Starting phenix.real_space_refine on Mon Mar 25 00:14:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjp_22358/03_2024/7jjp_22358_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjp_22358/03_2024/7jjp_22358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjp_22358/03_2024/7jjp_22358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjp_22358/03_2024/7jjp_22358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjp_22358/03_2024/7jjp_22358_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjp_22358/03_2024/7jjp_22358_trim_updated.pdb" } resolution = 1.94 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= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians S 120 5.16 5 C 14832 2.51 5 N 3204 2.21 5 O 3660 1.98 5 H 19104 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40920 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "D" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "E" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "F" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "G" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "H" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "I" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "J" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "K" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "L" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "E" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "F" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "G" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "H" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "K" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "L" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-2': 15, 'MC3:plan-1': 15} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Time building chain proxies: 19.63, per 1000 atoms: 0.48 Number of scatterers: 40920 At special positions: 0 Unit cell: (97.999, 99.297, 165.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 O 3660 8.00 N 3204 7.00 C 14832 6.00 H 19104 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 201 " distance=2.04 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 201 " distance=2.04 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 201 " distance=2.04 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 190 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 201 " distance=2.04 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 190 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 201 " distance=2.04 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 190 " distance=2.04 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 201 " distance=2.04 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 190 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 201 " distance=2.04 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 190 " distance=2.04 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 201 " distance=2.04 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 190 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 201 " distance=2.04 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 195 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 190 " distance=2.04 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 201 " distance=2.04 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 190 " distance=2.04 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: 33.01 Conformation dependent library (CDL) restraints added in 3.3 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 12 sheets defined 69.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 41 through 44 No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 74 through 108 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 153 through 180 Processing helix chain 'A' and resid 206 through 235 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 41 through 44 No H-bonds generated for 'chain 'B' and resid 41 through 44' Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 74 through 108 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 153 through 180 Processing helix chain 'B' and resid 206 through 235 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 41 through 44 No H-bonds generated for 'chain 'C' and resid 41 through 44' Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 74 through 108 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 153 through 180 Processing helix chain 'C' and resid 206 through 235 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 74 through 108 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 153 through 180 Processing helix chain 'D' and resid 206 through 235 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 20 through 32 Processing helix chain 'E' and resid 34 through 39 Processing helix chain 'E' and resid 41 through 44 No H-bonds generated for 'chain 'E' and resid 41 through 44' Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 74 through 108 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 153 through 180 Processing helix chain 'E' and resid 206 through 235 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 20 through 32 Processing helix chain 'F' and resid 34 through 39 Processing helix chain 'F' and resid 41 through 44 No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 61 through 69 Processing helix chain 'F' and resid 74 through 108 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 153 through 180 Processing helix chain 'F' and resid 206 through 235 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 20 through 32 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 41 through 44 No H-bonds generated for 'chain 'G' and resid 41 through 44' Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 74 through 108 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 153 through 180 Processing helix chain 'G' and resid 206 through 235 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 20 through 32 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 41 through 44 No H-bonds generated for 'chain 'H' and resid 41 through 44' Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 74 through 108 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 153 through 180 Processing helix chain 'H' and resid 206 through 235 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 20 through 32 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 44 No H-bonds generated for 'chain 'I' and resid 41 through 44' Processing helix chain 'I' and resid 61 through 69 Processing helix chain 'I' and resid 74 through 108 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 153 through 180 Processing helix chain 'I' and resid 206 through 235 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 20 through 32 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 44 No H-bonds generated for 'chain 'J' and resid 41 through 44' Processing helix chain 'J' and resid 61 through 69 Processing helix chain 'J' and resid 74 through 108 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 153 through 180 Processing helix chain 'J' and resid 206 through 235 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 20 through 32 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 41 through 44 No H-bonds generated for 'chain 'K' and resid 41 through 44' Processing helix chain 'K' and resid 61 through 69 Processing helix chain 'K' and resid 74 through 108 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 153 through 180 Processing helix chain 'K' and resid 206 through 235 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 20 through 32 Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 41 through 44 No H-bonds generated for 'chain 'L' and resid 41 through 44' Processing helix chain 'L' and resid 61 through 69 Processing helix chain 'L' and resid 74 through 108 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 153 through 180 Processing helix chain 'L' and resid 206 through 235 Processing sheet with id= A, first strand: chain 'A' and resid 187 through 190 Processing sheet with id= B, first strand: chain 'B' and resid 187 through 190 Processing sheet with id= C, first strand: chain 'C' and resid 187 through 190 Processing sheet with id= D, first strand: chain 'D' and resid 187 through 190 Processing sheet with id= E, first strand: chain 'E' and resid 187 through 190 Processing sheet with id= F, first strand: chain 'F' and resid 187 through 190 Processing sheet with id= G, first strand: chain 'G' and resid 187 through 190 Processing sheet with id= H, first strand: chain 'H' and resid 187 through 190 Processing sheet with id= I, first strand: chain 'I' and resid 187 through 190 Processing sheet with id= J, first strand: chain 'J' and resid 187 through 190 Processing sheet with id= K, first strand: chain 'K' and resid 187 through 190 Processing sheet with id= L, first strand: chain 'L' and resid 187 through 190 1260 hydrogen bonds defined for protein. 3744 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: 15.29 Time building geometry restraints manager: 34.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19092 1.03 - 1.22: 45 1.22 - 1.42: 8619 1.42 - 1.62: 12972 1.62 - 1.82: 156 Bond restraints: 40884 Sorted by residual: bond pdb=" CG1 ILE B 36 " pdb=" CD1 ILE B 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CG1 ILE L 36 " pdb=" CD1 ILE L 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CG1 ILE F 36 " pdb=" CD1 ILE F 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CG1 ILE C 36 " pdb=" CD1 ILE C 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CG1 ILE K 36 " pdb=" CD1 ILE K 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.28e+00 ... (remaining 40879 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.12: 2049 107.12 - 113.90: 44890 113.90 - 120.68: 15127 120.68 - 127.46: 9586 127.46 - 134.24: 300 Bond angle restraints: 71952 Sorted by residual: angle pdb=" N ALA I 41 " pdb=" CA ALA I 41 " pdb=" C ALA I 41 " ideal model delta sigma weight residual 111.11 114.29 -3.18 1.20e+00 6.94e-01 7.01e+00 angle pdb=" N ALA H 41 " pdb=" CA ALA H 41 " pdb=" C ALA H 41 " ideal model delta sigma weight residual 111.11 114.28 -3.17 1.20e+00 6.94e-01 6.97e+00 angle pdb=" N ALA L 41 " pdb=" CA ALA L 41 " pdb=" C ALA L 41 " ideal model delta sigma weight residual 111.11 114.28 -3.17 1.20e+00 6.94e-01 6.96e+00 angle pdb=" N ALA J 41 " pdb=" CA ALA J 41 " pdb=" C ALA J 41 " ideal model delta sigma weight residual 111.11 114.26 -3.15 1.20e+00 6.94e-01 6.88e+00 angle pdb=" N ALA D 41 " pdb=" CA ALA D 41 " pdb=" C ALA D 41 " ideal model delta sigma weight residual 111.11 114.26 -3.15 1.20e+00 6.94e-01 6.88e+00 ... (remaining 71947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 17453 15.80 - 31.59: 1671 31.59 - 47.39: 457 47.39 - 63.19: 339 63.19 - 78.98: 48 Dihedral angle restraints: 19968 sinusoidal: 11256 harmonic: 8712 Sorted by residual: dihedral pdb=" CA VAL L 14 " pdb=" C VAL L 14 " pdb=" N ASN L 15 " pdb=" CA ASN L 15 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA VAL I 14 " pdb=" C VAL I 14 " pdb=" N ASN I 15 " pdb=" CA ASN I 15 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA VAL E 14 " pdb=" C VAL E 14 " pdb=" N ASN E 15 " pdb=" CA ASN E 15 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 19965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1442 0.043 - 0.086: 1052 0.086 - 0.129: 375 0.129 - 0.172: 142 0.172 - 0.216: 37 Chirality restraints: 3048 Sorted by residual: chirality pdb=" CA ASP C 47 " pdb=" N ASP C 47 " pdb=" C ASP C 47 " pdb=" CB ASP C 47 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASP D 47 " pdb=" N ASP D 47 " pdb=" C ASP D 47 " pdb=" CB ASP D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASP B 47 " pdb=" N ASP B 47 " pdb=" C ASP B 47 " pdb=" CB ASP B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 3045 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 49 " 0.004 2.00e-02 2.50e+03 2.21e-02 7.31e+00 pdb=" CD GLN A 49 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN A 49 " 0.026 2.00e-02 2.50e+03 pdb=" NE2 GLN A 49 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 49 " 0.020 2.00e-02 2.50e+03 pdb="HE22 GLN A 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 49 " -0.003 2.00e-02 2.50e+03 2.19e-02 7.21e+00 pdb=" CD GLN J 49 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN J 49 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 GLN J 49 " -0.005 2.00e-02 2.50e+03 pdb="HE21 GLN J 49 " -0.019 2.00e-02 2.50e+03 pdb="HE22 GLN J 49 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 10 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.68e+00 pdb=" C ILE H 10 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE H 10 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU H 11 " -0.015 2.00e-02 2.50e+03 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 4693 2.25 - 2.83: 84799 2.83 - 3.42: 107376 3.42 - 4.01: 151575 4.01 - 4.60: 231044 Nonbonded interactions: 579487 Sorted by model distance: nonbonded pdb=" HG1 THR D 56 " pdb=" O HOH D 607 " model vdw 1.657 1.850 nonbonded pdb=" HG1 THR C 56 " pdb=" O HOH C 607 " model vdw 1.657 1.850 nonbonded pdb=" HG1 THR F 56 " pdb=" O HOH F 607 " model vdw 1.658 1.850 nonbonded pdb=" HG1 THR E 56 " pdb=" O HOH E 607 " model vdw 1.659 1.850 nonbonded pdb=" HG1 THR L 56 " pdb=" O HOH L 607 " model vdw 1.660 1.850 ... (remaining 579482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 236 or (resid 503 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23)) or (resid 504 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C2 \ 1 or name C22 or name C23 or name C24)) or (resid 506 through 507 and (name C15 \ or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or resid 509 through 512 or resid 514 through 515) \ ) selection = (chain 'B' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'C' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'D' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'E' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'F' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'G' and (resid 2 through 236 or (resid 503 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23)) or (resid 504 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C2 \ 1 or name C22 or name C23 or name C24)) or (resid 506 through 507 and (name C15 \ or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or resid 509 through 512 or resid 514 through 515) \ ) selection = (chain 'H' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'I' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'J' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'K' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'L' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) } 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: 9.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 9.040 Check model and map are aligned: 0.590 Set scattering table: 0.350 Process input model: 126.470 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.011 0.073 21780 Z= 0.752 Angle : 0.873 8.458 28704 Z= 0.456 Chirality : 0.067 0.216 3048 Planarity : 0.006 0.026 3324 Dihedral : 13.339 61.154 8580 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.56 % Allowed : 6.56 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.39 (0.16), residues: 2304 helix: 0.85 (0.12), residues: 1752 sheet: -0.86 (0.30), residues: 204 loop : -1.67 (0.26), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP E 193 HIS 0.007 0.002 HIS F 95 PHE 0.028 0.004 PHE I 84 TYR 0.017 0.003 TYR L 66 ARG 0.013 0.002 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 324 time to evaluate : 3.136 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 335 average time/residue: 2.6518 time to fit residues: 1015.4048 Evaluate side-chains 300 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 288 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 9 ASN F 9 ASN G 176 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21780 Z= 0.147 Angle : 0.509 4.979 28704 Z= 0.263 Chirality : 0.039 0.112 3048 Planarity : 0.004 0.043 3324 Dihedral : 6.669 56.365 4188 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.02 % Allowed : 7.82 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.17), residues: 2304 helix: 2.45 (0.12), residues: 1740 sheet: -0.76 (0.30), residues: 204 loop : -1.54 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 193 HIS 0.003 0.001 HIS H 176 PHE 0.014 0.001 PHE C 202 TYR 0.011 0.002 TYR J 66 ARG 0.004 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 302 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 316 average time/residue: 2.8741 time to fit residues: 1029.7976 Evaluate side-chains 308 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 294 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 166 optimal weight: 0.0020 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 9 ASN F 9 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21780 Z= 0.199 Angle : 0.517 4.218 28704 Z= 0.268 Chirality : 0.040 0.111 3048 Planarity : 0.004 0.045 3324 Dihedral : 6.544 56.626 4188 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.09 % Allowed : 7.36 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.17), residues: 2304 helix: 3.01 (0.12), residues: 1740 sheet: -0.21 (0.35), residues: 132 loop : -1.15 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 193 HIS 0.004 0.001 HIS J 161 PHE 0.019 0.002 PHE D 212 TYR 0.016 0.002 TYR J 66 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 317 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5328 (mpt) REVERT: B 102 MET cc_start: 0.5890 (OUTLIER) cc_final: 0.5240 (mpt) REVERT: C 231 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.6847 (mpp) REVERT: E 102 MET cc_start: 0.5868 (OUTLIER) cc_final: 0.5302 (mpt) REVERT: H 102 MET cc_start: 0.5611 (OUTLIER) cc_final: 0.5228 (mpt) outliers start: 45 outliers final: 27 residues processed: 339 average time/residue: 2.9583 time to fit residues: 1131.2587 Evaluate side-chains 343 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 311 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 33 ARG Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain I residue 102 MET Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN C 58 GLN E 58 GLN F 9 ASN F 58 GLN H 58 GLN I 58 GLN K 58 GLN L 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21780 Z= 0.272 Angle : 0.561 4.682 28704 Z= 0.294 Chirality : 0.042 0.114 3048 Planarity : 0.004 0.062 3324 Dihedral : 7.499 58.015 4188 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.72 % Allowed : 7.68 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.17), residues: 2304 helix: 2.98 (0.12), residues: 1740 sheet: -0.26 (0.34), residues: 132 loop : -1.14 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 193 HIS 0.005 0.001 HIS H 161 PHE 0.024 0.003 PHE J 212 TYR 0.019 0.002 TYR J 66 ARG 0.003 0.000 ARG H 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 333 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 ASP cc_start: 0.8129 (m-30) cc_final: 0.7895 (m-30) REVERT: E 231 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7205 (mpp) REVERT: F 51 ASP cc_start: 0.8120 (m-30) cc_final: 0.7903 (m-30) REVERT: H 102 MET cc_start: 0.5681 (OUTLIER) cc_final: 0.5266 (mpt) REVERT: J 231 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6903 (mpp) REVERT: K 102 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5174 (mpt) outliers start: 37 outliers final: 16 residues processed: 340 average time/residue: 2.7195 time to fit residues: 1056.4295 Evaluate side-chains 348 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 328 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 231 MET Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21780 Z= 0.319 Angle : 0.581 4.938 28704 Z= 0.304 Chirality : 0.043 0.119 3048 Planarity : 0.005 0.069 3324 Dihedral : 8.081 59.996 4188 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.44 % Allowed : 8.75 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.17), residues: 2304 helix: 2.92 (0.12), residues: 1740 sheet: -0.94 (0.28), residues: 204 loop : -1.39 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 193 HIS 0.005 0.001 HIS J 161 PHE 0.024 0.003 PHE J 212 TYR 0.019 0.003 TYR J 66 ARG 0.004 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 329 time to evaluate : 3.148 Fit side-chains REVERT: A 102 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5285 (mpt) REVERT: B 102 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5240 (mpt) REVERT: B 231 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7138 (mpp) REVERT: C 231 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6910 (mpp) REVERT: D 102 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5206 (mpt) REVERT: E 102 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.5375 (mpt) REVERT: G 102 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5184 (mpt) REVERT: H 102 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5236 (mpt) REVERT: H 231 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7087 (mpp) REVERT: K 102 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.5190 (mpt) REVERT: K 231 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7108 (mpp) outliers start: 31 outliers final: 13 residues processed: 342 average time/residue: 2.6180 time to fit residues: 1026.5594 Evaluate side-chains 344 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 320 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN D 58 GLN G 58 GLN J 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 21780 Z= 0.133 Angle : 0.462 3.842 28704 Z= 0.240 Chirality : 0.038 0.113 3048 Planarity : 0.004 0.059 3324 Dihedral : 6.632 59.987 4188 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.02 % Allowed : 9.82 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.17), residues: 2304 helix: 3.27 (0.12), residues: 1728 sheet: -0.15 (0.35), residues: 132 loop : -1.34 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 193 HIS 0.002 0.001 HIS D 176 PHE 0.015 0.001 PHE J 212 TYR 0.013 0.002 TYR J 66 ARG 0.007 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 354 time to evaluate : 2.813 Fit side-chains revert: symmetry clash REVERT: D 102 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5203 (mpt) REVERT: E 102 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5346 (mpt) REVERT: G 102 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.5189 (mpt) REVERT: H 102 MET cc_start: 0.5758 (OUTLIER) cc_final: 0.5199 (mpt) REVERT: J 102 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5368 (mpt) outliers start: 22 outliers final: 14 residues processed: 358 average time/residue: 2.5547 time to fit residues: 1051.4402 Evaluate side-chains 350 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 331 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 125 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 185 optimal weight: 0.3980 chunk 123 optimal weight: 6.9990 chunk 219 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN D 58 GLN G 58 GLN J 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21780 Z= 0.211 Angle : 0.507 4.067 28704 Z= 0.263 Chirality : 0.040 0.116 3048 Planarity : 0.004 0.061 3324 Dihedral : 6.973 59.825 4188 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.98 % Allowed : 10.01 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.17), residues: 2304 helix: 3.20 (0.12), residues: 1740 sheet: -0.21 (0.35), residues: 132 loop : -1.19 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 193 HIS 0.003 0.001 HIS A 161 PHE 0.019 0.002 PHE J 212 TYR 0.017 0.002 TYR J 66 ARG 0.006 0.000 ARG E 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 325 time to evaluate : 3.073 Fit side-chains REVERT: A 102 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5336 (mpt) REVERT: B 102 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5345 (mpt) REVERT: E 102 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5341 (mpt) REVERT: H 102 MET cc_start: 0.5771 (OUTLIER) cc_final: 0.5215 (mpt) REVERT: J 102 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.5333 (mpt) outliers start: 21 outliers final: 12 residues processed: 338 average time/residue: 2.6207 time to fit residues: 1015.8900 Evaluate side-chains 343 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 326 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN D 58 GLN G 58 GLN J 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21780 Z= 0.154 Angle : 0.471 3.807 28704 Z= 0.244 Chirality : 0.038 0.111 3048 Planarity : 0.004 0.066 3324 Dihedral : 6.489 59.269 4188 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.88 % Allowed : 10.01 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.17), residues: 2304 helix: 3.28 (0.12), residues: 1740 sheet: -0.16 (0.36), residues: 132 loop : -1.20 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 193 HIS 0.003 0.001 HIS D 161 PHE 0.017 0.002 PHE J 212 TYR 0.013 0.002 TYR G 66 ARG 0.007 0.000 ARG H 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 330 time to evaluate : 2.790 Fit side-chains REVERT: A 102 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5323 (mpt) REVERT: B 102 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5356 (mpt) REVERT: E 102 MET cc_start: 0.5960 (OUTLIER) cc_final: 0.5319 (mpt) outliers start: 19 outliers final: 13 residues processed: 343 average time/residue: 2.5878 time to fit residues: 1017.6317 Evaluate side-chains 338 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 322 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN D 58 GLN G 58 GLN J 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21780 Z= 0.155 Angle : 0.471 4.581 28704 Z= 0.244 Chirality : 0.038 0.111 3048 Planarity : 0.004 0.067 3324 Dihedral : 6.351 59.374 4188 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.84 % Allowed : 10.06 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.17), residues: 2304 helix: 3.36 (0.12), residues: 1740 sheet: -0.16 (0.36), residues: 132 loop : -1.21 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 193 HIS 0.003 0.001 HIS A 161 PHE 0.017 0.002 PHE J 212 TYR 0.014 0.002 TYR J 66 ARG 0.009 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 328 time to evaluate : 3.233 Fit side-chains REVERT: A 102 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5332 (mpt) REVERT: B 102 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5362 (mpt) REVERT: C 51 ASP cc_start: 0.8084 (m-30) cc_final: 0.7882 (m-30) REVERT: D 102 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5290 (mpt) REVERT: E 102 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5331 (mpt) REVERT: K 102 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5359 (mpt) outliers start: 18 outliers final: 13 residues processed: 340 average time/residue: 2.5936 time to fit residues: 1012.5133 Evaluate side-chains 344 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 326 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21780 Z= 0.262 Angle : 0.542 5.371 28704 Z= 0.282 Chirality : 0.041 0.135 3048 Planarity : 0.005 0.084 3324 Dihedral : 7.277 59.078 4188 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.88 % Allowed : 10.15 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.17), residues: 2304 helix: 3.18 (0.12), residues: 1740 sheet: -0.20 (0.34), residues: 132 loop : -1.24 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 193 HIS 0.004 0.001 HIS J 161 PHE 0.022 0.003 PHE H 212 TYR 0.019 0.002 TYR J 66 ARG 0.012 0.001 ARG L 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 328 time to evaluate : 3.130 Fit side-chains REVERT: A 102 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5336 (mpt) REVERT: B 102 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5359 (mpt) REVERT: D 102 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5262 (mpt) REVERT: K 102 MET cc_start: 0.5915 (OUTLIER) cc_final: 0.5374 (mpt) outliers start: 19 outliers final: 14 residues processed: 342 average time/residue: 2.5852 time to fit residues: 1016.0340 Evaluate side-chains 346 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 328 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 186 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN D 58 GLN G 58 GLN J 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.165298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107390 restraints weight = 48321.394| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.16 r_work: 0.3100 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21780 Z= 0.144 Angle : 0.468 5.349 28704 Z= 0.243 Chirality : 0.038 0.112 3048 Planarity : 0.004 0.068 3324 Dihedral : 6.409 58.480 4188 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.88 % Allowed : 10.34 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.17), residues: 2304 helix: 3.33 (0.12), residues: 1740 sheet: -0.08 (0.36), residues: 132 loop : -1.23 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 193 HIS 0.004 0.001 HIS B 17 PHE 0.017 0.001 PHE J 212 TYR 0.013 0.002 TYR J 66 ARG 0.009 0.000 ARG C 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16406.96 seconds wall clock time: 290 minutes 22.86 seconds (17422.86 seconds total)