Starting phenix.real_space_refine on Sat Mar 23 22:48:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/03_2024/7jfo_22308_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/03_2024/7jfo_22308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/03_2024/7jfo_22308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/03_2024/7jfo_22308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/03_2024/7jfo_22308_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jfo_22308/03_2024/7jfo_22308_updated.pdb" } resolution = 2.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 23904 2.51 5 N 6680 2.21 5 O 8094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 187": "NH1" <-> "NH2" Residue "G PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 305": "NH1" <-> "NH2" Residue "G PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 360": "NH1" <-> "NH2" Residue "H PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "I ARG 21": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "I TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 187": "NH1" <-> "NH2" Residue "I PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 305": "NH1" <-> "NH2" Residue "I PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 360": "NH1" <-> "NH2" Residue "J PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 125": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 131": "NH1" <-> "NH2" Residue "K ARG 187": "NH1" <-> "NH2" Residue "K PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 305": "NH1" <-> "NH2" Residue "K PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 360": "NH1" <-> "NH2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 125": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 79": "NH1" <-> "NH2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 305": "NH1" <-> "NH2" Residue "M PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 360": "NH1" <-> "NH2" Residue "N PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 84": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 125": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 79": "NH1" <-> "NH2" Residue "O TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 131": "NH1" <-> "NH2" Residue "O ARG 187": "NH1" <-> "NH2" Residue "O PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 360": "NH1" <-> "NH2" Residue "P PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "P ARG 91": "NH1" <-> "NH2" Residue "P TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "r GLU 68": "OE1" <-> "OE2" Residue "r ARG 71": "NH1" <-> "NH2" Residue "s GLU 68": "OE1" <-> "OE2" Residue "s ARG 71": "NH1" <-> "NH2" Residue "t GLU 68": "OE1" <-> "OE2" Residue "t ARG 71": "NH1" <-> "NH2" Residue "u GLU 68": "OE1" <-> "OE2" Residue "u ARG 71": "NH1" <-> "NH2" Residue "v ARG 71": "NH1" <-> "NH2" Residue "w GLU 68": "OE1" <-> "OE2" Residue "w ARG 71": "NH1" <-> "NH2" Residue "x GLU 68": "OE1" <-> "OE2" Residue "x ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38958 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "C" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "E" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "G" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "K" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "M" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "N" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "O" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "q" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "r" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "s" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "t" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "u" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "v" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "w" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "x" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "E" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "G" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "K" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "M" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "N" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Time building chain proxies: 20.29, per 1000 atoms: 0.52 Number of scatterers: 38958 At special positions: 0 Unit cell: (142.135, 142.135, 139.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 280 16.00 O 8094 8.00 N 6680 7.00 C 23904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.35 Conformation dependent library (CDL) restraints added in 6.3 seconds 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 32 sheets defined 38.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.95 Creating SS restraints... Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 142 through 147 removed outlier: 4.229A pdb=" N THR A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 405 through 408 No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 413 through 432 Processing helix chain 'A' and resid 437 through 451 removed outlier: 6.358A pdb=" N GLY A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 113 through 121 Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 142 through 147 removed outlier: 4.225A pdb=" N THR C 147 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 269 through 272 No H-bonds generated for 'chain 'C' and resid 269 through 272' Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 336 through 350 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 405 through 408 No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 413 through 432 Processing helix chain 'C' and resid 437 through 451 removed outlier: 6.348A pdb=" N GLY C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 460 Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 86 through 99 Processing helix chain 'E' and resid 50 through 59 Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 142 through 147 removed outlier: 4.225A pdb=" N THR E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 Processing helix chain 'E' and resid 182 through 194 Processing helix chain 'E' and resid 214 through 232 Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'E' and resid 269 through 272 No H-bonds generated for 'chain 'E' and resid 269 through 272' Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 311 through 321 Processing helix chain 'E' and resid 336 through 350 Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 387 through 394 Processing helix chain 'E' and resid 405 through 408 No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 413 through 432 Processing helix chain 'E' and resid 437 through 451 removed outlier: 6.385A pdb=" N GLY E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP E 443 " --> pdb=" O ARG E 439 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 460 Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 47 through 50 No H-bonds generated for 'chain 'F' and resid 47 through 50' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 86 through 99 Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 142 through 147 removed outlier: 4.217A pdb=" N THR G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 182 through 194 Processing helix chain 'G' and resid 214 through 232 Processing helix chain 'G' and resid 247 through 258 Processing helix chain 'G' and resid 269 through 272 No H-bonds generated for 'chain 'G' and resid 269 through 272' Processing helix chain 'G' and resid 274 through 287 Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 311 through 321 Processing helix chain 'G' and resid 336 through 350 Processing helix chain 'G' and resid 358 through 360 No H-bonds generated for 'chain 'G' and resid 358 through 360' Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 405 through 408 No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 413 through 432 Processing helix chain 'G' and resid 437 through 451 removed outlier: 6.377A pdb=" N GLY G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP G 443 " --> pdb=" O ARG G 439 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP G 451 " --> pdb=" O SER G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 460 Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 47 through 50 No H-bonds generated for 'chain 'H' and resid 47 through 50' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 86 through 99 Processing helix chain 'I' and resid 50 through 59 Processing helix chain 'I' and resid 105 through 107 No H-bonds generated for 'chain 'I' and resid 105 through 107' Processing helix chain 'I' and resid 113 through 121 Processing helix chain 'I' and resid 124 through 126 No H-bonds generated for 'chain 'I' and resid 124 through 126' Processing helix chain 'I' and resid 142 through 147 removed outlier: 4.217A pdb=" N THR I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 162 Processing helix chain 'I' and resid 182 through 194 Processing helix chain 'I' and resid 214 through 232 Processing helix chain 'I' and resid 247 through 258 Processing helix chain 'I' and resid 269 through 272 No H-bonds generated for 'chain 'I' and resid 269 through 272' Processing helix chain 'I' and resid 274 through 287 Processing helix chain 'I' and resid 298 through 302 Processing helix chain 'I' and resid 311 through 321 Processing helix chain 'I' and resid 336 through 350 Processing helix chain 'I' and resid 358 through 360 No H-bonds generated for 'chain 'I' and resid 358 through 360' Processing helix chain 'I' and resid 387 through 394 Processing helix chain 'I' and resid 405 through 408 No H-bonds generated for 'chain 'I' and resid 405 through 408' Processing helix chain 'I' and resid 413 through 432 Processing helix chain 'I' and resid 437 through 451 removed outlier: 6.378A pdb=" N GLY I 442 " --> pdb=" O ALA I 438 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP I 443 " --> pdb=" O ARG I 439 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP I 451 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 460 Processing helix chain 'J' and resid 23 through 35 Processing helix chain 'J' and resid 47 through 50 No H-bonds generated for 'chain 'J' and resid 47 through 50' Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'J' and resid 86 through 99 Processing helix chain 'K' and resid 50 through 59 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 121 Processing helix chain 'K' and resid 124 through 126 No H-bonds generated for 'chain 'K' and resid 124 through 126' Processing helix chain 'K' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR K 147 " --> pdb=" O ALA K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 162 Processing helix chain 'K' and resid 182 through 194 Processing helix chain 'K' and resid 214 through 232 Processing helix chain 'K' and resid 247 through 258 Processing helix chain 'K' and resid 269 through 272 No H-bonds generated for 'chain 'K' and resid 269 through 272' Processing helix chain 'K' and resid 274 through 287 Processing helix chain 'K' and resid 298 through 302 Processing helix chain 'K' and resid 311 through 321 Processing helix chain 'K' and resid 336 through 350 Processing helix chain 'K' and resid 358 through 360 No H-bonds generated for 'chain 'K' and resid 358 through 360' Processing helix chain 'K' and resid 387 through 394 Processing helix chain 'K' and resid 405 through 408 No H-bonds generated for 'chain 'K' and resid 405 through 408' Processing helix chain 'K' and resid 413 through 432 Processing helix chain 'K' and resid 437 through 451 removed outlier: 6.409A pdb=" N GLY K 442 " --> pdb=" O ALA K 438 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP K 443 " --> pdb=" O ARG K 439 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS K 450 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP K 451 " --> pdb=" O SER K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 460 Processing helix chain 'L' and resid 23 through 35 Processing helix chain 'L' and resid 47 through 50 No H-bonds generated for 'chain 'L' and resid 47 through 50' Processing helix chain 'L' and resid 55 through 59 Processing helix chain 'L' and resid 86 through 99 Processing helix chain 'M' and resid 50 through 59 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 113 through 121 Processing helix chain 'M' and resid 124 through 126 No H-bonds generated for 'chain 'M' and resid 124 through 126' Processing helix chain 'M' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 162 Processing helix chain 'M' and resid 182 through 194 Processing helix chain 'M' and resid 214 through 232 Processing helix chain 'M' and resid 247 through 258 Processing helix chain 'M' and resid 269 through 272 No H-bonds generated for 'chain 'M' and resid 269 through 272' Processing helix chain 'M' and resid 274 through 287 Processing helix chain 'M' and resid 298 through 302 Processing helix chain 'M' and resid 311 through 321 Processing helix chain 'M' and resid 336 through 350 Processing helix chain 'M' and resid 358 through 360 No H-bonds generated for 'chain 'M' and resid 358 through 360' Processing helix chain 'M' and resid 387 through 394 Processing helix chain 'M' and resid 405 through 408 No H-bonds generated for 'chain 'M' and resid 405 through 408' Processing helix chain 'M' and resid 413 through 432 Processing helix chain 'M' and resid 437 through 451 removed outlier: 6.388A pdb=" N GLY M 442 " --> pdb=" O ALA M 438 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP M 443 " --> pdb=" O ARG M 439 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP M 451 " --> pdb=" O SER M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 460 Processing helix chain 'N' and resid 23 through 35 Processing helix chain 'N' and resid 47 through 50 No H-bonds generated for 'chain 'N' and resid 47 through 50' Processing helix chain 'N' and resid 55 through 59 Processing helix chain 'N' and resid 86 through 99 Processing helix chain 'O' and resid 50 through 59 Processing helix chain 'O' and resid 105 through 107 No H-bonds generated for 'chain 'O' and resid 105 through 107' Processing helix chain 'O' and resid 113 through 121 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR O 147 " --> pdb=" O ALA O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 162 Processing helix chain 'O' and resid 182 through 194 Processing helix chain 'O' and resid 214 through 232 Processing helix chain 'O' and resid 247 through 258 Processing helix chain 'O' and resid 269 through 272 No H-bonds generated for 'chain 'O' and resid 269 through 272' Processing helix chain 'O' and resid 274 through 287 Processing helix chain 'O' and resid 298 through 302 Processing helix chain 'O' and resid 311 through 321 Processing helix chain 'O' and resid 336 through 350 Processing helix chain 'O' and resid 358 through 360 No H-bonds generated for 'chain 'O' and resid 358 through 360' Processing helix chain 'O' and resid 387 through 394 Processing helix chain 'O' and resid 405 through 408 No H-bonds generated for 'chain 'O' and resid 405 through 408' Processing helix chain 'O' and resid 413 through 432 Processing helix chain 'O' and resid 437 through 451 removed outlier: 6.349A pdb=" N GLY O 442 " --> pdb=" O ALA O 438 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP O 443 " --> pdb=" O ARG O 439 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP O 451 " --> pdb=" O SER O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 460 Processing helix chain 'P' and resid 23 through 35 Processing helix chain 'P' and resid 47 through 50 No H-bonds generated for 'chain 'P' and resid 47 through 50' Processing helix chain 'P' and resid 55 through 59 Processing helix chain 'P' and resid 86 through 99 Processing helix chain 'q' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER q 69 " --> pdb=" O GLN q 65 " (cutoff:3.500A) Processing helix chain 'r' and resid 63 through 71 removed outlier: 3.557A pdb=" N SER r 69 " --> pdb=" O GLN r 65 " (cutoff:3.500A) Processing helix chain 's' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER s 69 " --> pdb=" O GLN s 65 " (cutoff:3.500A) Processing helix chain 't' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER t 69 " --> pdb=" O GLN t 65 " (cutoff:3.500A) Processing helix chain 'u' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) Processing helix chain 'v' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER v 69 " --> pdb=" O GLN v 65 " (cutoff:3.500A) Processing helix chain 'w' and resid 63 through 71 removed outlier: 3.559A pdb=" N SER w 69 " --> pdb=" O GLN w 65 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 71 removed outlier: 3.558A pdb=" N SER x 69 " --> pdb=" O GLN x 65 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 139 removed outlier: 6.737A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.660A pdb=" N THR A 173 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.235A pdb=" N LEU A 290 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS A 267 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS A 292 " --> pdb=" O HIS A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU B 42 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU B 107 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 122 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA B 109 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLY B 120 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 132 through 139 removed outlier: 6.734A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.654A pdb=" N THR C 173 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.234A pdb=" N LEU C 290 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS C 267 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS C 292 " --> pdb=" O HIS C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 74 through 76 removed outlier: 4.651A pdb=" N LEU D 42 " --> pdb=" O TRP D 76 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU D 107 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU D 122 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA D 109 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY D 120 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 132 through 139 removed outlier: 6.733A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 237 through 239 removed outlier: 3.673A pdb=" N THR E 173 " --> pdb=" O PHE E 402 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN E 401 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA E 378 " --> pdb=" O GLN E 401 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 264 through 268 removed outlier: 6.232A pdb=" N LEU E 290 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N HIS E 267 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS E 292 " --> pdb=" O HIS E 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 74 through 76 removed outlier: 4.656A pdb=" N LEU F 42 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU F 107 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU F 122 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA F 109 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLY F 120 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 132 through 139 removed outlier: 6.732A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 237 through 239 removed outlier: 3.694A pdb=" N THR G 173 " --> pdb=" O PHE G 402 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLN G 401 " --> pdb=" O PRO G 376 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA G 378 " --> pdb=" O GLN G 401 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 264 through 268 removed outlier: 6.234A pdb=" N LEU G 290 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS G 267 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS G 292 " --> pdb=" O HIS G 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 74 through 76 removed outlier: 4.653A pdb=" N LEU H 42 " --> pdb=" O TRP H 76 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU H 107 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU H 122 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA H 109 " --> pdb=" O GLY H 120 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY H 120 " --> pdb=" O ALA H 109 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 132 through 139 removed outlier: 6.735A pdb=" N ALA I 39 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU I 138 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU I 37 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP I 86 " --> pdb=" O TYR I 100 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 237 through 239 removed outlier: 3.662A pdb=" N THR I 173 " --> pdb=" O PHE I 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN I 401 " --> pdb=" O PRO I 376 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA I 378 " --> pdb=" O GLN I 401 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 264 through 268 removed outlier: 6.232A pdb=" N LEU I 290 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS I 267 " --> pdb=" O LEU I 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS I 292 " --> pdb=" O HIS I 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'J' and resid 74 through 76 removed outlier: 4.660A pdb=" N LEU J 42 " --> pdb=" O TRP J 76 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU J 107 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU J 122 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA J 109 " --> pdb=" O GLY J 120 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY J 120 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 132 through 139 removed outlier: 6.734A pdb=" N ALA K 39 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU K 138 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU K 37 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP K 86 " --> pdb=" O TYR K 100 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA K 102 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS K 84 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 237 through 239 removed outlier: 3.646A pdb=" N THR K 173 " --> pdb=" O PHE K 402 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN K 401 " --> pdb=" O PRO K 376 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA K 378 " --> pdb=" O GLN K 401 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 264 through 268 removed outlier: 6.235A pdb=" N LEU K 290 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS K 267 " --> pdb=" O LEU K 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS K 292 " --> pdb=" O HIS K 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 74 through 76 removed outlier: 4.648A pdb=" N LEU L 42 " --> pdb=" O TRP L 76 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU L 107 " --> pdb=" O LEU L 122 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU L 122 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA L 109 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLY L 120 " --> pdb=" O ALA L 109 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 132 through 139 removed outlier: 6.737A pdb=" N ALA M 39 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU M 138 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU M 37 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP M 86 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA M 102 " --> pdb=" O CYS M 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS M 84 " --> pdb=" O ALA M 102 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 237 through 239 removed outlier: 3.659A pdb=" N THR M 173 " --> pdb=" O PHE M 402 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN M 401 " --> pdb=" O PRO M 376 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA M 378 " --> pdb=" O GLN M 401 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 264 through 268 removed outlier: 6.243A pdb=" N LEU M 290 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS M 267 " --> pdb=" O LEU M 290 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS M 292 " --> pdb=" O HIS M 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'N' and resid 74 through 76 removed outlier: 4.645A pdb=" N LEU N 42 " --> pdb=" O TRP N 76 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU N 107 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU N 122 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA N 109 " --> pdb=" O GLY N 120 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY N 120 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 132 through 139 removed outlier: 6.740A pdb=" N ALA O 39 " --> pdb=" O GLU O 136 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU O 138 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU O 37 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP O 86 " --> pdb=" O TYR O 100 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA O 102 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS O 84 " --> pdb=" O ALA O 102 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 237 through 239 removed outlier: 3.659A pdb=" N THR O 173 " --> pdb=" O PHE O 402 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN O 401 " --> pdb=" O PRO O 376 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA O 378 " --> pdb=" O GLN O 401 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 264 through 268 removed outlier: 6.245A pdb=" N LEU O 290 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N HIS O 267 " --> pdb=" O LEU O 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS O 292 " --> pdb=" O HIS O 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'P' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU P 42 " --> pdb=" O TRP P 76 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU P 107 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU P 122 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA P 109 " --> pdb=" O GLY P 120 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY P 120 " --> pdb=" O ALA P 109 " (cutoff:3.500A) 1398 hydrogen bonds defined for protein. 3999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.05 Time building geometry restraints manager: 17.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 6506 1.30 - 1.44: 10659 1.44 - 1.58: 20717 1.58 - 1.72: 362 1.72 - 1.86: 428 Bond restraints: 38672 Sorted by residual: bond pdb=" SD MET G 266 " pdb=" CE MET G 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.92e+01 bond pdb=" SD MET E 266 " pdb=" CE MET E 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET O 266 " pdb=" CE MET O 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET K 266 " pdb=" CE MET K 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" SD MET M 266 " pdb=" CE MET M 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 ... (remaining 38667 not shown) Histogram of bond angle deviations from ideal: 92.55 - 100.97: 75 100.97 - 109.40: 5019 109.40 - 117.83: 22906 117.83 - 126.26: 23669 126.26 - 134.69: 763 Bond angle restraints: 52432 Sorted by residual: angle pdb=" N TRP I 66 " pdb=" CA TRP I 66 " pdb=" C TRP I 66 " ideal model delta sigma weight residual 111.36 123.98 -12.62 1.09e+00 8.42e-01 1.34e+02 angle pdb=" N TRP M 66 " pdb=" CA TRP M 66 " pdb=" C TRP M 66 " ideal model delta sigma weight residual 111.36 123.74 -12.38 1.09e+00 8.42e-01 1.29e+02 angle pdb=" N TRP O 66 " pdb=" CA TRP O 66 " pdb=" C TRP O 66 " ideal model delta sigma weight residual 111.36 123.51 -12.15 1.09e+00 8.42e-01 1.24e+02 angle pdb=" N TRP A 66 " pdb=" CA TRP A 66 " pdb=" C TRP A 66 " ideal model delta sigma weight residual 111.36 119.71 -8.35 1.09e+00 8.42e-01 5.87e+01 angle pdb=" N TRP K 66 " pdb=" CA TRP K 66 " pdb=" C TRP K 66 " ideal model delta sigma weight residual 111.36 119.63 -8.27 1.09e+00 8.42e-01 5.76e+01 ... (remaining 52427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 20504 14.24 - 28.49: 2053 28.49 - 42.73: 324 42.73 - 56.97: 83 56.97 - 71.21: 44 Dihedral angle restraints: 23008 sinusoidal: 9128 harmonic: 13880 Sorted by residual: dihedral pdb=" CA PHE F 60 " pdb=" C PHE F 60 " pdb=" N GLY F 61 " pdb=" CA GLY F 61 " ideal model delta harmonic sigma weight residual 180.00 152.39 27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA PHE H 60 " pdb=" C PHE H 60 " pdb=" N GLY H 61 " pdb=" CA GLY H 61 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA PHE P 60 " pdb=" C PHE P 60 " pdb=" N GLY P 61 " pdb=" CA GLY P 61 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 23005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4369 0.114 - 0.228: 945 0.228 - 0.342: 194 0.342 - 0.456: 68 0.456 - 0.569: 8 Chirality restraints: 5584 Sorted by residual: chirality pdb=" CB ILE G 301 " pdb=" CA ILE G 301 " pdb=" CG1 ILE G 301 " pdb=" CG2 ILE G 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CB ILE K 301 " pdb=" CA ILE K 301 " pdb=" CG1 ILE K 301 " pdb=" CG2 ILE K 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CB ILE E 301 " pdb=" CA ILE E 301 " pdb=" CG1 ILE E 301 " pdb=" CG2 ILE E 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.90e+00 ... (remaining 5581 not shown) Planarity restraints: 6880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 153 " 0.066 2.00e-02 2.50e+03 5.82e-02 5.08e+01 pdb=" CG HIS I 153 " -0.102 2.00e-02 2.50e+03 pdb=" ND1 HIS I 153 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS I 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS I 153 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS I 153 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 153 " -0.066 2.00e-02 2.50e+03 5.81e-02 5.07e+01 pdb=" CG HIS G 153 " 0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS G 153 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS G 153 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS G 153 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS G 153 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 153 " 0.065 2.00e-02 2.50e+03 5.78e-02 5.02e+01 pdb=" CG HIS E 153 " -0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS E 153 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS E 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS E 153 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS E 153 " 0.067 2.00e-02 2.50e+03 ... (remaining 6877 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4106 2.74 - 3.28: 40769 3.28 - 3.82: 75120 3.82 - 4.36: 92924 4.36 - 4.90: 145860 Nonbonded interactions: 358779 Sorted by model distance: nonbonded pdb=" NE2 GLN A 156 " pdb=" OD2 ASP A 160 " model vdw 2.198 2.520 nonbonded pdb=" NE2 GLN G 156 " pdb=" OD2 ASP G 160 " model vdw 2.201 2.520 nonbonded pdb=" NE2 GLN O 156 " pdb=" OD2 ASP O 160 " model vdw 2.203 2.520 nonbonded pdb=" NE2 GLN I 156 " pdb=" OD2 ASP I 160 " model vdw 2.204 2.520 nonbonded pdb=" NE2 GLN C 156 " pdb=" OD2 ASP C 160 " model vdw 2.206 2.520 ... (remaining 358774 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 14.240 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 97.780 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.022 0.162 38672 Z= 1.420 Angle : 1.666 12.619 52432 Z= 0.976 Chirality : 0.109 0.569 5584 Planarity : 0.014 0.064 6880 Dihedral : 12.066 71.215 14144 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.23 % Allowed : 4.59 % Favored : 94.17 % Cbeta Deviations : 0.05 % 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: -0.96 (0.11), residues: 4760 helix: -0.72 (0.10), residues: 1856 sheet: -0.22 (0.20), residues: 752 loop : -0.52 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.008 TRP M 214 HIS 0.050 0.011 HIS M 153 PHE 0.103 0.012 PHE I 148 TYR 0.083 0.012 TYR O 363 ARG 0.033 0.005 ARG G 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 644 time to evaluate : 4.347 Fit side-chains REVERT: B 80 MET cc_start: 0.7538 (mtm) cc_final: 0.7202 (mpp) REVERT: D 80 MET cc_start: 0.7558 (mtm) cc_final: 0.7179 (mpp) REVERT: E 297 MET cc_start: 0.8201 (ttp) cc_final: 0.7759 (ttp) REVERT: I 297 MET cc_start: 0.8278 (ttp) cc_final: 0.7837 (ttp) REVERT: L 49 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7953 (mmtm) REVERT: L 80 MET cc_start: 0.7561 (mtm) cc_final: 0.7218 (mpp) REVERT: M 205 ASN cc_start: 0.7781 (p0) cc_final: 0.7413 (p0) REVERT: N 80 MET cc_start: 0.7555 (mtm) cc_final: 0.7195 (mpp) REVERT: P 80 MET cc_start: 0.7495 (mtm) cc_final: 0.7142 (mpp) REVERT: P 122 LEU cc_start: 0.9057 (tp) cc_final: 0.8824 (tp) REVERT: v 56 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.5591 (tpp-160) outliers start: 48 outliers final: 7 residues processed: 682 average time/residue: 1.6695 time to fit residues: 1356.2884 Evaluate side-chains 609 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 601 time to evaluate : 4.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain v residue 56 ARG Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 4.9990 chunk 357 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 369 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 428 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 163 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 241 ASN A 267 HIS A 277 ASN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 432 ASN B 8 ASN B 9 ASN B 29 GLN B 36 ASN C 45 GLN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 163 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS C 241 ASN C 267 HIS C 277 ASN ** C 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN C 432 ASN D 8 ASN D 9 ASN D 29 GLN D 36 ASN D 124 GLN E 45 GLN E 95 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 163 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 HIS E 241 ASN E 267 HIS E 277 ASN ** E 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 420 ASN E 432 ASN F 8 ASN F 9 ASN F 29 GLN F 36 ASN F 124 GLN G 45 GLN G 95 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 163 ASN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 HIS G 241 ASN G 267 HIS G 277 ASN ** G 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN G 432 ASN H 8 ASN H 9 ASN H 29 GLN H 36 ASN H 124 GLN I 45 GLN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 HIS I 241 ASN I 267 HIS I 277 ASN ** I 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 432 ASN J 8 ASN J 9 ASN J 29 GLN J 36 ASN J 124 GLN K 45 GLN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN K 163 ASN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 HIS K 241 ASN K 267 HIS K 277 ASN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 420 ASN K 432 ASN L 8 ASN L 9 ASN L 29 GLN L 36 ASN M 45 GLN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 163 ASN ** M 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 238 HIS M 241 ASN M 267 HIS M 277 ASN ** M 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 ASN M 432 ASN N 8 ASN N 9 ASN N 29 GLN N 36 ASN N 124 GLN O 45 GLN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN O 163 ASN ** O 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 238 HIS O 241 ASN O 267 HIS O 277 ASN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 420 ASN O 432 ASN P 8 ASN P 9 ASN P 29 GLN P 36 ASN P 124 GLN Total number of N/Q/H flips: 119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38672 Z= 0.207 Angle : 0.643 5.907 52432 Z= 0.351 Chirality : 0.045 0.181 5584 Planarity : 0.005 0.049 6880 Dihedral : 5.850 27.354 5372 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.90 % Allowed : 7.14 % Favored : 91.97 % 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: 0.45 (0.12), residues: 4760 helix: 0.92 (0.11), residues: 1864 sheet: 0.17 (0.19), residues: 696 loop : -0.08 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 368 HIS 0.013 0.002 HIS O 153 PHE 0.036 0.002 PHE E 345 TYR 0.016 0.002 TYR G 269 ARG 0.007 0.001 ARG M 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 694 time to evaluate : 4.646 Fit side-chains REVERT: B 13 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 80 MET cc_start: 0.7358 (mtm) cc_final: 0.6957 (mpp) REVERT: C 297 MET cc_start: 0.8242 (ttp) cc_final: 0.7853 (ttp) REVERT: D 80 MET cc_start: 0.7388 (mtm) cc_final: 0.6994 (mpp) REVERT: D 122 LEU cc_start: 0.8927 (tp) cc_final: 0.8705 (tp) REVERT: F 122 LEU cc_start: 0.8918 (tp) cc_final: 0.8706 (tp) REVERT: G 297 MET cc_start: 0.8176 (ttp) cc_final: 0.7793 (ttp) REVERT: J 122 LEU cc_start: 0.8943 (tp) cc_final: 0.8692 (tp) REVERT: K 297 MET cc_start: 0.8221 (ttp) cc_final: 0.7824 (ttp) REVERT: L 13 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7588 (mm-30) REVERT: L 80 MET cc_start: 0.7388 (mtm) cc_final: 0.6987 (mpp) REVERT: L 122 LEU cc_start: 0.8907 (tp) cc_final: 0.8676 (tp) REVERT: M 297 MET cc_start: 0.8211 (ttp) cc_final: 0.7781 (ttp) REVERT: N 80 MET cc_start: 0.7366 (mtm) cc_final: 0.6957 (mpp) REVERT: P 80 MET cc_start: 0.7325 (mtm) cc_final: 0.6918 (mpp) REVERT: P 122 LEU cc_start: 0.8903 (tp) cc_final: 0.8675 (tp) outliers start: 35 outliers final: 18 residues processed: 717 average time/residue: 1.6802 time to fit residues: 1447.5155 Evaluate side-chains 679 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 661 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain w residue 55 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 356 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 118 optimal weight: 40.0000 chunk 429 optimal weight: 10.0000 chunk 463 optimal weight: 30.0000 chunk 382 optimal weight: 20.0000 chunk 425 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 344 optimal weight: 20.0000 overall best weight: 5.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 95 ASN A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 45 GLN C 95 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 124 GLN E 45 GLN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN F 124 GLN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 124 GLN I 95 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN J 124 GLN K 45 GLN K 95 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 45 GLN M 95 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN N 124 GLN O 95 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN O 207 ASN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN P 124 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 38672 Z= 0.347 Angle : 0.756 6.407 52432 Z= 0.410 Chirality : 0.051 0.206 5584 Planarity : 0.007 0.064 6880 Dihedral : 6.027 28.274 5365 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.26 % Allowed : 8.62 % Favored : 90.12 % 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: 0.55 (0.12), residues: 4760 helix: 1.02 (0.12), residues: 1920 sheet: 0.23 (0.19), residues: 696 loop : -0.06 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 214 HIS 0.019 0.003 HIS M 153 PHE 0.037 0.004 PHE O 345 TYR 0.023 0.003 TYR G 269 ARG 0.007 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 644 time to evaluate : 4.347 Fit side-chains REVERT: A 297 MET cc_start: 0.8310 (ttp) cc_final: 0.7794 (ttp) REVERT: B 80 MET cc_start: 0.7410 (mtm) cc_final: 0.7085 (mpp) REVERT: C 297 MET cc_start: 0.8290 (ttp) cc_final: 0.7863 (ttp) REVERT: C 431 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7422 (tmm-80) REVERT: D 80 MET cc_start: 0.7439 (mtm) cc_final: 0.6993 (mpp) REVERT: D 122 LEU cc_start: 0.8994 (tp) cc_final: 0.8764 (tp) REVERT: E 297 MET cc_start: 0.8191 (ttp) cc_final: 0.7770 (ttp) REVERT: F 122 LEU cc_start: 0.8995 (tp) cc_final: 0.8760 (tp) REVERT: G 297 MET cc_start: 0.8225 (ttp) cc_final: 0.7720 (ttp) REVERT: G 431 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7283 (tmm-80) REVERT: H 122 LEU cc_start: 0.8989 (tp) cc_final: 0.8773 (tp) REVERT: I 431 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7322 (tmm-80) REVERT: J 122 LEU cc_start: 0.9014 (tp) cc_final: 0.8778 (tp) REVERT: K 297 MET cc_start: 0.8270 (ttp) cc_final: 0.7777 (ttp) REVERT: L 80 MET cc_start: 0.7430 (mtm) cc_final: 0.7141 (mpp) REVERT: L 122 LEU cc_start: 0.8971 (tp) cc_final: 0.8752 (tp) REVERT: M 297 MET cc_start: 0.8259 (ttp) cc_final: 0.7751 (ttp) REVERT: N 80 MET cc_start: 0.7409 (mtm) cc_final: 0.7077 (mpp) REVERT: O 297 MET cc_start: 0.8280 (ttp) cc_final: 0.7837 (ttp) REVERT: P 80 MET cc_start: 0.7359 (mtm) cc_final: 0.7040 (mpp) REVERT: P 122 LEU cc_start: 0.8981 (tp) cc_final: 0.8764 (tp) outliers start: 49 outliers final: 24 residues processed: 673 average time/residue: 1.7355 time to fit residues: 1387.6772 Evaluate side-chains 662 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 635 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 431 ARG Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 288 optimal weight: 0.8980 chunk 430 optimal weight: 5.9990 chunk 456 optimal weight: 30.0000 chunk 225 optimal weight: 10.0000 chunk 408 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 207 ASN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 207 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 207 ASN ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 207 ASN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 207 ASN ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN K 207 ASN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 207 ASN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 38672 Z= 0.245 Angle : 0.654 5.850 52432 Z= 0.354 Chirality : 0.046 0.190 5584 Planarity : 0.005 0.050 6880 Dihedral : 5.742 26.646 5365 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.33 % Allowed : 8.88 % Favored : 89.78 % 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: 0.85 (0.12), residues: 4760 helix: 1.43 (0.12), residues: 1872 sheet: 0.17 (0.19), residues: 696 loop : 0.04 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 132 HIS 0.014 0.002 HIS O 153 PHE 0.035 0.003 PHE E 345 TYR 0.018 0.002 TYR E 269 ARG 0.005 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 659 time to evaluate : 4.786 Fit side-chains REVERT: A 297 MET cc_start: 0.8327 (ttp) cc_final: 0.7842 (ttp) REVERT: B 80 MET cc_start: 0.7416 (mtm) cc_final: 0.7074 (mpp) REVERT: C 297 MET cc_start: 0.8307 (ttp) cc_final: 0.7884 (ttp) REVERT: C 431 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7324 (tmm-80) REVERT: D 80 MET cc_start: 0.7461 (mtm) cc_final: 0.6974 (mpp) REVERT: D 122 LEU cc_start: 0.8945 (tp) cc_final: 0.8721 (tp) REVERT: E 297 MET cc_start: 0.8210 (ttp) cc_final: 0.7757 (ttp) REVERT: E 327 HIS cc_start: 0.8433 (m-70) cc_final: 0.8121 (m90) REVERT: E 431 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7311 (tmm-80) REVERT: F 1 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.5817 (ttp) REVERT: F 122 LEU cc_start: 0.8944 (tp) cc_final: 0.8735 (tp) REVERT: G 297 MET cc_start: 0.8243 (ttp) cc_final: 0.7753 (ttp) REVERT: G 431 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7258 (tmm-80) REVERT: H 80 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7215 (mpp) REVERT: I 431 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7314 (tmm-80) REVERT: J 122 LEU cc_start: 0.8967 (tp) cc_final: 0.8752 (tp) REVERT: K 297 MET cc_start: 0.8285 (ttp) cc_final: 0.7794 (ttp) REVERT: L 1 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.5774 (ttp) REVERT: L 80 MET cc_start: 0.7418 (mtm) cc_final: 0.7041 (mpp) REVERT: L 122 LEU cc_start: 0.8927 (tp) cc_final: 0.8712 (tp) REVERT: M 297 MET cc_start: 0.8255 (ttp) cc_final: 0.7761 (ttp) REVERT: N 80 MET cc_start: 0.7432 (mtm) cc_final: 0.7071 (mpp) REVERT: O 297 MET cc_start: 0.8312 (ttp) cc_final: 0.7877 (ttp) REVERT: P 80 MET cc_start: 0.7366 (mtm) cc_final: 0.7030 (mpp) outliers start: 52 outliers final: 30 residues processed: 688 average time/residue: 1.7022 time to fit residues: 1394.0549 Evaluate side-chains 691 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 654 time to evaluate : 4.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 431 ARG Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 339 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 389 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 232 optimal weight: 30.0000 chunk 409 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 38672 Z= 0.456 Angle : 0.838 6.995 52432 Z= 0.455 Chirality : 0.055 0.233 5584 Planarity : 0.008 0.075 6880 Dihedral : 6.222 29.253 5365 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.69 % Allowed : 8.88 % Favored : 89.43 % 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: 0.60 (0.12), residues: 4760 helix: 1.17 (0.12), residues: 1872 sheet: 0.05 (0.19), residues: 712 loop : -0.05 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP M 214 HIS 0.020 0.004 HIS M 153 PHE 0.037 0.005 PHE O 345 TYR 0.028 0.004 TYR E 269 ARG 0.009 0.001 ARG M 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 638 time to evaluate : 4.192 Fit side-chains REVERT: A 297 MET cc_start: 0.8317 (ttp) cc_final: 0.7817 (ttp) REVERT: B 80 MET cc_start: 0.7478 (mtm) cc_final: 0.7083 (mpp) REVERT: C 297 MET cc_start: 0.8296 (ttp) cc_final: 0.7857 (ttp) REVERT: C 431 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7453 (tmm-80) REVERT: D 80 MET cc_start: 0.7498 (mtm) cc_final: 0.7081 (mpp) REVERT: E 297 MET cc_start: 0.8218 (ttp) cc_final: 0.7752 (ttp) REVERT: E 431 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7435 (tmm-80) REVERT: F 1 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.5744 (ttp) REVERT: G 297 MET cc_start: 0.8236 (ttp) cc_final: 0.7794 (ttp) REVERT: G 431 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7313 (tmm-80) REVERT: H 1 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.5874 (ttp) REVERT: I 431 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7440 (tmm-80) REVERT: K 297 MET cc_start: 0.8272 (ttp) cc_final: 0.7839 (ttp) REVERT: L 1 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5754 (ttp) REVERT: L 80 MET cc_start: 0.7479 (mtm) cc_final: 0.7072 (mpp) REVERT: M 297 MET cc_start: 0.8269 (ttp) cc_final: 0.7937 (ttp) REVERT: N 80 MET cc_start: 0.7495 (mtm) cc_final: 0.7065 (mpp) REVERT: O 297 MET cc_start: 0.8293 (ttp) cc_final: 0.7835 (ttp) REVERT: P 80 MET cc_start: 0.7448 (mtm) cc_final: 0.7004 (mpp) outliers start: 66 outliers final: 30 residues processed: 679 average time/residue: 1.6975 time to fit residues: 1371.4344 Evaluate side-chains 672 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 635 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 431 ARG Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 10.0000 chunk 410 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 267 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 456 optimal weight: 10.0000 chunk 379 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 151 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38672 Z= 0.222 Angle : 0.634 6.025 52432 Z= 0.342 Chirality : 0.046 0.185 5584 Planarity : 0.005 0.046 6880 Dihedral : 5.704 26.798 5365 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.98 % Allowed : 10.06 % Favored : 88.96 % 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: 0.97 (0.12), residues: 4760 helix: 1.54 (0.12), residues: 1872 sheet: 0.14 (0.19), residues: 696 loop : 0.14 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 132 HIS 0.012 0.002 HIS M 153 PHE 0.034 0.003 PHE E 345 TYR 0.017 0.002 TYR E 269 ARG 0.006 0.001 ARG C 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 672 time to evaluate : 3.966 Fit side-chains REVERT: A 297 MET cc_start: 0.8319 (ttp) cc_final: 0.7902 (ttp) REVERT: B 80 MET cc_start: 0.7454 (mtm) cc_final: 0.6988 (mpp) REVERT: C 297 MET cc_start: 0.8284 (ttp) cc_final: 0.7817 (ttp) REVERT: C 431 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7325 (tmm-80) REVERT: D 80 MET cc_start: 0.7468 (mtm) cc_final: 0.6995 (mpp) REVERT: E 297 MET cc_start: 0.8224 (ttp) cc_final: 0.7751 (ttp) REVERT: E 431 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7300 (tmm-80) REVERT: F 122 LEU cc_start: 0.8937 (tp) cc_final: 0.8724 (tp) REVERT: G 297 MET cc_start: 0.8230 (ttp) cc_final: 0.7871 (ttp) REVERT: G 431 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7291 (tmm-80) REVERT: H 80 MET cc_start: 0.7606 (mtp) cc_final: 0.7251 (mpp) REVERT: I 431 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7309 (tmm-80) REVERT: J 122 LEU cc_start: 0.8961 (tp) cc_final: 0.8741 (tp) REVERT: K 297 MET cc_start: 0.8269 (ttp) cc_final: 0.7924 (ttp) REVERT: L 80 MET cc_start: 0.7439 (mtm) cc_final: 0.6982 (mpp) REVERT: L 122 LEU cc_start: 0.8933 (tp) cc_final: 0.8731 (tp) REVERT: M 297 MET cc_start: 0.8278 (ttp) cc_final: 0.7817 (ttp) REVERT: N 80 MET cc_start: 0.7462 (mtm) cc_final: 0.6954 (mpp) REVERT: O 297 MET cc_start: 0.8300 (ttp) cc_final: 0.7809 (ttp) REVERT: P 80 MET cc_start: 0.7416 (mtm) cc_final: 0.6905 (mpp) outliers start: 38 outliers final: 26 residues processed: 695 average time/residue: 1.6746 time to fit residues: 1386.8458 Evaluate side-chains 694 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 664 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 431 ARG Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 53 SER Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 260 optimal weight: 20.0000 chunk 333 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 384 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 454 optimal weight: 4.9990 chunk 284 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38672 Z= 0.290 Angle : 0.697 6.565 52432 Z= 0.376 Chirality : 0.048 0.197 5584 Planarity : 0.006 0.058 6880 Dihedral : 5.817 25.955 5365 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.51 % Allowed : 10.29 % Favored : 88.19 % 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: 0.86 (0.12), residues: 4760 helix: 1.33 (0.12), residues: 1920 sheet: 0.15 (0.19), residues: 696 loop : 0.15 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 132 HIS 0.015 0.002 HIS M 153 PHE 0.034 0.003 PHE E 345 TYR 0.021 0.003 TYR E 269 ARG 0.006 0.001 ARG O 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 660 time to evaluate : 4.310 Fit side-chains REVERT: A 297 MET cc_start: 0.8315 (ttp) cc_final: 0.7809 (ttp) REVERT: B 80 MET cc_start: 0.7468 (mtm) cc_final: 0.7078 (mpp) REVERT: C 297 MET cc_start: 0.8303 (ttp) cc_final: 0.7856 (ttp) REVERT: C 431 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7353 (tmm-80) REVERT: D 80 MET cc_start: 0.7480 (mtm) cc_final: 0.6992 (mpp) REVERT: E 297 MET cc_start: 0.8215 (ttp) cc_final: 0.7729 (ttp) REVERT: E 431 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7306 (tmm-80) REVERT: F 122 LEU cc_start: 0.8965 (tp) cc_final: 0.8756 (tp) REVERT: G 297 MET cc_start: 0.8226 (ttp) cc_final: 0.7762 (ttp) REVERT: G 431 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7291 (tmm-80) REVERT: H 80 MET cc_start: 0.7621 (mtp) cc_final: 0.7252 (mpp) REVERT: I 431 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7335 (tmm-80) REVERT: K 297 MET cc_start: 0.8290 (ttp) cc_final: 0.7865 (ttp) REVERT: L 80 MET cc_start: 0.7432 (mtm) cc_final: 0.6986 (mpp) REVERT: M 297 MET cc_start: 0.8259 (ttp) cc_final: 0.7815 (ttp) REVERT: N 80 MET cc_start: 0.7461 (mtm) cc_final: 0.7057 (mpp) REVERT: O 297 MET cc_start: 0.8283 (ttp) cc_final: 0.7816 (ttp) REVERT: P 80 MET cc_start: 0.7411 (mtm) cc_final: 0.7011 (mpp) outliers start: 59 outliers final: 37 residues processed: 696 average time/residue: 1.7023 time to fit residues: 1411.4908 Evaluate side-chains 700 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 659 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 431 ARG Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 252 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 53 SER Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 53 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain w residue 53 SER Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 289 optimal weight: 0.0870 chunk 309 optimal weight: 0.3980 chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 357 optimal weight: 9.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 38672 Z= 0.153 Angle : 0.551 6.158 52432 Z= 0.295 Chirality : 0.043 0.171 5584 Planarity : 0.004 0.045 6880 Dihedral : 5.249 21.758 5365 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.82 % Allowed : 11.24 % Favored : 87.94 % 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: 1.26 (0.12), residues: 4760 helix: 1.81 (0.12), residues: 1872 sheet: 0.13 (0.18), residues: 696 loop : 0.34 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 132 HIS 0.007 0.001 HIS G 153 PHE 0.033 0.002 PHE G 345 TYR 0.012 0.001 TYR G 269 ARG 0.009 0.000 ARG C 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 665 time to evaluate : 4.473 Fit side-chains REVERT: A 297 MET cc_start: 0.8269 (ttp) cc_final: 0.7820 (ttp) REVERT: B 80 MET cc_start: 0.7405 (mtm) cc_final: 0.7009 (mpp) REVERT: C 431 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7282 (tmm-80) REVERT: D 80 MET cc_start: 0.7428 (mtm) cc_final: 0.7061 (mpp) REVERT: E 297 MET cc_start: 0.8167 (ttp) cc_final: 0.7753 (ttp) REVERT: E 327 HIS cc_start: 0.8373 (m-70) cc_final: 0.8070 (m90) REVERT: E 431 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7267 (tmm-80) REVERT: F 80 MET cc_start: 0.7497 (mtp) cc_final: 0.7214 (mpp) REVERT: G 431 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7279 (tmm-80) REVERT: H 80 MET cc_start: 0.7544 (mtp) cc_final: 0.7211 (mpp) REVERT: I 431 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7239 (tmm-80) REVERT: K 297 MET cc_start: 0.8221 (ttp) cc_final: 0.7813 (ttp) REVERT: K 327 HIS cc_start: 0.8415 (m-70) cc_final: 0.8157 (m90) REVERT: L 80 MET cc_start: 0.7403 (mtm) cc_final: 0.7004 (mpp) REVERT: N 80 MET cc_start: 0.7419 (mtm) cc_final: 0.7008 (mpp) REVERT: P 80 MET cc_start: 0.7371 (mtm) cc_final: 0.6939 (mpp) outliers start: 32 outliers final: 14 residues processed: 682 average time/residue: 1.7340 time to fit residues: 1403.1001 Evaluate side-chains 683 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 665 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 431 ARG Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 53 SER Chi-restraints excluded: chain v residue 53 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 9.9990 chunk 435 optimal weight: 20.0000 chunk 397 optimal weight: 5.9990 chunk 423 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 332 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 383 optimal weight: 10.0000 chunk 400 optimal weight: 8.9990 chunk 422 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 45 GLN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 45 GLN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 HIS ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 38672 Z= 0.404 Angle : 0.783 7.173 52432 Z= 0.424 Chirality : 0.053 0.209 5584 Planarity : 0.007 0.070 6880 Dihedral : 5.879 24.565 5360 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.46 % Allowed : 10.88 % Favored : 87.65 % 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: 0.83 (0.12), residues: 4760 helix: 1.28 (0.12), residues: 1920 sheet: 0.16 (0.19), residues: 696 loop : 0.14 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 214 HIS 0.018 0.003 HIS M 153 PHE 0.035 0.004 PHE E 345 TYR 0.025 0.003 TYR G 269 ARG 0.007 0.001 ARG M 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 660 time to evaluate : 4.488 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.8311 (ttp) cc_final: 0.7819 (ttp) REVERT: A 431 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7337 (tmm-80) REVERT: B 80 MET cc_start: 0.7449 (mtm) cc_final: 0.7059 (mpp) REVERT: C 297 MET cc_start: 0.8262 (ttp) cc_final: 0.7843 (ttp) REVERT: C 431 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7366 (tmm-80) REVERT: D 80 MET cc_start: 0.7464 (mtm) cc_final: 0.7136 (mpp) REVERT: E 297 MET cc_start: 0.8221 (ttp) cc_final: 0.7759 (ttp) REVERT: E 431 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7339 (tmm-80) REVERT: G 297 MET cc_start: 0.8204 (ttp) cc_final: 0.7791 (ttp) REVERT: G 431 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7302 (tmm-80) REVERT: I 431 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7364 (tmm-80) REVERT: K 297 MET cc_start: 0.8270 (ttp) cc_final: 0.7943 (ttp) REVERT: K 431 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7302 (tmm-80) REVERT: L 80 MET cc_start: 0.7458 (mtm) cc_final: 0.7082 (mpp) REVERT: M 297 MET cc_start: 0.8238 (ttp) cc_final: 0.7750 (ttp) REVERT: N 80 MET cc_start: 0.7465 (mtm) cc_final: 0.7064 (mpp) REVERT: O 297 MET cc_start: 0.8267 (ttp) cc_final: 0.7777 (ttp) REVERT: O 431 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7366 (tmm-80) REVERT: P 80 MET cc_start: 0.7425 (mtm) cc_final: 0.7008 (mpp) outliers start: 57 outliers final: 31 residues processed: 692 average time/residue: 1.7427 time to fit residues: 1437.9475 Evaluate side-chains 696 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 658 time to evaluate : 4.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 431 ARG Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 431 ARG Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain O residue 431 ARG Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 53 SER Chi-restraints excluded: chain r residue 53 SER Chi-restraints excluded: chain t residue 53 SER Chi-restraints excluded: chain u residue 53 SER Chi-restraints excluded: chain v residue 53 SER Chi-restraints excluded: chain v residue 64 ARG Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 7.9990 chunk 448 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 212 optimal weight: 10.0000 chunk 311 optimal weight: 0.7980 chunk 470 optimal weight: 6.9990 chunk 432 optimal weight: 0.8980 chunk 374 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 289 optimal weight: 20.0000 chunk 229 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 38672 Z= 0.159 Angle : 0.565 6.331 52432 Z= 0.302 Chirality : 0.043 0.171 5584 Planarity : 0.004 0.051 6880 Dihedral : 5.271 22.129 5360 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.80 % Allowed : 11.52 % Favored : 87.68 % 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: 1.25 (0.12), residues: 4760 helix: 1.80 (0.12), residues: 1872 sheet: 0.14 (0.18), residues: 696 loop : 0.33 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 132 HIS 0.008 0.001 HIS I 153 PHE 0.033 0.002 PHE I 345 TYR 0.013 0.001 TYR G 269 ARG 0.010 0.001 ARG C 305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 665 time to evaluate : 4.662 Fit side-chains REVERT: A 431 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7296 (tmm-80) REVERT: B 80 MET cc_start: 0.7397 (mtm) cc_final: 0.6960 (mpp) REVERT: C 297 MET cc_start: 0.8239 (ttp) cc_final: 0.7792 (ttp) REVERT: C 431 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7280 (tmm-80) REVERT: D 80 MET cc_start: 0.7439 (mtm) cc_final: 0.6988 (mpp) REVERT: E 297 MET cc_start: 0.8173 (ttp) cc_final: 0.7741 (ttp) REVERT: E 327 HIS cc_start: 0.8380 (m-70) cc_final: 0.8062 (m90) REVERT: E 431 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7275 (tmm-80) REVERT: F 80 MET cc_start: 0.7511 (mtp) cc_final: 0.7219 (mpp) REVERT: G 297 MET cc_start: 0.8187 (ttp) cc_final: 0.7735 (ttp) REVERT: G 327 HIS cc_start: 0.8386 (m-70) cc_final: 0.8076 (m90) REVERT: G 431 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7277 (tmm-80) REVERT: H 80 MET cc_start: 0.7511 (mtp) cc_final: 0.7259 (mpp) REVERT: I 431 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7251 (tmm-80) REVERT: K 297 MET cc_start: 0.8234 (ttp) cc_final: 0.7854 (ttp) REVERT: K 327 HIS cc_start: 0.8436 (m-70) cc_final: 0.8151 (m90) REVERT: K 431 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7264 (tmm-80) REVERT: L 80 MET cc_start: 0.7411 (mtm) cc_final: 0.7004 (mpp) REVERT: N 80 MET cc_start: 0.7424 (mtm) cc_final: 0.7021 (mpp) REVERT: O 431 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7261 (tmm-80) REVERT: P 80 MET cc_start: 0.7385 (mtm) cc_final: 0.7009 (mpp) outliers start: 31 outliers final: 17 residues processed: 681 average time/residue: 1.7087 time to fit residues: 1383.9362 Evaluate side-chains 688 residues out of total 3984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 664 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 431 ARG Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 431 ARG Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 431 ARG Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain O residue 431 ARG Chi-restraints excluded: chain O residue 461 VAL Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 53 SER Chi-restraints excluded: chain u residue 53 SER Chi-restraints excluded: chain v residue 53 SER Chi-restraints excluded: chain x residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 0.7980 chunk 398 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 345 optimal weight: 0.0030 chunk 55 optimal weight: 0.0050 chunk 104 optimal weight: 4.9990 chunk 375 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 385 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.9608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN H 36 ASN I 96 GLN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** M 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.197418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.158215 restraints weight = 214420.626| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 6.14 r_work: 0.2918 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 38672 Z= 0.184 Angle : 0.587 6.275 52432 Z= 0.314 Chirality : 0.044 0.179 5584 Planarity : 0.005 0.055 6880 Dihedral : 5.275 21.952 5360 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.69 % Allowed : 11.94 % Favored : 87.37 % 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: 1.29 (0.12), residues: 4760 helix: 1.82 (0.12), residues: 1872 sheet: 0.19 (0.18), residues: 696 loop : 0.36 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 132 HIS 0.009 0.001 HIS C 153 PHE 0.033 0.002 PHE E 345 TYR 0.016 0.002 TYR G 269 ARG 0.009 0.001 ARG A 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18358.56 seconds wall clock time: 324 minutes 15.57 seconds (19455.57 seconds total)