Starting phenix.real_space_refine on Fri Feb 23 06:36:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/02_2024/6oqu_20170_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/02_2024/6oqu_20170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/02_2024/6oqu_20170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/02_2024/6oqu_20170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/02_2024/6oqu_20170_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oqu_20170/02_2024/6oqu_20170_neut_updated.pdb" } resolution = 3.2 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 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 36": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 69": "OD1" <-> "OD2" Residue "W 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 107": "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 "W GLU 168": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C 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 ASP 336": "OD1" <-> "OD2" Residue "C PHE 354": "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 PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C GLU 497": "OE1" <-> "OE2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 412": "OD1" <-> "OD2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 458": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A 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 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 "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X ASP 55": "OD1" <-> "OD2" Residue "X GLU 71": "OE1" <-> "OE2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X GLU 93": "OE1" <-> "OE2" Residue "X GLU 97": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ARG 113": "NH1" <-> "NH2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X ASP 141": "OD1" <-> "OD2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 197": "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 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F ASP 236": "OD1" <-> "OD2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "F PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 422": "OD1" <-> "OD2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ASP 302": "OD1" <-> "OD2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E ASP 380": "OD1" <-> "OD2" Residue "E GLU 384": "OE1" <-> "OE2" Residue "E ASP 386": "OD1" <-> "OD2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D 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 "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ARG 50": "NH1" <-> "NH2" 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 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 7": "OD1" <-> "OD2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O TYR 73": "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 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 44": "OD1" <-> "OD2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q TYR 73": "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 ASP 42": "OD1" <-> "OD2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y GLU 71": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y GLU 97": "OE1" <-> "OE2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y GLU 110": "OE1" <-> "OE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y ASP 150": "OD1" <-> "OD2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 146": "OD1" <-> "OD2" Residue "a PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 7": "OD1" <-> "OD2" 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-5238/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: 19.36, per 1000 atoms: 0.52 Number of scatterers: 36971 At special positions: 0 Unit cell: (176.956, 220.116, 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: 14.84 Conformation dependent library (CDL) restraints added in 7.0 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: 179 helices and 25 sheets defined 55.7% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.52 Creating SS restraints... Processing helix chain 'W' and resid 6 through 20 removed outlier: 4.686A pdb=" N TYR W 10 " --> pdb=" O VAL W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.813A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.688A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 63 removed outlier: 4.047A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 82 removed outlier: 4.014A pdb=" N LEU W 75 " --> pdb=" O ASN W 71 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 102 Proline residue: W 89 - end of helix removed outlier: 3.970A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN W 94 " --> pdb=" O VAL W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 removed outlier: 4.518A pdb=" N GLU W 129 " --> pdb=" O SER W 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 168 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.924A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.631A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.957A pdb=" N ALA C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.632A pdb=" N MET C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.250A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 342 through 348 removed outlier: 4.009A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.748A pdb=" N ALA C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 412 removed outlier: 3.813A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 removed outlier: 3.645A pdb=" N LYS C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 477 removed outlier: 3.512A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL C 475 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.652A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'B' and resid 5 through 17 removed outlier: 4.053A 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 188 removed outlier: 3.673A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 removed outlier: 3.611A pdb=" N ARG B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.740A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.668A pdb=" N ALA B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.535A 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: 4.320A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.634A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 removed outlier: 3.533A pdb=" N LYS B 426 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 464 through 478 removed outlier: 3.672A pdb=" N ALA B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 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: 4.008A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.585A pdb=" N MET A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 4.078A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.607A pdb=" N ARG A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.380A 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: 3.566A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 409 removed outlier: 3.637A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.645A pdb=" N LYS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.375A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.583A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 22 removed outlier: 4.014A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE X 12 " --> pdb=" O GLY X 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE X 14 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA X 21 " --> pdb=" O VAL X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 135 removed outlier: 3.813A pdb=" N ILE X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU X 39 " --> pdb=" O LYS X 35 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP X 42 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU X 65 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS X 66 " --> pdb=" O THR X 62 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU X 71 " --> pdb=" O LYS X 67 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA X 92 " --> pdb=" O ASP X 88 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 155 removed outlier: 3.822A pdb=" N SER X 146 " --> pdb=" O ALA X 143 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP X 147 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP X 150 " --> pdb=" O ASP X 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 102 removed outlier: 3.610A pdb=" N ARG H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 130 through 133 No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.879A pdb=" N SER G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 90 through 108 removed outlier: 3.958A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 removed outlier: 3.683A pdb=" N SER G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 160 removed outlier: 4.397A pdb=" N GLY G 150 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Proline residue: G 151 - end of helix removed outlier: 3.775A pdb=" N VAL G 154 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP G 160 " --> pdb=" O GLN G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.964A pdb=" N LYS G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 202' Processing helix chain 'G' and resid 211 through 282 removed outlier: 3.551A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (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 168 removed outlier: 4.011A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 196 removed outlier: 3.742A pdb=" N PHE F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.998A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.636A pdb=" N GLU F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.729A 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 314 removed outlier: 4.710A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 removed outlier: 4.878A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 377 removed outlier: 7.294A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N GLU F 352 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS F 353 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS F 371 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.118A 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 384 through 399 removed outlier: 3.760A pdb=" N LEU F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 411 Processing helix chain 'F' and resid 421 through 431 removed outlier: 3.893A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) removed outlier: 3.816A 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 455 Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' 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 131 through 136 Processing helix chain 'E' and resid 155 through 168 Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.657A pdb=" N GLU E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 3.608A 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 233 removed outlier: 5.176A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 271 through 279 removed outlier: 3.537A pdb=" N GLY E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.737A 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 311 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: 4.064A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.754A pdb=" N ALA E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG E 394 " --> pdb=" O VAL E 390 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 432 removed outlier: 3.722A 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 452 through 456 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 198 through 201 Processing helix chain 'D' and resid 213 through 232 removed outlier: 5.014A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 271 through 279 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.726A pdb=" N THR D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 346 through 377 removed outlier: 7.233A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 384 through 399 removed outlier: 3.847A pdb=" N LEU D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.600A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 removed outlier: 3.514A pdb=" N GLY D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.688A pdb=" N VAL D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 41 removed outlier: 4.277A pdb=" N TYR J 10 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 77 removed outlier: 3.740A pdb=" N GLY J 58 " --> pdb=" O PHE J 54 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.871A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA L 14 " --> pdb=" O TYR L 10 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (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: 4.506A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA L 62 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 4.277A 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 41 removed outlier: 3.937A pdb=" N LEU M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 4.071A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.200A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 Proline residue: N 47 - end of helix removed outlier: 3.513A pdb=" N VAL N 56 " --> pdb=" O PHE N 53 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.686A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 41 removed outlier: 3.753A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET O 11 " --> pdb=" O ASP O 7 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.692A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 removed outlier: 3.546A pdb=" N ILE O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 41 removed outlier: 4.132A pdb=" N ALA P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 77 removed outlier: 3.706A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix Processing helix chain 'Q' and resid 4 through 39 removed outlier: 4.482A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA Q 20 " --> pdb=" O MET Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 3.886A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.737A pdb=" N ALA Q 67 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL Q 68 " --> pdb=" O MET Q 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.764A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR R 10 " --> pdb=" O MET R 6 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET R 11 " --> pdb=" O ASP R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 76 removed outlier: 3.711A pdb=" N VAL R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'Y' and resid 3 through 24 removed outlier: 3.528A pdb=" N PHE Y 20 " --> pdb=" O LEU Y 16 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 59 removed outlier: 3.603A pdb=" N GLY Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP Y 53 " --> pdb=" O ARG Y 49 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 101 removed outlier: 3.936A pdb=" N ILE Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA Y 94 " --> pdb=" O ALA Y 90 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN Y 96 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 138 removed outlier: 3.864A pdb=" N ALA Y 107 " --> pdb=" O GLN Y 104 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE Y 109 " --> pdb=" O GLN Y 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA Y 111 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU Y 133 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 removed outlier: 3.502A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU Y 155 " --> pdb=" O LYS Y 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 16 removed outlier: 3.660A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 66 removed outlier: 3.616A pdb=" N PHE a 48 " --> pdb=" O ASP a 44 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL a 50 " --> pdb=" O MET a 46 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS a 66 " --> pdb=" O SER a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 4.400A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 120 removed outlier: 3.813A pdb=" N ALA a 102 " --> pdb=" O LYS a 99 " (cutoff:3.500A) Proline residue: a 103 - end of helix removed outlier: 3.591A pdb=" N TRP a 111 " --> pdb=" O ILE a 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL a 112 " --> pdb=" O PHE a 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET a 118 " --> pdb=" O MET a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 133 removed outlier: 3.636A pdb=" N GLU a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS a 132 " --> pdb=" O TYR a 128 " (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 167 removed outlier: 3.907A pdb=" N LEU a 160 " --> pdb=" O GLY a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 180 removed outlier: 4.005A pdb=" N PHE a 174 " --> pdb=" O GLY a 170 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix removed outlier: 3.793A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE a 194 " --> pdb=" O VAL a 191 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.578A pdb=" N LEU a 209 " --> pdb=" O SER a 206 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY a 213 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN a 214 " --> pdb=" O LEU a 211 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA a 217 " --> pdb=" O ASN a 214 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU a 220 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 3.532A pdb=" N GLN a 234 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TRP a 235 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU a 237 " --> pdb=" O GLN a 234 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL a 239 " --> pdb=" O ILE a 236 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.164A pdb=" N ILE a 255 " --> pdb=" O GLN a 252 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER a 265 " --> pdb=" O VAL a 262 " (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 removed outlier: 3.580A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 Proline residue: I 47 - end of helix removed outlier: 4.675A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL I 60 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.620A pdb=" N ALA I 67 " --> pdb=" O PRO I 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR I 73 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL I 74 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 Processing helix chain 'S' and resid 43 through 75 Proline residue: S 47 - end of helix removed outlier: 3.600A pdb=" N ARG S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE S 55 " --> pdb=" O GLN S 52 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE S 63 " --> pdb=" O VAL S 60 " (cutoff:3.500A) Proline residue: S 64 - end of helix removed outlier: 3.918A pdb=" N LEU S 70 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU S 72 " --> pdb=" O GLY S 69 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL S 74 " --> pdb=" O GLY S 71 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 135 through 142 removed outlier: 3.644A pdb=" N VAL W 110 " --> pdb=" O ASN W 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.564A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.252A 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: 8.450A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C 327 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.648A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.457A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.083A 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: 6.581A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 169 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 221 through 226 removed outlier: 8.783A pdb=" N ILE B 222 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP B 255 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE B 194 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 257 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL B 196 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 259 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 198 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.520A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= L, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.672A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.882A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.065A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 180 through 188 removed outlier: 6.596A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.499A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.805A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.887A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLY F 149 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL F 296 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 4 through 9 removed outlier: 6.347A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.773A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 317 through 319 removed outlier: 3.536A pdb=" N GLY E 146 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR E 173 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE E 240 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL E 175 " --> pdb=" O PHE E 240 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.674A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= X, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.798A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'a' and resid 20 through 22 removed outlier: 4.483A pdb=" N GLN a 20 " --> pdb=" O VAL a 29 " (cutoff:3.500A) 1876 hydrogen bonds defined for protein. 4716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.66 Time building geometry restraints manager: 15.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6333 1.29 - 1.42: 8600 1.42 - 1.55: 22211 1.55 - 1.68: 24 1.68 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.91e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.83e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.38e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.48: 814 105.48 - 113.16: 20943 113.16 - 120.85: 18571 120.85 - 128.53: 10255 128.53 - 136.21: 214 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 139.87 115.95 23.92 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.31e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.91 21.96 1.00e+00 1.00e+00 4.82e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.85 19.98 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 119.58 17.25 1.00e+00 1.00e+00 2.97e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.97: 22044 30.97 - 61.95: 657 61.95 - 92.92: 88 92.92 - 123.90: 2 123.90 - 154.87: 3 Dihedral angle restraints: 22794 sinusoidal: 9010 harmonic: 13784 Sorted by residual: dihedral pdb=" C ASP C 261 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual -122.60 -145.64 23.04 0 2.50e+00 1.60e-01 8.49e+01 dihedral pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual 122.80 145.59 -22.79 0 2.50e+00 1.60e-01 8.31e+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 300.00 145.12 154.87 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 22791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 5897 0.197 - 0.394: 20 0.394 - 0.591: 2 0.591 - 0.789: 0 0.789 - 0.986: 1 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 1.52 0.99 2.00e-01 2.50e+01 2.43e+01 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 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ASP C 262 " pdb=" N ASP C 262 " pdb=" C ASP C 262 " pdb=" CB ASP C 262 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 14 " -0.022 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C ALA I 14 " 0.080 2.00e-02 2.50e+03 pdb=" O ALA I 14 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL I 15 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.022 2.00e-02 2.50e+03 4.53e-02 2.06e+01 pdb=" C ALA D 264 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.028 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 5 " 0.020 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C ASN L 5 " -0.072 2.00e-02 2.50e+03 pdb=" O ASN L 5 " 0.027 2.00e-02 2.50e+03 pdb=" N MET L 6 " 0.025 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 46 2.35 - 2.99: 21951 2.99 - 3.63: 53499 3.63 - 4.26: 84899 4.26 - 4.90: 143932 Nonbonded interactions: 304327 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.718 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.749 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.811 2.170 nonbonded pdb=" OG1 THR F 156 " pdb="MG MG F 501 " model vdw 1.833 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.848 2.170 ... (remaining 304322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 459 or resid 500)) selection = (chain 'E' and (resid 2 through 459 or resid 500)) selection = (chain 'F' and (resid 2 through 459 or resid 500)) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.350 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 95.930 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 0.113 37528 Z= 0.605 Angle : 0.927 23.924 50797 Z= 0.615 Chirality : 0.054 0.986 5920 Planarity : 0.005 0.055 6550 Dihedral : 15.072 154.874 13976 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 9.36 % Favored : 87.72 % Cbeta Deviations : 0.05 % 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: -2.70 (0.10), residues: 4807 helix: -1.84 (0.08), residues: 2579 sheet: -0.92 (0.19), residues: 564 loop : -1.67 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 39 HIS 0.007 0.001 HIS C 123 PHE 0.019 0.002 PHE E 410 TYR 0.031 0.002 TYR E 206 ARG 0.007 0.001 ARG Y 36 *********************** 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 873 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 761 time to evaluate : 4.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 123 LYS cc_start: 0.9192 (mtmt) cc_final: 0.8594 (mmmm) REVERT: W 143 ASP cc_start: 0.8772 (t0) cc_final: 0.8314 (t0) REVERT: C 76 MET cc_start: 0.9129 (mtm) cc_final: 0.8826 (mtm) REVERT: C 115 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8722 (pt) REVERT: C 236 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8852 (t80) REVERT: C 386 MET cc_start: 0.8847 (mmm) cc_final: 0.8278 (mmt) REVERT: C 501 LYS cc_start: 0.8895 (tttm) cc_final: 0.8615 (tttm) REVERT: B 14 GLN cc_start: 0.8253 (mm110) cc_final: 0.7864 (mm-40) REVERT: B 48 MET cc_start: 0.8855 (ptp) cc_final: 0.8449 (ptp) REVERT: B 386 MET cc_start: 0.8743 (mmm) cc_final: 0.8487 (mmt) REVERT: A 180 ILE cc_start: 0.8959 (pt) cc_final: 0.8700 (mm) REVERT: A 483 MET cc_start: 0.8407 (mmp) cc_final: 0.8188 (mmm) REVERT: A 511 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.5652 (tp-100) REVERT: X 20 PHE cc_start: 0.6781 (m-80) cc_final: 0.6404 (m-80) REVERT: X 37 GLN cc_start: 0.8066 (mm110) cc_final: 0.7840 (mm-40) REVERT: X 78 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7583 (tm-30) REVERT: X 146 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8467 (p) REVERT: X 150 ASP cc_start: 0.9105 (m-30) cc_final: 0.8878 (m-30) REVERT: H 51 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7694 (ttm110) REVERT: H 58 HIS cc_start: 0.7663 (m-70) cc_final: 0.7297 (m90) REVERT: G 57 HIS cc_start: 0.7308 (p-80) cc_final: 0.7002 (p-80) REVERT: G 116 MET cc_start: 0.9281 (mmm) cc_final: 0.8954 (mmm) REVERT: F 340 THR cc_start: 0.8653 (m) cc_final: 0.8430 (m) REVERT: E 97 MET cc_start: 0.8713 (mmt) cc_final: 0.8415 (mmm) REVERT: D 88 MET cc_start: 0.9105 (mtm) cc_final: 0.8899 (mtp) REVERT: D 301 ASP cc_start: 0.8293 (t0) cc_final: 0.7816 (t0) REVERT: D 322 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8436 (p) REVERT: J 55 ILE cc_start: 0.8362 (mm) cc_final: 0.8054 (mm) REVERT: L 63 ILE cc_start: 0.8522 (mm) cc_final: 0.8218 (mm) REVERT: L 68 VAL cc_start: 0.8930 (t) cc_final: 0.8574 (p) REVERT: L 73 TYR cc_start: 0.9004 (t80) cc_final: 0.8591 (t80) REVERT: M 6 MET cc_start: 0.6801 (mtt) cc_final: 0.6386 (mtm) REVERT: M 7 ASP cc_start: 0.7565 (m-30) cc_final: 0.7108 (p0) REVERT: N 16 MET cc_start: 0.7907 (mtp) cc_final: 0.7608 (tpp) REVERT: N 34 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7934 (mmtp) REVERT: O 7 ASP cc_start: 0.7021 (p0) cc_final: 0.6808 (p0) REVERT: O 8 LEU cc_start: 0.8431 (mt) cc_final: 0.7009 (tt) REVERT: O 42 GLN cc_start: 0.8789 (mm-40) cc_final: 0.7842 (mp10) REVERT: P 11 MET cc_start: 0.8391 (tpp) cc_final: 0.7738 (mmm) REVERT: P 17 MET cc_start: 0.8188 (mtm) cc_final: 0.7644 (mtt) REVERT: P 61 ASP cc_start: 0.8510 (m-30) cc_final: 0.8093 (m-30) REVERT: Q 16 MET cc_start: 0.8725 (ttm) cc_final: 0.8484 (ttm) REVERT: Q 35 PHE cc_start: 0.8651 (t80) cc_final: 0.8310 (t80) REVERT: Q 36 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8819 (tt) REVERT: R 34 LYS cc_start: 0.8176 (mmtm) cc_final: 0.7452 (mmtm) REVERT: R 48 LEU cc_start: 0.8310 (tp) cc_final: 0.7797 (tt) REVERT: R 51 THR cc_start: 0.9311 (m) cc_final: 0.8688 (p) REVERT: R 52 GLN cc_start: 0.8950 (mm110) cc_final: 0.8337 (mm110) REVERT: R 76 PHE cc_start: 0.8026 (m-80) cc_final: 0.7778 (m-80) REVERT: Y 85 GLN cc_start: 0.8652 (tp40) cc_final: 0.8235 (tp40) REVERT: Y 150 ASP cc_start: 0.8979 (m-30) cc_final: 0.8674 (m-30) REVERT: a 6 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.4085 (tpt) REVERT: a 9 GLN cc_start: 0.8768 (mt0) cc_final: 0.8565 (pm20) REVERT: a 94 TYR cc_start: 0.6622 (t80) cc_final: 0.6368 (t80) REVERT: a 99 LYS cc_start: 0.7473 (mppt) cc_final: 0.7026 (ttpt) REVERT: a 203 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8659 (mttp) REVERT: a 219 GLU cc_start: 0.9113 (tt0) cc_final: 0.8812 (tt0) REVERT: a 237 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8951 (tt) REVERT: a 263 TYR cc_start: 0.8672 (m-10) cc_final: 0.8453 (m-80) REVERT: I 17 MET cc_start: 0.8076 (ptp) cc_final: 0.7422 (ttp) REVERT: I 35 PHE cc_start: 0.8912 (t80) cc_final: 0.8493 (t80) REVERT: S 37 GLU cc_start: 0.8911 (tt0) cc_final: 0.8418 (tt0) REVERT: S 50 ARG cc_start: 0.8303 (ttm170) cc_final: 0.8034 (ttp-170) outliers start: 112 outliers final: 68 residues processed: 859 average time/residue: 0.5213 time to fit residues: 709.1081 Evaluate side-chains 668 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 592 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 115 ILE 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 374 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 46 SER Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 17 ASN Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 32 GLN Chi-restraints excluded: chain a residue 57 LEU Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 241 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 370 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 429 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 71 ASN W 94 GLN C 369 ASN B 26 HIS B 186 GLN B 408 GLN A 20 ASN A 65 ASN A 147 GLN A 408 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 145 ASN H 14 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN G 274 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN F 353 HIS F 437 HIS E 441 GLN D 73 HIS D 170 HIS D 437 HIS J 52 GLN L 3 ASN L 5 ASN M 5 ASN N 3 ASN O 3 ASN P 3 ASN R 52 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37528 Z= 0.192 Angle : 0.625 9.030 50797 Z= 0.325 Chirality : 0.043 0.307 5920 Planarity : 0.005 0.067 6550 Dihedral : 8.640 143.035 5464 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.52 % Allowed : 12.10 % Favored : 84.38 % 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: -0.97 (0.12), residues: 4807 helix: -0.34 (0.10), residues: 2625 sheet: -0.57 (0.21), residues: 522 loop : -0.90 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 513 HIS 0.005 0.001 HIS a 245 PHE 0.017 0.001 PHE Y 17 TYR 0.017 0.001 TYR B 236 ARG 0.007 0.001 ARG X 98 *********************** 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 791 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 656 time to evaluate : 4.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 43 MET cc_start: 0.9173 (tpt) cc_final: 0.8878 (tpp) REVERT: W 135 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8409 (ttpp) REVERT: W 143 ASP cc_start: 0.8723 (t0) cc_final: 0.8305 (t0) REVERT: C 27 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7957 (p0) REVERT: C 170 ASP cc_start: 0.7696 (m-30) cc_final: 0.7409 (m-30) REVERT: C 236 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.8685 (t80) REVERT: B 97 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8746 (m) REVERT: B 180 ILE cc_start: 0.8950 (pt) cc_final: 0.8723 (mt) REVERT: B 386 MET cc_start: 0.8823 (mmm) cc_final: 0.8500 (mmt) REVERT: B 415 ASP cc_start: 0.8118 (t0) cc_final: 0.7756 (t0) REVERT: B 419 LYS cc_start: 0.8231 (tptt) cc_final: 0.8024 (pttp) REVERT: A 49 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8931 (tp40) REVERT: A 418 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7469 (tpp-160) REVERT: A 501 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8807 (tptm) REVERT: X 20 PHE cc_start: 0.6560 (m-80) cc_final: 0.6179 (m-80) REVERT: X 49 ARG cc_start: 0.7615 (ttp80) cc_final: 0.7330 (ttp80) REVERT: X 96 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8699 (mm-40) REVERT: H 31 GLU cc_start: 0.7856 (tt0) cc_final: 0.7392 (tt0) REVERT: H 58 HIS cc_start: 0.7368 (m-70) cc_final: 0.7076 (m90) REVERT: H 65 SER cc_start: 0.8995 (m) cc_final: 0.8196 (t) REVERT: G 259 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7703 (mp0) REVERT: F 141 LYS cc_start: 0.9287 (tttt) cc_final: 0.8874 (ttpp) REVERT: F 366 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8367 (tpp-160) REVERT: E 14 ASP cc_start: 0.7901 (m-30) cc_final: 0.7527 (m-30) REVERT: E 97 MET cc_start: 0.8572 (mmt) cc_final: 0.8370 (mmm) REVERT: E 209 MET cc_start: 0.8482 (mtm) cc_final: 0.8213 (mtm) REVERT: E 316 ASP cc_start: 0.8288 (m-30) cc_final: 0.8030 (m-30) REVERT: E 410 PHE cc_start: 0.8201 (m-80) cc_final: 0.7958 (m-80) REVERT: D 166 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9005 (mp) REVERT: D 301 ASP cc_start: 0.8111 (t0) cc_final: 0.7689 (t0) REVERT: J 37 GLU cc_start: 0.8348 (pp20) cc_final: 0.7661 (pp20) REVERT: J 41 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.8004 (ttm110) REVERT: J 55 ILE cc_start: 0.8537 (mm) cc_final: 0.8203 (mm) REVERT: L 8 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7649 (tm) REVERT: L 37 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8346 (tp30) REVERT: L 41 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8532 (mtp180) REVERT: N 3 ASN cc_start: 0.4925 (OUTLIER) cc_final: 0.3904 (t0) REVERT: N 16 MET cc_start: 0.7873 (mtp) cc_final: 0.7641 (tpp) REVERT: N 17 MET cc_start: 0.8784 (mmm) cc_final: 0.8312 (mmm) REVERT: O 16 MET cc_start: 0.8081 (ttp) cc_final: 0.7035 (mmm) REVERT: O 42 GLN cc_start: 0.8556 (mm-40) cc_final: 0.7638 (mp10) REVERT: P 3 ASN cc_start: 0.0655 (OUTLIER) cc_final: 0.0359 (m-40) REVERT: P 11 MET cc_start: 0.8210 (tpp) cc_final: 0.7650 (mmm) REVERT: P 48 LEU cc_start: 0.9142 (tp) cc_final: 0.8791 (tp) REVERT: P 51 THR cc_start: 0.8843 (p) cc_final: 0.8499 (p) REVERT: P 52 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8562 (mm-40) REVERT: P 54 PHE cc_start: 0.8638 (m-80) cc_final: 0.8259 (m-80) REVERT: P 61 ASP cc_start: 0.8657 (m-30) cc_final: 0.8286 (m-30) REVERT: P 64 PRO cc_start: 0.9167 (Cg_exo) cc_final: 0.8967 (Cg_endo) REVERT: Q 11 MET cc_start: 0.8388 (tpp) cc_final: 0.8140 (tpp) REVERT: Q 16 MET cc_start: 0.8670 (ttm) cc_final: 0.8468 (ttm) REVERT: Q 51 THR cc_start: 0.8591 (m) cc_final: 0.8331 (p) REVERT: R 48 LEU cc_start: 0.8089 (tp) cc_final: 0.7856 (tt) REVERT: R 51 THR cc_start: 0.9357 (m) cc_final: 0.9151 (p) REVERT: R 70 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7857 (tp) REVERT: R 75 MET cc_start: 0.8647 (ttt) cc_final: 0.7820 (tpp) REVERT: Y 53 ASP cc_start: 0.6096 (t0) cc_final: 0.5769 (t0) REVERT: Y 80 ASN cc_start: 0.8180 (m-40) cc_final: 0.7455 (m110) REVERT: Y 150 ASP cc_start: 0.8912 (m-30) cc_final: 0.8525 (m-30) REVERT: a 11 TYR cc_start: 0.7975 (t80) cc_final: 0.7733 (t80) REVERT: a 56 PHE cc_start: 0.8263 (t80) cc_final: 0.8056 (t80) REVERT: a 76 GLN cc_start: 0.6667 (tt0) cc_final: 0.6185 (pt0) REVERT: a 99 LYS cc_start: 0.7382 (mppt) cc_final: 0.6922 (ttpt) REVERT: a 203 LYS cc_start: 0.9067 (mtpp) cc_final: 0.8806 (mttp) REVERT: a 219 GLU cc_start: 0.9049 (tt0) cc_final: 0.8737 (tt0) REVERT: a 237 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8925 (tt) REVERT: I 11 MET cc_start: 0.8595 (mmt) cc_final: 0.8334 (mmt) REVERT: I 16 MET cc_start: 0.8350 (tpp) cc_final: 0.8002 (mmm) REVERT: I 17 MET cc_start: 0.7941 (ptp) cc_final: 0.7433 (ttp) REVERT: I 61 ASP cc_start: 0.8635 (m-30) cc_final: 0.8403 (m-30) REVERT: I 65 MET cc_start: 0.8244 (mmm) cc_final: 0.7698 (mmp) REVERT: S 50 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7749 (ttp-170) REVERT: S 61 ASP cc_start: 0.7373 (p0) cc_final: 0.7048 (t0) outliers start: 135 outliers final: 60 residues processed: 750 average time/residue: 0.5188 time to fit residues: 639.1952 Evaluate side-chains 663 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 592 time to evaluate : 4.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 27 ASN 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 32 VAL 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 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 357 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 430 optimal weight: 1.9990 chunk 464 optimal weight: 2.9990 chunk 383 optimal weight: 8.9990 chunk 426 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 345 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN B 147 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN G 274 GLN F 368 GLN N 3 ASN O 52 GLN P 3 ASN Y 10 GLN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN S 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 37528 Z= 0.358 Angle : 0.643 11.460 50797 Z= 0.329 Chirality : 0.045 0.252 5920 Planarity : 0.005 0.049 6550 Dihedral : 7.888 153.540 5395 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.83 % Allowed : 13.95 % Favored : 82.22 % 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: -0.62 (0.12), residues: 4807 helix: -0.01 (0.10), residues: 2623 sheet: -0.46 (0.22), residues: 515 loop : -0.81 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 235 HIS 0.004 0.001 HIS G 64 PHE 0.032 0.002 PHE E 189 TYR 0.019 0.002 TYR B 400 ARG 0.007 0.000 ARG H 99 *********************** 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 757 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 610 time to evaluate : 4.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 43 MET cc_start: 0.9238 (tpt) cc_final: 0.8851 (tpp) REVERT: W 135 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8423 (ttpp) REVERT: W 143 ASP cc_start: 0.8627 (t0) cc_final: 0.8182 (t0) REVERT: C 27 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8166 (p0) REVERT: C 48 MET cc_start: 0.8580 (mtm) cc_final: 0.8133 (mtt) REVERT: C 170 ASP cc_start: 0.7714 (m-30) cc_final: 0.7440 (m-30) REVERT: C 236 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8835 (t80) REVERT: C 413 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8738 (mp) REVERT: B 97 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8773 (m) REVERT: B 180 ILE cc_start: 0.9016 (pt) cc_final: 0.8791 (mt) REVERT: B 386 MET cc_start: 0.8760 (mmm) cc_final: 0.8498 (mmt) REVERT: A 49 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.9003 (tp40) REVERT: A 418 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7583 (tpp-160) REVERT: X 2 ASN cc_start: 0.6507 (t0) cc_final: 0.6300 (t0) REVERT: X 15 VAL cc_start: 0.8005 (p) cc_final: 0.7707 (m) REVERT: X 20 PHE cc_start: 0.6625 (m-80) cc_final: 0.6159 (m-80) REVERT: X 96 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8690 (mm-40) REVERT: H 22 LYS cc_start: 0.8853 (ptpt) cc_final: 0.8476 (pttt) REVERT: H 58 HIS cc_start: 0.7363 (m-70) cc_final: 0.7039 (m90) REVERT: H 65 SER cc_start: 0.9057 (m) cc_final: 0.8477 (t) REVERT: H 72 GLN cc_start: 0.7113 (mt0) cc_final: 0.6865 (mp10) REVERT: G 116 MET cc_start: 0.9265 (mmm) cc_final: 0.8979 (mmm) REVERT: G 259 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7904 (mp0) REVERT: F 141 LYS cc_start: 0.9282 (tttt) cc_final: 0.8904 (ttpp) REVERT: F 366 ARG cc_start: 0.8644 (tpp80) cc_final: 0.8426 (tpp-160) REVERT: E 14 ASP cc_start: 0.8080 (m-30) cc_final: 0.7705 (m-30) REVERT: E 316 ASP cc_start: 0.8309 (m-30) cc_final: 0.7989 (m-30) REVERT: E 410 PHE cc_start: 0.8231 (m-80) cc_final: 0.7926 (m-80) REVERT: D 166 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9009 (mp) REVERT: D 301 ASP cc_start: 0.8057 (t0) cc_final: 0.7711 (t0) REVERT: D 458 LYS cc_start: 0.8020 (mmtm) cc_final: 0.7793 (mppt) REVERT: J 34 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7474 (mmtm) REVERT: J 37 GLU cc_start: 0.8195 (pp20) cc_final: 0.7810 (pp20) REVERT: J 41 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.7976 (ttm110) REVERT: J 55 ILE cc_start: 0.8595 (mm) cc_final: 0.8340 (mm) REVERT: L 11 MET cc_start: 0.8930 (mmm) cc_final: 0.8652 (mmm) REVERT: L 41 ARG cc_start: 0.8877 (mmm-85) cc_final: 0.8657 (mtm180) REVERT: L 42 GLN cc_start: 0.8300 (mp10) cc_final: 0.7900 (mp10) REVERT: M 10 TYR cc_start: 0.8307 (m-80) cc_final: 0.7651 (m-80) REVERT: M 37 GLU cc_start: 0.8195 (tt0) cc_final: 0.7947 (tt0) REVERT: N 3 ASN cc_start: 0.5072 (OUTLIER) cc_final: 0.3901 (p0) REVERT: N 9 LEU cc_start: 0.8011 (mm) cc_final: 0.7652 (mp) REVERT: N 16 MET cc_start: 0.7732 (mtp) cc_final: 0.7152 (tpp) REVERT: N 65 MET cc_start: 0.8716 (mmm) cc_final: 0.8412 (mmm) REVERT: O 42 GLN cc_start: 0.8495 (mm-40) cc_final: 0.7612 (mp10) REVERT: O 70 LEU cc_start: 0.8471 (mp) cc_final: 0.8191 (tp) REVERT: P 11 MET cc_start: 0.8433 (tpp) cc_final: 0.7773 (mmm) REVERT: P 52 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8849 (mp10) REVERT: P 54 PHE cc_start: 0.8661 (m-80) cc_final: 0.8304 (m-80) REVERT: P 61 ASP cc_start: 0.8606 (m-30) cc_final: 0.8346 (m-30) REVERT: Q 35 PHE cc_start: 0.8569 (t80) cc_final: 0.8324 (t80) REVERT: Q 42 GLN cc_start: 0.8932 (mt0) cc_final: 0.8605 (mp10) REVERT: Q 51 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8291 (p) REVERT: R 48 LEU cc_start: 0.8119 (tp) cc_final: 0.7621 (tt) REVERT: R 51 THR cc_start: 0.9365 (m) cc_final: 0.9022 (p) REVERT: R 52 GLN cc_start: 0.8925 (mm-40) cc_final: 0.8644 (mm110) REVERT: R 70 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7809 (tt) REVERT: Y 80 ASN cc_start: 0.8178 (m-40) cc_final: 0.7464 (m110) REVERT: Y 150 ASP cc_start: 0.8922 (m-30) cc_final: 0.8531 (m-30) REVERT: a 99 LYS cc_start: 0.7315 (mppt) cc_final: 0.6864 (ttpt) REVERT: a 203 LYS cc_start: 0.9247 (mtpp) cc_final: 0.8748 (mttp) REVERT: a 235 TRP cc_start: 0.8030 (p-90) cc_final: 0.7707 (p-90) REVERT: I 54 PHE cc_start: 0.9342 (m-80) cc_final: 0.8995 (m-80) REVERT: S 37 GLU cc_start: 0.9050 (tt0) cc_final: 0.8453 (tt0) REVERT: S 50 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7907 (ttp-170) REVERT: S 61 ASP cc_start: 0.7345 (p0) cc_final: 0.6987 (t0) outliers start: 147 outliers final: 100 residues processed: 713 average time/residue: 0.4968 time to fit residues: 574.3383 Evaluate side-chains 688 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 579 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 39 ILE 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 153 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 81 LYS 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 224 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 17 ASN Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 191 VAL Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 6.9990 chunk 323 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 431 optimal weight: 0.8980 chunk 457 optimal weight: 0.9980 chunk 225 optimal weight: 0.9980 chunk 409 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 94 GLN B 399 GLN A 358 ASN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN N 3 ASN O 3 ASN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2528 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= 0.197 Angle : 0.571 8.767 50797 Z= 0.291 Chirality : 0.042 0.193 5920 Planarity : 0.004 0.043 6550 Dihedral : 7.390 150.705 5390 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.21 % Allowed : 15.25 % Favored : 81.54 % 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: -0.24 (0.12), residues: 4807 helix: 0.33 (0.10), residues: 2616 sheet: -0.34 (0.22), residues: 513 loop : -0.69 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 235 HIS 0.003 0.001 HIS F 170 PHE 0.027 0.001 PHE E 189 TYR 0.015 0.001 TYR B 236 ARG 0.008 0.000 ARG I 50 *********************** 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 760 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 637 time to evaluate : 4.430 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 135 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8374 (ttpp) REVERT: W 143 ASP cc_start: 0.8636 (t0) cc_final: 0.8234 (t0) REVERT: W 146 VAL cc_start: 0.7360 (OUTLIER) cc_final: 0.6946 (p) REVERT: C 27 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8243 (p0) REVERT: C 48 MET cc_start: 0.8555 (mtm) cc_final: 0.8117 (mtt) REVERT: C 170 ASP cc_start: 0.7654 (m-30) cc_final: 0.7407 (m-30) REVERT: C 236 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8838 (t80) REVERT: B 415 ASP cc_start: 0.8007 (t70) cc_final: 0.7604 (t0) REVERT: A 49 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.9029 (tp40) REVERT: A 356 GLU cc_start: 0.7628 (tp30) cc_final: 0.7384 (tp30) REVERT: A 418 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7640 (tpp-160) REVERT: A 463 LYS cc_start: 0.6232 (tttt) cc_final: 0.5931 (tttp) REVERT: A 501 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8920 (tptm) REVERT: X 15 VAL cc_start: 0.8004 (p) cc_final: 0.7721 (m) REVERT: X 17 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: X 20 PHE cc_start: 0.6603 (m-80) cc_final: 0.6111 (m-80) REVERT: X 49 ARG cc_start: 0.7458 (ttp80) cc_final: 0.7167 (ttp80) REVERT: X 96 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8710 (mm-40) REVERT: H 52 ILE cc_start: 0.8959 (mm) cc_final: 0.8752 (mt) REVERT: H 58 HIS cc_start: 0.7241 (m-70) cc_final: 0.6862 (m90) REVERT: H 65 SER cc_start: 0.9028 (m) cc_final: 0.8338 (t) REVERT: H 72 GLN cc_start: 0.6941 (mt0) cc_final: 0.6713 (mp10) REVERT: F 141 LYS cc_start: 0.9228 (tttt) cc_final: 0.8867 (ttpp) REVERT: E 14 ASP cc_start: 0.8004 (m-30) cc_final: 0.7523 (m-30) REVERT: E 410 PHE cc_start: 0.8198 (m-80) cc_final: 0.7939 (m-80) REVERT: D 166 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9012 (mp) REVERT: D 301 ASP cc_start: 0.8075 (t0) cc_final: 0.7761 (t0) REVERT: J 37 GLU cc_start: 0.8194 (pp20) cc_final: 0.7966 (pp20) REVERT: J 55 ILE cc_start: 0.8539 (mm) cc_final: 0.8298 (mm) REVERT: L 41 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8600 (mtm180) REVERT: M 10 TYR cc_start: 0.8191 (m-80) cc_final: 0.7618 (m-80) REVERT: M 37 GLU cc_start: 0.8205 (tt0) cc_final: 0.7869 (tt0) REVERT: N 3 ASN cc_start: 0.4737 (OUTLIER) cc_final: 0.4192 (t0) REVERT: N 9 LEU cc_start: 0.7984 (mm) cc_final: 0.7618 (mp) REVERT: N 17 MET cc_start: 0.8951 (mmm) cc_final: 0.8655 (mmm) REVERT: N 65 MET cc_start: 0.8683 (mmm) cc_final: 0.8470 (tpp) REVERT: O 7 ASP cc_start: 0.5408 (p0) cc_final: 0.5021 (p0) REVERT: O 8 LEU cc_start: 0.8189 (mt) cc_final: 0.7173 (mp) REVERT: O 42 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7408 (mp10) REVERT: O 57 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7592 (ppp) REVERT: P 11 MET cc_start: 0.8505 (tpp) cc_final: 0.7818 (mmm) REVERT: P 42 GLN cc_start: 0.8348 (mm110) cc_final: 0.7941 (mm110) REVERT: P 46 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8634 (mm) REVERT: P 50 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.8021 (ptp-110) REVERT: P 52 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8772 (mp10) REVERT: P 54 PHE cc_start: 0.8489 (m-10) cc_final: 0.8090 (m-80) REVERT: Q 28 ILE cc_start: 0.8825 (mm) cc_final: 0.8526 (mm) REVERT: Q 35 PHE cc_start: 0.8607 (t80) cc_final: 0.8370 (t80) REVERT: Q 42 GLN cc_start: 0.8890 (mt0) cc_final: 0.8579 (mp10) REVERT: Q 51 THR cc_start: 0.8549 (m) cc_final: 0.8288 (p) REVERT: R 11 MET cc_start: 0.8599 (tpp) cc_final: 0.8344 (tpp) REVERT: R 48 LEU cc_start: 0.7988 (tp) cc_final: 0.7779 (tt) REVERT: R 75 MET cc_start: 0.8727 (tpt) cc_final: 0.8354 (tpt) REVERT: Y 80 ASN cc_start: 0.8192 (m-40) cc_final: 0.7488 (m110) REVERT: Y 150 ASP cc_start: 0.8863 (m-30) cc_final: 0.8644 (m-30) REVERT: a 99 LYS cc_start: 0.7292 (mppt) cc_final: 0.6884 (ttpt) REVERT: a 203 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8876 (mttp) REVERT: a 237 LEU cc_start: 0.9229 (mp) cc_final: 0.8879 (tt) REVERT: I 41 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7786 (ttm-80) REVERT: I 54 PHE cc_start: 0.9280 (m-80) cc_final: 0.8427 (m-80) REVERT: S 16 MET cc_start: 0.7987 (tpp) cc_final: 0.7615 (mtt) REVERT: S 37 GLU cc_start: 0.9080 (tt0) cc_final: 0.8491 (tt0) outliers start: 123 outliers final: 78 residues processed: 730 average time/residue: 0.4905 time to fit residues: 583.1563 Evaluate side-chains 673 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 585 time to evaluate : 4.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 17 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 81 LYS 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 224 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 219 GLU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 0.2980 chunk 259 optimal weight: 4.9990 chunk 6 optimal weight: 0.0770 chunk 340 optimal weight: 4.9990 chunk 188 optimal weight: 0.6980 chunk 390 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 233 optimal weight: 0.6980 chunk 410 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN L 3 ASN L 5 ASN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN a 20 GLN a 76 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 245 HIS S 3 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 37528 Z= 0.155 Angle : 0.557 10.939 50797 Z= 0.281 Chirality : 0.042 0.196 5920 Planarity : 0.004 0.043 6550 Dihedral : 6.886 148.433 5382 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.05 % Allowed : 15.90 % 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: 0.12 (0.12), residues: 4807 helix: 0.62 (0.10), residues: 2598 sheet: -0.15 (0.22), residues: 512 loop : -0.52 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 235 HIS 0.002 0.000 HIS a 95 PHE 0.024 0.001 PHE a 56 TYR 0.017 0.001 TYR Q 73 ARG 0.009 0.000 ARG I 50 *********************** 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 739 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 622 time to evaluate : 4.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 135 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8348 (ttpp) REVERT: W 143 ASP cc_start: 0.8559 (t0) cc_final: 0.8202 (t0) REVERT: W 146 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.6879 (p) REVERT: C 170 ASP cc_start: 0.7653 (m-30) cc_final: 0.7443 (m-30) REVERT: C 236 TYR cc_start: 0.9160 (OUTLIER) cc_final: 0.8749 (t80) REVERT: C 413 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 274 SER cc_start: 0.9151 (t) cc_final: 0.8894 (p) REVERT: A 356 GLU cc_start: 0.7585 (tp30) cc_final: 0.7323 (tp30) REVERT: A 418 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7544 (tpp-160) REVERT: A 463 LYS cc_start: 0.5897 (tttt) cc_final: 0.5489 (tttp) REVERT: A 501 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8897 (tptm) REVERT: X 15 VAL cc_start: 0.8028 (p) cc_final: 0.7733 (m) REVERT: X 20 PHE cc_start: 0.6405 (m-80) cc_final: 0.6037 (m-80) REVERT: X 83 ARG cc_start: 0.7376 (ttt90) cc_final: 0.7119 (ttt90) REVERT: H 22 LYS cc_start: 0.8831 (ptpt) cc_final: 0.8499 (pttt) REVERT: H 26 THR cc_start: 0.8986 (t) cc_final: 0.8700 (p) REVERT: H 58 HIS cc_start: 0.7094 (m-70) cc_final: 0.6656 (m90) REVERT: H 65 SER cc_start: 0.9028 (m) cc_final: 0.8262 (t) REVERT: G 83 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8513 (t0) REVERT: G 116 MET cc_start: 0.9353 (mmm) cc_final: 0.8964 (mmm) REVERT: G 259 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7814 (mp0) REVERT: F 141 LYS cc_start: 0.9215 (tttt) cc_final: 0.8898 (ttpp) REVERT: E 14 ASP cc_start: 0.7972 (m-30) cc_final: 0.7505 (m-30) REVERT: E 410 PHE cc_start: 0.8145 (m-80) cc_final: 0.7912 (m-80) REVERT: D 301 ASP cc_start: 0.8112 (t0) cc_final: 0.7828 (t0) REVERT: J 37 GLU cc_start: 0.8165 (pp20) cc_final: 0.7823 (pp20) REVERT: J 72 LEU cc_start: 0.9236 (mm) cc_final: 0.9027 (mm) REVERT: L 11 MET cc_start: 0.8815 (mmm) cc_final: 0.8587 (mmm) REVERT: N 3 ASN cc_start: 0.4477 (OUTLIER) cc_final: 0.4076 (m110) REVERT: N 9 LEU cc_start: 0.7971 (mm) cc_final: 0.7646 (mp) REVERT: N 17 MET cc_start: 0.8978 (mmm) cc_final: 0.8767 (mmm) REVERT: O 41 ARG cc_start: 0.8615 (ttm170) cc_final: 0.7967 (ttm-80) REVERT: O 42 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7340 (mp10) REVERT: O 57 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7625 (ppp) REVERT: O 63 ILE cc_start: 0.7984 (mm) cc_final: 0.7605 (mm) REVERT: P 11 MET cc_start: 0.8496 (tpp) cc_final: 0.7746 (mmm) REVERT: P 42 GLN cc_start: 0.8412 (mm110) cc_final: 0.7980 (mm110) REVERT: P 46 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8699 (mm) REVERT: P 52 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8818 (mp10) REVERT: P 54 PHE cc_start: 0.8505 (m-10) cc_final: 0.8199 (m-80) REVERT: P 61 ASP cc_start: 0.8858 (m-30) cc_final: 0.8455 (p0) REVERT: Q 35 PHE cc_start: 0.8602 (t80) cc_final: 0.8398 (t80) REVERT: Q 42 GLN cc_start: 0.8869 (mt0) cc_final: 0.8647 (mp10) REVERT: Q 51 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8165 (p) REVERT: R 48 LEU cc_start: 0.7716 (tp) cc_final: 0.7422 (tt) REVERT: R 52 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8762 (mm110) REVERT: R 75 MET cc_start: 0.8671 (tpt) cc_final: 0.8319 (tpt) REVERT: Y 80 ASN cc_start: 0.8277 (m-40) cc_final: 0.7613 (m110) REVERT: Y 82 ARG cc_start: 0.8148 (tpp-160) cc_final: 0.7920 (tpp-160) REVERT: Y 150 ASP cc_start: 0.8946 (m-30) cc_final: 0.8611 (m-30) REVERT: a 94 TYR cc_start: 0.6625 (t80) cc_final: 0.6346 (t80) REVERT: a 99 LYS cc_start: 0.7215 (mppt) cc_final: 0.6772 (ttpt) REVERT: a 203 LYS cc_start: 0.9219 (mtpp) cc_final: 0.8877 (mttt) REVERT: a 257 MET cc_start: 0.9115 (ttp) cc_final: 0.8642 (tmm) REVERT: I 16 MET cc_start: 0.8536 (tpp) cc_final: 0.7969 (mmm) REVERT: I 41 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7850 (ttm-80) REVERT: I 54 PHE cc_start: 0.9306 (m-80) cc_final: 0.8644 (m-80) REVERT: S 16 MET cc_start: 0.8066 (tpp) cc_final: 0.7674 (mtt) outliers start: 117 outliers final: 79 residues processed: 706 average time/residue: 0.4992 time to fit residues: 570.4827 Evaluate side-chains 678 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 590 time to evaluate : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 67 GLU 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 C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 57 MET Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 95 HIS Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 219 GLU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 4.9990 chunk 411 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 457 optimal weight: 2.9990 chunk 379 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 73 GLN X 64 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 37528 Z= 0.281 Angle : 0.597 9.921 50797 Z= 0.299 Chirality : 0.043 0.201 5920 Planarity : 0.004 0.053 6550 Dihedral : 6.873 152.886 5374 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.73 % Allowed : 15.85 % Favored : 80.42 % 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: 0.15 (0.12), residues: 4807 helix: 0.67 (0.10), residues: 2612 sheet: -0.18 (0.22), residues: 521 loop : -0.57 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP a 235 HIS 0.004 0.001 HIS a 132 PHE 0.020 0.001 PHE a 109 TYR 0.016 0.001 TYR B 236 ARG 0.013 0.000 ARG P 50 *********************** 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 741 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 598 time to evaluate : 4.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 135 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8333 (ttpp) REVERT: W 143 ASP cc_start: 0.8499 (t0) cc_final: 0.8129 (t0) REVERT: W 146 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.6939 (p) REVERT: C 170 ASP cc_start: 0.7686 (m-30) cc_final: 0.7388 (m-30) REVERT: C 236 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8853 (t80) REVERT: C 413 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8685 (mp) REVERT: B 14 GLN cc_start: 0.8090 (pt0) cc_final: 0.7756 (pt0) REVERT: A 356 GLU cc_start: 0.7560 (tp30) cc_final: 0.7316 (tp30) REVERT: A 418 ARG cc_start: 0.7843 (tpp80) cc_final: 0.7559 (tpp-160) REVERT: A 463 LYS cc_start: 0.6156 (tttt) cc_final: 0.5882 (tttp) REVERT: A 501 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8901 (tptm) REVERT: X 15 VAL cc_start: 0.8017 (p) cc_final: 0.7724 (m) REVERT: X 20 PHE cc_start: 0.6392 (m-80) cc_final: 0.6029 (m-80) REVERT: H 22 LYS cc_start: 0.8834 (ptpt) cc_final: 0.8499 (pttt) REVERT: H 26 THR cc_start: 0.9043 (t) cc_final: 0.8825 (p) REVERT: H 58 HIS cc_start: 0.7164 (m-70) cc_final: 0.6704 (m90) REVERT: H 65 SER cc_start: 0.9043 (m) cc_final: 0.8460 (t) REVERT: H 132 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: G 83 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8628 (t0) REVERT: F 141 LYS cc_start: 0.9212 (tttt) cc_final: 0.8892 (ttpp) REVERT: E 410 PHE cc_start: 0.8170 (m-80) cc_final: 0.7849 (m-80) REVERT: J 11 MET cc_start: 0.8606 (mmt) cc_final: 0.8359 (tpp) REVERT: J 37 GLU cc_start: 0.8061 (pp20) cc_final: 0.7810 (pp20) REVERT: L 63 ILE cc_start: 0.8718 (mp) cc_final: 0.8225 (mm) REVERT: N 3 ASN cc_start: 0.4486 (OUTLIER) cc_final: 0.4235 (m-40) REVERT: N 9 LEU cc_start: 0.8104 (mm) cc_final: 0.7778 (mp) REVERT: O 41 ARG cc_start: 0.8644 (ttm170) cc_final: 0.8173 (ttm170) REVERT: O 42 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7481 (mp10) REVERT: O 57 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7691 (ppp) REVERT: O 63 ILE cc_start: 0.8058 (mm) cc_final: 0.7651 (mm) REVERT: P 11 MET cc_start: 0.8511 (tpp) cc_final: 0.7769 (mmm) REVERT: P 42 GLN cc_start: 0.8418 (mm110) cc_final: 0.8140 (mm-40) REVERT: P 52 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8704 (mp10) REVERT: P 54 PHE cc_start: 0.8283 (m-10) cc_final: 0.7999 (m-80) REVERT: P 61 ASP cc_start: 0.8835 (m-30) cc_final: 0.8284 (m-30) REVERT: Q 35 PHE cc_start: 0.8616 (t80) cc_final: 0.8403 (t80) REVERT: Q 42 GLN cc_start: 0.8884 (mt0) cc_final: 0.8586 (mp10) REVERT: Q 51 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8207 (p) REVERT: R 11 MET cc_start: 0.8634 (tpp) cc_final: 0.8367 (tpp) REVERT: R 37 GLU cc_start: 0.7927 (pp20) cc_final: 0.7668 (pp20) REVERT: R 48 LEU cc_start: 0.7750 (tp) cc_final: 0.7476 (tt) REVERT: R 52 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8696 (mm110) REVERT: Y 80 ASN cc_start: 0.8249 (m-40) cc_final: 0.7576 (m110) REVERT: Y 150 ASP cc_start: 0.8959 (m-30) cc_final: 0.8623 (m-30) REVERT: a 94 TYR cc_start: 0.6808 (t80) cc_final: 0.6467 (t80) REVERT: a 99 LYS cc_start: 0.7295 (mppt) cc_final: 0.6789 (ttpt) REVERT: a 124 ASP cc_start: 0.6710 (OUTLIER) cc_final: 0.6478 (m-30) REVERT: a 203 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8879 (mttp) REVERT: a 257 MET cc_start: 0.9114 (ttp) cc_final: 0.8647 (tmm) REVERT: I 16 MET cc_start: 0.8602 (tpp) cc_final: 0.8143 (mmm) REVERT: I 41 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7755 (tpp80) REVERT: I 54 PHE cc_start: 0.9308 (m-80) cc_final: 0.8469 (m-80) REVERT: S 16 MET cc_start: 0.8036 (tpp) cc_final: 0.7728 (mtt) REVERT: S 37 GLU cc_start: 0.9135 (tt0) cc_final: 0.8533 (tt0) REVERT: S 65 MET cc_start: 0.8197 (tpp) cc_final: 0.7916 (tpt) outliers start: 143 outliers final: 103 residues processed: 700 average time/residue: 0.4966 time to fit residues: 562.7913 Evaluate side-chains 703 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 590 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 102 SER Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 42 HIS 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 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 57 MET Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 57 MET Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 95 HIS Chi-restraints excluded: chain a residue 124 ASP Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 61 ASP Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 258 optimal weight: 20.0000 chunk 385 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 455 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 277 optimal weight: 0.2980 chunk 210 optimal weight: 0.0670 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37528 Z= 0.170 Angle : 0.572 11.402 50797 Z= 0.286 Chirality : 0.041 0.187 5920 Planarity : 0.004 0.059 6550 Dihedral : 6.564 150.836 5372 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.79 % Allowed : 16.81 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.12), residues: 4807 helix: 0.84 (0.10), residues: 2599 sheet: -0.02 (0.22), residues: 515 loop : -0.49 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 235 HIS 0.004 0.000 HIS G 200 PHE 0.021 0.001 PHE a 109 TYR 0.020 0.001 TYR B 236 ARG 0.007 0.000 ARG H 99 *********************** 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 712 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 605 time to evaluate : 4.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 135 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8333 (ttpp) REVERT: W 143 ASP cc_start: 0.8465 (t0) cc_final: 0.8133 (t0) REVERT: W 146 VAL cc_start: 0.7430 (OUTLIER) cc_final: 0.7051 (p) REVERT: C 170 ASP cc_start: 0.7703 (m-30) cc_final: 0.7441 (m-30) REVERT: C 236 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8798 (t80) REVERT: C 413 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8615 (mp) REVERT: B 157 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9304 (mt) REVERT: B 262 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: B 376 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8284 (mtt180) REVERT: A 356 GLU cc_start: 0.7552 (tp30) cc_final: 0.7306 (tp30) REVERT: A 418 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7534 (tpp-160) REVERT: A 463 LYS cc_start: 0.6106 (tttt) cc_final: 0.5843 (tttp) REVERT: A 501 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8873 (tptm) REVERT: X 15 VAL cc_start: 0.8073 (p) cc_final: 0.7795 (m) REVERT: X 20 PHE cc_start: 0.6354 (m-80) cc_final: 0.5985 (m-80) REVERT: H 22 LYS cc_start: 0.8864 (ptpt) cc_final: 0.8505 (pttt) REVERT: H 24 GLN cc_start: 0.8116 (tp40) cc_final: 0.7846 (tp40) REVERT: H 26 THR cc_start: 0.9016 (t) cc_final: 0.8798 (p) REVERT: H 58 HIS cc_start: 0.7057 (m-70) cc_final: 0.6569 (m90) REVERT: H 65 SER cc_start: 0.9031 (m) cc_final: 0.8279 (t) REVERT: H 132 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: G 83 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8576 (t0) REVERT: F 141 LYS cc_start: 0.9181 (tttt) cc_final: 0.8877 (ttpp) REVERT: E 14 ASP cc_start: 0.8054 (m-30) cc_final: 0.7579 (m-30) REVERT: E 56 MET cc_start: 0.9578 (mmp) cc_final: 0.9361 (mmt) REVERT: E 410 PHE cc_start: 0.8144 (m-80) cc_final: 0.7824 (m-80) REVERT: D 103 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: J 37 GLU cc_start: 0.7997 (pp20) cc_final: 0.7710 (pp20) REVERT: J 51 THR cc_start: 0.8932 (m) cc_final: 0.8700 (p) REVERT: L 63 ILE cc_start: 0.8739 (mp) cc_final: 0.8267 (mm) REVERT: M 37 GLU cc_start: 0.8031 (tt0) cc_final: 0.7749 (tt0) REVERT: N 3 ASN cc_start: 0.5303 (OUTLIER) cc_final: 0.4420 (t0) REVERT: N 9 LEU cc_start: 0.8142 (mm) cc_final: 0.7840 (mp) REVERT: N 65 MET cc_start: 0.8840 (mmm) cc_final: 0.8266 (tpp) REVERT: O 41 ARG cc_start: 0.8619 (ttm170) cc_final: 0.7874 (ttm-80) REVERT: O 42 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7371 (mp10) REVERT: O 63 ILE cc_start: 0.8069 (mm) cc_final: 0.7699 (mm) REVERT: P 11 MET cc_start: 0.8498 (tpp) cc_final: 0.7738 (mmm) REVERT: P 41 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7326 (ttp80) REVERT: P 42 GLN cc_start: 0.8494 (mm110) cc_final: 0.8279 (mm-40) REVERT: P 52 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8704 (mp10) REVERT: P 61 ASP cc_start: 0.8770 (m-30) cc_final: 0.8105 (m-30) REVERT: Q 42 GLN cc_start: 0.8870 (mt0) cc_final: 0.8639 (mp10) REVERT: R 11 MET cc_start: 0.8555 (tpp) cc_final: 0.8322 (tpp) REVERT: R 17 MET cc_start: 0.9164 (mmm) cc_final: 0.8925 (mmt) REVERT: Y 19 LEU cc_start: 0.8568 (mt) cc_final: 0.8334 (tp) REVERT: Y 30 MET cc_start: 0.7900 (mmm) cc_final: 0.7647 (mmt) REVERT: Y 80 ASN cc_start: 0.8229 (m-40) cc_final: 0.7559 (m110) REVERT: Y 150 ASP cc_start: 0.8937 (m-30) cc_final: 0.8599 (m-30) REVERT: a 94 TYR cc_start: 0.6817 (t80) cc_final: 0.6489 (t80) REVERT: a 99 LYS cc_start: 0.7235 (mppt) cc_final: 0.6731 (ttpt) REVERT: a 119 ASP cc_start: 0.7914 (m-30) cc_final: 0.7130 (m-30) REVERT: a 203 LYS cc_start: 0.9219 (mtpp) cc_final: 0.8759 (mttm) REVERT: a 257 MET cc_start: 0.9111 (ttp) cc_final: 0.8674 (tmm) REVERT: I 16 MET cc_start: 0.8674 (tpp) cc_final: 0.8189 (mmm) REVERT: I 54 PHE cc_start: 0.9295 (m-80) cc_final: 0.8364 (m-80) REVERT: S 16 MET cc_start: 0.8011 (tpp) cc_final: 0.7661 (mtt) REVERT: S 65 MET cc_start: 0.8163 (tpp) cc_final: 0.7893 (tpt) outliers start: 107 outliers final: 81 residues processed: 687 average time/residue: 0.5075 time to fit residues: 563.9600 Evaluate side-chains 674 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 582 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 57 MET Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 95 HIS Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 0.4980 chunk 182 optimal weight: 0.0770 chunk 272 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 289 optimal weight: 0.3980 chunk 310 optimal weight: 7.9990 chunk 225 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 358 optimal weight: 6.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN F 7 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 37528 Z= 0.148 Angle : 0.565 12.051 50797 Z= 0.280 Chirality : 0.041 0.184 5920 Planarity : 0.004 0.062 6550 Dihedral : 6.222 148.040 5371 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.63 % Allowed : 17.21 % Favored : 80.16 % 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: 0.54 (0.12), residues: 4807 helix: 0.98 (0.10), residues: 2596 sheet: 0.09 (0.23), residues: 489 loop : -0.38 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 235 HIS 0.004 0.000 HIS G 200 PHE 0.022 0.001 PHE B 467 TYR 0.017 0.001 TYR B 236 ARG 0.010 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 8 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 736 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 635 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 135 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8286 (ttpp) REVERT: W 143 ASP cc_start: 0.8460 (t0) cc_final: 0.8158 (t0) REVERT: W 146 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7092 (p) REVERT: C 236 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8786 (t80) REVERT: C 413 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8519 (mp) REVERT: B 262 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: B 403 LEU cc_start: 0.6031 (tt) cc_final: 0.4898 (mt) REVERT: A 356 GLU cc_start: 0.7556 (tp30) cc_final: 0.7319 (tp30) REVERT: A 463 LYS cc_start: 0.6054 (tttt) cc_final: 0.5834 (tttp) REVERT: X 15 VAL cc_start: 0.8068 (p) cc_final: 0.7798 (m) REVERT: X 20 PHE cc_start: 0.6285 (m-80) cc_final: 0.5981 (m-80) REVERT: H 22 LYS cc_start: 0.8861 (ptpt) cc_final: 0.8515 (pttt) REVERT: H 24 GLN cc_start: 0.8114 (tp40) cc_final: 0.7834 (tp40) REVERT: H 32 LEU cc_start: 0.8426 (tp) cc_final: 0.8125 (mt) REVERT: H 58 HIS cc_start: 0.7083 (m-70) cc_final: 0.6840 (m90) REVERT: H 65 SER cc_start: 0.8973 (m) cc_final: 0.8153 (t) REVERT: H 132 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8182 (pt0) REVERT: G 83 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8558 (t0) REVERT: G 259 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7806 (mp0) REVERT: F 141 LYS cc_start: 0.9143 (tttt) cc_final: 0.8876 (ttpp) REVERT: E 14 ASP cc_start: 0.8023 (m-30) cc_final: 0.7547 (m-30) REVERT: E 56 MET cc_start: 0.9568 (mmp) cc_final: 0.9366 (mmt) REVERT: E 410 PHE cc_start: 0.8124 (m-80) cc_final: 0.7829 (m-80) REVERT: D 103 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: D 301 ASP cc_start: 0.8059 (t0) cc_final: 0.7784 (t0) REVERT: J 11 MET cc_start: 0.8576 (mmt) cc_final: 0.8333 (tpp) REVERT: J 37 GLU cc_start: 0.7854 (pp20) cc_final: 0.7589 (pp20) REVERT: J 51 THR cc_start: 0.8980 (m) cc_final: 0.8765 (p) REVERT: L 48 LEU cc_start: 0.9302 (mm) cc_final: 0.9032 (tt) REVERT: L 56 VAL cc_start: 0.8819 (p) cc_final: 0.8591 (p) REVERT: L 59 LEU cc_start: 0.7808 (mm) cc_final: 0.7487 (mm) REVERT: L 63 ILE cc_start: 0.8790 (mp) cc_final: 0.8299 (mm) REVERT: M 37 GLU cc_start: 0.8034 (tt0) cc_final: 0.7748 (tt0) REVERT: M 54 PHE cc_start: 0.7876 (m-80) cc_final: 0.7487 (m-10) REVERT: N 3 ASN cc_start: 0.5511 (OUTLIER) cc_final: 0.4607 (t0) REVERT: N 9 LEU cc_start: 0.8141 (mm) cc_final: 0.7828 (mp) REVERT: N 65 MET cc_start: 0.8762 (mmm) cc_final: 0.8227 (tpp) REVERT: O 41 ARG cc_start: 0.8618 (ttm170) cc_final: 0.7885 (ttm-80) REVERT: O 42 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7370 (mp10) REVERT: O 63 ILE cc_start: 0.8058 (mm) cc_final: 0.7674 (mm) REVERT: P 11 MET cc_start: 0.8494 (tpp) cc_final: 0.7760 (mmm) REVERT: P 41 ARG cc_start: 0.8089 (ttm-80) cc_final: 0.7395 (ttp80) REVERT: P 42 GLN cc_start: 0.8465 (mm110) cc_final: 0.8257 (mm-40) REVERT: P 54 PHE cc_start: 0.8128 (m-80) cc_final: 0.7784 (m-80) REVERT: P 61 ASP cc_start: 0.8897 (m-30) cc_final: 0.8261 (m-30) REVERT: Q 35 PHE cc_start: 0.8495 (t80) cc_final: 0.8216 (t80) REVERT: Y 19 LEU cc_start: 0.8526 (mt) cc_final: 0.8274 (tp) REVERT: Y 29 LEU cc_start: 0.8733 (mt) cc_final: 0.8525 (tp) REVERT: Y 30 MET cc_start: 0.7763 (mmm) cc_final: 0.7415 (tpp) REVERT: Y 80 ASN cc_start: 0.8223 (m-40) cc_final: 0.7527 (m-40) REVERT: Y 150 ASP cc_start: 0.8883 (m-30) cc_final: 0.8565 (m-30) REVERT: a 94 TYR cc_start: 0.6849 (t80) cc_final: 0.6595 (t80) REVERT: a 99 LYS cc_start: 0.7172 (mppt) cc_final: 0.6679 (ttpt) REVERT: a 119 ASP cc_start: 0.7460 (m-30) cc_final: 0.7249 (m-30) REVERT: a 203 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8743 (mttm) REVERT: a 237 LEU cc_start: 0.9205 (mp) cc_final: 0.8897 (tp) REVERT: a 257 MET cc_start: 0.9125 (ttp) cc_final: 0.8756 (tmm) REVERT: I 16 MET cc_start: 0.8669 (tpp) cc_final: 0.8301 (tpp) REVERT: I 54 PHE cc_start: 0.9213 (m-80) cc_final: 0.8378 (m-80) REVERT: S 6 MET cc_start: 0.8276 (ppp) cc_final: 0.7786 (pmm) REVERT: S 16 MET cc_start: 0.8011 (tpp) cc_final: 0.7671 (mtt) REVERT: S 65 MET cc_start: 0.8213 (tpp) cc_final: 0.7848 (tpt) outliers start: 101 outliers final: 72 residues processed: 705 average time/residue: 0.5006 time to fit residues: 569.9204 Evaluate side-chains 669 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 589 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 52 MET 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 C residue 293 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 431 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 95 HIS Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 8.9990 chunk 436 optimal weight: 9.9990 chunk 398 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 chunk 255 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 333 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 383 optimal weight: 0.0470 chunk 401 optimal weight: 0.0980 chunk 423 optimal weight: 6.9990 overall best weight: 1.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 37 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN F 7 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 145 ASN ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37528 Z= 0.180 Angle : 0.586 12.485 50797 Z= 0.289 Chirality : 0.042 0.201 5920 Planarity : 0.004 0.065 6550 Dihedral : 6.132 148.999 5364 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.89 % Allowed : 17.28 % Favored : 79.82 % 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: 0.58 (0.12), residues: 4807 helix: 1.01 (0.10), residues: 2602 sheet: 0.11 (0.23), residues: 503 loop : -0.36 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 235 HIS 0.003 0.000 HIS G 200 PHE 0.035 0.001 PHE E 189 TYR 0.016 0.001 TYR B 236 ARG 0.010 0.000 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 9 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 700 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 589 time to evaluate : 4.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 135 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8305 (ttpp) REVERT: W 143 ASP cc_start: 0.8459 (t0) cc_final: 0.8146 (t0) REVERT: W 146 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.7116 (p) REVERT: C 236 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8816 (t80) REVERT: C 413 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8513 (mp) REVERT: B 262 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: B 403 LEU cc_start: 0.6038 (tt) cc_final: 0.4799 (mt) REVERT: B 463 LYS cc_start: 0.8843 (mmtp) cc_final: 0.8415 (ttpt) REVERT: A 463 LYS cc_start: 0.6090 (tttt) cc_final: 0.5490 (tttm) REVERT: A 483 MET cc_start: 0.8122 (mmp) cc_final: 0.7855 (mmp) REVERT: X 15 VAL cc_start: 0.8074 (p) cc_final: 0.7806 (m) REVERT: X 20 PHE cc_start: 0.6280 (m-80) cc_final: 0.5980 (m-80) REVERT: X 83 ARG cc_start: 0.7456 (ttt90) cc_final: 0.6971 (ttt90) REVERT: H 22 LYS cc_start: 0.8862 (ptpt) cc_final: 0.8502 (pttt) REVERT: H 24 GLN cc_start: 0.7941 (tp40) cc_final: 0.7670 (tp40) REVERT: H 32 LEU cc_start: 0.8417 (tp) cc_final: 0.8148 (mt) REVERT: H 58 HIS cc_start: 0.7177 (m-70) cc_final: 0.6910 (m90) REVERT: H 65 SER cc_start: 0.8974 (m) cc_final: 0.8168 (t) REVERT: H 87 GLN cc_start: 0.8693 (tp40) cc_final: 0.8450 (tp40) REVERT: H 129 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.8004 (mtm-85) REVERT: H 132 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: G 83 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8598 (t0) REVERT: G 102 MET cc_start: 0.8166 (mtm) cc_final: 0.7828 (mtp) REVERT: G 259 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7773 (mp0) REVERT: F 9 ILE cc_start: 0.8991 (mm) cc_final: 0.8677 (mm) REVERT: F 141 LYS cc_start: 0.9147 (tttt) cc_final: 0.8888 (ttpp) REVERT: E 14 ASP cc_start: 0.8044 (m-30) cc_final: 0.7572 (m-30) REVERT: E 56 MET cc_start: 0.9573 (mmp) cc_final: 0.9351 (mmt) REVERT: E 410 PHE cc_start: 0.8163 (m-80) cc_final: 0.7805 (m-80) REVERT: D 103 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7331 (pt0) REVERT: D 301 ASP cc_start: 0.8046 (t0) cc_final: 0.7744 (t0) REVERT: J 11 MET cc_start: 0.8488 (mmt) cc_final: 0.8268 (tpp) REVERT: J 37 GLU cc_start: 0.7856 (pp20) cc_final: 0.7621 (pp20) REVERT: J 51 THR cc_start: 0.8995 (m) cc_final: 0.8686 (p) REVERT: L 63 ILE cc_start: 0.8725 (mp) cc_final: 0.8270 (mm) REVERT: M 8 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7577 (tp) REVERT: M 54 PHE cc_start: 0.7866 (m-80) cc_final: 0.7454 (m-10) REVERT: N 3 ASN cc_start: 0.5357 (OUTLIER) cc_final: 0.4823 (t0) REVERT: N 9 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7879 (mp) REVERT: O 41 ARG cc_start: 0.8613 (ttm170) cc_final: 0.7889 (ttm-80) REVERT: O 42 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7436 (mp10) REVERT: O 63 ILE cc_start: 0.8064 (mm) cc_final: 0.7692 (mm) REVERT: P 11 MET cc_start: 0.8490 (tpp) cc_final: 0.7728 (mmm) REVERT: P 41 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7305 (ttp80) REVERT: P 42 GLN cc_start: 0.8447 (mm110) cc_final: 0.8065 (mm110) REVERT: P 52 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8768 (mm-40) REVERT: P 61 ASP cc_start: 0.8933 (m-30) cc_final: 0.8574 (p0) REVERT: Q 35 PHE cc_start: 0.8511 (t80) cc_final: 0.8212 (t80) REVERT: Y 2 ASN cc_start: 0.5722 (t0) cc_final: 0.5456 (p0) REVERT: Y 19 LEU cc_start: 0.8525 (mt) cc_final: 0.8271 (tp) REVERT: Y 29 LEU cc_start: 0.8741 (mt) cc_final: 0.8529 (tp) REVERT: Y 80 ASN cc_start: 0.8206 (m-40) cc_final: 0.7532 (m110) REVERT: Y 150 ASP cc_start: 0.8884 (m-30) cc_final: 0.8577 (m-30) REVERT: a 94 TYR cc_start: 0.6783 (t80) cc_final: 0.6469 (t80) REVERT: a 99 LYS cc_start: 0.7169 (mppt) cc_final: 0.6736 (ttpt) REVERT: a 203 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8769 (mttm) REVERT: a 237 LEU cc_start: 0.9194 (mp) cc_final: 0.8891 (tp) REVERT: a 257 MET cc_start: 0.9111 (ttp) cc_final: 0.8645 (tmm) REVERT: I 16 MET cc_start: 0.8649 (tpp) cc_final: 0.8270 (mmm) REVERT: I 54 PHE cc_start: 0.9194 (m-80) cc_final: 0.8219 (m-80) REVERT: I 57 MET cc_start: 0.8779 (tmm) cc_final: 0.8271 (tmm) REVERT: S 6 MET cc_start: 0.8290 (ppp) cc_final: 0.7809 (pmm) REVERT: S 16 MET cc_start: 0.8012 (tpp) cc_final: 0.7662 (mtt) REVERT: S 37 GLU cc_start: 0.9137 (tt0) cc_final: 0.8575 (tt0) REVERT: S 46 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8440 (pt) REVERT: S 65 MET cc_start: 0.8244 (tpp) cc_final: 0.7899 (tpt) outliers start: 111 outliers final: 89 residues processed: 668 average time/residue: 0.5203 time to fit residues: 562.8040 Evaluate side-chains 686 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 586 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 3 ASN Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 95 HIS Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 3.9990 chunk 449 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 chunk 471 optimal weight: 4.9990 chunk 433 optimal weight: 4.9990 chunk 375 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 289 optimal weight: 0.5980 chunk 230 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37528 Z= 0.213 Angle : 0.603 12.257 50797 Z= 0.295 Chirality : 0.042 0.220 5920 Planarity : 0.004 0.067 6550 Dihedral : 6.188 151.296 5364 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.82 % Allowed : 17.70 % Favored : 79.48 % 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: 1.02 (0.10), residues: 2610 sheet: 0.11 (0.23), residues: 504 loop : -0.37 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 235 HIS 0.003 0.001 HIS G 200 PHE 0.023 0.001 PHE I 53 TYR 0.018 0.001 TYR B 236 ARG 0.010 0.000 ARG X 49 ********************** REFINEMENT MACRO_CYCLE 10 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 693 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 585 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 135 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8313 (ttpp) REVERT: W 143 ASP cc_start: 0.8466 (t0) cc_final: 0.8138 (t0) REVERT: W 146 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7135 (p) REVERT: C 236 TYR cc_start: 0.9226 (OUTLIER) cc_final: 0.8914 (t80) REVERT: C 413 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 262 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: B 403 LEU cc_start: 0.6075 (tt) cc_final: 0.4828 (mt) REVERT: B 463 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8412 (ttpt) REVERT: A 52 MET cc_start: 0.8780 (mtt) cc_final: 0.8425 (mtt) REVERT: A 418 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7482 (tpp-160) REVERT: A 463 LYS cc_start: 0.6031 (tttt) cc_final: 0.5356 (tttm) REVERT: A 483 MET cc_start: 0.8151 (mmp) cc_final: 0.7841 (mmp) REVERT: X 15 VAL cc_start: 0.8073 (p) cc_final: 0.7802 (m) REVERT: X 20 PHE cc_start: 0.6286 (m-80) cc_final: 0.5991 (m-80) REVERT: H 22 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8500 (pttt) REVERT: H 24 GLN cc_start: 0.7951 (tp40) cc_final: 0.7668 (tp40) REVERT: H 65 SER cc_start: 0.8985 (m) cc_final: 0.8195 (t) REVERT: H 87 GLN cc_start: 0.8740 (tp40) cc_final: 0.8503 (tp40) REVERT: H 132 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8249 (pt0) REVERT: G 83 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8625 (t0) REVERT: G 102 MET cc_start: 0.8146 (mtm) cc_final: 0.7906 (mtp) REVERT: F 141 LYS cc_start: 0.9175 (tttt) cc_final: 0.8910 (ttpp) REVERT: E 56 MET cc_start: 0.9581 (mmp) cc_final: 0.9347 (mmt) REVERT: E 410 PHE cc_start: 0.8215 (m-80) cc_final: 0.7860 (m-80) REVERT: D 103 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7029 (pt0) REVERT: D 301 ASP cc_start: 0.8161 (t0) cc_final: 0.7798 (t0) REVERT: J 11 MET cc_start: 0.8535 (mmt) cc_final: 0.8314 (tpp) REVERT: J 16 MET cc_start: 0.8756 (ptm) cc_final: 0.8498 (ppp) REVERT: J 37 GLU cc_start: 0.7872 (pp20) cc_final: 0.7574 (pp20) REVERT: J 53 PHE cc_start: 0.8912 (t80) cc_final: 0.8655 (t80) REVERT: L 63 ILE cc_start: 0.8775 (mp) cc_final: 0.8319 (mm) REVERT: M 54 PHE cc_start: 0.7886 (m-80) cc_final: 0.7479 (m-10) REVERT: N 9 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7884 (mp) REVERT: N 65 MET cc_start: 0.8607 (mmm) cc_final: 0.8402 (mmm) REVERT: O 41 ARG cc_start: 0.8644 (ttm170) cc_final: 0.8234 (ttm170) REVERT: O 42 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7453 (mp10) REVERT: O 63 ILE cc_start: 0.8098 (mm) cc_final: 0.7743 (mm) REVERT: P 11 MET cc_start: 0.8452 (tpp) cc_final: 0.7704 (mmm) REVERT: P 41 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7459 (ttp80) REVERT: P 52 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8624 (mp10) REVERT: P 61 ASP cc_start: 0.8997 (m-30) cc_final: 0.8557 (m-30) REVERT: Y 2 ASN cc_start: 0.5808 (t0) cc_final: 0.5521 (p0) REVERT: Y 19 LEU cc_start: 0.8548 (mt) cc_final: 0.8285 (tp) REVERT: Y 80 ASN cc_start: 0.8233 (m-40) cc_final: 0.7595 (m110) REVERT: Y 150 ASP cc_start: 0.8906 (m-30) cc_final: 0.8603 (m-30) REVERT: a 99 LYS cc_start: 0.7151 (mppt) cc_final: 0.6713 (ttpt) REVERT: a 119 ASP cc_start: 0.7813 (m-30) cc_final: 0.7593 (m-30) REVERT: a 203 LYS cc_start: 0.9131 (mtpp) cc_final: 0.8757 (mttm) REVERT: a 237 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8882 (tp) REVERT: a 257 MET cc_start: 0.9107 (ttp) cc_final: 0.8778 (tmm) REVERT: I 10 TYR cc_start: 0.8145 (m-80) cc_final: 0.7427 (m-80) REVERT: I 16 MET cc_start: 0.8604 (tpp) cc_final: 0.8213 (mmm) REVERT: I 54 PHE cc_start: 0.9193 (m-80) cc_final: 0.8208 (m-80) REVERT: I 57 MET cc_start: 0.8755 (tmm) cc_final: 0.8267 (tmm) REVERT: S 6 MET cc_start: 0.8265 (ppp) cc_final: 0.7898 (pmm) REVERT: S 16 MET cc_start: 0.8028 (tpp) cc_final: 0.7678 (mtt) REVERT: S 37 GLU cc_start: 0.9127 (tt0) cc_final: 0.8572 (tt0) REVERT: S 65 MET cc_start: 0.8295 (tpp) cc_final: 0.7974 (tpt) outliers start: 108 outliers final: 88 residues processed: 666 average time/residue: 0.4925 time to fit residues: 530.5237 Evaluate side-chains 671 residues out of total 3849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 574 time to evaluate : 4.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 133 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 147 MET Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain O residue 7 ASP Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain Y residue 7 ILE Chi-restraints excluded: chain Y residue 48 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 95 HIS Chi-restraints excluded: chain a residue 169 LYS Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 8.9990 chunk 399 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 385 optimal weight: 9.9990 chunk 47 optimal weight: 0.0770 chunk 69 optimal weight: 0.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN F 7 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.068285 restraints weight = 77981.027| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.05 r_work: 0.2786 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3428 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= 0.219 Angle : 0.606 12.344 50797 Z= 0.298 Chirality : 0.042 0.230 5920 Planarity : 0.004 0.067 6550 Dihedral : 6.216 152.995 5364 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.87 % Allowed : 17.60 % Favored : 79.54 % 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: 1.03 (0.10), residues: 2607 sheet: 0.14 (0.23), residues: 501 loop : -0.38 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 235 HIS 0.002 0.001 HIS A 42 PHE 0.022 0.001 PHE L 53 TYR 0.067 0.001 TYR a 94 ARG 0.010 0.000 ARG Y 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10761.07 seconds wall clock time: 194 minutes 11.25 seconds (11651.25 seconds total)