Starting phenix.real_space_refine on Sat Feb 24 13:38:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/02_2024/7jmc_22391_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/02_2024/7jmc_22391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/02_2024/7jmc_22391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/02_2024/7jmc_22391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/02_2024/7jmc_22391_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/02_2024/7jmc_22391_trim_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 120 5.16 5 C 14532 2.51 5 N 3084 2.21 5 O 3504 1.98 5 H 18576 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 ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39828 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "B" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "C" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "E" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "F" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "G" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "H" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "I" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "K" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "L" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "F" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "G" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "H" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "I" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "J" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "K" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "L" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 16.52, per 1000 atoms: 0.41 Number of scatterers: 39828 At special positions: 0 Unit cell: (95.403, 96.701, 161.601, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 12 15.00 O 3504 8.00 N 3084 7.00 C 14532 6.00 H 18576 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 201 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 201 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 201 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 201 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 201 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 201 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 201 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 201 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 201 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 201 " distance=2.03 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=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.31 Conformation dependent library (CDL) restraints added in 3.6 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 12 sheets defined 71.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.82 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 48 through 51 No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 61 through 69 Processing helix chain 'F' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'G' and resid 48 through 51' Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'H' and resid 48 through 51' Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'I' and resid 48 through 51' Processing helix chain 'I' and resid 61 through 69 Processing helix chain 'I' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'J' and resid 48 through 51' Processing helix chain 'J' and resid 61 through 69 Processing helix chain 'J' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 61 through 69 Processing helix chain 'K' and resid 74 through 105 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 48 through 51 No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'L' and resid 61 through 69 Processing helix chain 'L' and resid 74 through 105 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 1224 hydrogen bonds defined for protein. 3636 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: 14.82 Time building geometry restraints manager: 30.58 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: 18564 1.03 - 1.22: 72 1.22 - 1.42: 8535 1.42 - 1.61: 12705 1.61 - 1.80: 180 Bond restraints: 40056 Sorted by residual: bond pdb=" C11 MC3 A 506 " pdb=" O3 MC3 A 506 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C31 MC3 E 508 " pdb=" O2 MC3 E 508 " ideal model delta sigma weight residual 1.328 1.400 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 H 501 " pdb=" O3 MC3 H 501 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 K 501 " pdb=" O3 MC3 K 501 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 B 501 " pdb=" O3 MC3 B 501 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 40051 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.09: 446 106.09 - 113.11: 44963 113.11 - 120.14: 12620 120.14 - 127.16: 12147 127.16 - 134.18: 300 Bond angle restraints: 70476 Sorted by residual: angle pdb=" O3P MC3 L 508 " pdb=" P MC3 L 508 " pdb=" O4P MC3 L 508 " ideal model delta sigma weight residual 93.26 109.95 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 C 508 " pdb=" P MC3 C 508 " pdb=" O4P MC3 C 508 " ideal model delta sigma weight residual 93.26 109.95 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 J 508 " pdb=" P MC3 J 508 " pdb=" O4P MC3 J 508 " ideal model delta sigma weight residual 93.26 109.94 -16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 D 508 " pdb=" P MC3 D 508 " pdb=" O4P MC3 D 508 " ideal model delta sigma weight residual 93.26 109.94 -16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 G 501 " pdb=" P MC3 G 501 " pdb=" O4P MC3 G 501 " ideal model delta sigma weight residual 93.26 109.94 -16.68 3.00e+00 1.11e-01 3.09e+01 ... (remaining 70471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 19152 35.38 - 70.75: 492 70.75 - 106.13: 36 106.13 - 141.50: 0 141.50 - 176.88: 24 Dihedral angle restraints: 19704 sinusoidal: 11136 harmonic: 8568 Sorted by residual: dihedral pdb=" C33 MC3 E 501 " pdb=" C31 MC3 E 501 " pdb=" C32 MC3 E 501 " pdb=" O2 MC3 E 501 " ideal model delta sinusoidal sigma weight residual 175.52 -1.36 176.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 MC3 K 501 " pdb=" C31 MC3 K 501 " pdb=" C32 MC3 K 501 " pdb=" O2 MC3 K 501 " ideal model delta sinusoidal sigma weight residual 175.52 -1.36 176.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 MC3 B 501 " pdb=" C31 MC3 B 501 " pdb=" C32 MC3 B 501 " pdb=" O2 MC3 B 501 " ideal model delta sinusoidal sigma weight residual 175.52 -1.36 176.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 19701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2112 0.053 - 0.106: 735 0.106 - 0.159: 129 0.159 - 0.213: 12 0.213 - 0.266: 24 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA ASN I 197 " pdb=" N ASN I 197 " pdb=" C ASN I 197 " pdb=" CB ASN I 197 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASN F 197 " pdb=" N ASN F 197 " pdb=" C ASN F 197 " pdb=" CB ASN F 197 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASN A 197 " pdb=" N ASN A 197 " pdb=" C ASN A 197 " pdb=" CB ASN A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3009 not shown) Planarity restraints: 5484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 197 " 0.216 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CG ASN E 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 197 " -0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN E 197 " 0.014 2.00e-02 2.50e+03 pdb="HD21 ASN E 197 " 0.437 2.00e-02 2.50e+03 pdb="HD22 ASN E 197 " -0.434 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 197 " -0.217 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CG ASN C 197 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 197 " 0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN C 197 " -0.014 2.00e-02 2.50e+03 pdb="HD21 ASN C 197 " -0.437 2.00e-02 2.50e+03 pdb="HD22 ASN C 197 " 0.433 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 197 " -0.217 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CG ASN L 197 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN L 197 " 0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN L 197 " -0.014 2.00e-02 2.50e+03 pdb="HD21 ASN L 197 " -0.437 2.00e-02 2.50e+03 pdb="HD22 ASN L 197 " 0.433 2.00e-02 2.50e+03 ... (remaining 5481 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 3889 2.24 - 2.83: 84937 2.83 - 3.42: 101444 3.42 - 4.01: 143537 4.01 - 4.60: 227583 Nonbonded interactions: 561390 Sorted by model distance: nonbonded pdb=" O TYR H 158 " pdb=" HD1 HIS H 161 " model vdw 1.650 1.850 nonbonded pdb=" O TYR I 158 " pdb=" HD1 HIS I 161 " model vdw 1.650 1.850 nonbonded pdb=" O TYR F 158 " pdb=" HD1 HIS F 161 " model vdw 1.650 1.850 nonbonded pdb=" O TYR E 158 " pdb=" HD1 HIS E 161 " model vdw 1.651 1.850 nonbonded pdb=" O TYR K 158 " pdb=" HD1 HIS K 161 " model vdw 1.651 1.850 ... (remaining 561385 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 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or resid 502 through 504 or (resid 505 through 506 and (na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 o \ r name C22 or name C23 or name C24)) or (resid 507 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 C21 \ or name C22 or name C23 or name C24)) or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or resid 509 through 510 or (resid 511 and (name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23 or name C24)) or (resid 512 and (name 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 n \ ame C24)))) selection = (chain 'B' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) selection = (chain 'C' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) selection = (chain 'D' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) selection = (chain 'E' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) selection = (chain 'F' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) selection = (chain 'G' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or resid 502 through 504 or (resid 505 through 506 and (na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 o \ r name C22 or name C23 or name C24)) or (resid 507 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 C21 \ or name C22 or name C23 or name C24)) or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or resid 509 through 510 or (resid 511 and (name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23 or name C24)) or (resid 512 and (name 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 n \ ame C24)))) selection = (chain 'H' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) selection = (chain 'I' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) selection = (chain 'J' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) selection = (chain 'K' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) selection = (chain 'L' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e 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 name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 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 511 through 512)) } 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: 6.440 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: 0.600 Extract box with map and model: 16.290 Check model and map are aligned: 0.550 Set scattering table: 0.390 Process input model: 117.320 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 21480 Z= 0.636 Angle : 1.287 16.685 28440 Z= 0.530 Chirality : 0.057 0.266 3012 Planarity : 0.006 0.055 3288 Dihedral : 14.519 176.875 8496 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.57 % Allowed : 6.29 % Favored : 93.14 % 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: 3.40 (0.16), residues: 2256 helix: 3.16 (0.10), residues: 1704 sheet: 0.10 (0.46), residues: 132 loop : -1.18 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 193 HIS 0.005 0.002 HIS E 161 PHE 0.034 0.002 PHE C 202 TYR 0.014 0.003 TYR A 180 ARG 0.005 0.001 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6925 (mtt90) outliers start: 12 outliers final: 12 residues processed: 263 average time/residue: 2.0915 time to fit residues: 651.4699 Evaluate side-chains 223 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 2.897 ------------------------------------------------------------------------------- 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: 0.6980 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN E 15 ASN K 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21480 Z= 0.169 Angle : 0.503 5.066 28440 Z= 0.252 Chirality : 0.038 0.118 3012 Planarity : 0.004 0.042 3288 Dihedral : 13.092 171.419 4284 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.48 % Allowed : 9.62 % Favored : 88.90 % 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: 3.93 (0.17), residues: 2256 helix: 3.54 (0.11), residues: 1704 sheet: 0.56 (0.45), residues: 132 loop : -1.09 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 4 HIS 0.004 0.001 HIS C 98 PHE 0.015 0.001 PHE J 202 TYR 0.007 0.002 TYR C 158 ARG 0.001 0.000 ARG K 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 23 ARG cc_start: 0.7482 (mtt180) cc_final: 0.6926 (mtt90) REVERT: G 23 ARG cc_start: 0.7510 (mtt180) cc_final: 0.6945 (mtt90) REVERT: H 231 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6497 (mpp) REVERT: J 23 ARG cc_start: 0.7501 (mtt180) cc_final: 0.6925 (mtt90) outliers start: 31 outliers final: 29 residues processed: 251 average time/residue: 2.1927 time to fit residues: 653.8242 Evaluate side-chains 258 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8080 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21480 Z= 0.281 Angle : 0.514 5.308 28440 Z= 0.264 Chirality : 0.040 0.124 3012 Planarity : 0.004 0.037 3288 Dihedral : 12.470 156.946 4284 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.24 % Allowed : 9.19 % Favored : 88.57 % 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: 3.45 (0.17), residues: 2256 helix: 3.26 (0.12), residues: 1716 sheet: -0.80 (0.32), residues: 204 loop : -1.25 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 4 HIS 0.005 0.001 HIS J 98 PHE 0.021 0.002 PHE L 202 TYR 0.011 0.002 TYR D 66 ARG 0.001 0.000 ARG F 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 240 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6930 (mtt90) REVERT: B 23 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7075 (mtt90) REVERT: C 23 ARG cc_start: 0.7485 (mtt180) cc_final: 0.6957 (mtt90) REVERT: C 176 HIS cc_start: 0.8085 (t-90) cc_final: 0.7856 (t-170) REVERT: C 231 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6948 (mpp) REVERT: D 23 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7093 (mtt-85) REVERT: E 23 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7059 (mtt90) REVERT: F 23 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7026 (mtt90) REVERT: H 231 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6475 (mpp) outliers start: 47 outliers final: 36 residues processed: 258 average time/residue: 2.1460 time to fit residues: 654.0592 Evaluate side-chains 267 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS D 176 HIS E 176 HIS F 176 HIS G 176 HIS I 176 HIS J 176 HIS L 176 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21480 Z= 0.262 Angle : 0.493 5.036 28440 Z= 0.253 Chirality : 0.039 0.120 3012 Planarity : 0.004 0.034 3288 Dihedral : 10.737 135.378 4284 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.14 % Allowed : 9.86 % Favored : 88.00 % 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: 3.28 (0.17), residues: 2256 helix: 3.05 (0.12), residues: 1728 sheet: -0.59 (0.37), residues: 132 loop : -1.06 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 4 HIS 0.007 0.001 HIS L 176 PHE 0.022 0.002 PHE B 202 TYR 0.011 0.002 TYR A 66 ARG 0.001 0.000 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 243 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7078 (mtt90) REVERT: C 23 ARG cc_start: 0.7486 (mtt180) cc_final: 0.6976 (mtt90) REVERT: C 231 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6932 (mpp) REVERT: E 23 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7073 (mtt90) REVERT: F 23 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7025 (mtt90) REVERT: H 231 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6330 (mpp) outliers start: 45 outliers final: 37 residues processed: 260 average time/residue: 2.2104 time to fit residues: 674.4175 Evaluate side-chains 269 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS C 176 HIS D 9 ASN E 176 HIS F 176 HIS H 176 HIS I 176 HIS K 176 HIS L 176 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 21480 Z= 0.242 Angle : 0.470 4.412 28440 Z= 0.242 Chirality : 0.039 0.116 3012 Planarity : 0.003 0.033 3288 Dihedral : 10.039 115.347 4284 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.19 % Allowed : 9.24 % Favored : 87.57 % 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: 3.28 (0.17), residues: 2256 helix: 3.05 (0.12), residues: 1728 sheet: -0.71 (0.36), residues: 132 loop : -1.04 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 4 HIS 0.008 0.001 HIS B 176 PHE 0.019 0.002 PHE L 202 TYR 0.010 0.002 TYR A 66 ARG 0.001 0.000 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 243 time to evaluate : 2.966 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: B 23 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7113 (mtt90) REVERT: C 23 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7008 (mtt90) REVERT: D 23 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7115 (mtt-85) REVERT: E 23 ARG cc_start: 0.7507 (mtt180) cc_final: 0.7107 (mtt90) REVERT: F 23 ARG cc_start: 0.7540 (mtt180) cc_final: 0.7069 (mtt90) REVERT: I 23 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7066 (mtt90) REVERT: J 23 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7062 (mtt-85) REVERT: K 23 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7146 (mtt-85) REVERT: L 23 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7060 (mtt90) outliers start: 67 outliers final: 40 residues processed: 282 average time/residue: 2.6037 time to fit residues: 841.2392 Evaluate side-chains 275 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 176 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 176 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS B 176 HIS C 95 HIS C 176 HIS D 9 ASN E 176 HIS F 95 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 HIS H 176 HIS I 95 HIS ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 HIS L 95 HIS ** L 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21480 Z= 0.183 Angle : 0.460 4.163 28440 Z= 0.241 Chirality : 0.038 0.159 3012 Planarity : 0.005 0.062 3288 Dihedral : 9.304 101.617 4284 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.52 % Allowed : 10.14 % Favored : 87.33 % 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: 2256 helix: 2.94 (0.12), residues: 1728 sheet: -0.70 (0.37), residues: 132 loop : -1.04 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 4 HIS 0.037 0.002 HIS F 176 PHE 0.017 0.001 PHE C 202 TYR 0.009 0.002 TYR A 66 ARG 0.008 0.001 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 238 time to evaluate : 3.054 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: A 23 ARG cc_start: 0.7458 (mtt180) cc_final: 0.6952 (mtt-85) REVERT: B 23 ARG cc_start: 0.7506 (mtt180) cc_final: 0.7117 (mtt90) REVERT: C 23 ARG cc_start: 0.7471 (mtt180) cc_final: 0.7006 (mtt90) REVERT: D 23 ARG cc_start: 0.7512 (mtt180) cc_final: 0.7103 (mtt-85) REVERT: E 23 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7104 (mtt90) REVERT: F 23 ARG cc_start: 0.7519 (mtt180) cc_final: 0.7062 (mtt90) REVERT: G 23 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7070 (mtt-85) REVERT: I 23 ARG cc_start: 0.7517 (mtt180) cc_final: 0.7058 (mtt90) REVERT: J 23 ARG cc_start: 0.7469 (mtt180) cc_final: 0.7047 (mtt-85) REVERT: K 23 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7140 (mtt-85) REVERT: L 23 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7050 (mtt90) outliers start: 53 outliers final: 38 residues processed: 265 average time/residue: 2.1703 time to fit residues: 677.4086 Evaluate side-chains 274 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 176 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN D 95 HIS E 95 HIS E 176 HIS F 176 HIS G 95 HIS H 176 HIS I 176 HIS J 95 HIS K 95 HIS K 176 HIS K 233 HIS L 176 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 21480 Z= 0.309 Angle : 0.502 4.439 28440 Z= 0.260 Chirality : 0.040 0.124 3012 Planarity : 0.004 0.045 3288 Dihedral : 9.285 92.317 4284 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.52 % Allowed : 9.90 % Favored : 87.57 % 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: 2.94 (0.17), residues: 2256 helix: 2.80 (0.12), residues: 1728 sheet: -0.88 (0.36), residues: 132 loop : -1.08 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 193 HIS 0.025 0.002 HIS C 176 PHE 0.022 0.002 PHE C 202 TYR 0.015 0.003 TYR C 177 ARG 0.008 0.001 ARG L 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 251 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7484 (mtt180) cc_final: 0.6975 (mtt-85) REVERT: C 23 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7036 (mtt90) REVERT: D 23 ARG cc_start: 0.7521 (mtt180) cc_final: 0.7110 (mtt-85) REVERT: E 23 ARG cc_start: 0.7508 (mtt180) cc_final: 0.7114 (mtt90) REVERT: F 23 ARG cc_start: 0.7528 (mtt180) cc_final: 0.7067 (mtt90) REVERT: G 23 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7075 (mtt-85) REVERT: I 23 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7078 (mtt90) REVERT: J 23 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7068 (mtt-85) REVERT: K 23 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7155 (mtt-85) REVERT: L 23 ARG cc_start: 0.7549 (mtt180) cc_final: 0.7054 (mtt90) outliers start: 53 outliers final: 41 residues processed: 269 average time/residue: 2.1843 time to fit residues: 693.1272 Evaluate side-chains 284 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 231 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 0.0050 chunk 42 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS C 176 HIS D 9 ASN E 176 HIS F 176 HIS H 176 HIS I 176 HIS J 233 HIS K 176 HIS K 233 HIS L 176 HIS L 233 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 21480 Z= 0.210 Angle : 0.455 4.124 28440 Z= 0.235 Chirality : 0.038 0.117 3012 Planarity : 0.004 0.038 3288 Dihedral : 8.719 74.824 4284 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.29 % Allowed : 10.43 % Favored : 87.29 % 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: 3.10 (0.17), residues: 2256 helix: 2.92 (0.12), residues: 1716 sheet: -0.76 (0.37), residues: 132 loop : -1.00 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 193 HIS 0.015 0.002 HIS I 176 PHE 0.018 0.001 PHE C 202 TYR 0.010 0.002 TYR A 66 ARG 0.005 0.000 ARG G 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 250 time to evaluate : 3.074 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 23 ARG cc_start: 0.7482 (mtt180) cc_final: 0.6979 (mtt-85) REVERT: C 23 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7005 (mtt90) REVERT: E 23 ARG cc_start: 0.7497 (mtt180) cc_final: 0.7103 (mtt90) REVERT: F 23 ARG cc_start: 0.7526 (mtt180) cc_final: 0.7065 (mtt90) REVERT: G 23 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7071 (mtt-85) REVERT: I 23 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7064 (mtt90) REVERT: J 23 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7067 (mtt-85) REVERT: K 23 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7148 (mtt-85) REVERT: L 23 ARG cc_start: 0.7545 (mtt180) cc_final: 0.7055 (mtt90) outliers start: 48 outliers final: 38 residues processed: 269 average time/residue: 2.1180 time to fit residues: 671.1661 Evaluate side-chains 279 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 241 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS B 176 HIS B 233 HIS C 176 HIS D 9 ASN E 176 HIS F 176 HIS G 233 HIS H 176 HIS I 176 HIS I 233 HIS J 233 HIS K 176 HIS K 233 HIS L 176 HIS L 233 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21480 Z= 0.196 Angle : 0.452 8.546 28440 Z= 0.232 Chirality : 0.038 0.117 3012 Planarity : 0.004 0.032 3288 Dihedral : 8.533 64.012 4284 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.48 % Allowed : 10.57 % Favored : 86.95 % 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: 3.21 (0.17), residues: 2256 helix: 3.01 (0.12), residues: 1716 sheet: -0.71 (0.37), residues: 132 loop : -1.01 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 4 HIS 0.016 0.002 HIS L 176 PHE 0.017 0.001 PHE C 202 TYR 0.009 0.002 TYR A 66 ARG 0.005 0.000 ARG G 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 243 time to evaluate : 3.435 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: C 23 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7003 (mtt90) REVERT: D 23 ARG cc_start: 0.7520 (mtt180) cc_final: 0.6917 (mtt-85) REVERT: E 23 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7101 (mtt90) REVERT: F 23 ARG cc_start: 0.7527 (mtt180) cc_final: 0.7071 (mtt90) REVERT: G 23 ARG cc_start: 0.7499 (mtt180) cc_final: 0.7072 (mtt-85) REVERT: I 23 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7064 (mtt90) REVERT: J 23 ARG cc_start: 0.7496 (mtt180) cc_final: 0.7068 (mtt-85) REVERT: K 23 ARG cc_start: 0.7546 (mtt180) cc_final: 0.7144 (mtt-85) REVERT: L 23 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7061 (mtt90) outliers start: 52 outliers final: 45 residues processed: 266 average time/residue: 2.1864 time to fit residues: 683.4532 Evaluate side-chains 285 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 240 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 176 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 176 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 231 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 176 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 176 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS B 176 HIS B 233 HIS C 176 HIS D 9 ASN E 176 HIS F 176 HIS G 233 HIS H 176 HIS I 176 HIS I 233 HIS J 233 HIS K 176 HIS K 233 HIS L 176 HIS L 233 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 21480 Z= 0.263 Angle : 0.496 4.853 28440 Z= 0.263 Chirality : 0.039 0.118 3012 Planarity : 0.004 0.032 3288 Dihedral : 8.697 60.870 4284 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.48 % Allowed : 10.71 % Favored : 86.81 % 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: 2.87 (0.17), residues: 2256 helix: 2.75 (0.12), residues: 1716 sheet: -0.76 (0.37), residues: 132 loop : -1.05 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 193 HIS 0.015 0.002 HIS C 176 PHE 0.021 0.002 PHE A 202 TYR 0.015 0.003 TYR L 180 ARG 0.005 0.000 ARG G 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 254 time to evaluate : 2.923 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: C 23 ARG cc_start: 0.7505 (mtt180) cc_final: 0.7027 (mtt90) REVERT: D 23 ARG cc_start: 0.7526 (mtt180) cc_final: 0.6922 (mtt-85) REVERT: E 23 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7100 (mtt90) REVERT: F 23 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7070 (mtt90) REVERT: G 23 ARG cc_start: 0.7513 (mtt180) cc_final: 0.7087 (mtt-85) REVERT: I 23 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7079 (mtt90) REVERT: J 23 ARG cc_start: 0.7504 (mtt180) cc_final: 0.7078 (mtt-85) REVERT: K 23 ARG cc_start: 0.7554 (mtt180) cc_final: 0.7151 (mtt-85) REVERT: L 23 ARG cc_start: 0.7554 (mtt180) cc_final: 0.7064 (mtt90) outliers start: 52 outliers final: 37 residues processed: 271 average time/residue: 2.1721 time to fit residues: 694.8524 Evaluate side-chains 286 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 249 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 231 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 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: 3.9990 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 233 HIS B 176 HIS B 233 HIS C 176 HIS D 9 ASN E 176 HIS F 176 HIS G 233 HIS H 176 HIS I 176 HIS I 233 HIS J 233 HIS K 176 HIS K 233 HIS L 176 HIS L 233 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.161754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114642 restraints weight = 57465.249| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.39 r_work: 0.3219 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 21480 Z= 0.196 Angle : 0.448 4.363 28440 Z= 0.232 Chirality : 0.038 0.118 3012 Planarity : 0.004 0.031 3288 Dihedral : 8.493 55.446 4284 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.57 % Allowed : 10.71 % Favored : 86.71 % 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: 3.11 (0.17), residues: 2256 helix: 2.93 (0.12), residues: 1716 sheet: -0.66 (0.37), residues: 132 loop : -1.04 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 193 HIS 0.015 0.002 HIS E 176 PHE 0.017 0.001 PHE C 202 TYR 0.009 0.002 TYR A 66 ARG 0.005 0.000 ARG I 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12659.52 seconds wall clock time: 224 minutes 16.18 seconds (13456.18 seconds total)