Starting phenix.real_space_refine on Tue Apr 16 01:01:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbv_27310/04_2024/8dbv_27310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbv_27310/04_2024/8dbv_27310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbv_27310/04_2024/8dbv_27310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbv_27310/04_2024/8dbv_27310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbv_27310/04_2024/8dbv_27310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbv_27310/04_2024/8dbv_27310_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 178 5.16 5 C 23421 2.51 5 N 6300 2.21 5 O 6942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 476": "OD1" <-> "OD2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 412": "OD1" <-> "OD2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "D ASP 14": "OD1" <-> "OD2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 338": "OD1" <-> "OD2" Residue "D ASP 355": "OD1" <-> "OD2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 20": "OD1" <-> "OD2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E ASP 355": "OD1" <-> "OD2" Residue "E GLU 369": "OE1" <-> "OE2" Residue "E ASP 372": "OD1" <-> "OD2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E GLU 384": "OE1" <-> "OE2" Residue "E ASP 386": "OD1" <-> "OD2" Residue "E PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 372": "OD1" <-> "OD2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "F TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 432": "OE1" <-> "OE2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G ASP 216": "OD1" <-> "OD2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "H TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W ASP 156": "OD1" <-> "OD2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "W GLU 168": "OE1" <-> "OE2" Residue "I ASP 7": "OD1" <-> "OD2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" 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 "Q TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X GLU 89": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X GLU 110": "OE1" <-> "OE2" Residue "X ARG 113": "NH1" <-> "NH2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "X GLU 133": "OE1" <-> "OE2" Residue "X ASP 141": "OD1" <-> "OD2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y ASP 141": "OD1" <-> "OD2" Residue "Y ASP 150": "OD1" <-> "OD2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 44": "OD1" <-> "OD2" Residue "a PHE 48": "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 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36862 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3852 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Chain: "B" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3811 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 486} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} 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: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1021 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "W" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1317 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: "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: "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: "X" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1187 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1201 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 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: "F" 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} Time building chain proxies: 18.95, per 1000 atoms: 0.51 Number of scatterers: 36862 At special positions: 0 Unit cell: (175.877, 217.958, 133.796, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 16 15.00 Mg 5 11.99 O 6942 8.00 N 6300 7.00 C 23421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.18 Conformation dependent library (CDL) restraints added in 7.3 seconds 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 25 sheets defined 55.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.47 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.525A pdb=" N ALA A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 4.151A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.598A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 292 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A 294 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A 299 " --> 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 348 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 406 removed outlier: 4.588A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 455 through 458 removed outlier: 4.067A pdb=" N ASP A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 461 through 477 removed outlier: 4.360A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 9 through 17 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.620A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 4.109A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.527A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.386A 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 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 391 through 408 removed outlier: 3.880A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 462 through 478 removed outlier: 4.044A pdb=" N GLY B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 478 " --> pdb=" O VAL B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.852A pdb=" N ALA B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' 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 156 Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.859A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.610A pdb=" N TYR C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 236' Processing helix chain 'C' and resid 238 through 252 removed outlier: 3.688A pdb=" N MET C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 removed outlier: 4.146A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.747A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 357 through 360 No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 417 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 464 through 477 Processing helix chain 'C' and resid 481 through 488 removed outlier: 3.803A pdb=" N ILE C 486 " --> pdb=" O MET C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 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 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 removed outlier: 3.699A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 233 removed outlier: 4.899A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.565A pdb=" N THR D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 279 removed outlier: 3.632A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 314 removed outlier: 4.358A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 351 through 377 removed outlier: 3.525A pdb=" N GLU D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 370 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 168 Processing helix chain 'E' and resid 183 through 196 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: 4.560A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.989A 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: 3.701A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 314 removed outlier: 3.828A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 351 through 376 removed outlier: 4.150A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 384 through 400 Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.794A pdb=" N GLU E 408 " --> pdb=" O PHE E 405 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL E 409 " --> pdb=" O VAL E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 432 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.658A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 155 through 168 removed outlier: 3.592A pdb=" N ALA F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 215 through 232 removed outlier: 3.502A pdb=" N VAL F 219 " --> pdb=" O ASN F 215 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 255 removed outlier: 3.526A pdb=" N GLY F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 279 Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' Processing helix chain 'F' and resid 323 through 327 Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 377 removed outlier: 3.961A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (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 Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 420 through 431 Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'G' and resid 3 through 55 Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 90 through 107 Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 145 through 160 removed outlier: 4.548A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'G' and resid 211 through 283 removed outlier: 3.561A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU G 276 " --> pdb=" O ILE G 272 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR G 277 " --> pdb=" O THR G 273 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 107 Processing helix chain 'H' and resid 111 through 135 Processing helix chain 'W' and resid 4 through 18 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.675A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 48 removed outlier: 3.552A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 64 removed outlier: 4.397A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 81 removed outlier: 4.035A pdb=" N ARG W 77 " --> pdb=" O GLN W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 102 Proline residue: W 89 - end of helix removed outlier: 3.779A pdb=" N LEU W 92 " --> pdb=" O PRO W 89 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN W 94 " --> pdb=" O VAL W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 131 Processing helix chain 'W' and resid 144 through 146 No H-bonds generated for 'chain 'W' and resid 144 through 146' Processing helix chain 'W' and resid 163 through 173 Processing helix chain 'I' and resid 4 through 41 removed outlier: 4.110A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.933A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 3.646A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET I 57 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY I 58 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA I 62 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.517A pdb=" N LEU I 70 " --> pdb=" O ALA I 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.803A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 76 removed outlier: 3.834A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 5.128A 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: 3.555A pdb=" N LEU L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 13 " --> pdb=" O TYR L 10 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET L 17 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU L 19 " --> pdb=" O MET L 16 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA L 20 " --> pdb=" O MET L 17 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE L 26 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY L 27 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE L 28 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY L 32 " --> pdb=" O GLY L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.610A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.050A pdb=" N ARG L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 3.794A pdb=" N VAL L 68 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 Processing helix chain 'M' and resid 43 through 76 removed outlier: 3.609A pdb=" N ILE M 46 " --> pdb=" O PRO M 43 " (cutoff:3.500A) Proline residue: M 47 - end of helix removed outlier: 4.125A pdb=" N ARG M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE M 53 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.701A pdb=" N VAL M 68 " --> pdb=" O MET M 65 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU M 72 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.388A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU N 31 " --> pdb=" O GLY N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 60 removed outlier: 3.595A pdb=" N ILE N 46 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Proline residue: N 47 - end of helix removed outlier: 3.539A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 76 Processing helix chain 'O' and resid 4 through 39 removed outlier: 3.582A pdb=" N MET O 17 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY O 18 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY O 23 " --> pdb=" O ALA O 20 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA O 24 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE O 26 " --> pdb=" O GLY O 23 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE O 30 " --> pdb=" O GLY O 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU O 31 " --> pdb=" O ILE O 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE O 35 " --> pdb=" O GLY O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 76 removed outlier: 3.756A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 6 through 41 removed outlier: 3.779A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.875A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.911A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.551A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.149A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET Q 57 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 4.121A pdb=" N ALA Q 67 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL Q 68 " --> pdb=" O MET Q 65 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.571A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 77 removed outlier: 3.686A pdb=" N ILE R 46 " --> pdb=" O PRO R 43 " (cutoff:3.500A) Proline residue: R 47 - end of helix removed outlier: 3.589A pdb=" N VAL R 56 " --> pdb=" O PHE R 53 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.502A pdb=" N LEU R 72 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL R 74 " --> pdb=" O GLY R 71 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET R 75 " --> pdb=" O LEU R 72 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA R 77 " --> pdb=" O VAL R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 removed outlier: 4.670A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA S 13 " --> pdb=" O TYR S 10 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET S 17 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY S 18 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU S 19 " --> pdb=" O MET S 16 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA S 20 " --> pdb=" O MET S 17 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY S 23 " --> pdb=" O ALA S 20 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA S 25 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE S 26 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY S 27 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY S 32 " --> pdb=" O GLY S 29 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY S 33 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 77 Proline residue: S 47 - end of helix removed outlier: 4.221A pdb=" N ASP S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA S 62 " --> pdb=" O LEU S 59 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE S 63 " --> pdb=" O VAL S 60 " (cutoff:3.500A) Proline residue: S 64 - end of helix removed outlier: 3.549A pdb=" N LEU S 70 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL S 74 " --> pdb=" O GLY S 71 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET S 75 " --> pdb=" O LEU S 72 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA S 77 " --> pdb=" O VAL S 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 23 removed outlier: 4.582A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE X 12 " --> pdb=" O GLY X 9 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE X 14 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.601A pdb=" N LEU X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER X 46 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU X 48 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG X 49 " --> pdb=" O ALA X 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU X 65 " --> pdb=" O ALA X 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS X 66 " --> pdb=" O THR X 62 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA X 128 " --> pdb=" O VAL X 124 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU X 133 " --> pdb=" O VAL X 129 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE X 136 " --> pdb=" O ALA X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 145 No H-bonds generated for 'chain 'X' and resid 143 through 145' Processing helix chain 'X' and resid 149 through 152 No H-bonds generated for 'chain 'X' and resid 149 through 152' Processing helix chain 'Y' and resid 3 through 24 removed outlier: 3.743A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 39 removed outlier: 3.735A pdb=" N GLN Y 37 " --> pdb=" O ILE Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 138 removed outlier: 4.642A pdb=" N ALA Y 45 " --> pdb=" O ALA Y 41 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU Y 48 " --> pdb=" O LEU Y 44 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA Y 50 " --> pdb=" O SER Y 46 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS Y 51 " --> pdb=" O ALA Y 47 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU Y 56 " --> pdb=" O LYS Y 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA Y 57 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA Y 59 " --> pdb=" O ASP Y 55 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN Y 64 " --> pdb=" O SER Y 60 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN Y 80 " --> pdb=" O ILE Y 76 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 152 Processing helix chain 'a' and resid 8 through 16 Processing helix chain 'a' and resid 43 through 64 removed outlier: 3.541A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 93 removed outlier: 3.584A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 120 removed outlier: 3.653A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 132 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 Processing helix chain 'a' and resid 170 through 179 Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix removed outlier: 4.026A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL a 198 " --> pdb=" O LEU a 195 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU a 201 " --> pdb=" O VAL a 198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS a 203 " --> pdb=" O LEU a 200 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.590A pdb=" N GLY a 208 " --> pdb=" O VAL a 205 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU a 209 " --> pdb=" O SER a 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY a 213 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N TYR a 216 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA a 217 " --> pdb=" O ASN a 214 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU a 219 " --> pdb=" O TYR a 216 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 3.923A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.269A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.460A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 70 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.431A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL A 224 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.691A pdb=" N LEU A 166 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.463A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.355A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL B 224 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 198 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 327 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.616A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET C 76 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C 61 " --> pdb=" O MET C 76 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= J, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.453A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.939A pdb=" N ALA C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL C 224 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.528A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.373A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.196A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 3 through 9 removed outlier: 6.561A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.708A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 317 through 319 removed outlier: 3.530A pdb=" N ALA E 317 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.691A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'F' and resid 317 through 320 removed outlier: 7.640A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 181 through 186 removed outlier: 6.357A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N MET G 116 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN G 135 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 76 through 79 removed outlier: 6.262A pdb=" N SER H 10 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN H 14 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR H 82 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 22 through 25 Processing sheet with id= X, first strand: chain 'H' and resid 43 through 45 removed outlier: 4.192A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'W' and resid 139 through 142 1929 hydrogen bonds defined for protein. 4965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.35 Time building geometry restraints manager: 16.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8280 1.32 - 1.45: 6986 1.45 - 1.57: 21769 1.57 - 1.69: 28 1.69 - 1.81: 356 Bond restraints: 37419 Sorted by residual: bond pdb=" C4 ATP F 502 " pdb=" C5 ATP F 502 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.52e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.42e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.33e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.08e+01 bond pdb=" C4 ATP C 600 " pdb=" N9 ATP C 600 " ideal model delta sigma weight residual 1.374 1.313 0.061 1.00e-02 1.00e+04 3.75e+01 ... (remaining 37414 not shown) Histogram of bond angle deviations from ideal: 97.48 - 105.07: 825 105.07 - 112.66: 19245 112.66 - 120.25: 15553 120.25 - 127.85: 14795 127.85 - 135.44: 230 Bond angle restraints: 50648 Sorted by residual: angle pdb=" PA ATP F 502 " pdb=" O3A ATP F 502 " pdb=" PB ATP F 502 " ideal model delta sigma weight residual 136.83 113.59 23.24 1.00e+00 1.00e+00 5.40e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.91 22.96 1.00e+00 1.00e+00 5.27e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 117.28 22.59 1.00e+00 1.00e+00 5.10e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.85 22.02 1.00e+00 1.00e+00 4.85e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.39 18.44 1.00e+00 1.00e+00 3.40e+02 ... (remaining 50643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.25: 21915 29.25 - 58.50: 739 58.50 - 87.76: 87 87.76 - 117.01: 5 117.01 - 146.26: 2 Dihedral angle restraints: 22748 sinusoidal: 9006 harmonic: 13742 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 86.26 -146.26 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 62.78 -122.78 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" C ASP X 147 " pdb=" N ASP X 147 " pdb=" CA ASP X 147 " pdb=" CB ASP X 147 " ideal model delta harmonic sigma weight residual -122.60 -137.02 14.42 0 2.50e+00 1.60e-01 3.33e+01 ... (remaining 22745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 5545 0.119 - 0.237: 341 0.237 - 0.356: 14 0.356 - 0.474: 1 0.474 - 0.593: 1 Chirality restraints: 5902 Sorted by residual: chirality pdb=" CB ILE Q 63 " pdb=" CA ILE Q 63 " pdb=" CG1 ILE Q 63 " pdb=" CG2 ILE Q 63 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.59 2.00e-01 2.50e+01 8.78e+00 chirality pdb=" CA ASP X 147 " pdb=" N ASP X 147 " pdb=" C ASP X 147 " pdb=" CB ASP X 147 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CB ILE H 131 " pdb=" CA ILE H 131 " pdb=" CG1 ILE H 131 " pdb=" CG2 ILE H 131 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 5899 not shown) Planarity restraints: 6530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " -0.162 9.50e-02 1.11e+02 9.29e-02 4.55e+01 pdb=" NE ARG B 59 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 59 " -0.111 2.00e-02 2.50e+03 pdb=" NH1 ARG B 59 " 0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG B 59 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 376 " -0.162 9.50e-02 1.11e+02 8.89e-02 3.64e+01 pdb=" NE ARG A 376 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 376 " -0.098 2.00e-02 2.50e+03 pdb=" NH1 ARG A 376 " 0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG A 376 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 41 " -0.144 9.50e-02 1.11e+02 8.14e-02 3.31e+01 pdb=" NE ARG N 41 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG N 41 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG N 41 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG N 41 " 0.027 2.00e-02 2.50e+03 ... (remaining 6527 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 39 2.38 - 3.01: 21378 3.01 - 3.64: 55430 3.64 - 4.27: 84615 4.27 - 4.90: 142322 Nonbonded interactions: 303784 Sorted by model distance: nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.749 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.774 2.170 nonbonded pdb="MG MG F 501 " pdb=" O1G ATP F 502 " model vdw 1.783 2.170 nonbonded pdb=" O3B ATP B 600 " pdb="MG MG B 601 " model vdw 1.841 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.850 2.170 ... (remaining 303779 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 7 through 511 or resid 600 through 601)) selection = chain 'B' selection = (chain 'C' and (resid 7 through 511 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = (chain 'I' 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' and resid 1 through 153) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.670 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 98.930 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.240 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.103 37419 Z= 0.660 Angle : 1.229 23.244 50648 Z= 0.773 Chirality : 0.063 0.593 5902 Planarity : 0.010 0.146 6530 Dihedral : 14.766 146.259 13958 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 1.86 % Allowed : 7.69 % Favored : 90.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.11), residues: 4793 helix: -0.81 (0.09), residues: 2609 sheet: -0.55 (0.22), residues: 524 loop : -1.07 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.006 TRP a 186 HIS 0.014 0.003 HIS C 423 PHE 0.061 0.004 PHE O 54 TYR 0.052 0.007 TYR G 205 ARG 0.113 0.012 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 479 time to evaluate : 4.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8054 (p90) REVERT: H 34 ILE cc_start: 0.6632 (OUTLIER) cc_final: 0.6170 (mp) REVERT: H 58 HIS cc_start: 0.8476 (m-70) cc_final: 0.8268 (m-70) REVERT: H 63 TYR cc_start: 0.5814 (t80) cc_final: 0.4764 (t80) REVERT: H 75 ASN cc_start: 0.8414 (m110) cc_final: 0.8126 (t0) REVERT: H 100 LYS cc_start: 0.7275 (mttm) cc_final: 0.7066 (mttt) REVERT: H 109 HIS cc_start: 0.8049 (t70) cc_final: 0.7819 (m90) REVERT: W 28 GLN cc_start: 0.7202 (tt0) cc_final: 0.6664 (tm-30) REVERT: I 60 VAL cc_start: 0.2491 (t) cc_final: 0.1974 (t) REVERT: J 17 MET cc_start: 0.5579 (mtp) cc_final: 0.3965 (tpp) REVERT: J 61 ASP cc_start: 0.7202 (m-30) cc_final: 0.6798 (p0) REVERT: M 6 MET cc_start: 0.3807 (mtp) cc_final: 0.3369 (ptt) REVERT: M 17 MET cc_start: 0.6507 (mtm) cc_final: 0.5192 (tpt) REVERT: M 22 ILE cc_start: 0.6456 (mt) cc_final: 0.6140 (mt) REVERT: M 42 GLN cc_start: 0.7743 (pt0) cc_final: 0.7508 (pp30) REVERT: N 11 MET cc_start: 0.5942 (tpp) cc_final: 0.5417 (tmm) REVERT: O 17 MET cc_start: 0.7500 (ttm) cc_final: 0.7258 (mtm) REVERT: O 37 GLU cc_start: 0.8083 (tt0) cc_final: 0.7839 (tp30) REVERT: O 68 VAL cc_start: 0.6678 (t) cc_final: 0.6454 (m) REVERT: P 16 MET cc_start: 0.6548 (mtt) cc_final: 0.6032 (tpp) REVERT: Q 17 MET cc_start: 0.2662 (mtm) cc_final: 0.1313 (tpt) REVERT: Q 28 ILE cc_start: 0.7427 (mt) cc_final: 0.7126 (tp) REVERT: R 28 ILE cc_start: 0.7900 (mt) cc_final: 0.7277 (tt) REVERT: R 53 PHE cc_start: 0.7638 (t80) cc_final: 0.7337 (t80) REVERT: S 16 MET cc_start: 0.7113 (mtp) cc_final: 0.6830 (ttm) REVERT: S 51 THR cc_start: 0.8602 (p) cc_final: 0.7433 (p) REVERT: S 57 MET cc_start: 0.7148 (tmt) cc_final: 0.6731 (ptt) REVERT: S 75 MET cc_start: 0.1527 (ttt) cc_final: 0.1198 (mtt) REVERT: X 63 ASP cc_start: 0.3825 (t0) cc_final: 0.2970 (m-30) REVERT: X 66 LYS cc_start: 0.7433 (mmmt) cc_final: 0.7039 (mmtm) REVERT: X 124 VAL cc_start: 0.7808 (p) cc_final: 0.7601 (p) REVERT: Y 1 MET cc_start: 0.1469 (ptt) cc_final: 0.0940 (tpp) REVERT: Y 96 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8241 (tm-30) REVERT: a 46 MET cc_start: 0.3603 (mmm) cc_final: 0.2997 (mtt) REVERT: a 139 LEU cc_start: 0.1488 (OUTLIER) cc_final: 0.1273 (tp) outliers start: 71 outliers final: 13 residues processed: 543 average time/residue: 0.5701 time to fit residues: 484.3407 Evaluate side-chains 295 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 279 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 5.9990 chunk 358 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 370 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 429 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 294 HIS A 344 ASN A 484 GLN A 511 GLN B 58 ASN B 200 GLN B 294 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 4 ASN C 147 GLN C 186 GLN C 333 GLN C 443 GLN E 324 GLN F 279 GLN F 294 GLN F 437 HIS G 54 HIS G 91 ASN G 252 ASN G 265 ASN G 269 GLN H 75 ASN W 67 GLN W 82 ASN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 ASN R 5 ASN S 5 ASN X 37 GLN a 132 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37419 Z= 0.242 Angle : 0.661 11.099 50648 Z= 0.344 Chirality : 0.043 0.282 5902 Planarity : 0.005 0.048 6530 Dihedral : 7.760 134.677 5376 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.90 % Favored : 98.08 % Rotamer: Outliers : 2.07 % Allowed : 11.04 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.07 (0.12), residues: 4793 helix: 0.66 (0.10), residues: 2602 sheet: -0.12 (0.22), residues: 538 loop : -0.72 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 186 HIS 0.009 0.001 HIS H 5 PHE 0.038 0.002 PHE S 54 TYR 0.018 0.002 TYR G 205 ARG 0.009 0.001 ARG G 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 291 time to evaluate : 5.211 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: C 236 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8032 (p90) REVERT: H 58 HIS cc_start: 0.8366 (m-70) cc_final: 0.8040 (m-70) REVERT: H 75 ASN cc_start: 0.8545 (m-40) cc_final: 0.8277 (t0) REVERT: H 81 ASP cc_start: 0.7746 (m-30) cc_final: 0.6965 (t70) REVERT: H 100 LYS cc_start: 0.7314 (mttm) cc_final: 0.6842 (pttm) REVERT: H 109 HIS cc_start: 0.8191 (t70) cc_final: 0.7929 (m90) REVERT: W 28 GLN cc_start: 0.7335 (tt0) cc_final: 0.6768 (tm-30) REVERT: W 73 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: I 16 MET cc_start: 0.0134 (tpt) cc_final: -0.0233 (tpt) REVERT: I 19 LEU cc_start: 0.8107 (mt) cc_final: 0.7685 (tp) REVERT: J 17 MET cc_start: 0.5827 (mtp) cc_final: 0.4251 (tpp) REVERT: J 61 ASP cc_start: 0.7091 (m-30) cc_final: 0.6780 (p0) REVERT: M 6 MET cc_start: 0.4058 (mtp) cc_final: 0.3723 (ptt) REVERT: M 17 MET cc_start: 0.6905 (mtm) cc_final: 0.5234 (tpp) REVERT: N 11 MET cc_start: 0.5864 (tpp) cc_final: 0.5461 (tmm) REVERT: O 53 PHE cc_start: 0.7949 (t80) cc_final: 0.7491 (t80) REVERT: P 61 ASP cc_start: 0.0388 (OUTLIER) cc_final: 0.0089 (t0) REVERT: S 57 MET cc_start: 0.7289 (tmt) cc_final: 0.6982 (ptt) REVERT: X 48 GLU cc_start: 0.4229 (OUTLIER) cc_final: 0.3794 (tt0) REVERT: X 63 ASP cc_start: 0.3858 (t0) cc_final: 0.3382 (m-30) REVERT: Y 96 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8233 (tm-30) REVERT: Y 98 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7317 (mtp180) REVERT: a 46 MET cc_start: 0.3412 (mmm) cc_final: 0.2840 (mtt) REVERT: a 257 MET cc_start: 0.7183 (tmm) cc_final: 0.6708 (ptm) outliers start: 79 outliers final: 33 residues processed: 354 average time/residue: 0.5075 time to fit residues: 296.2395 Evaluate side-chains 284 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 247 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 6 MET Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain a residue 7 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 357 optimal weight: 5.9990 chunk 292 optimal weight: 0.0980 chunk 118 optimal weight: 0.9980 chunk 430 optimal weight: 10.0000 chunk 464 optimal weight: 10.0000 chunk 383 optimal weight: 6.9990 chunk 426 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS F 19 GLN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS a 32 GLN ** a 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37419 Z= 0.261 Angle : 0.613 11.963 50648 Z= 0.313 Chirality : 0.042 0.215 5902 Planarity : 0.004 0.044 6530 Dihedral : 7.173 138.140 5359 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 1.96 % Allowed : 12.13 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.43 (0.12), residues: 4793 helix: 0.97 (0.10), residues: 2599 sheet: -0.08 (0.22), residues: 526 loop : -0.55 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 186 HIS 0.005 0.001 HIS G 64 PHE 0.031 0.001 PHE S 54 TYR 0.012 0.001 TYR C 236 ARG 0.006 0.000 ARG G 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 267 time to evaluate : 4.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 PHE cc_start: 0.8525 (t80) cc_final: 0.8276 (t80) REVERT: C 236 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8334 (p90) REVERT: E 287 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8516 (p) REVERT: H 75 ASN cc_start: 0.8530 (m-40) cc_final: 0.8147 (t0) REVERT: W 28 GLN cc_start: 0.7580 (tt0) cc_final: 0.6932 (tm-30) REVERT: W 43 MET cc_start: 0.7640 (ttm) cc_final: 0.7401 (tpp) REVERT: I 19 LEU cc_start: 0.8021 (mt) cc_final: 0.7626 (tp) REVERT: J 17 MET cc_start: 0.5905 (mtp) cc_final: 0.4539 (tpp) REVERT: J 61 ASP cc_start: 0.7106 (m-30) cc_final: 0.6641 (p0) REVERT: L 65 MET cc_start: 0.3823 (mmm) cc_final: 0.2291 (ppp) REVERT: M 6 MET cc_start: 0.4023 (mtp) cc_final: 0.3701 (ptt) REVERT: M 17 MET cc_start: 0.7021 (mtm) cc_final: 0.5280 (tpt) REVERT: N 11 MET cc_start: 0.5769 (tpp) cc_final: 0.5369 (tmm) REVERT: O 65 MET cc_start: 0.0821 (mmm) cc_final: 0.0410 (ttm) REVERT: P 16 MET cc_start: 0.6871 (ttt) cc_final: 0.6105 (ttm) REVERT: P 61 ASP cc_start: 0.0867 (OUTLIER) cc_final: 0.0424 (t0) REVERT: R 53 PHE cc_start: 0.7517 (t80) cc_final: 0.6949 (t80) REVERT: R 57 MET cc_start: 0.8050 (tmm) cc_final: 0.7236 (mmm) REVERT: X 48 GLU cc_start: 0.4484 (OUTLIER) cc_final: 0.4078 (tt0) REVERT: X 63 ASP cc_start: 0.4420 (t0) cc_final: 0.3838 (m-30) REVERT: X 66 LYS cc_start: 0.7533 (pptt) cc_final: 0.7155 (pptt) REVERT: Y 24 TYR cc_start: 0.1332 (OUTLIER) cc_final: 0.0303 (m-80) REVERT: Y 96 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8223 (tm-30) REVERT: Y 98 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7326 (mtp180) REVERT: a 46 MET cc_start: 0.3740 (mmm) cc_final: 0.3224 (mtp) REVERT: a 139 LEU cc_start: 0.1409 (OUTLIER) cc_final: 0.1089 (tt) REVERT: a 168 MET cc_start: 0.3726 (mmm) cc_final: 0.3407 (mtt) REVERT: a 196 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6953 (mt-10) REVERT: a 257 MET cc_start: 0.7322 (tmm) cc_final: 0.7107 (ptm) outliers start: 75 outliers final: 35 residues processed: 327 average time/residue: 0.5090 time to fit residues: 277.1251 Evaluate side-chains 282 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 241 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain R residue 6 MET Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 210 ARG 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: 8.9990 chunk 223 optimal weight: 7.9990 chunk 47 optimal weight: 0.0980 chunk 205 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 431 optimal weight: 20.0000 chunk 457 optimal weight: 40.0000 chunk 225 optimal weight: 6.9990 chunk 409 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN B 294 HIS C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 43 GLN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 37419 Z= 0.308 Angle : 0.625 10.680 50648 Z= 0.317 Chirality : 0.042 0.165 5902 Planarity : 0.004 0.060 6530 Dihedral : 6.911 126.938 5359 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 2.43 % Allowed : 13.10 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.51 (0.12), residues: 4793 helix: 1.07 (0.10), residues: 2607 sheet: -0.02 (0.23), residues: 517 loop : -0.61 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 241 HIS 0.005 0.001 HIS G 64 PHE 0.030 0.002 PHE S 54 TYR 0.020 0.001 TYR C 150 ARG 0.006 0.001 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 260 time to evaluate : 4.509 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: A 262 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.6942 (m-30) REVERT: A 406 PHE cc_start: 0.8621 (t80) cc_final: 0.8386 (t80) REVERT: B 103 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8183 (pp) REVERT: B 156 MET cc_start: 0.8875 (tpp) cc_final: 0.8631 (tpp) REVERT: D 379 MET cc_start: 0.8094 (tmm) cc_final: 0.7238 (tpp) REVERT: E 287 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8484 (p) REVERT: H 95 MET cc_start: 0.7563 (tpt) cc_final: 0.6610 (mmm) REVERT: W 28 GLN cc_start: 0.7808 (tt0) cc_final: 0.6891 (tm-30) REVERT: W 76 ILE cc_start: 0.8655 (pt) cc_final: 0.8320 (pt) REVERT: I 17 MET cc_start: 0.6040 (ppp) cc_final: 0.5783 (ppp) REVERT: I 19 LEU cc_start: 0.7966 (mt) cc_final: 0.7510 (tp) REVERT: J 17 MET cc_start: 0.5643 (mtp) cc_final: 0.4362 (tpp) REVERT: J 61 ASP cc_start: 0.7033 (m-30) cc_final: 0.6642 (p0) REVERT: L 65 MET cc_start: 0.3954 (mmm) cc_final: 0.2613 (ppp) REVERT: M 6 MET cc_start: 0.4051 (mtp) cc_final: 0.3690 (ptt) REVERT: M 28 ILE cc_start: 0.6722 (mm) cc_final: 0.6247 (tt) REVERT: N 11 MET cc_start: 0.5704 (tpp) cc_final: 0.5415 (tmm) REVERT: N 75 MET cc_start: 0.1518 (mmm) cc_final: 0.0722 (tpp) REVERT: O 65 MET cc_start: 0.0984 (mmm) cc_final: 0.0456 (ttm) REVERT: P 11 MET cc_start: 0.4817 (mmm) cc_final: 0.4490 (mmm) REVERT: P 61 ASP cc_start: 0.1385 (OUTLIER) cc_final: 0.0996 (t0) REVERT: R 57 MET cc_start: 0.7902 (tmm) cc_final: 0.7145 (mmm) REVERT: S 36 LEU cc_start: 0.8304 (mp) cc_final: 0.8070 (tp) REVERT: X 48 GLU cc_start: 0.4594 (OUTLIER) cc_final: 0.4199 (tt0) REVERT: X 63 ASP cc_start: 0.4763 (t0) cc_final: 0.4177 (m-30) REVERT: X 66 LYS cc_start: 0.7568 (pptt) cc_final: 0.7237 (pptt) REVERT: Y 24 TYR cc_start: 0.1138 (OUTLIER) cc_final: 0.0129 (m-80) REVERT: Y 96 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8201 (tm-30) REVERT: Y 98 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7457 (mtp180) REVERT: a 6 MET cc_start: 0.3041 (ttp) cc_final: 0.2837 (ppp) REVERT: a 46 MET cc_start: 0.3879 (mmm) cc_final: 0.3080 (mtp) REVERT: a 168 MET cc_start: 0.3879 (mmm) cc_final: 0.3620 (mtt) REVERT: a 196 GLU cc_start: 0.7521 (mm-30) cc_final: 0.6973 (mt-10) outliers start: 93 outliers final: 48 residues processed: 341 average time/residue: 0.4808 time to fit residues: 276.2975 Evaluate side-chains 293 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 239 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 340 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 390 optimal weight: 30.0000 chunk 316 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 410 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37419 Z= 0.227 Angle : 0.577 10.561 50648 Z= 0.292 Chirality : 0.040 0.158 5902 Planarity : 0.004 0.062 6530 Dihedral : 6.580 133.144 5359 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.43 % Rotamer: Outliers : 2.01 % Allowed : 14.41 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.73 (0.12), residues: 4793 helix: 1.31 (0.10), residues: 2588 sheet: 0.14 (0.23), residues: 498 loop : -0.61 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 203 HIS 0.004 0.001 HIS G 64 PHE 0.028 0.001 PHE S 54 TYR 0.012 0.001 TYR C 236 ARG 0.006 0.000 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 250 time to evaluate : 4.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6912 (m-30) REVERT: A 406 PHE cc_start: 0.8610 (t80) cc_final: 0.8369 (t80) REVERT: B 103 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8157 (pp) REVERT: B 156 MET cc_start: 0.8883 (tpp) cc_final: 0.8645 (mmt) REVERT: D 379 MET cc_start: 0.8307 (tmm) cc_final: 0.7472 (tpp) REVERT: E 287 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8385 (p) REVERT: E 445 MET cc_start: 0.8110 (mmm) cc_final: 0.7642 (mmm) REVERT: F 136 MET cc_start: 0.8902 (mmm) cc_final: 0.8673 (mmm) REVERT: G 155 MET cc_start: 0.8580 (tpp) cc_final: 0.8368 (tpp) REVERT: H 100 LYS cc_start: 0.5249 (mttm) cc_final: 0.5009 (mmtt) REVERT: W 28 GLN cc_start: 0.7965 (tt0) cc_final: 0.7149 (tm-30) REVERT: I 19 LEU cc_start: 0.7819 (mt) cc_final: 0.7434 (tp) REVERT: J 17 MET cc_start: 0.5766 (mtp) cc_final: 0.4663 (tpp) REVERT: L 65 MET cc_start: 0.4110 (mmm) cc_final: 0.2954 (ppp) REVERT: M 6 MET cc_start: 0.4123 (mtp) cc_final: 0.3801 (ptt) REVERT: M 28 ILE cc_start: 0.6676 (mm) cc_final: 0.6169 (tt) REVERT: N 11 MET cc_start: 0.5720 (tpp) cc_final: 0.5441 (tmm) REVERT: N 75 MET cc_start: 0.1528 (mmm) cc_final: 0.0807 (tpp) REVERT: O 65 MET cc_start: 0.0798 (mmm) cc_final: 0.0204 (ttm) REVERT: P 11 MET cc_start: 0.4847 (mmm) cc_final: 0.4557 (mmm) REVERT: P 61 ASP cc_start: 0.1541 (OUTLIER) cc_final: 0.1204 (t0) REVERT: R 57 MET cc_start: 0.7993 (tmm) cc_final: 0.7153 (mmm) REVERT: X 48 GLU cc_start: 0.4729 (OUTLIER) cc_final: 0.3587 (tp30) REVERT: X 63 ASP cc_start: 0.4732 (t0) cc_final: 0.4165 (m-30) REVERT: X 66 LYS cc_start: 0.7815 (pptt) cc_final: 0.7494 (pptt) REVERT: Y 24 TYR cc_start: 0.0920 (OUTLIER) cc_final: -0.0089 (m-80) REVERT: Y 96 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8209 (tm-30) REVERT: Y 98 ARG cc_start: 0.7826 (ttp80) cc_final: 0.7476 (mtp180) REVERT: a 6 MET cc_start: 0.2769 (ttp) cc_final: 0.2434 (ppp) REVERT: a 46 MET cc_start: 0.3541 (mmm) cc_final: 0.3086 (mtp) REVERT: a 168 MET cc_start: 0.3865 (mmm) cc_final: 0.3579 (mtt) REVERT: a 196 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7009 (mt-10) REVERT: a 257 MET cc_start: 0.7316 (ptt) cc_final: 0.7012 (tmm) outliers start: 77 outliers final: 49 residues processed: 316 average time/residue: 0.4933 time to fit residues: 261.9337 Evaluate side-chains 296 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 241 time to evaluate : 4.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 7 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 8.9990 chunk 411 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 457 optimal weight: 9.9990 chunk 379 optimal weight: 0.0980 chunk 211 optimal weight: 0.0980 chunk 38 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 240 optimal weight: 0.6980 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 493 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37419 Z= 0.205 Angle : 0.567 14.182 50648 Z= 0.283 Chirality : 0.040 0.148 5902 Planarity : 0.004 0.064 6530 Dihedral : 6.308 135.559 5359 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.57 % Favored : 97.41 % Rotamer: Outliers : 2.12 % Allowed : 14.54 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.84 (0.12), residues: 4793 helix: 1.40 (0.10), residues: 2587 sheet: 0.19 (0.23), residues: 509 loop : -0.57 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 203 HIS 0.004 0.001 HIS G 64 PHE 0.026 0.001 PHE S 54 TYR 0.015 0.001 TYR L 73 ARG 0.011 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 263 time to evaluate : 4.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: A 406 PHE cc_start: 0.8611 (t80) cc_final: 0.8367 (t80) REVERT: B 103 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8187 (pp) REVERT: B 156 MET cc_start: 0.8905 (tpp) cc_final: 0.8648 (mmt) REVERT: C 318 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8130 (mtmt) REVERT: C 468 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8557 (tp30) REVERT: D 261 MET cc_start: 0.8603 (mtt) cc_final: 0.8395 (mtt) REVERT: D 379 MET cc_start: 0.8324 (tmm) cc_final: 0.7484 (tpp) REVERT: E 193 MET cc_start: 0.8230 (mpp) cc_final: 0.8026 (mpp) REVERT: E 287 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8289 (p) REVERT: H 81 ASP cc_start: 0.7976 (m-30) cc_final: 0.7311 (t70) REVERT: W 28 GLN cc_start: 0.8068 (tt0) cc_final: 0.7252 (tm-30) REVERT: W 76 ILE cc_start: 0.8760 (pt) cc_final: 0.8420 (pt) REVERT: I 19 LEU cc_start: 0.7777 (mt) cc_final: 0.7390 (tp) REVERT: J 17 MET cc_start: 0.5541 (mtp) cc_final: 0.4561 (tpp) REVERT: L 65 MET cc_start: 0.4103 (mmm) cc_final: 0.2906 (ppp) REVERT: M 6 MET cc_start: 0.4081 (mtp) cc_final: 0.3715 (ptt) REVERT: M 28 ILE cc_start: 0.6634 (mm) cc_final: 0.6218 (tt) REVERT: N 75 MET cc_start: 0.1449 (mmm) cc_final: 0.0737 (tpp) REVERT: P 11 MET cc_start: 0.4882 (mmm) cc_final: 0.4502 (mmm) REVERT: P 61 ASP cc_start: 0.1566 (OUTLIER) cc_final: 0.1272 (t0) REVERT: R 57 MET cc_start: 0.7986 (tmm) cc_final: 0.7148 (mmm) REVERT: X 48 GLU cc_start: 0.4695 (OUTLIER) cc_final: 0.3624 (tp30) REVERT: X 63 ASP cc_start: 0.4821 (t0) cc_final: 0.4270 (m-30) REVERT: X 66 LYS cc_start: 0.7800 (pptt) cc_final: 0.7499 (pptt) REVERT: X 82 ARG cc_start: 0.8605 (ttt180) cc_final: 0.8092 (mmm160) REVERT: Y 24 TYR cc_start: 0.1061 (OUTLIER) cc_final: 0.0109 (m-80) REVERT: Y 96 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8143 (tm-30) REVERT: Y 98 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7577 (mtp180) REVERT: a 46 MET cc_start: 0.3548 (mmm) cc_final: 0.3094 (mtp) REVERT: a 168 MET cc_start: 0.3830 (mmm) cc_final: 0.3577 (mtt) REVERT: a 196 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7061 (mt-10) outliers start: 81 outliers final: 52 residues processed: 330 average time/residue: 0.4849 time to fit residues: 269.7993 Evaluate side-chains 305 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 246 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain W residue 39 LYS Chi-restraints excluded: chain I residue 65 MET Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain X residue 44 LEU Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 24 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 260 optimal weight: 0.9990 chunk 334 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 385 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 455 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 277 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN X 51 HIS ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37419 Z= 0.198 Angle : 0.573 12.510 50648 Z= 0.286 Chirality : 0.040 0.160 5902 Planarity : 0.004 0.057 6530 Dihedral : 6.153 135.878 5358 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 2.04 % Allowed : 14.88 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.89 (0.12), residues: 4793 helix: 1.44 (0.10), residues: 2592 sheet: 0.25 (0.23), residues: 502 loop : -0.55 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 235 HIS 0.004 0.001 HIS B 123 PHE 0.026 0.001 PHE S 54 TYR 0.013 0.001 TYR C 492 ARG 0.004 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 253 time to evaluate : 4.379 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: A 188 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7995 (p0) REVERT: A 262 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6871 (m-30) REVERT: A 406 PHE cc_start: 0.8614 (t80) cc_final: 0.8363 (t80) REVERT: B 103 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8219 (pp) REVERT: B 156 MET cc_start: 0.8918 (tpp) cc_final: 0.8664 (mmt) REVERT: C 318 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8106 (mtmt) REVERT: C 418 ARG cc_start: 0.9125 (ttp-170) cc_final: 0.8847 (ttp-110) REVERT: C 468 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8556 (tp30) REVERT: D 379 MET cc_start: 0.8276 (tmm) cc_final: 0.7445 (tpp) REVERT: E 193 MET cc_start: 0.8149 (mpp) cc_final: 0.7911 (mpp) REVERT: E 246 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8127 (mtt-85) REVERT: E 287 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8261 (p) REVERT: F 136 MET cc_start: 0.8843 (mmm) cc_final: 0.8595 (mmm) REVERT: H 81 ASP cc_start: 0.7987 (m-30) cc_final: 0.7336 (t70) REVERT: H 95 MET cc_start: 0.7304 (tpt) cc_final: 0.6844 (tpp) REVERT: W 28 GLN cc_start: 0.8086 (tt0) cc_final: 0.7274 (tm-30) REVERT: W 76 ILE cc_start: 0.8749 (pt) cc_final: 0.8432 (pt) REVERT: I 19 LEU cc_start: 0.7820 (mt) cc_final: 0.7434 (tp) REVERT: J 17 MET cc_start: 0.5494 (mtp) cc_final: 0.4660 (tpp) REVERT: L 65 MET cc_start: 0.4312 (mmm) cc_final: 0.3206 (ppp) REVERT: M 6 MET cc_start: 0.4058 (mtp) cc_final: 0.3675 (ptt) REVERT: M 28 ILE cc_start: 0.6799 (mm) cc_final: 0.6316 (tt) REVERT: N 75 MET cc_start: 0.1448 (mmm) cc_final: 0.0804 (tpp) REVERT: P 61 ASP cc_start: 0.1912 (OUTLIER) cc_final: 0.1700 (t0) REVERT: R 57 MET cc_start: 0.7938 (tmm) cc_final: 0.7075 (mmm) REVERT: X 1 MET cc_start: 0.2951 (mtm) cc_final: 0.2634 (mtm) REVERT: X 63 ASP cc_start: 0.4858 (t0) cc_final: 0.4142 (m-30) REVERT: X 82 ARG cc_start: 0.8593 (ttt180) cc_final: 0.8081 (mmm160) REVERT: Y 24 TYR cc_start: 0.1069 (OUTLIER) cc_final: 0.0135 (m-80) REVERT: Y 96 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8123 (tm-30) REVERT: Y 98 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7644 (mtp180) REVERT: a 46 MET cc_start: 0.3772 (mmm) cc_final: 0.3328 (mtt) REVERT: a 168 MET cc_start: 0.3736 (mmm) cc_final: 0.3455 (mtt) REVERT: a 196 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7100 (mt-10) outliers start: 78 outliers final: 46 residues processed: 319 average time/residue: 0.4915 time to fit residues: 262.4866 Evaluate side-chains 303 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 4.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain W residue 39 LYS Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain O residue 41 ARG Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 272 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 289 optimal weight: 0.8980 chunk 310 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 358 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37419 Z= 0.145 Angle : 0.578 13.589 50648 Z= 0.283 Chirality : 0.039 0.151 5902 Planarity : 0.004 0.055 6530 Dihedral : 5.926 134.093 5358 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 1.73 % Allowed : 15.32 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 0.96 (0.12), residues: 4793 helix: 1.49 (0.10), residues: 2593 sheet: 0.32 (0.23), residues: 506 loop : -0.53 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 26 HIS 0.003 0.000 HIS B 123 PHE 0.028 0.001 PHE S 54 TYR 0.012 0.001 TYR C 492 ARG 0.004 0.000 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 259 time to evaluate : 4.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7987 (p0) REVERT: A 406 PHE cc_start: 0.8607 (t80) cc_final: 0.8357 (t80) REVERT: B 103 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8135 (pp) REVERT: C 318 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8039 (mtmt) REVERT: C 418 ARG cc_start: 0.9101 (ttp-170) cc_final: 0.8820 (ttp-110) REVERT: D 379 MET cc_start: 0.8559 (tmm) cc_final: 0.7817 (tpp) REVERT: E 287 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8232 (p) REVERT: F 136 MET cc_start: 0.8865 (mmm) cc_final: 0.8632 (mmm) REVERT: H 81 ASP cc_start: 0.7958 (m-30) cc_final: 0.7368 (t70) REVERT: H 95 MET cc_start: 0.7058 (tpt) cc_final: 0.5988 (tpp) REVERT: W 28 GLN cc_start: 0.8115 (tt0) cc_final: 0.7370 (tm-30) REVERT: W 76 ILE cc_start: 0.8840 (pt) cc_final: 0.8386 (mp) REVERT: I 19 LEU cc_start: 0.7840 (mt) cc_final: 0.7497 (tp) REVERT: J 17 MET cc_start: 0.5323 (mtp) cc_final: 0.4516 (tpp) REVERT: L 65 MET cc_start: 0.4292 (mmm) cc_final: 0.3278 (ppp) REVERT: M 6 MET cc_start: 0.4123 (mtp) cc_final: 0.3664 (ptt) REVERT: M 28 ILE cc_start: 0.6854 (mm) cc_final: 0.6318 (tt) REVERT: N 65 MET cc_start: 0.3677 (mmm) cc_final: 0.3231 (mmm) REVERT: N 75 MET cc_start: 0.1399 (mmm) cc_final: 0.0700 (tpp) REVERT: P 11 MET cc_start: 0.4210 (mmm) cc_final: 0.3450 (mmm) REVERT: P 16 MET cc_start: 0.6325 (ttt) cc_final: 0.5564 (ttm) REVERT: Q 17 MET cc_start: 0.1531 (ptp) cc_final: 0.0065 (tpp) REVERT: R 57 MET cc_start: 0.7621 (tmm) cc_final: 0.6900 (mmt) REVERT: X 1 MET cc_start: 0.2669 (mtm) cc_final: 0.2290 (mtm) REVERT: X 63 ASP cc_start: 0.4894 (t0) cc_final: 0.3881 (m-30) REVERT: X 66 LYS cc_start: 0.7671 (pptt) cc_final: 0.6623 (mmtm) REVERT: X 82 ARG cc_start: 0.8658 (ttt180) cc_final: 0.8129 (mmm160) REVERT: Y 24 TYR cc_start: 0.1085 (OUTLIER) cc_final: 0.0182 (m-80) REVERT: Y 96 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8084 (tm-30) REVERT: Y 98 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7586 (mtp180) REVERT: a 6 MET cc_start: 0.4644 (ppp) cc_final: 0.3743 (tmm) REVERT: a 46 MET cc_start: 0.3662 (mmm) cc_final: 0.3288 (mtt) REVERT: a 168 MET cc_start: 0.3732 (mmm) cc_final: 0.3422 (mtt) REVERT: a 196 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7112 (mt-10) outliers start: 66 outliers final: 41 residues processed: 316 average time/residue: 0.4804 time to fit residues: 251.4280 Evaluate side-chains 291 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 4.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 513 TRP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain W residue 39 LYS Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 20.0000 chunk 436 optimal weight: 0.0070 chunk 398 optimal weight: 20.0000 chunk 424 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 333 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 383 optimal weight: 8.9990 chunk 401 optimal weight: 7.9990 chunk 423 optimal weight: 20.0000 overall best weight: 5.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS B 186 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 37419 Z= 0.340 Angle : 0.661 15.270 50648 Z= 0.328 Chirality : 0.042 0.181 5902 Planarity : 0.004 0.054 6530 Dihedral : 6.126 135.062 5358 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 1.75 % Allowed : 15.27 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.91 (0.12), residues: 4793 helix: 1.44 (0.10), residues: 2576 sheet: 0.27 (0.23), residues: 508 loop : -0.51 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 203 HIS 0.005 0.001 HIS B 123 PHE 0.024 0.002 PHE S 54 TYR 0.015 0.001 TYR L 73 ARG 0.007 0.001 ARG E 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 245 time to evaluate : 4.858 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: A 188 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8080 (p0) REVERT: B 103 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8406 (pp) REVERT: C 318 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8080 (mtmt) REVERT: D 0 MET cc_start: 0.7713 (ppp) cc_final: 0.7405 (ppp) REVERT: D 379 MET cc_start: 0.8500 (tmm) cc_final: 0.7676 (tpp) REVERT: E 193 MET cc_start: 0.8219 (mpp) cc_final: 0.7924 (mpp) REVERT: E 287 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8349 (p) REVERT: W 28 GLN cc_start: 0.8347 (tt0) cc_final: 0.7523 (tm-30) REVERT: W 76 ILE cc_start: 0.8951 (pt) cc_final: 0.8585 (mp) REVERT: I 19 LEU cc_start: 0.7683 (mt) cc_final: 0.7270 (tp) REVERT: I 75 MET cc_start: 0.4233 (tpt) cc_final: 0.3923 (tpt) REVERT: J 16 MET cc_start: 0.3288 (mmm) cc_final: 0.2976 (mmm) REVERT: L 17 MET cc_start: 0.2537 (mpp) cc_final: 0.2274 (ptp) REVERT: L 65 MET cc_start: 0.4250 (mmm) cc_final: 0.3115 (ppp) REVERT: M 6 MET cc_start: 0.4416 (mtp) cc_final: 0.3993 (ptt) REVERT: M 17 MET cc_start: 0.6756 (mpp) cc_final: 0.3524 (tmm) REVERT: M 28 ILE cc_start: 0.6812 (mm) cc_final: 0.6320 (tt) REVERT: N 65 MET cc_start: 0.3326 (mmm) cc_final: 0.2926 (mmm) REVERT: N 75 MET cc_start: 0.1470 (mmm) cc_final: 0.0687 (tpp) REVERT: Q 17 MET cc_start: 0.1381 (ptp) cc_final: -0.0076 (tpp) REVERT: R 57 MET cc_start: 0.7675 (tmm) cc_final: 0.6905 (mmm) REVERT: X 1 MET cc_start: 0.2952 (mtm) cc_final: 0.2613 (mtm) REVERT: X 63 ASP cc_start: 0.4933 (t0) cc_final: 0.4182 (m-30) REVERT: X 82 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8070 (mmm160) REVERT: Y 24 TYR cc_start: 0.1231 (OUTLIER) cc_final: 0.0318 (m-80) REVERT: Y 96 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8088 (tm-30) REVERT: Y 98 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7631 (mtp180) REVERT: a 46 MET cc_start: 0.3727 (mmm) cc_final: 0.3268 (mtt) REVERT: a 168 MET cc_start: 0.3846 (mmm) cc_final: 0.3490 (mtt) outliers start: 67 outliers final: 47 residues processed: 303 average time/residue: 0.4929 time to fit residues: 251.1647 Evaluate side-chains 290 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 238 time to evaluate : 4.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 4.9990 chunk 449 optimal weight: 6.9990 chunk 274 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 471 optimal weight: 6.9990 chunk 433 optimal weight: 10.0000 chunk 375 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 230 optimal weight: 0.0670 overall best weight: 2.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37419 Z= 0.220 Angle : 0.619 13.499 50648 Z= 0.304 Chirality : 0.040 0.183 5902 Planarity : 0.004 0.062 6530 Dihedral : 6.012 132.206 5356 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 1.44 % Allowed : 16.00 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: 0.95 (0.12), residues: 4793 helix: 1.47 (0.10), residues: 2587 sheet: 0.26 (0.23), residues: 518 loop : -0.48 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 203 HIS 0.004 0.001 HIS B 123 PHE 0.029 0.001 PHE F 189 TYR 0.012 0.001 TYR C 492 ARG 0.008 0.000 ARG H 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 243 time to evaluate : 4.750 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: A 188 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8027 (p0) REVERT: B 103 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8218 (pp) REVERT: C 318 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8107 (mtmt) REVERT: D 0 MET cc_start: 0.7715 (ppp) cc_final: 0.7426 (ppp) REVERT: D 379 MET cc_start: 0.8619 (tmm) cc_final: 0.7898 (tpp) REVERT: E 193 MET cc_start: 0.8123 (mpp) cc_final: 0.7896 (mpp) REVERT: E 287 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8215 (p) REVERT: F 209 MET cc_start: 0.8497 (ptp) cc_final: 0.7970 (mtm) REVERT: G 116 MET cc_start: 0.7061 (mmp) cc_final: 0.6812 (mmp) REVERT: W 28 GLN cc_start: 0.8354 (tt0) cc_final: 0.7579 (tm-30) REVERT: W 76 ILE cc_start: 0.8957 (pt) cc_final: 0.8626 (mp) REVERT: I 19 LEU cc_start: 0.7799 (mt) cc_final: 0.7418 (tp) REVERT: I 75 MET cc_start: 0.4484 (tpt) cc_final: 0.4199 (tpt) REVERT: J 17 MET cc_start: 0.5155 (mmt) cc_final: 0.3944 (tpp) REVERT: L 65 MET cc_start: 0.4275 (mmm) cc_final: 0.3199 (ppp) REVERT: M 28 ILE cc_start: 0.6859 (mm) cc_final: 0.6306 (tt) REVERT: N 65 MET cc_start: 0.3300 (mmm) cc_final: 0.2899 (mmm) REVERT: N 75 MET cc_start: 0.1625 (mmm) cc_final: 0.0857 (tpp) REVERT: Q 17 MET cc_start: 0.1367 (ptp) cc_final: -0.0089 (tpp) REVERT: R 57 MET cc_start: 0.7654 (tmm) cc_final: 0.6929 (mmt) REVERT: X 1 MET cc_start: 0.2809 (mtm) cc_final: 0.2408 (mtm) REVERT: X 63 ASP cc_start: 0.5154 (t0) cc_final: 0.4148 (m-30) REVERT: X 66 LYS cc_start: 0.7568 (pptt) cc_final: 0.6351 (mmtm) REVERT: X 82 ARG cc_start: 0.8661 (ttt180) cc_final: 0.8106 (mmm160) REVERT: Y 24 TYR cc_start: 0.1235 (OUTLIER) cc_final: 0.0327 (m-80) REVERT: Y 96 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8063 (tm-30) REVERT: Y 98 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7620 (mtp180) REVERT: a 6 MET cc_start: 0.4844 (ppp) cc_final: 0.4299 (tmm) REVERT: a 46 MET cc_start: 0.3774 (mmm) cc_final: 0.3269 (mtm) REVERT: a 153 MET cc_start: -0.0351 (mtm) cc_final: -0.1002 (ttt) REVERT: a 168 MET cc_start: 0.3923 (mmm) cc_final: 0.3564 (mtt) outliers start: 55 outliers final: 44 residues processed: 290 average time/residue: 0.5084 time to fit residues: 246.5180 Evaluate side-chains 288 residues out of total 3827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 239 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain O residue 30 ILE Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 24 TYR Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 210 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 0.9990 chunk 399 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 375 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 385 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** Q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.068970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.045912 restraints weight = 203686.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.046649 restraints weight = 104714.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.046670 restraints weight = 68452.243| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 37419 Z= 0.161 Angle : 0.606 15.083 50648 Z= 0.296 Chirality : 0.040 0.273 5902 Planarity : 0.004 0.056 6530 Dihedral : 5.835 127.877 5356 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.82 % Favored : 97.16 % Rotamer: Outliers : 1.52 % Allowed : 16.16 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.12), residues: 4793 helix: 1.51 (0.10), residues: 2590 sheet: 0.33 (0.23), residues: 524 loop : -0.46 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 203 HIS 0.003 0.000 HIS B 123 PHE 0.027 0.001 PHE S 54 TYR 0.012 0.001 TYR C 492 ARG 0.016 0.000 ARG H 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7021.92 seconds wall clock time: 129 minutes 27.97 seconds (7767.97 seconds total)