S 34 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8305 (mmtm) REVERT: S 42 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7954 (mm-40) REVERT: S 57 MET cc_start: 0.8702 (tmm) cc_final: 0.8354 (tmm) outliers start: 112 outliers final: 69 residues processed: 681 average time/residue: 0.4928 time to fit residues: 544.6871 Evaluate side-chains 657 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 581 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain X residue 14 PHE Chi-restraints excluded: chain X residue 112 GLU Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 119 GLU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain S residue 7 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 0.0470 chunk 259 optimal weight: 3.9990 chunk 6 optimal weight: 0.0070 chunk 340 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 390 optimal weight: 20.0000 chunk 316 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 410 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 119 GLN B 26 HIS B 399 GLN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37506 Z= 0.203 Angle : 0.556 9.949 50766 Z= 0.283 Chirality : 0.042 0.171 5918 Planarity : 0.004 0.048 6547 Dihedral : 7.177 120.321 5369 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.45 % Allowed : 16.30 % Favored : 81.25 % 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: 0.13 (0.12), residues: 4805 helix: 0.65 (0.10), residues: 2586 sheet: -0.36 (0.22), residues: 529 loop : -0.46 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 39 HIS 0.007 0.001 HIS a 14 PHE 0.028 0.001 PHE Y 14 TYR 0.014 0.001 TYR A 236 ARG 0.009 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 599 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.7856 (p0) cc_final: 0.7108 (p0) REVERT: C 236 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.8510 (t80) REVERT: C 386 MET cc_start: 0.8922 (mmm) cc_final: 0.8614 (mmm) REVERT: C 402 GLU cc_start: 0.8182 (tp30) cc_final: 0.7896 (tp30) REVERT: B 402 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7610 (tm-30) REVERT: A 49 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: A 52 MET cc_start: 0.9025 (mtp) cc_final: 0.8808 (mtm) REVERT: A 86 MET cc_start: 0.8539 (mtt) cc_final: 0.8282 (mtt) REVERT: A 343 THR cc_start: 0.9596 (OUTLIER) cc_final: 0.9328 (p) REVERT: X 17 PHE cc_start: 0.7981 (m-10) cc_final: 0.7708 (m-10) REVERT: X 49 ARG cc_start: 0.8684 (ptp-110) cc_final: 0.8473 (ptp-170) REVERT: X 104 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8886 (pp30) REVERT: H 22 LYS cc_start: 0.8492 (ptpp) cc_final: 0.8162 (ptmm) REVERT: H 111 ASP cc_start: 0.8747 (t0) cc_final: 0.8384 (t0) REVERT: G 157 GLN cc_start: 0.8426 (tt0) cc_final: 0.8045 (tt0) REVERT: G 168 TYR cc_start: 0.8973 (m-80) cc_final: 0.8539 (m-80) REVERT: G 201 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.7009 (mppt) REVERT: F 115 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8441 (p) REVERT: F 159 MET cc_start: 0.9025 (ttp) cc_final: 0.8810 (ttm) REVERT: F 385 GLU cc_start: 0.8055 (pm20) cc_final: 0.7745 (pm20) REVERT: F 424 ILE cc_start: 0.8572 (pt) cc_final: 0.8350 (mt) REVERT: E 366 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7595 (mmm160) REVERT: E 371 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8255 (ttpp) REVERT: D 381 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7995 (mm-30) REVERT: J 17 MET cc_start: 0.8367 (mtm) cc_final: 0.7923 (mmt) REVERT: J 42 GLN cc_start: 0.8468 (mt0) cc_final: 0.8242 (mp10) REVERT: J 57 MET cc_start: 0.8786 (tmm) cc_final: 0.8544 (tmm) REVERT: J 65 MET cc_start: 0.8712 (mmm) cc_final: 0.8484 (mmm) REVERT: L 17 MET cc_start: 0.8387 (mpp) cc_final: 0.8032 (mmp) REVERT: L 37 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8210 (mt-10) REVERT: L 57 MET cc_start: 0.9143 (tmm) cc_final: 0.8852 (tmm) REVERT: L 61 ASP cc_start: 0.8566 (m-30) cc_final: 0.7871 (m-30) REVERT: L 65 MET cc_start: 0.8582 (mmm) cc_final: 0.8298 (mmp) REVERT: M 46 ILE cc_start: 0.9100 (mt) cc_final: 0.8812 (mt) REVERT: N 16 MET cc_start: 0.7369 (mmm) cc_final: 0.6824 (tpp) REVERT: N 17 MET cc_start: 0.7865 (ttt) cc_final: 0.7361 (tmm) REVERT: N 42 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7166 (mt0) REVERT: N 76 PHE cc_start: 0.8599 (m-10) cc_final: 0.8233 (m-10) REVERT: O 31 LEU cc_start: 0.8684 (mt) cc_final: 0.8374 (mt) REVERT: O 42 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7647 (mp10) REVERT: O 52 GLN cc_start: 0.8553 (mm110) cc_final: 0.8286 (mp10) REVERT: O 57 MET cc_start: 0.8402 (tmm) cc_final: 0.8105 (ptm) REVERT: P 31 LEU cc_start: 0.8177 (tp) cc_final: 0.7822 (tp) REVERT: P 42 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7831 (mp10) REVERT: P 50 ARG cc_start: 0.7911 (ptt180) cc_final: 0.7404 (ptp90) REVERT: P 54 PHE cc_start: 0.8665 (m-80) cc_final: 0.8325 (m-80) REVERT: P 73 TYR cc_start: 0.7181 (t80) cc_final: 0.6276 (t80) REVERT: Q 52 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8610 (mp10) REVERT: Q 57 MET cc_start: 0.8261 (tmm) cc_final: 0.8007 (tmm) REVERT: R 6 MET cc_start: 0.7351 (mmt) cc_final: 0.6852 (mtm) REVERT: R 11 MET cc_start: 0.8607 (tpp) cc_final: 0.8347 (tpp) REVERT: R 57 MET cc_start: 0.8604 (ttp) cc_final: 0.7965 (tmm) REVERT: Y 1 MET cc_start: 0.4447 (ptt) cc_final: 0.4222 (ptp) REVERT: Y 49 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7689 (ptp-170) REVERT: Y 83 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7767 (ttp80) REVERT: Y 84 SER cc_start: 0.9408 (OUTLIER) cc_final: 0.9065 (p) REVERT: a 6 MET cc_start: 0.5208 (mmt) cc_final: 0.4662 (ptt) REVERT: a 54 LEU cc_start: 0.7482 (mp) cc_final: 0.6835 (tt) REVERT: a 56 PHE cc_start: 0.6873 (t80) cc_final: 0.6532 (t80) REVERT: a 153 MET cc_start: 0.8469 (mtp) cc_final: 0.8230 (mtt) REVERT: a 203 LYS cc_start: 0.8616 (mttp) cc_final: 0.8317 (mmtm) REVERT: a 215 MET cc_start: 0.8866 (mmm) cc_final: 0.8607 (mmm) REVERT: I 42 GLN cc_start: 0.6945 (mp10) cc_final: 0.6316 (mp10) REVERT: I 52 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8440 (mp10) REVERT: I 73 TYR cc_start: 0.7007 (t80) cc_final: 0.6642 (t80) REVERT: S 6 MET cc_start: 0.7178 (mmt) cc_final: 0.6563 (mmp) REVERT: S 7 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.5568 (m-30) REVERT: S 17 MET cc_start: 0.8596 (mmm) cc_final: 0.8377 (mmp) REVERT: S 34 LYS cc_start: 0.8537 (mmtm) cc_final: 0.7937 (mmmt) REVERT: S 41 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8153 (ttt90) REVERT: S 57 MET cc_start: 0.8731 (tmm) cc_final: 0.8388 (tmm) outliers start: 94 outliers final: 64 residues processed: 666 average time/residue: 0.4980 time to fit residues: 537.0413 Evaluate side-chains 644 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 573 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 119 GLU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 175 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain S residue 7 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 2.9990 chunk 411 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 268 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 457 optimal weight: 0.9980 chunk 379 optimal weight: 0.9990 chunk 211 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37506 Z= 0.167 Angle : 0.543 11.027 50766 Z= 0.275 Chirality : 0.041 0.352 5918 Planarity : 0.004 0.047 6547 Dihedral : 6.749 119.878 5362 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.16 % Allowed : 17.16 % Favored : 80.67 % 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: 0.34 (0.12), residues: 4805 helix: 0.84 (0.10), residues: 2591 sheet: -0.26 (0.22), residues: 529 loop : -0.42 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 39 HIS 0.007 0.001 HIS a 14 PHE 0.018 0.001 PHE Q 35 TYR 0.011 0.001 TYR C 236 ARG 0.010 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 611 time to evaluate : 4.345 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: W 22 GLN cc_start: 0.9000 (mp10) cc_final: 0.8540 (mp10) REVERT: W 156 ASP cc_start: 0.7859 (p0) cc_final: 0.7111 (p0) REVERT: C 236 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8487 (t80) REVERT: C 386 MET cc_start: 0.8936 (mmm) cc_final: 0.8642 (mmm) REVERT: C 402 GLU cc_start: 0.8188 (tp30) cc_final: 0.7903 (tp30) REVERT: B 402 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 483 MET cc_start: 0.8115 (mmp) cc_final: 0.7710 (mmp) REVERT: A 49 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: A 52 MET cc_start: 0.9022 (mtp) cc_final: 0.8790 (mtm) REVERT: A 86 MET cc_start: 0.8538 (mtt) cc_final: 0.8302 (mtt) REVERT: A 343 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9310 (p) REVERT: A 463 LYS cc_start: 0.5898 (tttt) cc_final: 0.5415 (tttp) REVERT: A 484 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 488 GLN cc_start: 0.8280 (mt0) cc_final: 0.8019 (mt0) REVERT: X 17 PHE cc_start: 0.8029 (m-10) cc_final: 0.7789 (m-10) REVERT: X 49 ARG cc_start: 0.8677 (ptp-110) cc_final: 0.8461 (ptp-170) REVERT: X 104 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8802 (pp30) REVERT: H 87 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7424 (tp-100) REVERT: H 111 ASP cc_start: 0.8725 (t0) cc_final: 0.8413 (t0) REVERT: G 102 MET cc_start: 0.8708 (mtp) cc_final: 0.8499 (mtp) REVERT: G 157 GLN cc_start: 0.8431 (tt0) cc_final: 0.8103 (tt0) REVERT: G 168 TYR cc_start: 0.8931 (m-80) cc_final: 0.8640 (m-80) REVERT: G 201 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6826 (mppt) REVERT: F 159 MET cc_start: 0.8982 (ttp) cc_final: 0.8781 (ttm) REVERT: F 342 ARG cc_start: 0.8366 (tpp-160) cc_final: 0.8164 (tpp-160) REVERT: E 366 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7712 (mmm160) REVERT: E 371 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8229 (ttpp) REVERT: D 381 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7998 (mm-30) REVERT: D 445 MET cc_start: 0.9235 (mmp) cc_final: 0.9009 (mmt) REVERT: J 19 LEU cc_start: 0.8413 (mt) cc_final: 0.8206 (tp) REVERT: J 57 MET cc_start: 0.8749 (tmm) cc_final: 0.8432 (tmm) REVERT: J 65 MET cc_start: 0.8805 (mmm) cc_final: 0.8574 (mmm) REVERT: L 17 MET cc_start: 0.8410 (mpp) cc_final: 0.8080 (mmp) REVERT: L 37 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8035 (mt-10) REVERT: L 57 MET cc_start: 0.9107 (tmm) cc_final: 0.8879 (tmm) REVERT: L 65 MET cc_start: 0.8618 (mmm) cc_final: 0.8358 (mmm) REVERT: L 73 TYR cc_start: 0.7969 (t80) cc_final: 0.7751 (t80) REVERT: M 46 ILE cc_start: 0.9068 (mt) cc_final: 0.8748 (mt) REVERT: N 17 MET cc_start: 0.7842 (ttt) cc_final: 0.7505 (tmm) REVERT: N 42 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7122 (mt0) REVERT: N 75 MET cc_start: 0.8401 (mmm) cc_final: 0.8153 (mmp) REVERT: N 76 PHE cc_start: 0.8093 (m-10) cc_final: 0.7833 (m-10) REVERT: O 31 LEU cc_start: 0.8724 (mt) cc_final: 0.8426 (mp) REVERT: O 42 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7616 (mp10) REVERT: O 52 GLN cc_start: 0.8539 (mm110) cc_final: 0.8188 (mp10) REVERT: O 61 ASP cc_start: 0.7599 (p0) cc_final: 0.7379 (p0) REVERT: P 31 LEU cc_start: 0.8138 (tp) cc_final: 0.7785 (tp) REVERT: P 41 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7526 (ttm-80) REVERT: P 42 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7725 (mp10) REVERT: P 50 ARG cc_start: 0.7812 (ptt180) cc_final: 0.7444 (ptp-110) REVERT: P 54 PHE cc_start: 0.8675 (m-80) cc_final: 0.8378 (m-80) REVERT: Q 57 MET cc_start: 0.8383 (tmm) cc_final: 0.8072 (tmm) REVERT: Q 75 MET cc_start: 0.8815 (mmm) cc_final: 0.8396 (mmm) REVERT: R 6 MET cc_start: 0.7327 (mmt) cc_final: 0.6844 (mtm) REVERT: R 11 MET cc_start: 0.8579 (tpp) cc_final: 0.8334 (tpp) REVERT: R 57 MET cc_start: 0.8564 (ttp) cc_final: 0.7894 (tmm) REVERT: Y 1 MET cc_start: 0.4616 (ptt) cc_final: 0.4370 (ptp) REVERT: Y 22 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5120 (mmp) REVERT: Y 49 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7678 (ptp-170) REVERT: Y 64 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8577 (mm-40) REVERT: Y 83 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7768 (ttp80) REVERT: Y 84 SER cc_start: 0.9379 (OUTLIER) cc_final: 0.9050 (p) REVERT: a 6 MET cc_start: 0.5171 (mmt) cc_final: 0.4671 (ptt) REVERT: a 54 LEU cc_start: 0.7555 (mp) cc_final: 0.6915 (tt) REVERT: a 56 PHE cc_start: 0.6773 (t80) cc_final: 0.6420 (t80) REVERT: a 215 MET cc_start: 0.8856 (mmm) cc_final: 0.8512 (mmm) REVERT: I 42 GLN cc_start: 0.6935 (mp10) cc_final: 0.6304 (mp10) REVERT: I 52 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8313 (mp10) REVERT: I 73 TYR cc_start: 0.7007 (t80) cc_final: 0.6600 (t80) REVERT: S 6 MET cc_start: 0.7176 (mmt) cc_final: 0.6670 (mmp) REVERT: S 16 MET cc_start: 0.8764 (mtp) cc_final: 0.8184 (mmt) REVERT: S 34 LYS cc_start: 0.8562 (mmtm) cc_final: 0.7725 (mmmt) REVERT: S 37 GLU cc_start: 0.8252 (tt0) cc_final: 0.7276 (tt0) REVERT: S 57 MET cc_start: 0.8749 (tmm) cc_final: 0.8352 (tmm) outliers start: 83 outliers final: 53 residues processed: 666 average time/residue: 0.5014 time to fit residues: 537.1088 Evaluate side-chains 643 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 584 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 119 GLU Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 175 THR Chi-restraints excluded: chain I residue 55 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 385 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 455 optimal weight: 4.9990 chunk 285 optimal weight: 0.2980 chunk 277 optimal weight: 5.9990 chunk 210 optimal weight: 0.4980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN a 184 ASN ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 37506 Z= 0.203 Angle : 0.552 11.078 50766 Z= 0.279 Chirality : 0.041 0.250 5918 Planarity : 0.004 0.048 6547 Dihedral : 6.629 123.437 5358 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.32 % Allowed : 17.37 % Favored : 80.31 % 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: 4805 helix: 0.92 (0.10), residues: 2592 sheet: -0.20 (0.22), residues: 520 loop : -0.36 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP a 39 HIS 0.006 0.001 HIS a 14 PHE 0.027 0.001 PHE N 53 TYR 0.018 0.001 TYR a 216 ARG 0.009 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 599 time to evaluate : 4.422 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: W 22 GLN cc_start: 0.9004 (mp10) cc_final: 0.8547 (mp10) REVERT: W 67 GLN cc_start: 0.8688 (mt0) cc_final: 0.8462 (mt0) REVERT: W 156 ASP cc_start: 0.7855 (p0) cc_final: 0.7098 (p0) REVERT: C 236 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.8527 (t80) REVERT: C 386 MET cc_start: 0.8949 (mmm) cc_final: 0.8678 (mmm) REVERT: C 402 GLU cc_start: 0.8209 (tp30) cc_final: 0.7924 (tp30) REVERT: B 402 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 49 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: A 86 MET cc_start: 0.8530 (mtt) cc_final: 0.8282 (mtt) REVERT: A 236 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8618 (t80) REVERT: A 343 THR cc_start: 0.9598 (OUTLIER) cc_final: 0.9306 (p) REVERT: A 463 LYS cc_start: 0.5894 (tttt) cc_final: 0.5371 (tttp) REVERT: A 484 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7515 (tm-30) REVERT: X 17 PHE cc_start: 0.7977 (m-10) cc_final: 0.7715 (m-10) REVERT: X 49 ARG cc_start: 0.8657 (ptp-110) cc_final: 0.8433 (ptp-170) REVERT: X 104 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8784 (pp30) REVERT: H 111 ASP cc_start: 0.8757 (t0) cc_final: 0.8437 (t0) REVERT: G 157 GLN cc_start: 0.8450 (tt0) cc_final: 0.8115 (tt0) REVERT: G 168 TYR cc_start: 0.8925 (m-80) cc_final: 0.8632 (m-80) REVERT: F 115 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8408 (p) REVERT: F 342 ARG cc_start: 0.8412 (tpp-160) cc_final: 0.8182 (tpp-160) REVERT: E 193 MET cc_start: 0.9078 (mtp) cc_final: 0.8841 (mtm) REVERT: E 366 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7618 (mmm160) REVERT: E 371 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8229 (ttpp) REVERT: D 381 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8110 (mm-30) REVERT: D 445 MET cc_start: 0.9234 (mmt) cc_final: 0.9027 (mmt) REVERT: J 57 MET cc_start: 0.8708 (tmm) cc_final: 0.8247 (tmm) REVERT: L 65 MET cc_start: 0.8599 (mmm) cc_final: 0.8304 (mmm) REVERT: L 73 TYR cc_start: 0.7979 (t80) cc_final: 0.7721 (t80) REVERT: M 46 ILE cc_start: 0.9084 (mt) cc_final: 0.8780 (mt) REVERT: N 17 MET cc_start: 0.7990 (ttt) cc_final: 0.7230 (tmm) REVERT: N 42 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7183 (mt0) REVERT: N 75 MET cc_start: 0.8504 (mmm) cc_final: 0.8128 (mmp) REVERT: N 76 PHE cc_start: 0.8142 (m-10) cc_final: 0.7878 (m-10) REVERT: O 16 MET cc_start: 0.6853 (mmm) cc_final: 0.6413 (mmm) REVERT: O 31 LEU cc_start: 0.8724 (mt) cc_final: 0.8443 (mp) REVERT: O 42 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7635 (mp10) REVERT: O 52 GLN cc_start: 0.8525 (mm110) cc_final: 0.8194 (mp10) REVERT: O 57 MET cc_start: 0.7645 (ptm) cc_final: 0.7388 (ptm) REVERT: P 16 MET cc_start: 0.7573 (mtp) cc_final: 0.7216 (mpp) REVERT: P 31 LEU cc_start: 0.8168 (tp) cc_final: 0.7842 (tp) REVERT: P 42 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7724 (mp10) REVERT: P 50 ARG cc_start: 0.7933 (ptt180) cc_final: 0.7538 (ptp-110) REVERT: P 54 PHE cc_start: 0.8665 (m-10) cc_final: 0.8142 (m-80) REVERT: P 70 LEU cc_start: 0.7891 (tt) cc_final: 0.7656 (tp) REVERT: Q 57 MET cc_start: 0.8416 (tmm) cc_final: 0.8093 (tmm) REVERT: Q 75 MET cc_start: 0.8819 (mmm) cc_final: 0.8386 (mmm) REVERT: R 6 MET cc_start: 0.7335 (mmt) cc_final: 0.6842 (mtm) REVERT: R 11 MET cc_start: 0.8593 (tpp) cc_final: 0.8355 (tpp) REVERT: R 57 MET cc_start: 0.8526 (ttp) cc_final: 0.7854 (tmm) REVERT: Y 1 MET cc_start: 0.4568 (ptt) cc_final: 0.4334 (ptp) REVERT: Y 22 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5126 (mmp) REVERT: Y 83 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7781 (ttp80) REVERT: Y 84 SER cc_start: 0.9378 (OUTLIER) cc_final: 0.9052 (p) REVERT: a 6 MET cc_start: 0.5192 (mmt) cc_final: 0.4694 (ptt) REVERT: a 54 LEU cc_start: 0.7535 (mp) cc_final: 0.6890 (tt) REVERT: a 56 PHE cc_start: 0.6824 (t80) cc_final: 0.6439 (t80) REVERT: a 93 MET cc_start: 0.8393 (mpp) cc_final: 0.8130 (mpp) REVERT: a 181 GLN cc_start: 0.8165 (pm20) cc_final: 0.7812 (pm20) REVERT: a 215 MET cc_start: 0.8805 (mmm) cc_final: 0.8492 (mmm) REVERT: a 252 GLN cc_start: 0.7748 (mt0) cc_final: 0.7523 (mt0) REVERT: I 11 MET cc_start: 0.8657 (tpt) cc_final: 0.8379 (tpp) REVERT: I 34 LYS cc_start: 0.9228 (mtmm) cc_final: 0.8532 (mtmm) REVERT: I 42 GLN cc_start: 0.6958 (mp10) cc_final: 0.6217 (mp10) REVERT: I 52 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8219 (mp10) REVERT: I 73 TYR cc_start: 0.7113 (t80) cc_final: 0.6624 (t80) REVERT: S 6 MET cc_start: 0.7128 (mmt) cc_final: 0.6630 (mmp) REVERT: S 34 LYS cc_start: 0.8542 (mmtm) cc_final: 0.7686 (mmmt) REVERT: S 37 GLU cc_start: 0.8261 (tt0) cc_final: 0.7245 (tt0) REVERT: S 57 MET cc_start: 0.8754 (tmm) cc_final: 0.8337 (tmm) outliers start: 89 outliers final: 61 residues processed: 661 average time/residue: 0.5265 time to fit residues: 561.5695 Evaluate side-chains 646 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 578 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 175 THR Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain I residue 22 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 225 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 358 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 37506 Z= 0.161 Angle : 0.558 9.523 50766 Z= 0.279 Chirality : 0.041 0.228 5918 Planarity : 0.004 0.050 6547 Dihedral : 6.315 121.906 5351 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.93 % Allowed : 17.92 % Favored : 80.15 % 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: 0.56 (0.12), residues: 4805 helix: 0.97 (0.10), residues: 2633 sheet: -0.06 (0.22), residues: 527 loop : -0.29 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 39 HIS 0.007 0.001 HIS a 14 PHE 0.031 0.001 PHE N 53 TYR 0.011 0.001 TYR B 492 ARG 0.011 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 605 time to evaluate : 4.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.7845 (p0) cc_final: 0.7091 (p0) REVERT: C 236 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.8406 (t80) REVERT: C 402 GLU cc_start: 0.8199 (tp30) cc_final: 0.7944 (tp30) REVERT: B 402 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 483 MET cc_start: 0.8216 (mmp) cc_final: 0.7725 (mmp) REVERT: A 49 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: A 52 MET cc_start: 0.9115 (mtm) cc_final: 0.8893 (mtp) REVERT: A 86 MET cc_start: 0.8524 (mtt) cc_final: 0.8264 (mtt) REVERT: A 236 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.8412 (t80) REVERT: A 343 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9324 (p) REVERT: A 463 LYS cc_start: 0.5769 (tttt) cc_final: 0.5191 (tttp) REVERT: X 49 ARG cc_start: 0.8664 (ptp-110) cc_final: 0.8447 (ptp-170) REVERT: X 104 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8710 (pp30) REVERT: H 58 HIS cc_start: 0.8068 (m-70) cc_final: 0.7845 (m90) REVERT: H 111 ASP cc_start: 0.8733 (t0) cc_final: 0.8427 (t0) REVERT: G 116 MET cc_start: 0.9020 (mmm) cc_final: 0.8731 (mmm) REVERT: G 157 GLN cc_start: 0.8435 (tt0) cc_final: 0.8136 (tt0) REVERT: G 168 TYR cc_start: 0.8886 (m-80) cc_final: 0.8635 (m-80) REVERT: F 236 ASP cc_start: 0.8060 (p0) cc_final: 0.7834 (p0) REVERT: E 193 MET cc_start: 0.9064 (mtp) cc_final: 0.8822 (mtm) REVERT: E 366 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7855 (mmm160) REVERT: E 371 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8201 (ttpp) REVERT: D 381 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8098 (mm-30) REVERT: J 37 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7952 (mt-10) REVERT: J 42 GLN cc_start: 0.8472 (mp10) cc_final: 0.8270 (mp10) REVERT: J 57 MET cc_start: 0.8731 (tmm) cc_final: 0.8199 (tmm) REVERT: L 17 MET cc_start: 0.7740 (mmt) cc_final: 0.7506 (mmm) REVERT: L 61 ASP cc_start: 0.8761 (m-30) cc_final: 0.8197 (p0) REVERT: L 65 MET cc_start: 0.8589 (mmm) cc_final: 0.8235 (mmm) REVERT: M 46 ILE cc_start: 0.9080 (mt) cc_final: 0.8775 (mt) REVERT: N 17 MET cc_start: 0.8062 (ttt) cc_final: 0.7837 (ttt) REVERT: N 42 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7183 (mt0) REVERT: N 75 MET cc_start: 0.8507 (mmm) cc_final: 0.8165 (mmp) REVERT: O 16 MET cc_start: 0.6857 (mmm) cc_final: 0.6409 (mmm) REVERT: O 42 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7596 (mp10) REVERT: O 52 GLN cc_start: 0.8523 (mm110) cc_final: 0.8178 (mp10) REVERT: P 31 LEU cc_start: 0.8027 (tp) cc_final: 0.7740 (tp) REVERT: P 42 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7822 (mp10) REVERT: P 50 ARG cc_start: 0.7906 (ptt180) cc_final: 0.7578 (ptp-110) REVERT: P 73 TYR cc_start: 0.6740 (t80) cc_final: 0.6022 (t80) REVERT: Q 75 MET cc_start: 0.8807 (mmm) cc_final: 0.8402 (mmm) REVERT: R 6 MET cc_start: 0.7200 (mmt) cc_final: 0.6613 (mtm) REVERT: R 11 MET cc_start: 0.8587 (tpp) cc_final: 0.8350 (tpp) REVERT: R 57 MET cc_start: 0.8494 (ttp) cc_final: 0.8117 (tmm) REVERT: R 64 PRO cc_start: 0.9006 (Cg_exo) cc_final: 0.8780 (Cg_endo) REVERT: Y 22 MET cc_start: 0.5817 (OUTLIER) cc_final: 0.5105 (mmp) REVERT: Y 64 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8570 (mm-40) REVERT: Y 83 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7744 (ttp80) REVERT: Y 84 SER cc_start: 0.9340 (OUTLIER) cc_final: 0.9012 (p) REVERT: a 6 MET cc_start: 0.5055 (mmt) cc_final: 0.4730 (ptt) REVERT: a 54 LEU cc_start: 0.7491 (mp) cc_final: 0.7004 (tt) REVERT: a 56 PHE cc_start: 0.6779 (t80) cc_final: 0.6386 (t80) REVERT: a 93 MET cc_start: 0.8437 (mpp) cc_final: 0.8185 (mpp) REVERT: a 131 GLU cc_start: 0.8038 (tt0) cc_final: 0.7734 (tp30) REVERT: a 215 MET cc_start: 0.8791 (mmm) cc_final: 0.8350 (mmm) REVERT: I 11 MET cc_start: 0.8571 (tpt) cc_final: 0.8340 (tpp) REVERT: I 42 GLN cc_start: 0.6896 (mp10) cc_final: 0.6259 (mp10) REVERT: I 52 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8244 (mp10) REVERT: I 73 TYR cc_start: 0.7144 (t80) cc_final: 0.6613 (t80) REVERT: S 6 MET cc_start: 0.7103 (mmt) cc_final: 0.6629 (mmp) REVERT: S 16 MET cc_start: 0.8798 (mtp) cc_final: 0.8069 (mmt) REVERT: S 17 MET cc_start: 0.8662 (mmm) cc_final: 0.8366 (mmp) REVERT: S 34 LYS cc_start: 0.8563 (mmtm) cc_final: 0.7794 (mmmt) REVERT: S 37 GLU cc_start: 0.8258 (tt0) cc_final: 0.7241 (tt0) REVERT: S 57 MET cc_start: 0.8747 (tmm) cc_final: 0.8322 (tmm) outliers start: 74 outliers final: 56 residues processed: 660 average time/residue: 0.5214 time to fit residues: 553.6153 Evaluate side-chains 641 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 579 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 175 THR Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain I residue 22 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 2.9990 chunk 436 optimal weight: 8.9990 chunk 398 optimal weight: 0.9990 chunk 424 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 333 optimal weight: 0.0670 chunk 130 optimal weight: 0.0980 chunk 383 optimal weight: 0.9990 chunk 401 optimal weight: 1.9990 chunk 423 optimal weight: 5.9990 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN D 121 ASN L 42 GLN Q 3 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN ** a 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37506 Z= 0.154 Angle : 0.553 12.743 50766 Z= 0.277 Chirality : 0.041 0.217 5918 Planarity : 0.004 0.056 6547 Dihedral : 6.060 122.518 5349 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.83 % Allowed : 18.23 % Favored : 79.94 % 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: 0.65 (0.12), residues: 4805 helix: 1.04 (0.10), residues: 2629 sheet: 0.04 (0.22), residues: 527 loop : -0.27 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 39 HIS 0.009 0.001 HIS a 14 PHE 0.022 0.001 PHE Q 35 TYR 0.014 0.001 TYR L 73 ARG 0.010 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 595 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.7837 (p0) cc_final: 0.7087 (p0) REVERT: C 236 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8402 (t80) REVERT: C 402 GLU cc_start: 0.8186 (tp30) cc_final: 0.7945 (tp30) REVERT: C 439 MET cc_start: 0.8834 (mtt) cc_final: 0.8602 (mtt) REVERT: B 402 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7527 (tm-30) REVERT: B 483 MET cc_start: 0.8199 (mmp) cc_final: 0.7714 (mmp) REVERT: A 49 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: A 86 MET cc_start: 0.8531 (mtt) cc_final: 0.8273 (mtt) REVERT: A 236 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8431 (t80) REVERT: A 343 THR cc_start: 0.9581 (OUTLIER) cc_final: 0.9326 (p) REVERT: A 463 LYS cc_start: 0.5573 (tttt) cc_final: 0.5118 (tttp) REVERT: X 17 PHE cc_start: 0.7689 (m-80) cc_final: 0.7183 (m-80) REVERT: X 49 ARG cc_start: 0.8650 (ptp-110) cc_final: 0.8437 (ptp-170) REVERT: X 104 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8863 (pp30) REVERT: H 58 HIS cc_start: 0.8024 (m-70) cc_final: 0.7807 (m90) REVERT: H 72 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6892 (mm-40) REVERT: H 111 ASP cc_start: 0.8725 (t0) cc_final: 0.8438 (t0) REVERT: G 116 MET cc_start: 0.8988 (mmm) cc_final: 0.8778 (mmm) REVERT: G 157 GLN cc_start: 0.8427 (tt0) cc_final: 0.8138 (tt0) REVERT: G 168 TYR cc_start: 0.8835 (m-80) cc_final: 0.8604 (m-80) REVERT: F 236 ASP cc_start: 0.8004 (p0) cc_final: 0.7761 (p0) REVERT: F 385 GLU cc_start: 0.7981 (pm20) cc_final: 0.7682 (pm20) REVERT: F 454 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7840 (tm-30) REVERT: E 193 MET cc_start: 0.9066 (mtp) cc_final: 0.8824 (mtm) REVERT: E 366 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7856 (mmm160) REVERT: E 371 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8205 (ttpp) REVERT: D 381 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8028 (mm-30) REVERT: J 17 MET cc_start: 0.8523 (tpp) cc_final: 0.8312 (mmt) REVERT: J 37 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8151 (mt-10) REVERT: J 41 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.8136 (mtm-85) REVERT: J 42 GLN cc_start: 0.8479 (mp10) cc_final: 0.8251 (mp10) REVERT: J 57 MET cc_start: 0.8724 (tmm) cc_final: 0.8162 (tmm) REVERT: J 75 MET cc_start: 0.9083 (tpp) cc_final: 0.8694 (tpp) REVERT: L 17 MET cc_start: 0.7864 (mmt) cc_final: 0.7581 (mmm) REVERT: L 37 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8046 (mt-10) REVERT: L 61 ASP cc_start: 0.8724 (m-30) cc_final: 0.8210 (p0) REVERT: L 65 MET cc_start: 0.8622 (mmm) cc_final: 0.8303 (mmm) REVERT: M 46 ILE cc_start: 0.9056 (mt) cc_final: 0.8748 (mt) REVERT: M 50 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8270 (ptp90) REVERT: N 17 MET cc_start: 0.8009 (ttt) cc_final: 0.7701 (ttt) REVERT: N 37 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8135 (tm-30) REVERT: N 42 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7176 (mt0) REVERT: N 75 MET cc_start: 0.8559 (mmm) cc_final: 0.8242 (mmp) REVERT: O 16 MET cc_start: 0.6810 (mmm) cc_final: 0.6385 (mmm) REVERT: O 42 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7556 (mp10) REVERT: O 52 GLN cc_start: 0.8488 (mm110) cc_final: 0.8134 (mp10) REVERT: P 31 LEU cc_start: 0.8063 (tp) cc_final: 0.7778 (tp) REVERT: P 42 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7675 (mp10) REVERT: P 50 ARG cc_start: 0.7918 (ptt180) cc_final: 0.7557 (ptp-110) REVERT: P 73 TYR cc_start: 0.6637 (t80) cc_final: 0.5946 (t80) REVERT: Q 28 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7580 (pp) REVERT: Q 52 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8551 (mp10) REVERT: Q 57 MET cc_start: 0.8285 (tmm) cc_final: 0.7972 (tpt) REVERT: Q 75 MET cc_start: 0.8742 (mmm) cc_final: 0.8360 (mmm) REVERT: R 6 MET cc_start: 0.7166 (mmt) cc_final: 0.6624 (mtm) REVERT: R 11 MET cc_start: 0.8596 (tpp) cc_final: 0.8363 (tpp) REVERT: R 57 MET cc_start: 0.8642 (ttp) cc_final: 0.8161 (tmm) REVERT: R 64 PRO cc_start: 0.8852 (Cg_exo) cc_final: 0.8549 (Cg_endo) REVERT: Y 1 MET cc_start: 0.3228 (ptp) cc_final: 0.1613 (mmm) REVERT: Y 22 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5085 (mmp) REVERT: Y 64 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8569 (mm-40) REVERT: Y 83 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7744 (ttp80) REVERT: Y 84 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.9056 (p) REVERT: a 6 MET cc_start: 0.5106 (mmt) cc_final: 0.4257 (ptt) REVERT: a 54 LEU cc_start: 0.7526 (mp) cc_final: 0.6875 (tt) REVERT: a 56 PHE cc_start: 0.6728 (t80) cc_final: 0.6323 (t80) REVERT: a 93 MET cc_start: 0.8496 (mpp) cc_final: 0.8286 (mpp) REVERT: a 131 GLU cc_start: 0.8009 (tt0) cc_final: 0.7724 (tp30) REVERT: I 42 GLN cc_start: 0.6899 (mp10) cc_final: 0.6233 (mp10) REVERT: I 52 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8258 (mp10) REVERT: I 73 TYR cc_start: 0.7051 (t80) cc_final: 0.6579 (t80) REVERT: S 6 MET cc_start: 0.7021 (mmt) cc_final: 0.6540 (mmp) REVERT: S 16 MET cc_start: 0.8792 (mtp) cc_final: 0.8098 (mmt) REVERT: S 17 MET cc_start: 0.8732 (mmm) cc_final: 0.8432 (mmp) REVERT: S 34 LYS cc_start: 0.8544 (mmtm) cc_final: 0.7794 (mmmt) REVERT: S 37 GLU cc_start: 0.8218 (tt0) cc_final: 0.7272 (tt0) REVERT: S 57 MET cc_start: 0.8769 (tmm) cc_final: 0.8495 (tmm) outliers start: 70 outliers final: 53 residues processed: 647 average time/residue: 0.4984 time to fit residues: 523.1230 Evaluate side-chains 639 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 579 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain I residue 22 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 0.7980 chunk 449 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 471 optimal weight: 4.9990 chunk 433 optimal weight: 8.9990 chunk 375 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 73 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 145 ASN H 55 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 35 ASN F 197 ASN D 121 ASN L 42 GLN Q 3 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37506 Z= 0.261 Angle : 0.591 10.243 50766 Z= 0.299 Chirality : 0.042 0.215 5918 Planarity : 0.004 0.050 6547 Dihedral : 6.146 128.672 5348 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.98 % Allowed : 18.49 % Favored : 79.53 % 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: 0.60 (0.12), residues: 4805 helix: 1.02 (0.10), residues: 2623 sheet: -0.01 (0.22), residues: 527 loop : -0.31 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 39 HIS 0.009 0.001 HIS a 14 PHE 0.024 0.001 PHE Q 35 TYR 0.014 0.001 TYR A 236 ARG 0.008 0.000 ARG M 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 580 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.7852 (p0) cc_final: 0.7218 (p0) REVERT: C 236 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8572 (t80) REVERT: C 402 GLU cc_start: 0.8196 (tp30) cc_final: 0.7939 (tp30) REVERT: B 67 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8574 (mm-30) REVERT: B 402 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7574 (tm-30) REVERT: B 483 MET cc_start: 0.8214 (mmp) cc_final: 0.7717 (mmp) REVERT: A 49 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: A 86 MET cc_start: 0.8522 (mtt) cc_final: 0.8259 (mtp) REVERT: A 236 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8518 (t80) REVERT: A 343 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9349 (p) REVERT: X 17 PHE cc_start: 0.7678 (m-80) cc_final: 0.7269 (m-80) REVERT: X 49 ARG cc_start: 0.8638 (ptp-110) cc_final: 0.8428 (ptp-170) REVERT: X 104 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8868 (pp30) REVERT: H 58 HIS cc_start: 0.8225 (m-70) cc_final: 0.8013 (m90) REVERT: H 111 ASP cc_start: 0.8776 (t0) cc_final: 0.8454 (t0) REVERT: G 116 MET cc_start: 0.9002 (mmm) cc_final: 0.8756 (mmm) REVERT: G 157 GLN cc_start: 0.8440 (tt0) cc_final: 0.8087 (tt0) REVERT: G 168 TYR cc_start: 0.8919 (m-80) cc_final: 0.8663 (m-80) REVERT: F 115 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8434 (p) REVERT: F 236 ASP cc_start: 0.8081 (p0) cc_final: 0.7823 (p0) REVERT: E 366 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7865 (mmm160) REVERT: E 371 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8183 (ttpp) REVERT: D 381 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8005 (mm-30) REVERT: J 17 MET cc_start: 0.8379 (tpp) cc_final: 0.7967 (mmt) REVERT: J 37 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8151 (mt-10) REVERT: J 42 GLN cc_start: 0.8498 (mp10) cc_final: 0.8235 (mp10) REVERT: J 57 MET cc_start: 0.8784 (tmm) cc_final: 0.8237 (tmm) REVERT: J 75 MET cc_start: 0.9078 (tpp) cc_final: 0.8702 (tpp) REVERT: L 17 MET cc_start: 0.7756 (mmt) cc_final: 0.7459 (mmm) REVERT: L 61 ASP cc_start: 0.8711 (m-30) cc_final: 0.8246 (p0) REVERT: L 65 MET cc_start: 0.8508 (mmm) cc_final: 0.8236 (mmm) REVERT: M 46 ILE cc_start: 0.9032 (mt) cc_final: 0.8683 (mt) REVERT: M 50 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8278 (ptp90) REVERT: N 37 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8129 (tm-30) REVERT: N 42 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7353 (mt0) REVERT: N 75 MET cc_start: 0.8535 (mmm) cc_final: 0.8193 (mmp) REVERT: O 16 MET cc_start: 0.6852 (mmm) cc_final: 0.6433 (mmm) REVERT: O 42 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7683 (mp10) REVERT: O 52 GLN cc_start: 0.8511 (mm110) cc_final: 0.8157 (mp10) REVERT: O 66 ILE cc_start: 0.8044 (pt) cc_final: 0.7817 (pt) REVERT: P 31 LEU cc_start: 0.8099 (tp) cc_final: 0.7794 (tp) REVERT: P 42 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7668 (mp10) REVERT: P 50 ARG cc_start: 0.7888 (ptt180) cc_final: 0.7501 (ptp-110) REVERT: P 73 TYR cc_start: 0.6545 (t80) cc_final: 0.5858 (t80) REVERT: Q 16 MET cc_start: 0.7030 (mmm) cc_final: 0.6811 (mmp) REVERT: Q 17 MET cc_start: 0.8038 (mmm) cc_final: 0.7757 (mmm) REVERT: Q 28 ILE cc_start: 0.8118 (pt) cc_final: 0.7786 (pp) REVERT: Q 36 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8236 (tt) REVERT: Q 52 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8522 (mp10) REVERT: Q 57 MET cc_start: 0.8257 (tmm) cc_final: 0.7975 (tpt) REVERT: Q 75 MET cc_start: 0.8741 (mmm) cc_final: 0.8338 (mmm) REVERT: R 11 MET cc_start: 0.8580 (tpp) cc_final: 0.8344 (tpp) REVERT: R 57 MET cc_start: 0.8631 (ttp) cc_final: 0.8120 (tmm) REVERT: R 64 PRO cc_start: 0.8832 (Cg_exo) cc_final: 0.8522 (Cg_endo) REVERT: Y 1 MET cc_start: 0.3215 (ptp) cc_final: 0.1449 (mmm) REVERT: Y 22 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.5147 (mmp) REVERT: Y 64 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8564 (mm-40) REVERT: Y 83 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7785 (ttp80) REVERT: Y 84 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9052 (p) REVERT: a 6 MET cc_start: 0.5167 (mmt) cc_final: 0.4276 (ptt) REVERT: a 54 LEU cc_start: 0.7522 (mp) cc_final: 0.6918 (tt) REVERT: a 56 PHE cc_start: 0.6945 (t80) cc_final: 0.6536 (t80) REVERT: a 93 MET cc_start: 0.8512 (mpp) cc_final: 0.8299 (mpp) REVERT: I 42 GLN cc_start: 0.6911 (mp10) cc_final: 0.6261 (mp10) REVERT: I 52 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8321 (mp10) REVERT: I 73 TYR cc_start: 0.6980 (t80) cc_final: 0.6573 (t80) REVERT: S 6 MET cc_start: 0.6939 (mmt) cc_final: 0.6475 (mmp) REVERT: S 16 MET cc_start: 0.8793 (mtp) cc_final: 0.8168 (mmt) REVERT: S 17 MET cc_start: 0.8662 (mmm) cc_final: 0.8429 (mmp) REVERT: S 34 LYS cc_start: 0.8537 (mmtm) cc_final: 0.7741 (mmmt) REVERT: S 37 GLU cc_start: 0.8254 (tt0) cc_final: 0.7286 (tt0) REVERT: S 57 MET cc_start: 0.8778 (tmm) cc_final: 0.8318 (tmm) outliers start: 76 outliers final: 55 residues processed: 636 average time/residue: 0.5331 time to fit residues: 552.3799 Evaluate side-chains 631 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 568 time to evaluate : 4.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 ASP Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 129 VAL Chi-restraints excluded: chain Y residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 1.9990 chunk 399 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 375 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 385 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN D 121 ASN L 42 GLN Q 3 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN R 52 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.099812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.066280 restraints weight = 75620.934| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.04 r_work: 0.2766 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37506 Z= 0.188 Angle : 0.580 10.614 50766 Z= 0.292 Chirality : 0.042 0.220 5918 Planarity : 0.004 0.048 6547 Dihedral : 6.054 126.954 5348 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.83 % Allowed : 18.60 % Favored : 79.58 % 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: 0.63 (0.12), residues: 4805 helix: 1.03 (0.10), residues: 2633 sheet: 0.05 (0.22), residues: 525 loop : -0.29 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP a 39 HIS 0.009 0.001 HIS a 14 PHE 0.045 0.001 PHE E 189 TYR 0.017 0.001 TYR a 263 ARG 0.008 0.000 ARG M 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11144.47 seconds wall clock time: 200 minutes 31.08 seconds (12031.08 seconds total)