Starting phenix.real_space_refine on Wed Feb 21 16:32:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzz_0563/02_2024/6nzz_0563_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzz_0563/02_2024/6nzz_0563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzz_0563/02_2024/6nzz_0563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzz_0563/02_2024/6nzz_0563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzz_0563/02_2024/6nzz_0563_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzz_0563/02_2024/6nzz_0563_neut_trim_updated.pdb" } resolution = 3.32 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= 1.000 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 S 102 5.16 5 Cl 2 4.86 5 C 10390 2.51 5 N 2466 2.21 5 O 2698 1.98 5 H 15330 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30988 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "B" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "C" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "D" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "E" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "F" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5123 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 2 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'L9Y': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 13.67, per 1000 atoms: 0.44 Number of scatterers: 30988 At special positions: 0 Unit cell: (112.064, 107.712, 127.296, 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) Cl 2 17.00 S 102 16.00 O 2698 8.00 N 2466 7.00 C 10390 6.00 H 15330 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 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: 24.71 Conformation dependent library (CDL) restraints added in 3.2 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 6 sheets defined 61.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 24 through 47 removed outlier: 3.986A pdb=" N ASP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 39 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.712A pdb=" N ALA A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 144 Proline residue: A 126 - end of helix removed outlier: 3.593A pdb=" N LEU A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 164 removed outlier: 4.662A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.864A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.579A pdb=" N LEU A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.502A pdb=" N MET A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 315 through 345 removed outlier: 3.745A pdb=" N SER A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 340 " --> pdb=" O CYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 360 No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 373 through 382 removed outlier: 4.030A pdb=" N ILE A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.606A pdb=" N PHE A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'B' and resid 24 through 47 removed outlier: 3.986A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 39 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.712A pdb=" N ALA B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 144 Proline residue: B 126 - end of helix removed outlier: 3.592A pdb=" N LEU B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 164 removed outlier: 4.661A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.863A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.580A pdb=" N LEU B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.502A pdb=" N MET B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 315 through 345 removed outlier: 3.745A pdb=" N SER B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 340 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 360 No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 373 through 382 removed outlier: 4.030A pdb=" N ILE B 379 " --> pdb=" O MET B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.607A pdb=" N PHE B 390 " --> pdb=" O TYR B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'C' and resid 24 through 47 removed outlier: 3.986A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 39 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY C 42 " --> pdb=" O ILE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.713A pdb=" N ALA C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 144 Proline residue: C 126 - end of helix removed outlier: 3.592A pdb=" N LEU C 130 " --> pdb=" O PRO C 126 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 removed outlier: 4.662A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 removed outlier: 3.863A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 253 removed outlier: 3.579A pdb=" N LEU C 243 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.502A pdb=" N MET C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 315 through 345 removed outlier: 3.745A pdb=" N SER C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR C 332 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 340 " --> pdb=" O CYS C 336 " (cutoff:3.500A) 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 373 through 382 removed outlier: 4.030A pdb=" N ILE C 379 " --> pdb=" O MET C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.608A pdb=" N PHE C 390 " --> pdb=" O TYR C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'D' and resid 24 through 47 removed outlier: 3.985A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 39 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.713A pdb=" N ALA D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 144 Proline residue: D 126 - end of helix removed outlier: 3.592A pdb=" N LEU D 130 " --> pdb=" O PRO D 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 4.661A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.863A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 253 removed outlier: 3.579A pdb=" N LEU D 243 " --> pdb=" O GLN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.501A pdb=" N MET D 265 " --> pdb=" O TYR D 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 315 through 345 removed outlier: 3.745A pdb=" N SER D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 340 " --> pdb=" O CYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 360 No H-bonds generated for 'chain 'D' and resid 357 through 360' Processing helix chain 'D' and resid 373 through 382 removed outlier: 4.029A pdb=" N ILE D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.607A pdb=" N PHE D 390 " --> pdb=" O TYR D 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 390' Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'E' and resid 24 through 47 removed outlier: 3.985A pdb=" N ASP E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 39 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY E 42 " --> pdb=" O ILE E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 115 removed outlier: 3.712A pdb=" N ALA E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 144 Proline residue: E 126 - end of helix removed outlier: 3.592A pdb=" N LEU E 130 " --> pdb=" O PRO E 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 164 removed outlier: 4.662A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.864A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 253 removed outlier: 3.579A pdb=" N LEU E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 282 removed outlier: 3.502A pdb=" N MET E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL E 272 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE E 273 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE E 275 " --> pdb=" O LYS E 271 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 315 through 345 removed outlier: 3.745A pdb=" N SER E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 340 " --> pdb=" O CYS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 360 No H-bonds generated for 'chain 'E' and resid 357 through 360' Processing helix chain 'E' and resid 373 through 382 removed outlier: 4.030A pdb=" N ILE E 379 " --> pdb=" O MET E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 removed outlier: 3.606A pdb=" N PHE E 390 " --> pdb=" O TYR E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 390' Processing helix chain 'E' and resid 396 through 403 Processing helix chain 'F' and resid 24 through 47 removed outlier: 3.986A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 39 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 42 " --> pdb=" O ILE F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.713A pdb=" N ALA F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 144 Proline residue: F 126 - end of helix removed outlier: 3.592A pdb=" N LEU F 130 " --> pdb=" O PRO F 126 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER F 140 " --> pdb=" O PHE F 136 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 164 removed outlier: 4.662A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 removed outlier: 3.864A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 253 removed outlier: 3.579A pdb=" N LEU F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 282 removed outlier: 3.503A pdb=" N MET F 265 " --> pdb=" O TYR F 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE F 273 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 315 through 345 removed outlier: 3.746A pdb=" N SER F 327 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 338 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 340 " --> pdb=" O CYS F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 360 No H-bonds generated for 'chain 'F' and resid 357 through 360' Processing helix chain 'F' and resid 373 through 382 removed outlier: 4.030A pdb=" N ILE F 379 " --> pdb=" O MET F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 390 removed outlier: 3.607A pdb=" N PHE F 390 " --> pdb=" O TYR F 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 386 through 390' Processing helix chain 'F' and resid 396 through 403 Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= B, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= C, first strand: chain 'C' and resid 53 through 56 Processing sheet with id= D, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= E, first strand: chain 'E' and resid 53 through 56 Processing sheet with id= F, first strand: chain 'F' and resid 53 through 56 660 hydrogen bonds defined for protein. 1962 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: 11.33 Time building geometry restraints manager: 25.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15306 1.03 - 1.22: 42 1.22 - 1.42: 7002 1.42 - 1.61: 8924 1.61 - 1.81: 148 Bond restraints: 31422 Sorted by residual: bond pdb=" C31 POV E 901 " pdb=" O32 POV E 901 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C31 POV B 901 " pdb=" O32 POV B 901 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C31 POV A 901 " pdb=" O32 POV A 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C31 POV D 901 " pdb=" O32 POV D 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C31 POV C 901 " pdb=" O32 POV C 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 31417 not shown) Histogram of bond angle deviations from ideal: 91.60 - 100.59: 8 100.59 - 109.58: 21079 109.58 - 118.57: 20147 118.57 - 127.56: 15027 127.56 - 136.55: 200 Bond angle restraints: 56461 Sorted by residual: angle pdb=" C32 POV E 901 " pdb=" C31 POV E 901 " pdb=" O31 POV E 901 " ideal model delta sigma weight residual 110.66 124.84 -14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C32 POV A 901 " pdb=" C31 POV A 901 " pdb=" O31 POV A 901 " ideal model delta sigma weight residual 110.66 124.80 -14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C32 POV F 901 " pdb=" C31 POV F 901 " pdb=" O31 POV F 901 " ideal model delta sigma weight residual 110.66 124.79 -14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C32 POV B 901 " pdb=" C31 POV B 901 " pdb=" O31 POV B 901 " ideal model delta sigma weight residual 110.66 124.78 -14.12 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C32 POV D 901 " pdb=" C31 POV D 901 " pdb=" O31 POV D 901 " ideal model delta sigma weight residual 110.66 124.76 -14.10 3.00e+00 1.11e-01 2.21e+01 ... (remaining 56456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 13190 17.43 - 34.86: 1359 34.86 - 52.28: 314 52.28 - 69.71: 85 69.71 - 87.14: 14 Dihedral angle restraints: 14962 sinusoidal: 7816 harmonic: 7146 Sorted by residual: dihedral pdb=" CA THR B 296 " pdb=" C THR B 296 " pdb=" N VAL B 297 " pdb=" CA VAL B 297 " ideal model delta harmonic sigma weight residual -180.00 -158.82 -21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA THR E 296 " pdb=" C THR E 296 " pdb=" N VAL E 297 " pdb=" CA VAL E 297 " ideal model delta harmonic sigma weight residual 180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA THR C 296 " pdb=" C THR C 296 " pdb=" N VAL C 297 " pdb=" CA VAL C 297 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 14959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2045 0.060 - 0.120: 283 0.120 - 0.180: 25 0.180 - 0.240: 0 0.240 - 0.300: 1 Chirality restraints: 2354 Sorted by residual: chirality pdb=" C24 L9Y F 904 " pdb=" C05 L9Y F 904 " pdb=" C25 L9Y F 904 " pdb=" C28 L9Y F 904 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C05 L9Y F 904 " pdb=" C06 L9Y F 904 " pdb=" C09 L9Y F 904 " pdb=" C24 L9Y F 904 " both_signs ideal model delta sigma weight residual False 2.95 3.12 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CG LEU B 376 " pdb=" CB LEU B 376 " pdb=" CD1 LEU B 376 " pdb=" CD2 LEU B 376 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2351 not shown) Planarity restraints: 4377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 166 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 167 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 166 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO F 167 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 166 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO D 167 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " -0.022 5.00e-02 4.00e+02 ... (remaining 4374 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 5001 2.28 - 2.86: 68185 2.86 - 3.44: 77367 3.44 - 4.02: 101791 4.02 - 4.60: 157364 Nonbonded interactions: 409708 Sorted by model distance: nonbonded pdb=" O PHE E 164 " pdb="HH11 ARG E 389 " model vdw 1.701 1.850 nonbonded pdb=" O PHE C 164 " pdb="HH11 ARG C 389 " model vdw 1.701 1.850 nonbonded pdb=" O PHE D 164 " pdb="HH11 ARG D 389 " model vdw 1.701 1.850 nonbonded pdb=" O PHE B 164 " pdb="HH11 ARG B 389 " model vdw 1.702 1.850 nonbonded pdb=" O PHE A 164 " pdb="HH11 ARG A 389 " model vdw 1.702 1.850 ... (remaining 409703 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 15 through 404 or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 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: 0.430 Extract box with map and model: 11.890 Check model and map are aligned: 0.460 Set scattering table: 0.320 Process input model: 96.110 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.200 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.007 0.151 16092 Z= 0.401 Angle : 0.942 14.178 21727 Z= 0.466 Chirality : 0.042 0.300 2354 Planarity : 0.004 0.040 2613 Dihedral : 14.226 71.524 5878 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.17 % Allowed : 13.38 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.79 (0.16), residues: 1800 helix: -3.61 (0.10), residues: 1152 sheet: -0.43 (0.46), residues: 96 loop : -2.08 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 143 HIS 0.009 0.002 HIS A 155 PHE 0.022 0.002 PHE A 125 TYR 0.014 0.002 TYR A 281 ARG 0.003 0.001 ARG F 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 252 time to evaluate : 2.449 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.7157 (OUTLIER) cc_final: 0.6807 (m) REVERT: A 140 SER cc_start: 0.7404 (t) cc_final: 0.7180 (p) REVERT: A 145 LYS cc_start: 0.7684 (mmtt) cc_final: 0.6860 (ttpt) REVERT: A 279 ILE cc_start: 0.6695 (mm) cc_final: 0.6346 (pt) REVERT: A 286 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7402 (t) REVERT: A 335 ILE cc_start: 0.5602 (OUTLIER) cc_final: 0.5199 (mt) REVERT: A 358 GLU cc_start: 0.5873 (tt0) cc_final: 0.5624 (mm-30) REVERT: B 28 THR cc_start: 0.7243 (OUTLIER) cc_final: 0.6920 (m) REVERT: B 124 TYR cc_start: 0.8022 (m-10) cc_final: 0.7757 (m-10) REVERT: B 140 SER cc_start: 0.7962 (t) cc_final: 0.7626 (p) REVERT: B 145 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7076 (ttpt) REVERT: B 149 THR cc_start: 0.7611 (p) cc_final: 0.7383 (t) REVERT: B 279 ILE cc_start: 0.6701 (mm) cc_final: 0.6389 (pt) REVERT: B 329 VAL cc_start: 0.6895 (OUTLIER) cc_final: 0.6454 (t) REVERT: B 335 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5452 (mt) REVERT: B 376 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5769 (tp) REVERT: C 28 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6824 (m) REVERT: C 145 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7071 (ttpp) REVERT: C 279 ILE cc_start: 0.6458 (mm) cc_final: 0.6135 (pt) REVERT: C 286 VAL cc_start: 0.7573 (OUTLIER) cc_final: 0.7165 (t) REVERT: C 335 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5308 (mt) REVERT: D 28 THR cc_start: 0.7186 (OUTLIER) cc_final: 0.6744 (m) REVERT: D 140 SER cc_start: 0.7148 (t) cc_final: 0.6937 (p) REVERT: D 145 LYS cc_start: 0.7608 (mmtt) cc_final: 0.6807 (ttpt) REVERT: D 265 MET cc_start: 0.6606 (tpt) cc_final: 0.6387 (tpt) REVERT: D 279 ILE cc_start: 0.6812 (mm) cc_final: 0.6468 (pt) REVERT: D 286 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7349 (t) REVERT: D 335 ILE cc_start: 0.5654 (OUTLIER) cc_final: 0.5309 (mt) REVERT: E 28 THR cc_start: 0.6945 (OUTLIER) cc_final: 0.6262 (p) REVERT: E 50 ASP cc_start: 0.8075 (t70) cc_final: 0.7779 (t70) REVERT: E 140 SER cc_start: 0.7736 (t) cc_final: 0.7458 (p) REVERT: E 149 THR cc_start: 0.7517 (p) cc_final: 0.7099 (t) REVERT: E 329 VAL cc_start: 0.6879 (OUTLIER) cc_final: 0.6527 (t) REVERT: E 335 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5583 (mt) REVERT: E 358 GLU cc_start: 0.5869 (tt0) cc_final: 0.5067 (mp0) REVERT: F 28 THR cc_start: 0.7148 (OUTLIER) cc_final: 0.6775 (m) REVERT: F 145 LYS cc_start: 0.7699 (mmtt) cc_final: 0.6884 (ttpt) REVERT: F 279 ILE cc_start: 0.6713 (mm) cc_final: 0.6331 (pt) REVERT: F 286 VAL cc_start: 0.7590 (OUTLIER) cc_final: 0.7243 (t) REVERT: F 335 ILE cc_start: 0.6013 (OUTLIER) cc_final: 0.5589 (mt) REVERT: F 376 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5655 (tp) outliers start: 54 outliers final: 9 residues processed: 300 average time/residue: 0.4928 time to fit residues: 233.5794 Evaluate side-chains 211 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A 132 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 155 HIS E 253 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS F 155 HIS ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16092 Z= 0.194 Angle : 0.569 5.273 21727 Z= 0.317 Chirality : 0.037 0.124 2354 Planarity : 0.004 0.046 2613 Dihedral : 9.196 59.827 2268 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.35 % Allowed : 17.84 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.27 (0.18), residues: 1800 helix: -2.30 (0.12), residues: 1140 sheet: -0.43 (0.42), residues: 96 loop : -1.70 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 143 HIS 0.008 0.001 HIS E 253 PHE 0.017 0.002 PHE D 331 TYR 0.013 0.001 TYR B 332 ARG 0.002 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 227 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.6996 (tp30) cc_final: 0.6636 (tp30) REVERT: A 140 SER cc_start: 0.7541 (t) cc_final: 0.7305 (p) REVERT: A 145 LYS cc_start: 0.7678 (mmtt) cc_final: 0.6944 (ttpt) REVERT: A 279 ILE cc_start: 0.6748 (mm) cc_final: 0.6341 (pt) REVERT: A 286 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7403 (t) REVERT: A 377 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6360 (t-170) REVERT: B 140 SER cc_start: 0.8124 (t) cc_final: 0.7750 (p) REVERT: B 279 ILE cc_start: 0.6939 (mm) cc_final: 0.6602 (pt) REVERT: B 329 VAL cc_start: 0.6801 (OUTLIER) cc_final: 0.6276 (t) REVERT: B 337 MET cc_start: 0.6468 (ppp) cc_final: 0.6144 (ppp) REVERT: B 375 MET cc_start: 0.7571 (mtm) cc_final: 0.7338 (mtt) REVERT: B 377 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6338 (t-170) REVERT: C 133 THR cc_start: 0.7786 (OUTLIER) cc_final: 0.7576 (t) REVERT: C 145 LYS cc_start: 0.7508 (mmtt) cc_final: 0.6948 (ttpp) REVERT: C 279 ILE cc_start: 0.6523 (mm) cc_final: 0.6246 (pt) REVERT: C 286 VAL cc_start: 0.7313 (OUTLIER) cc_final: 0.6881 (t) REVERT: C 377 HIS cc_start: 0.7071 (OUTLIER) cc_final: 0.6331 (t-170) REVERT: D 115 GLU cc_start: 0.6936 (tp30) cc_final: 0.6507 (tp30) REVERT: D 133 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7617 (t) REVERT: D 140 SER cc_start: 0.7362 (t) cc_final: 0.7089 (p) REVERT: D 145 LYS cc_start: 0.7669 (mmtt) cc_final: 0.6811 (ttpt) REVERT: D 279 ILE cc_start: 0.6728 (mm) cc_final: 0.6264 (pt) REVERT: D 284 TYR cc_start: 0.7031 (t80) cc_final: 0.6814 (t80) REVERT: D 286 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7526 (t) REVERT: E 115 GLU cc_start: 0.7266 (tp30) cc_final: 0.7023 (tp30) REVERT: E 140 SER cc_start: 0.7879 (t) cc_final: 0.7557 (p) REVERT: E 329 VAL cc_start: 0.6731 (OUTLIER) cc_final: 0.6308 (t) REVERT: E 358 GLU cc_start: 0.5748 (tt0) cc_final: 0.4889 (mp0) REVERT: E 377 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.6351 (t-170) REVERT: F 145 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7073 (ttpp) REVERT: F 279 ILE cc_start: 0.6937 (mm) cc_final: 0.6497 (pt) REVERT: F 286 VAL cc_start: 0.7540 (OUTLIER) cc_final: 0.7116 (t) outliers start: 40 outliers final: 14 residues processed: 257 average time/residue: 0.5197 time to fit residues: 206.5800 Evaluate side-chains 220 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS C 155 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16092 Z= 0.386 Angle : 0.640 4.680 21727 Z= 0.361 Chirality : 0.042 0.148 2354 Planarity : 0.004 0.033 2613 Dihedral : 9.382 59.464 2243 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.93 % Allowed : 18.90 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.11 (0.18), residues: 1800 helix: -1.98 (0.13), residues: 1176 sheet: 0.33 (0.45), residues: 96 loop : -2.26 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 143 HIS 0.019 0.002 HIS E 253 PHE 0.022 0.002 PHE E 125 TYR 0.012 0.002 TYR C 338 ARG 0.003 0.001 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 225 time to evaluate : 2.468 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: symmetry clash REVERT: A 133 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7881 (t) REVERT: A 140 SER cc_start: 0.7868 (t) cc_final: 0.7467 (p) REVERT: A 145 LYS cc_start: 0.7718 (mmtt) cc_final: 0.6989 (ttpt) REVERT: A 265 MET cc_start: 0.6696 (tpt) cc_final: 0.6489 (tpt) REVERT: A 279 ILE cc_start: 0.7203 (mm) cc_final: 0.6683 (pt) REVERT: A 286 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7499 (t) REVERT: A 309 ARG cc_start: 0.7814 (tpt-90) cc_final: 0.7579 (tpp80) REVERT: A 331 PHE cc_start: 0.6814 (t80) cc_final: 0.6506 (m-10) REVERT: A 377 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6259 (t-170) REVERT: A 399 GLU cc_start: 0.7028 (tt0) cc_final: 0.6751 (tt0) REVERT: B 140 SER cc_start: 0.8197 (t) cc_final: 0.7714 (p) REVERT: B 145 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7182 (ttpt) REVERT: B 279 ILE cc_start: 0.7053 (mm) cc_final: 0.6634 (pt) REVERT: B 329 VAL cc_start: 0.7236 (OUTLIER) cc_final: 0.6841 (t) REVERT: B 331 PHE cc_start: 0.6938 (t80) cc_final: 0.6609 (m-10) REVERT: B 335 ILE cc_start: 0.5756 (OUTLIER) cc_final: 0.5488 (mt) REVERT: B 377 HIS cc_start: 0.6992 (OUTLIER) cc_final: 0.6232 (t-170) REVERT: C 45 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8435 (tt) REVERT: C 133 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7812 (t) REVERT: C 255 GLU cc_start: 0.6792 (pt0) cc_final: 0.6503 (pt0) REVERT: C 265 MET cc_start: 0.6648 (tpt) cc_final: 0.6446 (tpt) REVERT: C 279 ILE cc_start: 0.6950 (mm) cc_final: 0.6551 (pt) REVERT: C 286 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7255 (t) REVERT: C 292 ASP cc_start: 0.7814 (m-30) cc_final: 0.7585 (m-30) REVERT: C 375 MET cc_start: 0.7328 (mtt) cc_final: 0.6838 (mtm) REVERT: C 377 HIS cc_start: 0.7123 (OUTLIER) cc_final: 0.6338 (t-170) REVERT: D 140 SER cc_start: 0.7686 (t) cc_final: 0.7284 (p) REVERT: D 145 LYS cc_start: 0.7705 (mmtt) cc_final: 0.6874 (ttpt) REVERT: D 279 ILE cc_start: 0.7219 (mm) cc_final: 0.6703 (pt) REVERT: D 284 TYR cc_start: 0.7436 (t80) cc_final: 0.7147 (t80) REVERT: D 286 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7583 (t) REVERT: D 302 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8374 (mp) REVERT: D 331 PHE cc_start: 0.7012 (t80) cc_final: 0.6670 (m-10) REVERT: E 133 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7697 (t) REVERT: E 140 SER cc_start: 0.8058 (t) cc_final: 0.7660 (p) REVERT: E 329 VAL cc_start: 0.7083 (OUTLIER) cc_final: 0.6623 (t) REVERT: E 335 ILE cc_start: 0.5752 (OUTLIER) cc_final: 0.5500 (mt) REVERT: E 358 GLU cc_start: 0.5434 (tt0) cc_final: 0.4968 (mp0) REVERT: E 377 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.6225 (t-170) REVERT: F 145 LYS cc_start: 0.7633 (mmtt) cc_final: 0.6960 (ttpp) REVERT: F 279 ILE cc_start: 0.7317 (mm) cc_final: 0.6673 (pt) REVERT: F 286 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7299 (t) REVERT: F 331 PHE cc_start: 0.6745 (t80) cc_final: 0.6503 (m-10) REVERT: F 375 MET cc_start: 0.7397 (mtt) cc_final: 0.6915 (mtm) outliers start: 67 outliers final: 39 residues processed: 285 average time/residue: 0.6196 time to fit residues: 272.7337 Evaluate side-chains 262 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 368 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 0.0470 chunk 46 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16092 Z= 0.146 Angle : 0.494 4.242 21727 Z= 0.276 Chirality : 0.036 0.123 2354 Planarity : 0.003 0.033 2613 Dihedral : 8.047 54.843 2243 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.76 % Allowed : 19.42 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.19), residues: 1800 helix: -1.22 (0.14), residues: 1176 sheet: 0.19 (0.44), residues: 96 loop : -1.90 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 143 HIS 0.006 0.001 HIS E 253 PHE 0.011 0.001 PHE B 331 TYR 0.017 0.001 TYR A 332 ARG 0.002 0.000 ARG E 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 210 time to evaluate : 2.540 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: A 133 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7854 (t) REVERT: A 140 SER cc_start: 0.7841 (t) cc_final: 0.7453 (p) REVERT: A 265 MET cc_start: 0.6404 (tpt) cc_final: 0.6164 (tpt) REVERT: A 279 ILE cc_start: 0.7188 (mm) cc_final: 0.6611 (pt) REVERT: A 286 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7559 (t) REVERT: A 377 HIS cc_start: 0.6877 (OUTLIER) cc_final: 0.6135 (t-170) REVERT: B 50 ASP cc_start: 0.8162 (t70) cc_final: 0.7961 (t70) REVERT: B 140 SER cc_start: 0.8162 (t) cc_final: 0.7696 (p) REVERT: B 279 ILE cc_start: 0.6859 (mm) cc_final: 0.6178 (pt) REVERT: B 329 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6517 (t) REVERT: B 337 MET cc_start: 0.6193 (ppp) cc_final: 0.5848 (ppp) REVERT: B 348 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.4954 (pp) REVERT: B 377 HIS cc_start: 0.7002 (OUTLIER) cc_final: 0.6360 (t-170) REVERT: C 255 GLU cc_start: 0.6741 (pt0) cc_final: 0.6374 (pt0) REVERT: C 279 ILE cc_start: 0.6805 (mm) cc_final: 0.6100 (pt) REVERT: C 286 VAL cc_start: 0.7401 (OUTLIER) cc_final: 0.6916 (t) REVERT: C 377 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6311 (t-170) REVERT: D 140 SER cc_start: 0.7686 (t) cc_final: 0.7275 (p) REVERT: D 279 ILE cc_start: 0.7261 (mm) cc_final: 0.6664 (pt) REVERT: D 286 VAL cc_start: 0.7942 (OUTLIER) cc_final: 0.7582 (t) REVERT: D 309 ARG cc_start: 0.7686 (tpt-90) cc_final: 0.7251 (tpp80) REVERT: E 124 TYR cc_start: 0.8363 (m-10) cc_final: 0.8150 (m-10) REVERT: E 133 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7653 (t) REVERT: E 140 SER cc_start: 0.8027 (t) cc_final: 0.7620 (p) REVERT: E 329 VAL cc_start: 0.6895 (OUTLIER) cc_final: 0.6400 (t) REVERT: E 337 MET cc_start: 0.6233 (ppp) cc_final: 0.5880 (ppp) REVERT: E 348 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4844 (pp) REVERT: E 358 GLU cc_start: 0.5395 (tt0) cc_final: 0.5005 (mp0) REVERT: E 377 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.6276 (t-170) REVERT: F 265 MET cc_start: 0.6192 (tpt) cc_final: 0.5934 (tpt) REVERT: F 279 ILE cc_start: 0.7192 (mm) cc_final: 0.6626 (pt) REVERT: F 286 VAL cc_start: 0.7568 (OUTLIER) cc_final: 0.7161 (t) REVERT: F 375 MET cc_start: 0.7112 (mtt) cc_final: 0.6899 (mtt) outliers start: 47 outliers final: 19 residues processed: 251 average time/residue: 0.5226 time to fit residues: 204.3761 Evaluate side-chains 227 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 329 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.0270 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16092 Z= 0.163 Angle : 0.492 4.129 21727 Z= 0.274 Chirality : 0.036 0.125 2354 Planarity : 0.003 0.030 2613 Dihedral : 7.670 55.301 2243 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.46 % Allowed : 20.01 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.66 (0.19), residues: 1800 helix: -0.82 (0.14), residues: 1176 sheet: 0.53 (0.47), residues: 96 loop : -1.76 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 143 HIS 0.009 0.001 HIS E 253 PHE 0.010 0.001 PHE E 125 TYR 0.011 0.001 TYR A 332 ARG 0.004 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 2.490 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: A 133 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7815 (t) REVERT: A 140 SER cc_start: 0.7895 (t) cc_final: 0.7508 (p) REVERT: A 265 MET cc_start: 0.6317 (tpt) cc_final: 0.6062 (tpt) REVERT: A 279 ILE cc_start: 0.7322 (mm) cc_final: 0.6700 (pt) REVERT: A 286 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7542 (t) REVERT: A 377 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.6121 (t-170) REVERT: B 50 ASP cc_start: 0.8144 (t70) cc_final: 0.7886 (t70) REVERT: B 140 SER cc_start: 0.8199 (t) cc_final: 0.7730 (p) REVERT: B 265 MET cc_start: 0.6246 (tpt) cc_final: 0.5981 (tpt) REVERT: B 279 ILE cc_start: 0.7065 (mm) cc_final: 0.6377 (pt) REVERT: B 329 VAL cc_start: 0.7021 (OUTLIER) cc_final: 0.6642 (t) REVERT: B 337 MET cc_start: 0.6236 (ppp) cc_final: 0.5898 (ppp) REVERT: B 348 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4815 (pp) REVERT: B 351 TYR cc_start: 0.6580 (t80) cc_final: 0.6315 (t80) REVERT: B 377 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6356 (t-170) REVERT: C 279 ILE cc_start: 0.6987 (mm) cc_final: 0.6332 (pt) REVERT: C 286 VAL cc_start: 0.7381 (OUTLIER) cc_final: 0.6947 (t) REVERT: C 377 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.6247 (t-170) REVERT: D 140 SER cc_start: 0.7722 (t) cc_final: 0.7314 (p) REVERT: D 279 ILE cc_start: 0.7233 (mm) cc_final: 0.6595 (pt) REVERT: D 284 TYR cc_start: 0.7291 (t80) cc_final: 0.7029 (t80) REVERT: D 286 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7550 (t) REVERT: D 309 ARG cc_start: 0.7679 (tpt-90) cc_final: 0.7328 (tpp80) REVERT: E 124 TYR cc_start: 0.8383 (m-10) cc_final: 0.8150 (m-10) REVERT: E 133 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7666 (t) REVERT: E 140 SER cc_start: 0.8028 (t) cc_final: 0.7600 (p) REVERT: E 337 MET cc_start: 0.6277 (ppp) cc_final: 0.5936 (ppp) REVERT: E 348 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.4644 (pp) REVERT: E 358 GLU cc_start: 0.5433 (tt0) cc_final: 0.5030 (mp0) REVERT: E 377 HIS cc_start: 0.6903 (OUTLIER) cc_final: 0.6268 (t-170) REVERT: F 265 MET cc_start: 0.6256 (tpt) cc_final: 0.5884 (tpt) REVERT: F 279 ILE cc_start: 0.7189 (mm) cc_final: 0.6389 (pt) REVERT: F 286 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7106 (t) REVERT: F 335 ILE cc_start: 0.5883 (OUTLIER) cc_final: 0.5541 (mt) REVERT: F 375 MET cc_start: 0.7112 (mtt) cc_final: 0.6905 (mtt) outliers start: 42 outliers final: 22 residues processed: 237 average time/residue: 0.4953 time to fit residues: 186.4018 Evaluate side-chains 229 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16092 Z= 0.215 Angle : 0.517 4.791 21727 Z= 0.289 Chirality : 0.038 0.128 2354 Planarity : 0.003 0.033 2613 Dihedral : 7.959 57.487 2242 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.11 % Allowed : 19.31 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.19), residues: 1800 helix: -0.73 (0.15), residues: 1176 sheet: 0.68 (0.49), residues: 96 loop : -1.81 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 143 HIS 0.011 0.002 HIS E 253 PHE 0.013 0.001 PHE E 125 TYR 0.019 0.001 TYR C 332 ARG 0.002 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 204 time to evaluate : 2.782 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: symmetry clash REVERT: A 133 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7847 (t) REVERT: A 140 SER cc_start: 0.7961 (t) cc_final: 0.7562 (p) REVERT: A 265 MET cc_start: 0.6411 (tpt) cc_final: 0.6173 (tpt) REVERT: A 279 ILE cc_start: 0.7403 (mm) cc_final: 0.6791 (pt) REVERT: A 286 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7585 (t) REVERT: A 302 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8236 (mp) REVERT: A 332 TYR cc_start: 0.7865 (t80) cc_final: 0.7613 (t80) REVERT: A 335 ILE cc_start: 0.5724 (OUTLIER) cc_final: 0.5432 (mt) REVERT: A 377 HIS cc_start: 0.6935 (OUTLIER) cc_final: 0.6101 (t-170) REVERT: B 50 ASP cc_start: 0.8119 (t70) cc_final: 0.7780 (t70) REVERT: B 140 SER cc_start: 0.8237 (t) cc_final: 0.7788 (p) REVERT: B 265 MET cc_start: 0.6302 (tpt) cc_final: 0.6006 (tpt) REVERT: B 279 ILE cc_start: 0.7001 (mm) cc_final: 0.6668 (tp) REVERT: B 309 ARG cc_start: 0.7657 (tpt-90) cc_final: 0.7179 (tpp80) REVERT: B 337 MET cc_start: 0.6350 (ppp) cc_final: 0.6044 (ppp) REVERT: B 348 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4805 (pp) REVERT: B 351 TYR cc_start: 0.6600 (t80) cc_final: 0.6349 (t80) REVERT: B 377 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6343 (t-170) REVERT: C 286 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7019 (t) REVERT: C 335 ILE cc_start: 0.5854 (OUTLIER) cc_final: 0.5381 (mt) REVERT: C 377 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.6254 (t-170) REVERT: D 140 SER cc_start: 0.7819 (t) cc_final: 0.7388 (p) REVERT: D 279 ILE cc_start: 0.7479 (mm) cc_final: 0.6818 (pt) REVERT: D 284 TYR cc_start: 0.7374 (t80) cc_final: 0.7094 (t80) REVERT: D 286 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7608 (t) REVERT: D 309 ARG cc_start: 0.7687 (tpt-90) cc_final: 0.7344 (tpp80) REVERT: D 335 ILE cc_start: 0.5654 (OUTLIER) cc_final: 0.5341 (mt) REVERT: E 133 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7645 (t) REVERT: E 140 SER cc_start: 0.8062 (t) cc_final: 0.7631 (p) REVERT: E 337 MET cc_start: 0.6265 (ppp) cc_final: 0.5897 (ppp) REVERT: E 348 LEU cc_start: 0.5122 (OUTLIER) cc_final: 0.4812 (pp) REVERT: E 358 GLU cc_start: 0.5431 (tt0) cc_final: 0.5049 (mp0) REVERT: E 377 HIS cc_start: 0.6958 (OUTLIER) cc_final: 0.6273 (t-170) REVERT: F 265 MET cc_start: 0.6382 (tpt) cc_final: 0.6006 (tpt) REVERT: F 279 ILE cc_start: 0.7251 (mm) cc_final: 0.7009 (tp) REVERT: F 286 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7199 (t) REVERT: F 335 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5677 (mt) outliers start: 70 outliers final: 37 residues processed: 267 average time/residue: 0.5143 time to fit residues: 214.3372 Evaluate side-chains 251 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 197 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 368 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 chunk 108 optimal weight: 0.0770 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16092 Z= 0.143 Angle : 0.475 4.787 21727 Z= 0.264 Chirality : 0.036 0.141 2354 Planarity : 0.003 0.031 2613 Dihedral : 7.349 56.624 2240 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.88 % Allowed : 20.19 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.20), residues: 1800 helix: -0.45 (0.15), residues: 1176 sheet: 0.68 (0.48), residues: 96 loop : -1.70 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 143 HIS 0.007 0.001 HIS E 253 PHE 0.008 0.001 PHE E 125 TYR 0.014 0.001 TYR E 332 ARG 0.002 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 203 time to evaluate : 2.355 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: symmetry clash REVERT: A 133 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7721 (t) REVERT: A 140 SER cc_start: 0.7955 (t) cc_final: 0.7555 (p) REVERT: A 279 ILE cc_start: 0.7342 (mm) cc_final: 0.6719 (pt) REVERT: A 286 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7535 (t) REVERT: A 377 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.5932 (t-170) REVERT: B 50 ASP cc_start: 0.8033 (t70) cc_final: 0.7779 (t70) REVERT: B 140 SER cc_start: 0.8204 (t) cc_final: 0.7756 (p) REVERT: B 279 ILE cc_start: 0.7007 (mm) cc_final: 0.6747 (tp) REVERT: B 309 ARG cc_start: 0.7661 (tpt-90) cc_final: 0.7190 (tpp80) REVERT: B 337 MET cc_start: 0.6329 (ppp) cc_final: 0.6038 (ppp) REVERT: B 351 TYR cc_start: 0.6531 (t80) cc_final: 0.6326 (t80) REVERT: B 377 HIS cc_start: 0.6982 (OUTLIER) cc_final: 0.6327 (t-170) REVERT: C 67 ASP cc_start: 0.6112 (m-30) cc_final: 0.5728 (m-30) REVERT: C 279 ILE cc_start: 0.7096 (mm) cc_final: 0.6816 (tp) REVERT: C 286 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7002 (t) REVERT: C 375 MET cc_start: 0.6691 (mtt) cc_final: 0.6302 (mtt) REVERT: C 377 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6204 (t-170) REVERT: D 140 SER cc_start: 0.7766 (t) cc_final: 0.7351 (p) REVERT: D 279 ILE cc_start: 0.7441 (mm) cc_final: 0.6791 (pt) REVERT: D 286 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7536 (t) REVERT: D 309 ARG cc_start: 0.7700 (tpt-90) cc_final: 0.7295 (tpp80) REVERT: E 124 TYR cc_start: 0.8341 (m-10) cc_final: 0.8110 (m-10) REVERT: E 133 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7688 (t) REVERT: E 140 SER cc_start: 0.8063 (t) cc_final: 0.7608 (p) REVERT: E 337 MET cc_start: 0.6299 (ppp) cc_final: 0.5947 (ppp) REVERT: E 358 GLU cc_start: 0.5437 (tt0) cc_final: 0.5053 (mp0) REVERT: E 377 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.6192 (t-170) REVERT: F 27 PHE cc_start: 0.5664 (m-10) cc_final: 0.5452 (m-10) REVERT: F 265 MET cc_start: 0.6237 (tpt) cc_final: 0.5922 (tpt) REVERT: F 286 VAL cc_start: 0.7547 (OUTLIER) cc_final: 0.7093 (t) outliers start: 49 outliers final: 29 residues processed: 244 average time/residue: 0.5010 time to fit residues: 192.7633 Evaluate side-chains 237 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 289 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.0570 chunk 136 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16092 Z= 0.140 Angle : 0.479 6.539 21727 Z= 0.263 Chirality : 0.037 0.215 2354 Planarity : 0.003 0.031 2613 Dihedral : 7.003 56.694 2240 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.58 % Allowed : 20.77 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1800 helix: -0.25 (0.15), residues: 1176 sheet: 0.64 (0.48), residues: 96 loop : -1.60 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 143 HIS 0.008 0.001 HIS E 253 PHE 0.010 0.001 PHE B 136 TYR 0.017 0.001 TYR B 332 ARG 0.002 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 2.377 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: A 133 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7725 (t) REVERT: A 140 SER cc_start: 0.7975 (t) cc_final: 0.7513 (p) REVERT: A 279 ILE cc_start: 0.7374 (mm) cc_final: 0.6747 (pt) REVERT: A 377 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.5946 (t-170) REVERT: B 140 SER cc_start: 0.8205 (t) cc_final: 0.7759 (p) REVERT: B 309 ARG cc_start: 0.7658 (tpt-90) cc_final: 0.7108 (tpp80) REVERT: B 337 MET cc_start: 0.6309 (ppp) cc_final: 0.6021 (ppp) REVERT: B 348 LEU cc_start: 0.4962 (OUTLIER) cc_final: 0.4576 (pp) REVERT: B 351 TYR cc_start: 0.6512 (t80) cc_final: 0.6291 (t80) REVERT: B 377 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6279 (t-170) REVERT: C 67 ASP cc_start: 0.6047 (m-30) cc_final: 0.5655 (m-30) REVERT: C 279 ILE cc_start: 0.7053 (mm) cc_final: 0.6818 (tp) REVERT: C 286 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.6930 (t) REVERT: C 340 LEU cc_start: 0.4574 (OUTLIER) cc_final: 0.4191 (tp) REVERT: C 377 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6215 (t-170) REVERT: D 140 SER cc_start: 0.7776 (t) cc_final: 0.7344 (p) REVERT: D 279 ILE cc_start: 0.7414 (mm) cc_final: 0.6765 (pt) REVERT: D 284 TYR cc_start: 0.7259 (t80) cc_final: 0.7025 (t80) REVERT: D 286 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7405 (t) REVERT: D 309 ARG cc_start: 0.7767 (tpt-90) cc_final: 0.7370 (tpp80) REVERT: E 133 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7817 (t) REVERT: E 140 SER cc_start: 0.8067 (t) cc_final: 0.7606 (p) REVERT: E 337 MET cc_start: 0.6370 (ppp) cc_final: 0.6072 (ppp) REVERT: E 358 GLU cc_start: 0.5443 (tt0) cc_final: 0.5064 (mp0) REVERT: E 377 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6248 (t-170) REVERT: F 265 MET cc_start: 0.6136 (tpt) cc_final: 0.5805 (tpt) outliers start: 44 outliers final: 30 residues processed: 243 average time/residue: 0.5007 time to fit residues: 192.1418 Evaluate side-chains 242 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 202 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 289 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.8980 chunk 166 optimal weight: 0.0000 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16092 Z= 0.152 Angle : 0.488 5.826 21727 Z= 0.269 Chirality : 0.037 0.214 2354 Planarity : 0.003 0.031 2613 Dihedral : 6.856 57.116 2238 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.46 % Allowed : 21.13 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.20), residues: 1800 helix: -0.15 (0.16), residues: 1176 sheet: 0.66 (0.49), residues: 96 loop : -1.58 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 143 HIS 0.006 0.001 HIS A 155 PHE 0.009 0.001 PHE C 136 TYR 0.014 0.001 TYR B 332 ARG 0.002 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 2.442 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: A 133 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7732 (t) REVERT: A 140 SER cc_start: 0.7962 (t) cc_final: 0.7487 (p) REVERT: A 279 ILE cc_start: 0.7403 (mm) cc_final: 0.6778 (pt) REVERT: A 340 LEU cc_start: 0.4804 (OUTLIER) cc_final: 0.4511 (tp) REVERT: A 377 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.5951 (t-170) REVERT: B 140 SER cc_start: 0.8257 (t) cc_final: 0.7805 (p) REVERT: B 309 ARG cc_start: 0.7653 (tpt-90) cc_final: 0.7125 (tpp80) REVERT: B 337 MET cc_start: 0.6306 (ppp) cc_final: 0.6021 (ppp) REVERT: B 348 LEU cc_start: 0.4977 (OUTLIER) cc_final: 0.4550 (pp) REVERT: B 351 TYR cc_start: 0.6560 (t80) cc_final: 0.6340 (t80) REVERT: B 377 HIS cc_start: 0.6863 (OUTLIER) cc_final: 0.6184 (t-170) REVERT: C 67 ASP cc_start: 0.6057 (m-30) cc_final: 0.5660 (m-30) REVERT: C 284 TYR cc_start: 0.7057 (t80) cc_final: 0.6719 (t80) REVERT: C 340 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4204 (tp) REVERT: C 377 HIS cc_start: 0.6904 (OUTLIER) cc_final: 0.6205 (t-170) REVERT: D 140 SER cc_start: 0.7800 (t) cc_final: 0.7339 (p) REVERT: D 284 TYR cc_start: 0.7270 (t80) cc_final: 0.6984 (t80) REVERT: D 309 ARG cc_start: 0.7787 (tpt-90) cc_final: 0.7391 (tpp80) REVERT: E 133 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7817 (t) REVERT: E 140 SER cc_start: 0.8051 (t) cc_final: 0.7569 (p) REVERT: E 337 MET cc_start: 0.6333 (ppp) cc_final: 0.6067 (ppp) REVERT: E 358 GLU cc_start: 0.5459 (tt0) cc_final: 0.5069 (mp0) REVERT: E 377 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6202 (t-170) REVERT: F 265 MET cc_start: 0.6223 (tpt) cc_final: 0.5871 (tpt) REVERT: F 340 LEU cc_start: 0.4816 (OUTLIER) cc_final: 0.4538 (tp) outliers start: 42 outliers final: 30 residues processed: 239 average time/residue: 0.4995 time to fit residues: 188.4176 Evaluate side-chains 239 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 0.3980 chunk 179 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 113 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16092 Z= 0.183 Angle : 0.505 7.231 21727 Z= 0.277 Chirality : 0.037 0.190 2354 Planarity : 0.003 0.032 2613 Dihedral : 6.958 57.155 2236 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.41 % Allowed : 21.65 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.20), residues: 1800 helix: -0.15 (0.15), residues: 1176 sheet: 0.75 (0.49), residues: 96 loop : -1.60 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 143 HIS 0.007 0.001 HIS A 155 PHE 0.010 0.001 PHE E 125 TYR 0.018 0.001 TYR A 332 ARG 0.002 0.000 ARG E 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 2.597 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: A 133 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7774 (t) REVERT: A 140 SER cc_start: 0.7973 (t) cc_final: 0.7494 (p) REVERT: A 377 HIS cc_start: 0.6670 (OUTLIER) cc_final: 0.5896 (t-170) REVERT: B 140 SER cc_start: 0.8269 (t) cc_final: 0.7814 (p) REVERT: B 309 ARG cc_start: 0.7666 (tpt-90) cc_final: 0.7202 (tpp80) REVERT: B 337 MET cc_start: 0.6311 (ppp) cc_final: 0.6028 (ppp) REVERT: B 348 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4581 (pp) REVERT: B 351 TYR cc_start: 0.6663 (t80) cc_final: 0.6447 (t80) REVERT: B 377 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.6210 (t-170) REVERT: C 67 ASP cc_start: 0.6080 (m-30) cc_final: 0.5690 (m-30) REVERT: C 340 LEU cc_start: 0.4558 (OUTLIER) cc_final: 0.4223 (tp) REVERT: C 377 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6193 (t-170) REVERT: D 140 SER cc_start: 0.7815 (t) cc_final: 0.7356 (p) REVERT: D 284 TYR cc_start: 0.7293 (t80) cc_final: 0.7042 (t80) REVERT: D 309 ARG cc_start: 0.7723 (tpt-90) cc_final: 0.7319 (tpp80) REVERT: E 140 SER cc_start: 0.8070 (t) cc_final: 0.7601 (p) REVERT: E 337 MET cc_start: 0.6317 (ppp) cc_final: 0.6049 (ppp) REVERT: E 358 GLU cc_start: 0.5610 (tt0) cc_final: 0.5096 (mp0) REVERT: E 377 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.6250 (t-170) REVERT: F 265 MET cc_start: 0.6305 (tpt) cc_final: 0.5944 (tpt) REVERT: F 340 LEU cc_start: 0.4564 (OUTLIER) cc_final: 0.4252 (tp) outliers start: 41 outliers final: 32 residues processed: 236 average time/residue: 0.5188 time to fit residues: 192.7439 Evaluate side-chains 241 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.207354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.161885 restraints weight = 51635.856| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.98 r_work: 0.3824 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16092 Z= 0.157 Angle : 0.490 6.603 21727 Z= 0.270 Chirality : 0.037 0.188 2354 Planarity : 0.003 0.032 2613 Dihedral : 6.769 57.645 2236 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.58 % Allowed : 21.48 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.20), residues: 1800 helix: -0.03 (0.16), residues: 1170 sheet: 0.69 (0.48), residues: 96 loop : -1.60 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 143 HIS 0.009 0.001 HIS E 253 PHE 0.008 0.001 PHE B 136 TYR 0.014 0.001 TYR B 332 ARG 0.001 0.000 ARG E 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6552.45 seconds wall clock time: 117 minutes 4.89 seconds (7024.89 seconds total)