Starting phenix.real_space_refine on Tue Apr 16 02:23:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqv_20454/04_2024/6pqv_20454_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqv_20454/04_2024/6pqv_20454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqv_20454/04_2024/6pqv_20454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqv_20454/04_2024/6pqv_20454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqv_20454/04_2024/6pqv_20454_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqv_20454/04_2024/6pqv_20454_neut_updated.pdb" } resolution = 3.3 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 23485 2.51 5 N 6317 2.21 5 O 6968 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 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W GLU 36": "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 GLU 70": "OE1" <-> "OE2" 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 143": "OD1" <-> "OD2" Residue "W ASP 160": "OD1" <-> "OD2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C 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 PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 7": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" 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 415": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A 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 TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A 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 PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "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 ARG 49": "NH1" <-> "NH2" Residue "X ASP 55": "OD1" <-> "OD2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X 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 155": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 88": "OD1" <-> "OD2" 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 ASP 69": "OD1" <-> "OD2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G ARG 84": "NH1" <-> "NH2" 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 PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 197": "OD1" <-> "OD2" Residue "G ASP 210": "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 GLU 127": "OE1" <-> "OE2" 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 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 ASP 338": "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 GLU 440": "OE1" <-> "OE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 36": "OE1" <-> "OE2" 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 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 228": "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 372": "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 "J ASP 7": "OD1" <-> "OD2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 50": "NH1" <-> "NH2" 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 "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y GLU 110": "OE1" <-> "OE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y ASP 141": "OD1" <-> "OD2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 196": "OE1" <-> "OE2" Residue "a TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ARG 50": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36971 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: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3871 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} 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} Link IDs: {'PTRANS': 2, 'TRANS': 153} 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} Link IDs: {'PTRANS': 2, 'TRANS': 153} 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: 17.00, per 1000 atoms: 0.46 Number of scatterers: 36971 At special positions: 0 Unit cell: (178.035, 221.195, 139.191, 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 6968 8.00 N 6317 7.00 C 23485 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: 13.27 Conformation dependent library (CDL) restraints added in 6.8 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 182 helices and 25 sheets defined 55.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.69 Creating SS restraints... Processing helix chain 'W' and resid 4 through 20 removed outlier: 3.638A pdb=" N ARG W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Proline residue: W 9 - end of helix removed outlier: 3.632A pdb=" N GLU W 20 " --> pdb=" O ASP W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.825A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.644A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 3.854A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 82 Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 4.126A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN W 94 " --> pdb=" O VAL W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 removed outlier: 4.034A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG W 131 " --> pdb=" O ALA W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 173 removed outlier: 3.711A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 removed outlier: 4.213A pdb=" N GLN C 14 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) 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: 3.580A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 156' Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.037A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.899A 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: 3.607A pdb=" N MET C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.547A pdb=" N ALA C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.981A 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: 4.357A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 313 removed outlier: 3.543A pdb=" N GLU C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) 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: 3.956A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 409 removed outlier: 3.931A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 431 Processing helix chain 'C' and resid 441 through 452 removed outlier: 3.731A pdb=" N VAL C 447 " --> pdb=" O GLN C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 477 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: 3.688A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.584A pdb=" N GLY C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.694A pdb=" N ARG B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.552A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (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 removed outlier: 3.711A pdb=" N LEU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.627A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.570A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) 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: 4.534A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 298 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.569A pdb=" N LYS B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 removed outlier: 4.122A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 3.509A pdb=" N LYS B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.636A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 477 removed outlier: 3.990A pdb=" N ALA B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 removed outlier: 3.524A pdb=" N GLN B 488 " --> pdb=" O GLN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.551A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 removed outlier: 3.737A pdb=" N LYS A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) 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 252 Proline residue: A 239 - end of helix removed outlier: 3.622A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.527A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (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 291 through 300 removed outlier: 3.626A pdb=" N ARG A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.792A 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: 3.508A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.827A pdb=" N ALA A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 408 removed outlier: 5.538A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.584A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.800A pdb=" N GLU A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 509 removed outlier: 4.183A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 22 removed outlier: 4.249A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL X 15 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 3.737A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS X 81 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU X 87 " --> pdb=" O ARG X 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA X 90 " --> pdb=" O ILE X 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA X 92 " --> pdb=" O ASP X 88 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG X 121 " --> pdb=" O ARG X 117 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 155 removed outlier: 4.182A pdb=" N LYS X 151 " --> pdb=" O ASP X 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 102 removed outlier: 3.584A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.679A pdb=" N SER G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 3.515A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) 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 90 through 108 removed outlier: 3.832A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 3.539A pdb=" N ILE G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.694A 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 199 through 202 removed outlier: 3.775A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 199 through 202' Processing helix chain 'G' and resid 211 through 282 removed outlier: 3.866A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 239 " --> pdb=" O LEU G 235 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU G 278 " --> pdb=" O GLN G 274 " (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 166 Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'F' and resid 198 through 201 Processing helix chain 'F' and resid 213 through 232 removed outlier: 3.914A pdb=" N ARG F 218 " --> pdb=" O GLY F 214 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 255 removed outlier: 3.796A pdb=" N GLY F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.731A 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: 4.796A 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: 3.554A pdb=" N LYS F 371 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.137A 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 387 through 399 removed outlier: 3.540A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) 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 431 removed outlier: 3.653A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS F 428 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.807A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (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 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.765A pdb=" N GLU E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 232 removed outlier: 3.626A pdb=" N ARG E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.880A 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: 3.883A 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 313 removed outlier: 4.030A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) 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: 4.207A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.629A 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 386 through 400 removed outlier: 3.642A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 411 Processing helix chain 'E' and resid 420 through 432 removed outlier: 3.745A pdb=" N GLU E 432 " --> pdb=" O LYS E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 449 through 458 removed outlier: 4.612A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 4.268A 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 170 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.592A pdb=" N TYR D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 232 removed outlier: 4.915A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.758A 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 removed outlier: 3.617A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) 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 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 346 through 377 removed outlier: 7.909A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (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 386 through 399 removed outlier: 3.510A pdb=" N LYS D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 411 removed outlier: 3.757A pdb=" N VAL D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 430 Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 450 through 456 Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.892A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA J 13 " --> pdb=" O LEU J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 76 removed outlier: 3.555A pdb=" N ILE J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL J 56 " --> pdb=" O GLN J 52 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY J 58 " --> pdb=" O PHE J 54 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.949A 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 6 through 39 removed outlier: 3.515A pdb=" N VAL L 15 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 31 " --> pdb=" O GLY L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.699A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.318A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 5 through 40 removed outlier: 3.611A pdb=" N ALA M 20 " --> pdb=" O MET M 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 28 " --> pdb=" O ALA M 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU M 37 " --> pdb=" O GLY M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 61 Proline residue: M 47 - end of helix removed outlier: 4.456A pdb=" N ARG M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE M 53 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 76 removed outlier: 4.063A pdb=" N GLY M 69 " --> pdb=" O MET M 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 6 No H-bonds generated for 'chain 'N' and resid 4 through 6' Processing helix chain 'N' and resid 8 through 40 removed outlier: 4.105A pdb=" N ALA N 13 " --> pdb=" O LEU N 9 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 76 removed outlier: 3.586A pdb=" N GLN N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA N 62 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 5 through 41 removed outlier: 3.862A pdb=" N TYR O 10 " --> pdb=" O ASP O 7 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL O 15 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 60 removed outlier: 3.661A pdb=" N ILE O 46 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Proline residue: O 47 - end of helix removed outlier: 4.248A pdb=" N GLY O 58 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 75 removed outlier: 3.990A pdb=" N GLY O 69 " --> pdb=" O MET O 65 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL O 74 " --> pdb=" O LEU O 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 41 removed outlier: 3.900A pdb=" N MET P 11 " --> pdb=" O ASP P 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU P 31 " --> pdb=" O GLY P 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG P 41 " --> pdb=" O GLU P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 75 Proline residue: P 47 - end of helix removed outlier: 3.927A pdb=" N ARG P 50 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY P 58 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP P 61 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA P 62 " --> pdb=" O LEU P 59 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE P 63 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.591A pdb=" N LEU P 70 " --> pdb=" O ALA P 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 41 removed outlier: 4.620A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA Q 13 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA Q 20 " --> pdb=" O MET Q 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA Q 21 " --> pdb=" O MET Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 61 removed outlier: 3.917A pdb=" N ILE Q 46 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Proline residue: Q 47 - end of helix removed outlier: 4.513A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY Q 58 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 76 removed outlier: 3.873A pdb=" N GLY Q 69 " --> pdb=" O MET Q 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 41 removed outlier: 3.786A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 76 Proline residue: R 47 - end of helix removed outlier: 3.540A pdb=" N GLY R 58 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA R 62 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.536A pdb=" N LEU R 70 " --> pdb=" O ALA R 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 24 Processing helix chain 'Y' and resid 26 through 138 removed outlier: 4.394A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU Y 56 " --> pdb=" O LYS Y 52 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS Y 67 " --> pdb=" O ASP Y 63 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA Y 105 " --> pdb=" O ILE Y 101 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN Y 106 " --> pdb=" O VAL Y 102 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU Y 108 " --> pdb=" O GLN Y 104 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE Y 109 " --> pdb=" O ALA Y 105 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU Y 112 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN Y 123 " --> pdb=" O GLU Y 119 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL Y 129 " --> pdb=" O ALA Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 155 removed outlier: 3.977A pdb=" N VAL Y 149 " --> pdb=" O SER Y 146 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU Y 152 " --> pdb=" O VAL Y 149 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL Y 153 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Y 154 " --> pdb=" O LYS Y 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 15 removed outlier: 3.606A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS a 14 " --> pdb=" O ASP a 10 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 66 removed outlier: 3.834A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS a 65 " --> pdb=" O ARG a 61 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS a 66 " --> pdb=" O SER a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.890A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 5.092A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 131 removed outlier: 3.590A pdb=" N ILE a 129 " --> pdb=" O LEU a 125 " (cutoff:3.500A) 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: 7.429A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS a 176 " --> pdb=" O GLY a 172 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 removed outlier: 3.603A pdb=" N ILE a 189 " --> pdb=" O TRP a 186 " (cutoff:3.500A) Proline residue: a 190 - end of helix removed outlier: 3.626A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL a 198 " --> pdb=" O LEU a 195 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER a 202 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.926A pdb=" N ARG a 210 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY a 213 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA a 217 " --> pdb=" O ASN a 214 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU a 220 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 4.120A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.492A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA a 267 " --> pdb=" O TYR a 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 7 No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 9 through 41 Processing helix chain 'I' and resid 46 through 60 removed outlier: 3.796A pdb=" N GLY I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 76 Processing helix chain 'S' and resid 7 through 41 removed outlier: 3.684A pdb=" N ALA S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA S 13 " --> pdb=" O TYR S 10 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N MET S 16 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU S 19 " --> pdb=" O MET S 16 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE S 26 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE S 30 " --> pdb=" O GLY S 27 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY S 33 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG S 41 " --> pdb=" O GLY S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 76 Proline residue: S 47 - end of helix removed outlier: 3.563A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE S 63 " --> pdb=" O VAL S 60 " (cutoff:3.500A) Proline residue: S 64 - end of helix Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.511A pdb=" N VAL W 150 " --> pdb=" O GLY W 161 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.577A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 70 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET C 76 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA C 61 " --> pdb=" O MET C 76 " (cutoff:3.500A) removed outlier: 4.120A 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: 8.369A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.766A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 169 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.592A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.458A 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 352 through 355 removed outlier: 6.681A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.906A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 198 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.475A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ARG A 93 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR A 91 " --> pdb=" O SER A 54 " (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 352 through 355 removed outlier: 6.545A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 323 through 326 removed outlier: 6.231A pdb=" N LYS A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE A 259 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 194 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 41 through 45 removed outlier: 3.818A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY H 18 " --> pdb=" O LEU H 6 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.904A 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 removed outlier: 3.501A pdb=" N ILE H 23 " --> pdb=" O ILE H 34 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 180 through 188 removed outlier: 6.429A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.383A 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: 6.695A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.539A 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: 7.907A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.126A 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: 6.523A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.789A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 317 through 319 removed outlier: 8.412A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR E 173 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE E 240 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL E 175 " --> pdb=" O PHE E 240 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.630A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N HIS D 73 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLU D 30 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU D 71 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLN D 32 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 9.697A 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: 4.591A 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 320 removed outlier: 8.762A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) 1857 hydrogen bonds defined for protein. 4830 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: 12.36 Time building geometry restraints manager: 14.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6332 1.30 - 1.43: 8616 1.43 - 1.56: 22196 1.56 - 1.69: 24 1.69 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.59e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.40e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.83e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.09e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.83e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.47: 818 105.47 - 113.19: 20976 113.19 - 120.91: 18829 120.91 - 128.63: 9980 128.63 - 136.34: 194 Bond angle restraints: 50797 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 139.87 116.27 23.60 1.00e+00 1.00e+00 5.57e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.99 22.88 1.00e+00 1.00e+00 5.23e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.66 22.21 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.59 20.24 1.00e+00 1.00e+00 4.10e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 117.70 19.13 1.00e+00 1.00e+00 3.66e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.70: 22116 31.70 - 63.40: 606 63.40 - 95.10: 66 95.10 - 126.80: 4 126.80 - 158.50: 2 Dihedral angle restraints: 22794 sinusoidal: 9010 harmonic: 13784 Sorted by residual: dihedral pdb=" C5' ADP D 500 " pdb=" O5' ADP D 500 " pdb=" PA ADP D 500 " pdb=" O2A ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 98.51 -158.50 1 2.00e+01 2.50e-03 4.63e+01 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 300.00 168.92 131.07 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O2A ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PA ADP D 500 " pdb=" PB ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 59.50 -119.50 1 2.00e+01 2.50e-03 3.58e+01 ... (remaining 22791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5494 0.095 - 0.190: 406 0.190 - 0.285: 16 0.285 - 0.380: 2 0.380 - 0.475: 2 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 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 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ARG a 24 " pdb=" N ARG a 24 " pdb=" C ARG a 24 " pdb=" CB ARG a 24 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.023 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C ALA D 264 " -0.081 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 262 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C PRO E 262 " -0.077 2.00e-02 2.50e+03 pdb=" O PRO E 262 " 0.030 2.00e-02 2.50e+03 pdb=" N SER E 263 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 336 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C ASP B 336 " 0.074 2.00e-02 2.50e+03 pdb=" O ASP B 336 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL B 337 " -0.024 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 62 2.39 - 3.01: 23690 3.01 - 3.64: 53311 3.64 - 4.27: 84598 4.27 - 4.90: 142015 Nonbonded interactions: 303676 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.757 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.780 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.830 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.862 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.871 2.170 ... (remaining 303671 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: 1.770 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: 0.040 Extract box with map and model: 11.140 Check model and map are aligned: 0.530 Set scattering table: 0.350 Process input model: 88.730 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.260 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.009 0.078 37528 Z= 0.580 Angle : 0.928 23.601 50797 Z= 0.616 Chirality : 0.053 0.475 5920 Planarity : 0.005 0.061 6550 Dihedral : 14.821 158.502 13976 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 2.58 % Allowed : 8.45 % Favored : 88.97 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.10), residues: 4807 helix: -2.00 (0.08), residues: 2575 sheet: -0.73 (0.20), residues: 513 loop : -1.54 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 203 HIS 0.008 0.001 HIS C 215 PHE 0.030 0.002 PHE D 139 TYR 0.042 0.002 TYR B 492 ARG 0.009 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 740 time to evaluate : 4.406 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 109 ASP cc_start: 0.8308 (m-30) cc_final: 0.8105 (m-30) REVERT: W 143 ASP cc_start: 0.8309 (t0) cc_final: 0.8078 (t0) REVERT: W 156 ASP cc_start: 0.7647 (p0) cc_final: 0.6780 (p0) REVERT: W 159 ILE cc_start: 0.8826 (mp) cc_final: 0.8308 (tt) REVERT: C 236 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.7439 (t80) REVERT: C 484 GLN cc_start: 0.8448 (tp40) cc_final: 0.7773 (tp-100) REVERT: C 488 GLN cc_start: 0.8932 (tt0) cc_final: 0.8498 (tt0) REVERT: B 86 MET cc_start: 0.8774 (mtt) cc_final: 0.8518 (mtt) REVERT: B 295 SER cc_start: 0.9324 (t) cc_final: 0.9103 (p) REVERT: A 401 ARG cc_start: 0.8661 (mtp-110) cc_final: 0.8382 (ttm-80) REVERT: A 415 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8081 (t70) REVERT: A 511 GLN cc_start: 0.3928 (OUTLIER) cc_final: 0.3692 (tp-100) REVERT: X 42 ASP cc_start: 0.7112 (m-30) cc_final: 0.6842 (m-30) REVERT: X 121 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7706 (mtp85) REVERT: X 129 VAL cc_start: 0.9197 (t) cc_final: 0.8978 (p) REVERT: H 62 ILE cc_start: 0.8816 (mt) cc_final: 0.8475 (mm) REVERT: G 31 MET cc_start: 0.8448 (ttp) cc_final: 0.8154 (ttp) REVERT: G 155 MET cc_start: 0.9270 (mmm) cc_final: 0.9067 (mmt) REVERT: G 259 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7755 (mp0) REVERT: F 209 MET cc_start: 0.8669 (ptp) cc_final: 0.8277 (ptp) REVERT: F 211 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8439 (mt-10) REVERT: F 372 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: E 242 ASP cc_start: 0.7583 (t0) cc_final: 0.7348 (t0) REVERT: E 323 ARG cc_start: 0.8073 (tpp80) cc_final: 0.7714 (mmm-85) REVERT: E 368 GLN cc_start: 0.8636 (tp40) cc_final: 0.8095 (tp40) REVERT: D 88 MET cc_start: 0.9106 (mtm) cc_final: 0.8905 (mtp) REVERT: D 343 GLN cc_start: 0.8284 (mp10) cc_final: 0.7941 (mt0) REVERT: D 379 MET cc_start: 0.8300 (ttt) cc_final: 0.8098 (tpp) REVERT: D 384 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: L 6 MET cc_start: 0.7537 (ttp) cc_final: 0.7337 (mmt) REVERT: L 11 MET cc_start: 0.7388 (tpt) cc_final: 0.7084 (tpt) REVERT: L 57 MET cc_start: 0.8996 (tmm) cc_final: 0.8542 (tmm) REVERT: L 63 ILE cc_start: 0.7548 (mm) cc_final: 0.7341 (mm) REVERT: L 76 PHE cc_start: 0.7488 (m-80) cc_final: 0.7185 (m-80) REVERT: M 11 MET cc_start: 0.8405 (tpt) cc_final: 0.7994 (tpp) REVERT: M 16 MET cc_start: 0.8420 (ttp) cc_final: 0.8208 (ttm) REVERT: M 17 MET cc_start: 0.8455 (mtm) cc_final: 0.8131 (mtm) REVERT: M 41 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7567 (mtm-85) REVERT: M 42 GLN cc_start: 0.7319 (pt0) cc_final: 0.7084 (pt0) REVERT: M 65 MET cc_start: 0.8402 (mtp) cc_final: 0.8113 (ptt) REVERT: N 76 PHE cc_start: 0.6368 (m-80) cc_final: 0.5447 (t80) REVERT: P 36 LEU cc_start: 0.8567 (mt) cc_final: 0.8338 (tt) REVERT: P 55 ILE cc_start: 0.8806 (mm) cc_final: 0.8597 (mt) REVERT: Q 34 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7836 (mmtt) REVERT: Q 75 MET cc_start: 0.8997 (mtm) cc_final: 0.8675 (mtp) REVERT: R 10 TYR cc_start: 0.8054 (m-80) cc_final: 0.7637 (m-80) REVERT: R 11 MET cc_start: 0.8312 (tpt) cc_final: 0.7768 (tpt) REVERT: R 16 MET cc_start: 0.8503 (mtp) cc_final: 0.7884 (ttm) REVERT: R 63 ILE cc_start: 0.8832 (mm) cc_final: 0.8496 (mt) REVERT: R 65 MET cc_start: 0.9070 (mmm) cc_final: 0.8868 (mmm) REVERT: R 75 MET cc_start: 0.7765 (ttt) cc_final: 0.7422 (tpp) REVERT: R 76 PHE cc_start: 0.7086 (m-80) cc_final: 0.6504 (m-80) REVERT: Y 20 PHE cc_start: 0.8097 (t80) cc_final: 0.7786 (t80) REVERT: Y 38 LYS cc_start: 0.8836 (tptt) cc_final: 0.8633 (tmtt) REVERT: Y 56 LEU cc_start: 0.7469 (mp) cc_final: 0.7176 (tp) REVERT: Y 96 GLN cc_start: 0.8661 (tt0) cc_final: 0.8446 (tp40) REVERT: a 33 ASN cc_start: 0.4643 (OUTLIER) cc_final: 0.4376 (p0) REVERT: a 61 ARG cc_start: 0.6190 (tpt170) cc_final: 0.5601 (mtm110) REVERT: a 65 LYS cc_start: 0.5875 (tttt) cc_final: 0.5345 (mmtm) REVERT: a 94 TYR cc_start: 0.5315 (t80) cc_final: 0.5004 (t80) REVERT: a 215 MET cc_start: 0.8652 (mmt) cc_final: 0.8391 (mmm) REVERT: a 220 LEU cc_start: 0.8744 (tp) cc_final: 0.8477 (mt) REVERT: I 16 MET cc_start: 0.7256 (ttm) cc_final: 0.7003 (ttm) REVERT: S 6 MET cc_start: 0.7644 (mmt) cc_final: 0.7438 (mmp) REVERT: S 63 ILE cc_start: 0.8855 (mm) cc_final: 0.8613 (mt) REVERT: S 73 TYR cc_start: 0.8079 (t80) cc_final: 0.7252 (t80) outliers start: 99 outliers final: 50 residues processed: 822 average time/residue: 0.5495 time to fit residues: 723.6989 Evaluate side-chains 600 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 544 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 139 ASN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain Q residue 11 MET Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain a residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 3.9990 chunk 358 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 370 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 429 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN C 58 ASN B 18 GLN B 42 HIS B 58 ASN B 186 GLN B 333 GLN B 443 GLN A 65 ASN A 123 HIS A 147 GLN A 344 ASN A 484 GLN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 10 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 ASN H 127 GLN G 57 HIS G 64 HIS G 91 ASN G 126 ASN G 252 ASN G 265 ASN G 269 GLN F 7 GLN E 353 HIS J 3 ASN J 52 GLN L 42 GLN M 5 ASN M 52 GLN N 5 ASN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 184 ASN a 238 ASN S 5 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37528 Z= 0.192 Angle : 0.640 9.661 50797 Z= 0.334 Chirality : 0.044 0.225 5920 Planarity : 0.005 0.053 6550 Dihedral : 8.636 162.641 5425 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.92 % Allowed : 11.86 % Favored : 85.22 % 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: -0.90 (0.11), residues: 4807 helix: -0.40 (0.10), residues: 2547 sheet: -0.29 (0.21), residues: 526 loop : -0.75 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 111 HIS 0.007 0.001 HIS G 57 PHE 0.023 0.002 PHE I 53 TYR 0.022 0.001 TYR L 10 ARG 0.008 0.000 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 616 time to evaluate : 4.144 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 143 ASP cc_start: 0.8151 (t0) cc_final: 0.7832 (t0) REVERT: W 156 ASP cc_start: 0.7673 (p0) cc_final: 0.7074 (p0) REVERT: W 159 ILE cc_start: 0.8799 (mp) cc_final: 0.8580 (mp) REVERT: C 245 MET cc_start: 0.9086 (mtt) cc_final: 0.8775 (mtt) REVERT: C 484 GLN cc_start: 0.8408 (tp40) cc_final: 0.7844 (tp-100) REVERT: C 488 GLN cc_start: 0.8862 (tt0) cc_final: 0.8470 (tt0) REVERT: B 295 SER cc_start: 0.9238 (t) cc_final: 0.8749 (p) REVERT: A 172 GLN cc_start: 0.8571 (tt0) cc_final: 0.8070 (tt0) REVERT: A 180 ILE cc_start: 0.9226 (pt) cc_final: 0.8893 (mm) REVERT: A 343 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8941 (p) REVERT: A 386 MET cc_start: 0.8927 (mmm) cc_final: 0.8498 (mmt) REVERT: A 401 ARG cc_start: 0.8479 (mtp-110) cc_final: 0.8236 (ttm-80) REVERT: X 42 ASP cc_start: 0.7050 (m-30) cc_final: 0.6757 (m-30) REVERT: H 23 ILE cc_start: 0.8892 (pt) cc_final: 0.8466 (mm) REVERT: H 132 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: G 31 MET cc_start: 0.8468 (ttp) cc_final: 0.8234 (ttp) REVERT: F 209 MET cc_start: 0.8780 (ptp) cc_final: 0.8427 (ptp) REVERT: E 209 MET cc_start: 0.8880 (mtm) cc_final: 0.8583 (mtm) REVERT: E 323 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7660 (mmm-85) REVERT: E 368 GLN cc_start: 0.8535 (tp40) cc_final: 0.7792 (tp-100) REVERT: D 166 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8891 (mp) REVERT: J 37 GLU cc_start: 0.8790 (tp30) cc_final: 0.8543 (tp30) REVERT: L 11 MET cc_start: 0.7125 (tpt) cc_final: 0.6711 (tpt) REVERT: L 17 MET cc_start: 0.7811 (mtm) cc_final: 0.7387 (mtt) REVERT: L 34 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7896 (mmpt) REVERT: L 75 MET cc_start: 0.7796 (mmm) cc_final: 0.7254 (tpt) REVERT: L 76 PHE cc_start: 0.7392 (m-80) cc_final: 0.6972 (m-80) REVERT: M 34 LYS cc_start: 0.7951 (mmtm) cc_final: 0.7741 (mmtt) REVERT: M 42 GLN cc_start: 0.7312 (pt0) cc_final: 0.7007 (pt0) REVERT: M 54 PHE cc_start: 0.8614 (m-80) cc_final: 0.8390 (m-10) REVERT: N 10 TYR cc_start: 0.6811 (m-80) cc_final: 0.6587 (m-80) REVERT: N 75 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7417 (tmm) REVERT: N 76 PHE cc_start: 0.6076 (m-80) cc_final: 0.5264 (t80) REVERT: O 17 MET cc_start: 0.8057 (ttm) cc_final: 0.7509 (tpp) REVERT: O 72 LEU cc_start: 0.8763 (mt) cc_final: 0.8550 (pp) REVERT: P 6 MET cc_start: 0.4697 (mpp) cc_final: 0.4390 (mpp) REVERT: P 10 TYR cc_start: 0.6933 (m-80) cc_final: 0.6541 (m-80) REVERT: P 17 MET cc_start: 0.7461 (ppp) cc_final: 0.7158 (tmm) REVERT: P 36 LEU cc_start: 0.8569 (mt) cc_final: 0.8340 (tt) REVERT: P 42 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7550 (mp10) REVERT: P 64 PRO cc_start: 0.7895 (Cg_exo) cc_final: 0.7650 (Cg_endo) REVERT: Q 11 MET cc_start: 0.8410 (ttm) cc_final: 0.7445 (tpt) REVERT: Q 35 PHE cc_start: 0.8830 (t80) cc_final: 0.8320 (t80) REVERT: Q 54 PHE cc_start: 0.8024 (m-80) cc_final: 0.7711 (m-80) REVERT: Q 74 VAL cc_start: 0.8429 (t) cc_final: 0.8224 (t) REVERT: Q 75 MET cc_start: 0.9153 (mtm) cc_final: 0.8914 (mtp) REVERT: R 10 TYR cc_start: 0.8055 (m-80) cc_final: 0.7703 (m-80) REVERT: R 16 MET cc_start: 0.8355 (mtp) cc_final: 0.7924 (ttm) REVERT: R 76 PHE cc_start: 0.6811 (m-80) cc_final: 0.6564 (m-80) REVERT: Y 20 PHE cc_start: 0.7905 (t80) cc_final: 0.7628 (t80) REVERT: Y 38 LYS cc_start: 0.8892 (tptt) cc_final: 0.8686 (tmtt) REVERT: Y 82 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8275 (tpp-160) REVERT: Y 98 ARG cc_start: 0.7303 (mtp-110) cc_final: 0.7058 (ttm-80) REVERT: a 65 LYS cc_start: 0.5525 (tttt) cc_final: 0.5036 (pptt) REVERT: a 99 LYS cc_start: 0.7045 (ptmt) cc_final: 0.6274 (ttmt) REVERT: a 195 LEU cc_start: 0.8414 (mt) cc_final: 0.8194 (mp) REVERT: a 215 MET cc_start: 0.8455 (mmt) cc_final: 0.8158 (mmm) REVERT: a 256 PHE cc_start: 0.9347 (t80) cc_final: 0.9122 (t80) REVERT: I 75 MET cc_start: 0.7959 (ttm) cc_final: 0.7699 (ptm) REVERT: S 65 MET cc_start: 0.7417 (mtt) cc_final: 0.7085 (mtp) REVERT: S 73 TYR cc_start: 0.7827 (t80) cc_final: 0.7481 (t80) outliers start: 112 outliers final: 65 residues processed: 691 average time/residue: 0.5146 time to fit residues: 576.9037 Evaluate side-chains 607 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 538 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 357 optimal weight: 0.5980 chunk 292 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 430 optimal weight: 0.7980 chunk 464 optimal weight: 10.0000 chunk 383 optimal weight: 1.9990 chunk 426 optimal weight: 20.0000 chunk 146 optimal weight: 0.6980 chunk 345 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS F 7 GLN F 187 ASN L 5 ASN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN I 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37528 Z= 0.219 Angle : 0.590 10.215 50797 Z= 0.304 Chirality : 0.043 0.232 5920 Planarity : 0.004 0.054 6550 Dihedral : 7.732 153.683 5372 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.52 % Allowed : 12.93 % Favored : 83.55 % 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: -0.33 (0.12), residues: 4807 helix: 0.11 (0.10), residues: 2581 sheet: -0.06 (0.21), residues: 541 loop : -0.58 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 111 HIS 0.006 0.001 HIS G 57 PHE 0.037 0.001 PHE E 189 TYR 0.022 0.001 TYR a 263 ARG 0.006 0.000 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 574 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 143 ASP cc_start: 0.8055 (t0) cc_final: 0.7722 (t0) REVERT: W 159 ILE cc_start: 0.8781 (mp) cc_final: 0.8561 (mp) REVERT: C 245 MET cc_start: 0.9087 (mtt) cc_final: 0.8807 (mtt) REVERT: C 484 GLN cc_start: 0.8457 (tp40) cc_final: 0.7852 (tp-100) REVERT: C 488 GLN cc_start: 0.8816 (tt0) cc_final: 0.8436 (tt0) REVERT: B 295 SER cc_start: 0.9157 (t) cc_final: 0.8723 (p) REVERT: A 49 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: A 172 GLN cc_start: 0.8600 (tt0) cc_final: 0.8118 (tt0) REVERT: A 386 MET cc_start: 0.8961 (mmm) cc_final: 0.8629 (mmt) REVERT: X 42 ASP cc_start: 0.7068 (m-30) cc_final: 0.6784 (m-30) REVERT: H 22 LYS cc_start: 0.8278 (pttp) cc_final: 0.7783 (pttm) REVERT: H 23 ILE cc_start: 0.8826 (pt) cc_final: 0.8428 (mm) REVERT: H 65 SER cc_start: 0.8512 (m) cc_final: 0.7824 (t) REVERT: H 132 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: G 31 MET cc_start: 0.8479 (ttp) cc_final: 0.8250 (ttp) REVERT: G 187 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8417 (pp) REVERT: F 209 MET cc_start: 0.8851 (ptp) cc_final: 0.8538 (ptp) REVERT: E 323 ARG cc_start: 0.7962 (tpp80) cc_final: 0.7629 (mmm-85) REVERT: E 368 GLN cc_start: 0.8542 (tp40) cc_final: 0.7769 (tp-100) REVERT: D 166 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8702 (mp) REVERT: J 11 MET cc_start: 0.8516 (mmm) cc_final: 0.8058 (mmm) REVERT: L 6 MET cc_start: 0.6608 (mmt) cc_final: 0.5895 (mmt) REVERT: L 11 MET cc_start: 0.6937 (tpt) cc_final: 0.6376 (tpt) REVERT: L 17 MET cc_start: 0.7768 (mtm) cc_final: 0.7410 (mtm) REVERT: L 37 GLU cc_start: 0.7641 (pp20) cc_final: 0.7252 (mm-30) REVERT: L 41 ARG cc_start: 0.7146 (mmp80) cc_final: 0.6484 (mmp80) REVERT: L 75 MET cc_start: 0.7670 (mmm) cc_final: 0.7270 (tpt) REVERT: M 41 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7219 (mtm-85) REVERT: M 42 GLN cc_start: 0.7486 (pt0) cc_final: 0.6481 (pm20) REVERT: M 46 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8977 (mp) REVERT: M 75 MET cc_start: 0.8186 (ttt) cc_final: 0.7817 (tmm) REVERT: N 75 MET cc_start: 0.8170 (tmm) cc_final: 0.7112 (tmm) REVERT: O 17 MET cc_start: 0.8183 (ttm) cc_final: 0.7622 (tpp) REVERT: O 65 MET cc_start: 0.7494 (mmp) cc_final: 0.7231 (mmp) REVERT: O 72 LEU cc_start: 0.8773 (mt) cc_final: 0.8562 (pp) REVERT: P 6 MET cc_start: 0.4479 (mpp) cc_final: 0.4263 (mpp) REVERT: P 10 TYR cc_start: 0.6980 (m-80) cc_final: 0.6658 (m-80) REVERT: P 16 MET cc_start: 0.8128 (ttm) cc_final: 0.7805 (ptm) REVERT: P 36 LEU cc_start: 0.8632 (mt) cc_final: 0.8367 (tt) REVERT: P 42 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7884 (mp10) REVERT: P 64 PRO cc_start: 0.7918 (Cg_exo) cc_final: 0.7633 (Cg_endo) REVERT: Q 11 MET cc_start: 0.8404 (ttm) cc_final: 0.7509 (tpt) REVERT: Q 35 PHE cc_start: 0.8797 (t80) cc_final: 0.8320 (t80) REVERT: Q 41 ARG cc_start: 0.7378 (mtm-85) cc_final: 0.7029 (mtm-85) REVERT: Q 54 PHE cc_start: 0.8029 (m-80) cc_final: 0.7716 (m-80) REVERT: Q 75 MET cc_start: 0.9159 (mtm) cc_final: 0.8905 (mtp) REVERT: R 10 TYR cc_start: 0.8162 (m-80) cc_final: 0.7877 (m-80) REVERT: R 11 MET cc_start: 0.7895 (tpp) cc_final: 0.7202 (tpt) REVERT: R 16 MET cc_start: 0.8336 (mtp) cc_final: 0.8025 (ttt) REVERT: R 75 MET cc_start: 0.8349 (tpp) cc_final: 0.8103 (tpp) REVERT: Y 10 GLN cc_start: 0.6828 (tp-100) cc_final: 0.6492 (tt0) REVERT: Y 20 PHE cc_start: 0.7822 (t80) cc_final: 0.7511 (t80) REVERT: Y 82 ARG cc_start: 0.8682 (tpp-160) cc_final: 0.8371 (tpp-160) REVERT: Y 98 ARG cc_start: 0.7317 (mtp-110) cc_final: 0.7035 (ttm-80) REVERT: a 9 GLN cc_start: 0.6998 (mp10) cc_final: 0.6219 (mt0) REVERT: a 11 TYR cc_start: 0.8050 (t80) cc_final: 0.7837 (t80) REVERT: a 65 LYS cc_start: 0.5416 (tttt) cc_final: 0.5100 (pptt) REVERT: a 94 TYR cc_start: 0.5932 (t80) cc_final: 0.5540 (t80) REVERT: a 99 LYS cc_start: 0.7018 (ptmt) cc_final: 0.6274 (ttmt) REVERT: a 121 LEU cc_start: 0.7161 (mp) cc_final: 0.6854 (tt) REVERT: a 241 TRP cc_start: 0.8216 (t-100) cc_final: 0.7880 (t-100) REVERT: a 264 LEU cc_start: 0.9038 (mt) cc_final: 0.8582 (pp) REVERT: I 50 ARG cc_start: 0.8939 (mtm110) cc_final: 0.8709 (mtm110) REVERT: S 78 VAL cc_start: 0.8225 (t) cc_final: 0.7764 (t) outliers start: 135 outliers final: 88 residues processed: 670 average time/residue: 0.5034 time to fit residues: 551.1321 Evaluate side-chains 627 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 534 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 29 ASP Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 360 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 51 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 7.9990 chunk 323 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 288 optimal weight: 0.0980 chunk 431 optimal weight: 5.9990 chunk 457 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 409 optimal weight: 0.0980 chunk 123 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN X 73 GLN H 127 GLN G 57 HIS F 7 GLN D 170 HIS P 52 GLN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS I 42 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37528 Z= 0.192 Angle : 0.562 9.472 50797 Z= 0.288 Chirality : 0.042 0.237 5920 Planarity : 0.004 0.057 6550 Dihedral : 7.347 146.172 5370 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.49 % Allowed : 14.57 % Favored : 81.93 % 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: -0.06 (0.12), residues: 4807 helix: 0.39 (0.10), residues: 2625 sheet: 0.01 (0.22), residues: 536 loop : -0.54 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 111 HIS 0.006 0.001 HIS G 57 PHE 0.027 0.001 PHE I 53 TYR 0.018 0.001 TYR B 236 ARG 0.005 0.000 ARG P 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 565 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 143 ASP cc_start: 0.8020 (t0) cc_final: 0.7697 (t0) REVERT: W 159 ILE cc_start: 0.8695 (mp) cc_final: 0.8462 (mp) REVERT: C 484 GLN cc_start: 0.8451 (tp40) cc_final: 0.7941 (tp-100) REVERT: C 488 GLN cc_start: 0.8796 (tt0) cc_final: 0.8519 (tt0) REVERT: B 237 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9068 (mp) REVERT: B 295 SER cc_start: 0.9086 (t) cc_final: 0.8661 (p) REVERT: A 49 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8986 (tp40) REVERT: A 343 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8947 (p) REVERT: A 386 MET cc_start: 0.8955 (mmm) cc_final: 0.8676 (mmt) REVERT: A 415 ASP cc_start: 0.8088 (m-30) cc_final: 0.7567 (t70) REVERT: X 26 TRP cc_start: 0.7565 (t-100) cc_final: 0.7310 (t-100) REVERT: X 42 ASP cc_start: 0.7073 (m-30) cc_final: 0.6762 (m-30) REVERT: X 53 ASP cc_start: 0.7536 (t70) cc_final: 0.7285 (t0) REVERT: H 22 LYS cc_start: 0.8251 (pttp) cc_final: 0.7801 (pttm) REVERT: H 23 ILE cc_start: 0.8831 (pt) cc_final: 0.8496 (mm) REVERT: H 65 SER cc_start: 0.8454 (m) cc_final: 0.7779 (t) REVERT: H 127 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8029 (tp40) REVERT: H 132 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: H 138 MET cc_start: 0.6944 (ttm) cc_final: 0.6398 (ttp) REVERT: G 116 MET cc_start: 0.8727 (mmm) cc_final: 0.8377 (mmm) REVERT: G 187 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8333 (pp) REVERT: G 259 GLU cc_start: 0.7913 (mp0) cc_final: 0.7620 (mp0) REVERT: F 209 MET cc_start: 0.8886 (ptp) cc_final: 0.8623 (ptp) REVERT: E 368 GLN cc_start: 0.8528 (tp40) cc_final: 0.7788 (tp-100) REVERT: D 166 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8650 (mp) REVERT: J 53 PHE cc_start: 0.8630 (t80) cc_final: 0.8253 (t80) REVERT: L 11 MET cc_start: 0.6772 (tpt) cc_final: 0.6413 (tpt) REVERT: L 17 MET cc_start: 0.7760 (mtm) cc_final: 0.7468 (mtm) REVERT: L 37 GLU cc_start: 0.7529 (pp20) cc_final: 0.7251 (mm-30) REVERT: L 41 ARG cc_start: 0.7118 (mmp80) cc_final: 0.6591 (mmp80) REVERT: L 75 MET cc_start: 0.7467 (mmm) cc_final: 0.7205 (tpt) REVERT: M 41 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.7287 (mtm-85) REVERT: M 42 GLN cc_start: 0.7415 (pt0) cc_final: 0.6600 (pm20) REVERT: M 46 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8951 (mp) REVERT: M 75 MET cc_start: 0.8112 (ttt) cc_final: 0.7729 (tmm) REVERT: N 41 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7461 (mtp85) REVERT: O 17 MET cc_start: 0.8214 (ttm) cc_final: 0.7651 (tpp) REVERT: P 10 TYR cc_start: 0.6936 (m-80) cc_final: 0.6589 (m-80) REVERT: P 16 MET cc_start: 0.8111 (ttm) cc_final: 0.7754 (ptm) REVERT: P 17 MET cc_start: 0.7517 (ppp) cc_final: 0.7277 (ttp) REVERT: P 36 LEU cc_start: 0.8625 (mt) cc_final: 0.8412 (tt) REVERT: P 41 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7742 (ttp80) REVERT: P 42 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7997 (mp10) REVERT: P 64 PRO cc_start: 0.8026 (Cg_exo) cc_final: 0.7734 (Cg_endo) REVERT: Q 41 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7234 (mtm-85) REVERT: Q 54 PHE cc_start: 0.8099 (m-80) cc_final: 0.7802 (m-80) REVERT: Q 75 MET cc_start: 0.9126 (mtm) cc_final: 0.8856 (mtp) REVERT: R 10 TYR cc_start: 0.8186 (m-80) cc_final: 0.7618 (m-80) REVERT: R 16 MET cc_start: 0.8364 (mtp) cc_final: 0.7979 (ttm) REVERT: R 55 ILE cc_start: 0.8950 (tt) cc_final: 0.8583 (pt) REVERT: Y 10 GLN cc_start: 0.6794 (tp-100) cc_final: 0.6179 (mt0) REVERT: Y 20 PHE cc_start: 0.7849 (t80) cc_final: 0.7545 (t80) REVERT: Y 82 ARG cc_start: 0.8661 (tpp-160) cc_final: 0.8406 (tpp-160) REVERT: Y 119 GLU cc_start: 0.8719 (tp30) cc_final: 0.8421 (tm-30) REVERT: a 9 GLN cc_start: 0.7001 (mp10) cc_final: 0.6137 (mt0) REVERT: a 65 LYS cc_start: 0.5484 (tttt) cc_final: 0.5074 (pptt) REVERT: a 94 TYR cc_start: 0.6091 (t80) cc_final: 0.5729 (t80) REVERT: a 241 TRP cc_start: 0.8169 (t-100) cc_final: 0.7867 (t-100) REVERT: a 263 TYR cc_start: 0.8861 (m-80) cc_final: 0.8564 (m-80) REVERT: a 264 LEU cc_start: 0.9018 (mt) cc_final: 0.8590 (pp) REVERT: I 43 PRO cc_start: 0.9073 (Cg_endo) cc_final: 0.8765 (Cg_exo) REVERT: I 50 ARG cc_start: 0.8908 (mtm110) cc_final: 0.8676 (mtm110) outliers start: 134 outliers final: 83 residues processed: 655 average time/residue: 0.4998 time to fit residues: 534.7431 Evaluate side-chains 619 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 528 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 29 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 121 ARG Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 249 LEU 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 68 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain S residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 9.9990 chunk 259 optimal weight: 0.0000 chunk 6 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 390 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 chunk 410 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS G 57 HIS D 215 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37528 Z= 0.177 Angle : 0.550 9.208 50797 Z= 0.281 Chirality : 0.041 0.232 5920 Planarity : 0.004 0.057 6550 Dihedral : 7.069 141.612 5368 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.47 % Allowed : 15.48 % Favored : 81.05 % 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: 0.20 (0.12), residues: 4807 helix: 0.61 (0.10), residues: 2623 sheet: 0.10 (0.22), residues: 533 loop : -0.45 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 111 HIS 0.006 0.001 HIS G 57 PHE 0.026 0.001 PHE I 53 TYR 0.016 0.001 TYR B 236 ARG 0.008 0.000 ARG H 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 551 time to evaluate : 4.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 143 ASP cc_start: 0.7962 (t0) cc_final: 0.7634 (t0) REVERT: W 159 ILE cc_start: 0.8658 (mp) cc_final: 0.8409 (mp) REVERT: C 236 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.7678 (t80) REVERT: C 356 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7972 (mt-10) REVERT: C 484 GLN cc_start: 0.8505 (tp40) cc_final: 0.7977 (tp-100) REVERT: C 488 GLN cc_start: 0.8760 (tt0) cc_final: 0.8519 (tt0) REVERT: B 237 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9053 (mp) REVERT: B 295 SER cc_start: 0.9057 (t) cc_final: 0.8654 (p) REVERT: B 406 PHE cc_start: 0.6190 (OUTLIER) cc_final: 0.5767 (m-10) REVERT: B 419 LYS cc_start: 0.7666 (tptt) cc_final: 0.7251 (tppt) REVERT: A 252 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8736 (mtt180) REVERT: A 343 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8977 (p) REVERT: A 386 MET cc_start: 0.8935 (mmm) cc_final: 0.8693 (mmt) REVERT: X 42 ASP cc_start: 0.7046 (m-30) cc_final: 0.6768 (m-30) REVERT: X 53 ASP cc_start: 0.7564 (t70) cc_final: 0.7344 (t0) REVERT: X 121 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7558 (mtp-110) REVERT: H 23 ILE cc_start: 0.8812 (pt) cc_final: 0.8580 (mm) REVERT: H 65 SER cc_start: 0.8443 (m) cc_final: 0.7799 (t) REVERT: H 132 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: H 138 MET cc_start: 0.6981 (ttm) cc_final: 0.6448 (ttp) REVERT: G 187 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8259 (pp) REVERT: G 259 GLU cc_start: 0.7904 (mp0) cc_final: 0.7659 (mp0) REVERT: F 209 MET cc_start: 0.8845 (ptp) cc_final: 0.8636 (ptp) REVERT: F 224 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8916 (tt) REVERT: E 368 GLN cc_start: 0.8481 (tp40) cc_final: 0.7761 (tp-100) REVERT: D 166 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8641 (mp) REVERT: J 11 MET cc_start: 0.8401 (mmm) cc_final: 0.7983 (mmm) REVERT: L 10 TYR cc_start: 0.7012 (m-80) cc_final: 0.6590 (m-80) REVERT: L 11 MET cc_start: 0.6813 (tpt) cc_final: 0.6413 (tpt) REVERT: L 17 MET cc_start: 0.7736 (mtm) cc_final: 0.7414 (mtm) REVERT: L 37 GLU cc_start: 0.7518 (pp20) cc_final: 0.7174 (mm-30) REVERT: L 41 ARG cc_start: 0.7079 (mmp80) cc_final: 0.6584 (mmp80) REVERT: M 46 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8977 (mp) REVERT: M 75 MET cc_start: 0.8079 (ttt) cc_final: 0.7771 (tmm) REVERT: N 41 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7496 (mtp85) REVERT: O 6 MET cc_start: 0.4706 (ptp) cc_final: 0.4479 (ptp) REVERT: O 11 MET cc_start: 0.6161 (mmm) cc_final: 0.4500 (mtt) REVERT: O 17 MET cc_start: 0.8217 (ttm) cc_final: 0.7627 (tpp) REVERT: O 28 ILE cc_start: 0.8583 (mm) cc_final: 0.8045 (mm) REVERT: O 57 MET cc_start: 0.8651 (tmm) cc_final: 0.8204 (tpp) REVERT: P 10 TYR cc_start: 0.6799 (m-80) cc_final: 0.6539 (m-80) REVERT: P 16 MET cc_start: 0.8078 (ttm) cc_final: 0.7785 (ptm) REVERT: P 17 MET cc_start: 0.7516 (ppp) cc_final: 0.7269 (ttp) REVERT: P 41 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7651 (ttp80) REVERT: P 42 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8020 (mp10) REVERT: P 52 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8445 (mp10) REVERT: P 64 PRO cc_start: 0.8107 (Cg_exo) cc_final: 0.7652 (Cg_endo) REVERT: Q 41 ARG cc_start: 0.7533 (mtm-85) cc_final: 0.7215 (mtm-85) REVERT: Q 54 PHE cc_start: 0.8090 (m-80) cc_final: 0.7795 (m-80) REVERT: Q 75 MET cc_start: 0.9156 (mtm) cc_final: 0.8774 (mtp) REVERT: R 10 TYR cc_start: 0.8172 (m-80) cc_final: 0.7646 (m-80) REVERT: R 11 MET cc_start: 0.8387 (tpp) cc_final: 0.8164 (mmm) REVERT: R 16 MET cc_start: 0.8379 (mtp) cc_final: 0.8041 (ttm) REVERT: R 55 ILE cc_start: 0.8909 (tt) cc_final: 0.8528 (pt) REVERT: Y 10 GLN cc_start: 0.6651 (tp-100) cc_final: 0.6336 (mp10) REVERT: Y 20 PHE cc_start: 0.7862 (t80) cc_final: 0.7573 (t80) REVERT: Y 64 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8413 (pp30) REVERT: Y 82 ARG cc_start: 0.8708 (tpp-160) cc_final: 0.8488 (tpp-160) REVERT: Y 119 GLU cc_start: 0.8680 (tp30) cc_final: 0.8474 (tm-30) REVERT: a 9 GLN cc_start: 0.7158 (mp10) cc_final: 0.6330 (mt0) REVERT: a 65 LYS cc_start: 0.5484 (tttt) cc_final: 0.5077 (pptt) REVERT: a 94 TYR cc_start: 0.6208 (t80) cc_final: 0.5754 (t80) REVERT: a 219 GLU cc_start: 0.8567 (tt0) cc_final: 0.8227 (tt0) REVERT: a 241 TRP cc_start: 0.8184 (t-100) cc_final: 0.7942 (t-100) REVERT: a 263 TYR cc_start: 0.8950 (m-10) cc_final: 0.8702 (m-80) REVERT: a 264 LEU cc_start: 0.8968 (mt) cc_final: 0.8549 (pp) REVERT: I 43 PRO cc_start: 0.9097 (Cg_endo) cc_final: 0.8777 (Cg_exo) REVERT: I 50 ARG cc_start: 0.8901 (mtm110) cc_final: 0.8681 (mtm110) REVERT: I 54 PHE cc_start: 0.8625 (m-80) cc_final: 0.8378 (m-80) REVERT: S 16 MET cc_start: 0.6541 (ttp) cc_final: 0.6281 (tmm) outliers start: 133 outliers final: 85 residues processed: 642 average time/residue: 0.5212 time to fit residues: 545.8288 Evaluate side-chains 625 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 528 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 29 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 80 ASN Chi-restraints excluded: chain X residue 121 ARG Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 73 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 0.6980 chunk 411 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 457 optimal weight: 7.9990 chunk 379 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS I 42 GLN S 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37528 Z= 0.198 Angle : 0.556 9.739 50797 Z= 0.282 Chirality : 0.041 0.159 5920 Planarity : 0.004 0.054 6550 Dihedral : 6.845 137.417 5359 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.68 % Allowed : 15.69 % Favored : 80.63 % 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: 0.38 (0.12), residues: 4807 helix: 0.79 (0.10), residues: 2612 sheet: 0.19 (0.22), residues: 532 loop : -0.44 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 203 HIS 0.003 0.001 HIS H 58 PHE 0.030 0.001 PHE P 35 TYR 0.017 0.001 TYR B 236 ARG 0.006 0.000 ARG Y 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 551 time to evaluate : 4.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 143 ASP cc_start: 0.7915 (t0) cc_final: 0.7590 (t0) REVERT: W 159 ILE cc_start: 0.8629 (mp) cc_final: 0.8396 (mp) REVERT: C 236 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.7831 (t80) REVERT: C 356 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 484 GLN cc_start: 0.8489 (tp40) cc_final: 0.7901 (tp-100) REVERT: B 295 SER cc_start: 0.9054 (t) cc_final: 0.8674 (p) REVERT: B 406 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.5829 (m-10) REVERT: B 419 LYS cc_start: 0.7625 (tptt) cc_final: 0.7263 (tppt) REVERT: A 172 GLN cc_start: 0.8588 (tt0) cc_final: 0.8102 (tt0) REVERT: A 252 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8719 (mtt180) REVERT: A 343 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.9017 (p) REVERT: A 386 MET cc_start: 0.8905 (mmm) cc_final: 0.8674 (mmt) REVERT: X 42 ASP cc_start: 0.7064 (m-30) cc_final: 0.6717 (m-30) REVERT: X 121 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7591 (mtp-110) REVERT: H 23 ILE cc_start: 0.8880 (pt) cc_final: 0.8637 (mm) REVERT: H 24 GLN cc_start: 0.8784 (tt0) cc_final: 0.8022 (tt0) REVERT: H 65 SER cc_start: 0.8537 (m) cc_final: 0.7888 (t) REVERT: H 129 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7638 (mtm-85) REVERT: H 132 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: H 138 MET cc_start: 0.7166 (ttm) cc_final: 0.6624 (ttp) REVERT: G 187 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8228 (pp) REVERT: G 259 GLU cc_start: 0.7910 (mp0) cc_final: 0.7633 (mp0) REVERT: E 193 MET cc_start: 0.8405 (mtt) cc_final: 0.8107 (mtt) REVERT: E 368 GLN cc_start: 0.8465 (tp40) cc_final: 0.7707 (tp-100) REVERT: D 166 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8651 (mp) REVERT: J 11 MET cc_start: 0.8102 (mmm) cc_final: 0.7786 (mmm) REVERT: J 53 PHE cc_start: 0.8677 (t80) cc_final: 0.8164 (t80) REVERT: L 11 MET cc_start: 0.6724 (tpt) cc_final: 0.6414 (tpt) REVERT: L 17 MET cc_start: 0.7741 (mtm) cc_final: 0.7436 (mtm) REVERT: L 37 GLU cc_start: 0.7476 (pp20) cc_final: 0.7200 (mm-30) REVERT: L 41 ARG cc_start: 0.7104 (mmp80) cc_final: 0.6677 (mmp80) REVERT: M 11 MET cc_start: 0.8275 (tpp) cc_final: 0.8022 (tpp) REVERT: M 46 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8962 (mp) REVERT: M 64 PRO cc_start: 0.8401 (Cg_exo) cc_final: 0.8178 (Cg_endo) REVERT: M 75 MET cc_start: 0.8045 (ttt) cc_final: 0.7685 (tmm) REVERT: N 41 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7498 (mtp85) REVERT: O 6 MET cc_start: 0.4679 (ptp) cc_final: 0.4427 (ptp) REVERT: O 16 MET cc_start: 0.7936 (ptm) cc_final: 0.7664 (tpt) REVERT: O 17 MET cc_start: 0.8235 (ttm) cc_final: 0.7603 (tpp) REVERT: P 41 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7600 (ttp80) REVERT: P 42 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7954 (mp10) REVERT: P 64 PRO cc_start: 0.7925 (Cg_exo) cc_final: 0.7683 (Cg_endo) REVERT: Q 41 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7153 (mtm-85) REVERT: R 10 TYR cc_start: 0.8216 (m-80) cc_final: 0.7632 (m-80) REVERT: R 11 MET cc_start: 0.8389 (tpp) cc_final: 0.7686 (tpt) REVERT: R 16 MET cc_start: 0.8390 (mtp) cc_final: 0.8073 (ttm) REVERT: Y 10 GLN cc_start: 0.6714 (tp-100) cc_final: 0.6184 (mt0) REVERT: Y 20 PHE cc_start: 0.7789 (t80) cc_final: 0.7498 (t80) REVERT: Y 64 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8408 (pp30) REVERT: Y 82 ARG cc_start: 0.8831 (tpp-160) cc_final: 0.8590 (tpp-160) REVERT: a 9 GLN cc_start: 0.7112 (mp10) cc_final: 0.6356 (mt0) REVERT: a 65 LYS cc_start: 0.5495 (tttt) cc_final: 0.5096 (pptt) REVERT: a 94 TYR cc_start: 0.6498 (t80) cc_final: 0.5999 (t80) REVERT: a 115 MET cc_start: 0.6790 (ptp) cc_final: 0.6590 (ptp) REVERT: a 241 TRP cc_start: 0.8154 (t-100) cc_final: 0.7886 (t-100) REVERT: a 264 LEU cc_start: 0.8951 (mt) cc_final: 0.8529 (pp) REVERT: I 43 PRO cc_start: 0.9125 (Cg_endo) cc_final: 0.8772 (Cg_exo) REVERT: I 50 ARG cc_start: 0.8906 (mtm110) cc_final: 0.8682 (mtm110) REVERT: I 54 PHE cc_start: 0.8623 (m-80) cc_final: 0.8406 (m-80) REVERT: S 10 TYR cc_start: 0.7591 (m-80) cc_final: 0.7291 (m-80) REVERT: S 44 ASP cc_start: 0.8548 (m-30) cc_final: 0.8224 (p0) outliers start: 141 outliers final: 103 residues processed: 641 average time/residue: 0.5122 time to fit residues: 536.6899 Evaluate side-chains 644 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 531 time to evaluate : 4.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 29 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 80 ASN Chi-restraints excluded: chain X residue 121 ARG Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 148 ILE Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 76 PHE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 55 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 73 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 260 optimal weight: 0.6980 chunk 334 optimal weight: 6.9990 chunk 258 optimal weight: 30.0000 chunk 385 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 455 optimal weight: 6.9990 chunk 285 optimal weight: 0.0470 chunk 277 optimal weight: 0.8980 chunk 210 optimal weight: 0.3980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN F 7 GLN D 243 ASN Y 64 GLN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 37528 Z= 0.143 Angle : 0.542 9.285 50797 Z= 0.275 Chirality : 0.041 0.218 5920 Planarity : 0.004 0.051 6550 Dihedral : 6.570 125.274 5359 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.79 % Allowed : 17.15 % Favored : 80.06 % 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: 0.59 (0.12), residues: 4807 helix: 0.97 (0.10), residues: 2605 sheet: 0.21 (0.22), residues: 538 loop : -0.31 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 203 HIS 0.003 0.000 HIS B 479 PHE 0.027 0.001 PHE L 35 TYR 0.039 0.001 TYR L 10 ARG 0.008 0.000 ARG S 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 563 time to evaluate : 4.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 143 ASP cc_start: 0.7851 (t0) cc_final: 0.7554 (t0) REVERT: W 159 ILE cc_start: 0.8565 (mp) cc_final: 0.8330 (mp) REVERT: C 48 MET cc_start: 0.8380 (mtp) cc_final: 0.8151 (mtt) REVERT: C 356 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7968 (mt-10) REVERT: C 484 GLN cc_start: 0.8444 (tp40) cc_final: 0.7884 (tp-100) REVERT: B 295 SER cc_start: 0.9000 (t) cc_final: 0.8634 (p) REVERT: B 419 LYS cc_start: 0.7706 (tptt) cc_final: 0.7370 (tppt) REVERT: B 448 LEU cc_start: 0.8333 (mm) cc_final: 0.8091 (mm) REVERT: A 172 GLN cc_start: 0.8520 (tt0) cc_final: 0.8067 (tp40) REVERT: A 343 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8970 (p) REVERT: A 386 MET cc_start: 0.8862 (mmm) cc_final: 0.8636 (mmt) REVERT: A 483 MET cc_start: 0.8519 (mmm) cc_final: 0.8284 (mmm) REVERT: X 42 ASP cc_start: 0.6950 (m-30) cc_final: 0.6636 (m-30) REVERT: X 121 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7529 (mtp-110) REVERT: H 24 GLN cc_start: 0.8694 (tt0) cc_final: 0.7827 (mm-40) REVERT: H 65 SER cc_start: 0.8457 (m) cc_final: 0.8246 (p) REVERT: H 129 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7689 (mtm-85) REVERT: H 138 MET cc_start: 0.7220 (ttm) cc_final: 0.6682 (ttp) REVERT: G 187 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8087 (pp) REVERT: G 259 GLU cc_start: 0.7878 (mp0) cc_final: 0.7641 (mp0) REVERT: F 224 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8916 (tt) REVERT: E 368 GLN cc_start: 0.8399 (tp40) cc_final: 0.7656 (tp-100) REVERT: D 166 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8552 (mp) REVERT: J 53 PHE cc_start: 0.8624 (t80) cc_final: 0.8245 (t80) REVERT: J 65 MET cc_start: 0.8734 (mmt) cc_final: 0.8476 (mmp) REVERT: L 11 MET cc_start: 0.6661 (tpt) cc_final: 0.6321 (tpt) REVERT: L 17 MET cc_start: 0.7689 (mtm) cc_final: 0.7374 (mtm) REVERT: L 41 ARG cc_start: 0.7078 (mmp80) cc_final: 0.6697 (mmp80) REVERT: M 11 MET cc_start: 0.8274 (tpp) cc_final: 0.8023 (tpp) REVERT: M 46 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9015 (mp) REVERT: M 75 MET cc_start: 0.8021 (ttt) cc_final: 0.7623 (tmm) REVERT: O 11 MET cc_start: 0.6194 (mmm) cc_final: 0.4506 (mtt) REVERT: O 17 MET cc_start: 0.8181 (ttm) cc_final: 0.7632 (tpp) REVERT: O 28 ILE cc_start: 0.8551 (mm) cc_final: 0.8236 (mm) REVERT: P 16 MET cc_start: 0.8023 (ttm) cc_final: 0.7684 (ptm) REVERT: P 41 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7632 (ttp80) REVERT: P 42 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7968 (mp10) REVERT: P 52 GLN cc_start: 0.8752 (mm110) cc_final: 0.8225 (mp10) REVERT: P 64 PRO cc_start: 0.7870 (Cg_exo) cc_final: 0.7602 (Cg_endo) REVERT: Q 35 PHE cc_start: 0.8700 (t80) cc_final: 0.8446 (t80) REVERT: Q 52 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8775 (pm20) REVERT: R 10 TYR cc_start: 0.8219 (m-80) cc_final: 0.7560 (m-80) REVERT: R 11 MET cc_start: 0.8511 (tpp) cc_final: 0.7860 (tpt) REVERT: R 16 MET cc_start: 0.8348 (mtp) cc_final: 0.7928 (ttm) REVERT: Y 1 MET cc_start: 0.1799 (mtm) cc_final: 0.0578 (ttt) REVERT: Y 10 GLN cc_start: 0.6903 (tp-100) cc_final: 0.6443 (mt0) REVERT: Y 64 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8400 (pp30) REVERT: Y 82 ARG cc_start: 0.8830 (tpp-160) cc_final: 0.8607 (tpp-160) REVERT: a 9 GLN cc_start: 0.7055 (mp10) cc_final: 0.6371 (mt0) REVERT: a 65 LYS cc_start: 0.5449 (tttt) cc_final: 0.5056 (pptt) REVERT: a 72 PRO cc_start: 0.7173 (Cg_exo) cc_final: 0.6718 (Cg_endo) REVERT: a 140 ARG cc_start: 0.6178 (ptm160) cc_final: 0.5647 (ptm160) REVERT: a 200 LEU cc_start: 0.8772 (tt) cc_final: 0.8484 (pp) REVERT: a 241 TRP cc_start: 0.8118 (t-100) cc_final: 0.7874 (t-100) REVERT: a 264 LEU cc_start: 0.8868 (mt) cc_final: 0.8378 (pp) REVERT: I 42 GLN cc_start: 0.7756 (mm110) cc_final: 0.7285 (tp40) REVERT: I 50 ARG cc_start: 0.8894 (mtm110) cc_final: 0.8614 (mtm110) REVERT: I 54 PHE cc_start: 0.8505 (m-80) cc_final: 0.7973 (m-80) REVERT: S 10 TYR cc_start: 0.7551 (m-80) cc_final: 0.7346 (m-80) REVERT: S 16 MET cc_start: 0.6813 (tmm) cc_final: 0.6537 (ttt) REVERT: S 37 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7520 (mm-30) REVERT: S 42 GLN cc_start: 0.8547 (mm110) cc_final: 0.7485 (mm-40) REVERT: S 44 ASP cc_start: 0.8513 (m-30) cc_final: 0.8154 (p0) outliers start: 107 outliers final: 75 residues processed: 633 average time/residue: 0.5095 time to fit residues: 526.9159 Evaluate side-chains 616 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 533 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 80 ASN Chi-restraints excluded: chain X residue 121 ARG Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 0 MET Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 65 MET Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 77 GLU Chi-restraints excluded: chain a residue 15 HIS Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 85 PHE Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 186 TRP Chi-restraints excluded: chain I residue 41 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 289 optimal weight: 0.4980 chunk 310 optimal weight: 0.0060 chunk 225 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 358 optimal weight: 6.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 24 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 243 ASN P 52 GLN Y 2 ASN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3559 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: