Starting phenix.real_space_refine on Sat Mar 23 21:14:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/03_2024/7jsx_22462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/03_2024/7jsx_22462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/03_2024/7jsx_22462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/03_2024/7jsx_22462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/03_2024/7jsx_22462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsx_22462/03_2024/7jsx_22462_updated.pdb" } resolution = 2.06 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 23856 2.51 5 N 6632 2.21 5 O 8045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ASP 28": "OD1" <-> "OD2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 187": "NH1" <-> "NH2" Residue "G PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 305": "NH1" <-> "NH2" Residue "G PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 360": "NH1" <-> "NH2" Residue "H PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "I ARG 21": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "I TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 187": "NH1" <-> "NH2" Residue "I PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 305": "NH1" <-> "NH2" Residue "I PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 360": "NH1" <-> "NH2" Residue "J PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 125": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 131": "NH1" <-> "NH2" Residue "K ARG 187": "NH1" <-> "NH2" Residue "K PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 305": "NH1" <-> "NH2" Residue "K PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 360": "NH1" <-> "NH2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 125": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 79": "NH1" <-> "NH2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 305": "NH1" <-> "NH2" Residue "M PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 360": "NH1" <-> "NH2" Residue "N PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 84": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 125": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 79": "NH1" <-> "NH2" Residue "O TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 131": "NH1" <-> "NH2" Residue "O ARG 187": "NH1" <-> "NH2" Residue "O PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 360": "NH1" <-> "NH2" Residue "P PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "P ARG 91": "NH1" <-> "NH2" Residue "P TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 125": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38813 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "C" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "E" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "G" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "K" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "M" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "N" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "O" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'SMC:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "q" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "r" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "s" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "t" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "u" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "v" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "w" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "x" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "E" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "K" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "M" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "O" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "P" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Time building chain proxies: 19.33, per 1000 atoms: 0.50 Number of scatterers: 38813 At special positions: 0 Unit cell: (142.636, 142.636, 139.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 280 16.00 O 8045 8.00 N 6632 7.00 C 23856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS C 247 " distance=2.19 Simple disulfide: pdb=" SG CYS E 247 " - pdb=" SG CYS G 247 " distance=2.20 Simple disulfide: pdb=" SG CYS I 247 " - pdb=" SG CYS K 247 " distance=2.20 Simple disulfide: pdb=" SG CYS M 247 " - pdb=" SG CYS O 247 " distance=2.15 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.64 Conformation dependent library (CDL) restraints added in 6.3 seconds 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 32 sheets defined 38.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.97 Creating SS restraints... Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 142 through 147 removed outlier: 4.229A pdb=" N THR A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 405 through 408 No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 413 through 432 Processing helix chain 'A' and resid 437 through 451 removed outlier: 6.358A pdb=" N GLY A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 113 through 121 Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 142 through 147 removed outlier: 4.225A pdb=" N THR C 147 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 269 through 272 No H-bonds generated for 'chain 'C' and resid 269 through 272' Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 336 through 350 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 405 through 408 No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 413 through 432 Processing helix chain 'C' and resid 437 through 451 removed outlier: 6.348A pdb=" N GLY C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 460 Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 86 through 99 Processing helix chain 'E' and resid 50 through 59 Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 142 through 147 removed outlier: 4.226A pdb=" N THR E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 Processing helix chain 'E' and resid 182 through 194 Processing helix chain 'E' and resid 214 through 232 Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'E' and resid 269 through 272 No H-bonds generated for 'chain 'E' and resid 269 through 272' Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 311 through 321 Processing helix chain 'E' and resid 336 through 350 Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 387 through 394 Processing helix chain 'E' and resid 405 through 408 No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 413 through 432 Processing helix chain 'E' and resid 437 through 451 removed outlier: 6.385A pdb=" N GLY E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP E 443 " --> pdb=" O ARG E 439 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 460 Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 47 through 50 No H-bonds generated for 'chain 'F' and resid 47 through 50' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 86 through 99 Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 142 through 147 removed outlier: 4.217A pdb=" N THR G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 182 through 194 Processing helix chain 'G' and resid 214 through 232 Processing helix chain 'G' and resid 247 through 258 Processing helix chain 'G' and resid 269 through 272 No H-bonds generated for 'chain 'G' and resid 269 through 272' Processing helix chain 'G' and resid 274 through 287 Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 311 through 321 Processing helix chain 'G' and resid 336 through 350 Processing helix chain 'G' and resid 358 through 360 No H-bonds generated for 'chain 'G' and resid 358 through 360' Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 405 through 408 No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 413 through 432 Processing helix chain 'G' and resid 437 through 451 removed outlier: 6.377A pdb=" N GLY G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP G 443 " --> pdb=" O ARG G 439 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP G 451 " --> pdb=" O SER G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 460 Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 47 through 50 No H-bonds generated for 'chain 'H' and resid 47 through 50' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 86 through 99 Processing helix chain 'I' and resid 50 through 59 Processing helix chain 'I' and resid 105 through 107 No H-bonds generated for 'chain 'I' and resid 105 through 107' Processing helix chain 'I' and resid 113 through 121 Processing helix chain 'I' and resid 124 through 126 No H-bonds generated for 'chain 'I' and resid 124 through 126' Processing helix chain 'I' and resid 142 through 147 removed outlier: 4.217A pdb=" N THR I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 162 Processing helix chain 'I' and resid 182 through 194 Processing helix chain 'I' and resid 214 through 232 Processing helix chain 'I' and resid 247 through 258 Processing helix chain 'I' and resid 269 through 272 No H-bonds generated for 'chain 'I' and resid 269 through 272' Processing helix chain 'I' and resid 274 through 287 Processing helix chain 'I' and resid 298 through 302 Processing helix chain 'I' and resid 311 through 321 Processing helix chain 'I' and resid 336 through 350 Processing helix chain 'I' and resid 358 through 360 No H-bonds generated for 'chain 'I' and resid 358 through 360' Processing helix chain 'I' and resid 387 through 394 Processing helix chain 'I' and resid 405 through 408 No H-bonds generated for 'chain 'I' and resid 405 through 408' Processing helix chain 'I' and resid 413 through 432 Processing helix chain 'I' and resid 437 through 451 removed outlier: 6.378A pdb=" N GLY I 442 " --> pdb=" O ALA I 438 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP I 443 " --> pdb=" O ARG I 439 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP I 451 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 460 Processing helix chain 'J' and resid 23 through 35 Processing helix chain 'J' and resid 47 through 50 No H-bonds generated for 'chain 'J' and resid 47 through 50' Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'J' and resid 86 through 99 Processing helix chain 'K' and resid 50 through 59 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 121 Processing helix chain 'K' and resid 124 through 126 No H-bonds generated for 'chain 'K' and resid 124 through 126' Processing helix chain 'K' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR K 147 " --> pdb=" O ALA K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 162 Processing helix chain 'K' and resid 182 through 194 Processing helix chain 'K' and resid 214 through 232 Processing helix chain 'K' and resid 247 through 258 Processing helix chain 'K' and resid 269 through 272 No H-bonds generated for 'chain 'K' and resid 269 through 272' Processing helix chain 'K' and resid 274 through 287 Processing helix chain 'K' and resid 298 through 302 Processing helix chain 'K' and resid 311 through 321 Processing helix chain 'K' and resid 336 through 350 Processing helix chain 'K' and resid 358 through 360 No H-bonds generated for 'chain 'K' and resid 358 through 360' Processing helix chain 'K' and resid 387 through 394 Processing helix chain 'K' and resid 405 through 408 No H-bonds generated for 'chain 'K' and resid 405 through 408' Processing helix chain 'K' and resid 413 through 432 Processing helix chain 'K' and resid 437 through 451 removed outlier: 6.409A pdb=" N GLY K 442 " --> pdb=" O ALA K 438 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP K 443 " --> pdb=" O ARG K 439 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS K 450 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP K 451 " --> pdb=" O SER K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 460 Processing helix chain 'L' and resid 23 through 35 Processing helix chain 'L' and resid 47 through 50 No H-bonds generated for 'chain 'L' and resid 47 through 50' Processing helix chain 'L' and resid 55 through 59 Processing helix chain 'L' and resid 86 through 99 Processing helix chain 'M' and resid 50 through 59 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 113 through 121 Processing helix chain 'M' and resid 124 through 126 No H-bonds generated for 'chain 'M' and resid 124 through 126' Processing helix chain 'M' and resid 142 through 147 removed outlier: 4.232A pdb=" N THR M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 162 Processing helix chain 'M' and resid 182 through 194 Processing helix chain 'M' and resid 214 through 232 Processing helix chain 'M' and resid 247 through 258 Processing helix chain 'M' and resid 269 through 272 No H-bonds generated for 'chain 'M' and resid 269 through 272' Processing helix chain 'M' and resid 274 through 287 Processing helix chain 'M' and resid 298 through 302 Processing helix chain 'M' and resid 311 through 321 Processing helix chain 'M' and resid 336 through 350 Processing helix chain 'M' and resid 358 through 360 No H-bonds generated for 'chain 'M' and resid 358 through 360' Processing helix chain 'M' and resid 387 through 394 Processing helix chain 'M' and resid 405 through 408 No H-bonds generated for 'chain 'M' and resid 405 through 408' Processing helix chain 'M' and resid 413 through 432 Processing helix chain 'M' and resid 437 through 451 removed outlier: 6.387A pdb=" N GLY M 442 " --> pdb=" O ALA M 438 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP M 443 " --> pdb=" O ARG M 439 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP M 451 " --> pdb=" O SER M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 460 Processing helix chain 'N' and resid 23 through 35 Processing helix chain 'N' and resid 47 through 50 No H-bonds generated for 'chain 'N' and resid 47 through 50' Processing helix chain 'N' and resid 55 through 59 Processing helix chain 'N' and resid 86 through 99 Processing helix chain 'O' and resid 50 through 59 Processing helix chain 'O' and resid 105 through 107 No H-bonds generated for 'chain 'O' and resid 105 through 107' Processing helix chain 'O' and resid 113 through 121 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 142 through 147 removed outlier: 4.231A pdb=" N THR O 147 " --> pdb=" O ALA O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 162 Processing helix chain 'O' and resid 182 through 194 Processing helix chain 'O' and resid 214 through 232 Processing helix chain 'O' and resid 247 through 258 Processing helix chain 'O' and resid 269 through 272 No H-bonds generated for 'chain 'O' and resid 269 through 272' Processing helix chain 'O' and resid 274 through 287 Processing helix chain 'O' and resid 298 through 302 Processing helix chain 'O' and resid 311 through 321 Processing helix chain 'O' and resid 336 through 350 Processing helix chain 'O' and resid 358 through 360 No H-bonds generated for 'chain 'O' and resid 358 through 360' Processing helix chain 'O' and resid 387 through 394 Processing helix chain 'O' and resid 405 through 408 No H-bonds generated for 'chain 'O' and resid 405 through 408' Processing helix chain 'O' and resid 413 through 432 Processing helix chain 'O' and resid 437 through 451 removed outlier: 6.349A pdb=" N GLY O 442 " --> pdb=" O ALA O 438 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP O 443 " --> pdb=" O ARG O 439 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP O 451 " --> pdb=" O SER O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 460 Processing helix chain 'P' and resid 23 through 35 Processing helix chain 'P' and resid 47 through 50 No H-bonds generated for 'chain 'P' and resid 47 through 50' Processing helix chain 'P' and resid 55 through 59 Processing helix chain 'P' and resid 86 through 99 Processing helix chain 'q' and resid 126 through 134 Processing helix chain 'r' and resid 126 through 134 Processing helix chain 's' and resid 126 through 134 Processing helix chain 't' and resid 126 through 134 Processing helix chain 'u' and resid 126 through 134 Processing helix chain 'v' and resid 126 through 134 Processing helix chain 'w' and resid 126 through 134 Processing helix chain 'x' and resid 126 through 134 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 139 removed outlier: 6.737A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 239 removed outlier: 4.048A pdb=" N THR A 173 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.235A pdb=" N LEU A 290 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS A 267 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS A 292 " --> pdb=" O HIS A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU B 42 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU B 107 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 122 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA B 109 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLY B 120 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 132 through 139 removed outlier: 6.734A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.654A pdb=" N THR C 173 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.234A pdb=" N LEU C 290 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS C 267 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS C 292 " --> pdb=" O HIS C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 74 through 76 removed outlier: 4.650A pdb=" N LEU D 42 " --> pdb=" O TRP D 76 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU D 107 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU D 122 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA D 109 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY D 120 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 132 through 139 removed outlier: 6.733A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 237 through 239 removed outlier: 3.672A pdb=" N THR E 173 " --> pdb=" O PHE E 402 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN E 401 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA E 378 " --> pdb=" O GLN E 401 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 264 through 268 removed outlier: 6.233A pdb=" N LEU E 290 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N HIS E 267 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS E 292 " --> pdb=" O HIS E 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 74 through 76 removed outlier: 4.656A pdb=" N LEU F 42 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU F 107 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU F 122 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA F 109 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLY F 120 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 132 through 139 removed outlier: 6.732A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 237 through 239 removed outlier: 3.694A pdb=" N THR G 173 " --> pdb=" O PHE G 402 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLN G 401 " --> pdb=" O PRO G 376 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA G 378 " --> pdb=" O GLN G 401 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 264 through 268 removed outlier: 6.233A pdb=" N LEU G 290 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N HIS G 267 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS G 292 " --> pdb=" O HIS G 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 74 through 76 removed outlier: 4.652A pdb=" N LEU H 42 " --> pdb=" O TRP H 76 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU H 107 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU H 122 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA H 109 " --> pdb=" O GLY H 120 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY H 120 " --> pdb=" O ALA H 109 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 132 through 139 removed outlier: 6.736A pdb=" N ALA I 39 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU I 138 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU I 37 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP I 86 " --> pdb=" O TYR I 100 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 237 through 239 removed outlier: 3.662A pdb=" N THR I 173 " --> pdb=" O PHE I 402 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN I 401 " --> pdb=" O PRO I 376 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA I 378 " --> pdb=" O GLN I 401 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 264 through 268 removed outlier: 6.231A pdb=" N LEU I 290 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N HIS I 267 " --> pdb=" O LEU I 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS I 292 " --> pdb=" O HIS I 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'J' and resid 74 through 76 removed outlier: 4.660A pdb=" N LEU J 42 " --> pdb=" O TRP J 76 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU J 107 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU J 122 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA J 109 " --> pdb=" O GLY J 120 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY J 120 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 132 through 139 removed outlier: 6.734A pdb=" N ALA K 39 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU K 138 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU K 37 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP K 86 " --> pdb=" O TYR K 100 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA K 102 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS K 84 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 237 through 239 removed outlier: 3.646A pdb=" N THR K 173 " --> pdb=" O PHE K 402 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN K 401 " --> pdb=" O PRO K 376 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA K 378 " --> pdb=" O GLN K 401 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 264 through 268 removed outlier: 6.236A pdb=" N LEU K 290 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS K 267 " --> pdb=" O LEU K 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS K 292 " --> pdb=" O HIS K 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 74 through 76 removed outlier: 4.648A pdb=" N LEU L 42 " --> pdb=" O TRP L 76 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU L 107 " --> pdb=" O LEU L 122 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU L 122 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA L 109 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLY L 120 " --> pdb=" O ALA L 109 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 132 through 139 removed outlier: 6.737A pdb=" N ALA M 39 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU M 138 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU M 37 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP M 86 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA M 102 " --> pdb=" O CYS M 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS M 84 " --> pdb=" O ALA M 102 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 237 through 239 removed outlier: 3.658A pdb=" N THR M 173 " --> pdb=" O PHE M 402 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN M 401 " --> pdb=" O PRO M 376 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA M 378 " --> pdb=" O GLN M 401 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 264 through 268 removed outlier: 6.244A pdb=" N LEU M 290 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS M 267 " --> pdb=" O LEU M 290 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS M 292 " --> pdb=" O HIS M 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'N' and resid 74 through 76 removed outlier: 4.645A pdb=" N LEU N 42 " --> pdb=" O TRP N 76 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU N 107 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU N 122 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA N 109 " --> pdb=" O GLY N 120 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY N 120 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 132 through 139 removed outlier: 6.740A pdb=" N ALA O 39 " --> pdb=" O GLU O 136 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU O 138 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU O 37 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP O 86 " --> pdb=" O TYR O 100 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA O 102 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N CYS O 84 " --> pdb=" O ALA O 102 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 237 through 239 removed outlier: 3.659A pdb=" N THR O 173 " --> pdb=" O PHE O 402 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN O 401 " --> pdb=" O PRO O 376 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA O 378 " --> pdb=" O GLN O 401 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 264 through 268 removed outlier: 6.244A pdb=" N LEU O 290 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N HIS O 267 " --> pdb=" O LEU O 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS O 292 " --> pdb=" O HIS O 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'P' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU P 42 " --> pdb=" O TRP P 76 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU P 107 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU P 122 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA P 109 " --> pdb=" O GLY P 120 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY P 120 " --> pdb=" O ALA P 109 " (cutoff:3.500A) 1406 hydrogen bonds defined for protein. 4023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.66 Time building geometry restraints manager: 16.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 6504 1.30 - 1.44: 10625 1.44 - 1.58: 20677 1.58 - 1.72: 351 1.72 - 1.86: 427 Bond restraints: 38584 Sorted by residual: bond pdb=" SD MET E 266 " pdb=" CE MET E 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET O 266 " pdb=" CE MET O 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET K 266 " pdb=" CE MET K 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" SD MET M 266 " pdb=" CE MET M 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" SD MET G 266 " pdb=" CE MET G 266 " ideal model delta sigma weight residual 1.791 1.657 0.134 2.50e-02 1.60e+03 2.88e+01 ... (remaining 38579 not shown) Histogram of bond angle deviations from ideal: 92.55 - 100.97: 76 100.97 - 109.40: 5019 109.40 - 117.83: 22860 117.83 - 126.26: 23586 126.26 - 134.69: 771 Bond angle restraints: 52312 Sorted by residual: angle pdb=" N TRP I 66 " pdb=" CA TRP I 66 " pdb=" C TRP I 66 " ideal model delta sigma weight residual 111.36 124.01 -12.65 1.09e+00 8.42e-01 1.35e+02 angle pdb=" N TRP M 66 " pdb=" CA TRP M 66 " pdb=" C TRP M 66 " ideal model delta sigma weight residual 111.36 123.73 -12.37 1.09e+00 8.42e-01 1.29e+02 angle pdb=" N TRP O 66 " pdb=" CA TRP O 66 " pdb=" C TRP O 66 " ideal model delta sigma weight residual 111.36 123.51 -12.15 1.09e+00 8.42e-01 1.24e+02 angle pdb=" N TRP A 66 " pdb=" CA TRP A 66 " pdb=" C TRP A 66 " ideal model delta sigma weight residual 111.36 119.71 -8.35 1.09e+00 8.42e-01 5.87e+01 angle pdb=" N TRP K 66 " pdb=" CA TRP K 66 " pdb=" C TRP K 66 " ideal model delta sigma weight residual 111.36 119.63 -8.27 1.09e+00 8.42e-01 5.76e+01 ... (remaining 52307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 20477 14.24 - 28.49: 2049 28.49 - 42.73: 306 42.73 - 56.97: 88 56.97 - 71.21: 44 Dihedral angle restraints: 22964 sinusoidal: 9084 harmonic: 13880 Sorted by residual: dihedral pdb=" CB CYS M 247 " pdb=" SG CYS M 247 " pdb=" SG CYS O 247 " pdb=" CB CYS O 247 " ideal model delta sinusoidal sigma weight residual -86.00 -36.93 -49.07 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " pdb=" SG CYS C 247 " pdb=" CB CYS C 247 " ideal model delta sinusoidal sigma weight residual -86.00 -37.59 -48.41 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CA PHE H 60 " pdb=" C PHE H 60 " pdb=" N GLY H 61 " pdb=" CA GLY H 61 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 22961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4358 0.114 - 0.228: 949 0.228 - 0.342: 193 0.342 - 0.456: 68 0.456 - 0.569: 8 Chirality restraints: 5576 Sorted by residual: chirality pdb=" CB ILE G 301 " pdb=" CA ILE G 301 " pdb=" CG1 ILE G 301 " pdb=" CG2 ILE G 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CB ILE K 301 " pdb=" CA ILE K 301 " pdb=" CG1 ILE K 301 " pdb=" CG2 ILE K 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CB ILE E 301 " pdb=" CA ILE E 301 " pdb=" CG1 ILE E 301 " pdb=" CG2 ILE E 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.92e+00 ... (remaining 5573 not shown) Planarity restraints: 6856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 153 " 0.066 2.00e-02 2.50e+03 5.82e-02 5.08e+01 pdb=" CG HIS I 153 " -0.102 2.00e-02 2.50e+03 pdb=" ND1 HIS I 153 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS I 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS I 153 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS I 153 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 153 " -0.066 2.00e-02 2.50e+03 5.81e-02 5.07e+01 pdb=" CG HIS G 153 " 0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS G 153 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS G 153 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS G 153 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS G 153 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 153 " 0.065 2.00e-02 2.50e+03 5.78e-02 5.02e+01 pdb=" CG HIS E 153 " -0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS E 153 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS E 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS E 153 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS E 153 " 0.067 2.00e-02 2.50e+03 ... (remaining 6853 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4280 2.74 - 3.28: 40498 3.28 - 3.82: 74775 3.82 - 4.36: 92597 4.36 - 4.90: 145182 Nonbonded interactions: 357332 Sorted by model distance: nonbonded pdb=" NE2 GLN G 156 " pdb=" OD2 ASP G 160 " model vdw 2.201 2.520 nonbonded pdb=" NE2 GLN O 156 " pdb=" OD2 ASP O 160 " model vdw 2.203 2.520 nonbonded pdb=" NE2 GLN I 156 " pdb=" OD2 ASP I 160 " model vdw 2.205 2.520 nonbonded pdb=" NE2 GLN C 156 " pdb=" OD2 ASP C 160 " model vdw 2.206 2.520 nonbonded pdb=" NE2 GLN E 156 " pdb=" OD2 ASP E 160 " model vdw 2.206 2.520 ... (remaining 357327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.910 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 99.060 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 38584 Z= 1.423 Angle : 1.671 12.654 52312 Z= 0.981 Chirality : 0.110 0.569 5576 Planarity : 0.014 0.064 6856 Dihedral : 11.972 71.215 14088 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.26 % Allowed : 4.01 % Favored : 94.73 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.11), residues: 4760 helix: -0.73 (0.10), residues: 1872 sheet: -0.23 (0.19), residues: 784 loop : -0.64 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.008 TRP M 214 HIS 0.050 0.011 HIS M 153 PHE 0.103 0.012 PHE I 148 TYR 0.083 0.011 TYR O 363 ARG 0.033 0.005 ARG G 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 805 time to evaluate : 4.687 Fit side-chains revert: symmetry clash REVERT: q 131 GLU cc_start: 0.4096 (OUTLIER) cc_final: 0.3686 (tp30) REVERT: r 131 GLU cc_start: 0.4148 (OUTLIER) cc_final: 0.3553 (tp30) REVERT: s 131 GLU cc_start: 0.4028 (OUTLIER) cc_final: 0.3457 (tp30) REVERT: u 131 GLU cc_start: 0.4235 (OUTLIER) cc_final: 0.3671 (tp30) REVERT: v 131 GLU cc_start: 0.4077 (OUTLIER) cc_final: 0.3505 (tp30) REVERT: w 131 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.3970 (tp30) REVERT: x 131 GLU cc_start: 0.4121 (OUTLIER) cc_final: 0.3541 (tp30) outliers start: 49 outliers final: 3 residues processed: 848 average time/residue: 1.7014 time to fit residues: 1710.4991 Evaluate side-chains 610 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 600 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain r residue 131 GLU Chi-restraints excluded: chain s residue 131 GLU Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain u residue 131 GLU Chi-restraints excluded: chain v residue 131 GLU Chi-restraints excluded: chain w residue 131 GLU Chi-restraints excluded: chain x residue 131 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 369 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 428 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 207 ASN A 238 HIS A 241 ASN A 267 HIS A 277 ASN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN B 8 ASN B 9 ASN B 29 GLN B 36 ASN C 115 ASN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 207 ASN C 238 HIS C 241 ASN C 267 HIS C 277 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN C 432 ASN D 8 ASN D 9 ASN D 29 GLN D 36 ASN E 96 GLN E 115 ASN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 207 ASN E 238 HIS E 241 ASN E 267 HIS E 277 ASN E 420 ASN E 432 ASN F 8 ASN F 9 ASN F 29 GLN F 36 ASN G 115 ASN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 207 ASN G 238 HIS G 241 ASN G 267 HIS G 277 ASN G 432 ASN H 8 ASN H 9 ASN H 29 GLN H 36 ASN H 115 GLN I 115 ASN I 123 ASN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN I 207 ASN I 238 HIS I 241 ASN I 267 HIS I 277 ASN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 432 ASN J 8 ASN J 9 ASN J 29 GLN J 36 ASN K 96 GLN K 115 ASN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 ASN K 207 ASN K 238 HIS K 241 ASN K 267 HIS K 277 ASN K 420 ASN K 432 ASN L 8 ASN L 9 ASN L 29 GLN M 96 GLN M 115 ASN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN M 207 ASN M 238 HIS M 241 ASN M 267 HIS M 277 ASN M 420 ASN M 432 ASN N 8 ASN N 9 ASN N 29 GLN N 36 ASN O 115 ASN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 163 ASN O 207 ASN O 238 HIS O 241 ASN O 267 HIS O 277 ASN O 432 ASN P 8 ASN P 9 ASN P 29 GLN P 36 ASN Total number of N/Q/H flips: 112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 38584 Z= 0.238 Angle : 0.648 6.041 52312 Z= 0.348 Chirality : 0.044 0.193 5576 Planarity : 0.005 0.038 6856 Dihedral : 5.898 46.070 5370 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.64 % Allowed : 6.87 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4760 helix: 0.98 (0.11), residues: 1856 sheet: 0.37 (0.19), residues: 680 loop : 0.00 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 368 HIS 0.009 0.002 HIS C 153 PHE 0.037 0.003 PHE I 345 TYR 0.014 0.002 TYR I 226 ARG 0.006 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 695 time to evaluate : 4.471 Fit side-chains REVERT: B 66 LEU cc_start: 0.8707 (mt) cc_final: 0.8460 (mt) REVERT: D 66 LEU cc_start: 0.8766 (mt) cc_final: 0.8520 (mt) REVERT: F 66 LEU cc_start: 0.8736 (mt) cc_final: 0.8479 (mt) REVERT: H 66 LEU cc_start: 0.8754 (mt) cc_final: 0.8497 (mt) REVERT: I 130 LEU cc_start: 0.8193 (mt) cc_final: 0.7560 (mt) REVERT: J 66 LEU cc_start: 0.8765 (mt) cc_final: 0.8524 (mt) REVERT: N 66 LEU cc_start: 0.8778 (mt) cc_final: 0.8536 (mt) REVERT: N 68 TYR cc_start: 0.8515 (m-80) cc_final: 0.8311 (m-80) REVERT: P 66 LEU cc_start: 0.8714 (mt) cc_final: 0.8455 (mt) outliers start: 25 outliers final: 10 residues processed: 696 average time/residue: 1.7765 time to fit residues: 1461.3596 Evaluate side-chains 657 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 647 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain O residue 447 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 356 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 463 optimal weight: 8.9990 chunk 382 optimal weight: 7.9990 chunk 425 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 123 ASN A 420 ASN A 429 GLN B 36 ASN C 45 GLN C 123 ASN C 429 GLN D 8 ASN D 36 ASN D 124 GLN E 45 GLN E 123 ASN E 429 GLN F 36 ASN F 124 GLN G 45 GLN G 123 ASN G 156 GLN G 420 ASN G 429 GLN H 36 ASN H 124 GLN I 45 GLN I 123 ASN I 429 GLN J 36 ASN J 124 GLN K 45 GLN K 123 ASN K 429 GLN L 8 ASN L 36 ASN M 45 GLN M 96 GLN M 123 ASN M 429 GLN N 36 ASN N 124 GLN O 45 GLN O 123 ASN O 420 ASN O 429 GLN P 8 ASN P 36 ASN P 124 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 38584 Z= 0.434 Angle : 0.791 8.056 52312 Z= 0.425 Chirality : 0.051 0.224 5576 Planarity : 0.006 0.045 6856 Dihedral : 5.952 43.607 5345 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.93 % Allowed : 7.07 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 4760 helix: 0.98 (0.11), residues: 1904 sheet: -0.08 (0.18), residues: 744 loop : 0.07 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 368 HIS 0.020 0.004 HIS M 153 PHE 0.038 0.005 PHE O 345 TYR 0.024 0.003 TYR D 67 ARG 0.011 0.001 ARG O 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 717 time to evaluate : 4.139 Fit side-chains REVERT: C 305 ARG cc_start: 0.7708 (tpt170) cc_final: 0.7226 (tpt170) REVERT: E 305 ARG cc_start: 0.7771 (tpt170) cc_final: 0.7209 (tpp80) REVERT: G 305 ARG cc_start: 0.7720 (tpt170) cc_final: 0.7187 (tpp80) REVERT: I 42 MET cc_start: 0.8547 (mtm) cc_final: 0.8287 (mtp) REVERT: K 42 MET cc_start: 0.8510 (mtm) cc_final: 0.8301 (mtp) outliers start: 36 outliers final: 15 residues processed: 730 average time/residue: 1.8007 time to fit residues: 1547.4545 Evaluate side-chains 690 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 675 time to evaluate : 4.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 252 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 0.9980 chunk 322 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 288 optimal weight: 0.6980 chunk 430 optimal weight: 6.9990 chunk 456 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 408 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN D 36 ASN E 123 ASN E 153 HIS F 36 ASN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 123 ASN J 36 ASN K 96 GLN K 123 ASN L 36 ASN M 96 GLN M 123 ASN M 153 HIS N 36 ASN O 123 ASN P 36 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38584 Z= 0.196 Angle : 0.573 5.680 52312 Z= 0.305 Chirality : 0.043 0.182 5576 Planarity : 0.004 0.044 6856 Dihedral : 5.320 43.407 5345 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.46 % Allowed : 7.95 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.12), residues: 4760 helix: 1.35 (0.12), residues: 1904 sheet: 0.25 (0.19), residues: 688 loop : 0.18 (0.14), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 368 HIS 0.011 0.002 HIS K 153 PHE 0.035 0.002 PHE G 345 TYR 0.012 0.002 TYR O 269 ARG 0.008 0.001 ARG G 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 707 time to evaluate : 4.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8731 (mt) cc_final: 0.8498 (mt) REVERT: C 305 ARG cc_start: 0.7629 (tpt170) cc_final: 0.7159 (tpt170) REVERT: E 305 ARG cc_start: 0.7683 (tpt170) cc_final: 0.7294 (tpp80) REVERT: F 66 LEU cc_start: 0.8759 (mt) cc_final: 0.8529 (mt) REVERT: G 305 ARG cc_start: 0.7676 (tpt170) cc_final: 0.7231 (tpp80) REVERT: G 375 MET cc_start: 0.7969 (tpp) cc_final: 0.7746 (tpp) REVERT: H 66 LEU cc_start: 0.8761 (mt) cc_final: 0.8536 (mt) REVERT: I 305 ARG cc_start: 0.7688 (tpt170) cc_final: 0.7255 (tpp80) REVERT: I 375 MET cc_start: 0.7957 (tpp) cc_final: 0.7736 (tpp) REVERT: J 66 LEU cc_start: 0.8789 (mt) cc_final: 0.8565 (mt) REVERT: M 305 ARG cc_start: 0.7620 (tpt170) cc_final: 0.7003 (tpp80) REVERT: N 66 LEU cc_start: 0.8804 (mt) cc_final: 0.8566 (mt) REVERT: O 305 ARG cc_start: 0.7585 (tpt170) cc_final: 0.6994 (tpp80) REVERT: O 387 MET cc_start: 0.8496 (tpp) cc_final: 0.8281 (tpp) REVERT: P 66 LEU cc_start: 0.8746 (mt) cc_final: 0.8506 (mt) outliers start: 18 outliers final: 5 residues processed: 712 average time/residue: 1.8279 time to fit residues: 1533.4291 Evaluate side-chains 681 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 676 time to evaluate : 4.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain O residue 252 LYS Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 389 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 409 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 123 ASN A 304 GLN A 401 GLN B 36 ASN C 95 ASN C 123 ASN C 401 GLN D 36 ASN E 96 GLN E 123 ASN E 401 GLN F 36 ASN G 95 ASN G 123 ASN G 401 GLN H 36 ASN I 95 ASN I 123 ASN I 401 GLN J 36 ASN K 95 ASN K 96 GLN K 123 ASN K 401 GLN L 36 ASN M 95 ASN M 96 GLN M 123 ASN M 401 GLN N 36 ASN O 123 ASN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 401 GLN P 36 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 38584 Z= 0.574 Angle : 0.881 10.129 52312 Z= 0.474 Chirality : 0.056 0.245 5576 Planarity : 0.007 0.059 6856 Dihedral : 6.185 43.864 5345 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.21 % Allowed : 7.41 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.12), residues: 4760 helix: 0.70 (0.11), residues: 1952 sheet: -0.35 (0.18), residues: 720 loop : 0.37 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 368 HIS 0.019 0.004 HIS K 153 PHE 0.041 0.005 PHE O 345 TYR 0.028 0.004 TYR B 67 ARG 0.014 0.002 ARG O 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 689 time to evaluate : 4.572 Fit side-chains REVERT: C 305 ARG cc_start: 0.7721 (tpt170) cc_final: 0.7360 (tpp80) REVERT: D 68 TYR cc_start: 0.8592 (m-80) cc_final: 0.8322 (m-80) REVERT: E 305 ARG cc_start: 0.7745 (tpt170) cc_final: 0.7408 (tpp80) REVERT: G 305 ARG cc_start: 0.7745 (tpt170) cc_final: 0.7411 (tpp80) REVERT: I 305 ARG cc_start: 0.7722 (tpt170) cc_final: 0.7335 (tpp80) REVERT: J 68 TYR cc_start: 0.8581 (m-80) cc_final: 0.8335 (m-80) REVERT: K 305 ARG cc_start: 0.7743 (tpt170) cc_final: 0.7356 (tpp80) REVERT: M 305 ARG cc_start: 0.7707 (tpt170) cc_final: 0.7322 (tpp80) REVERT: N 68 TYR cc_start: 0.8570 (m-80) cc_final: 0.8277 (m-80) REVERT: O 305 ARG cc_start: 0.7654 (tpt170) cc_final: 0.7214 (tpp80) outliers start: 47 outliers final: 37 residues processed: 727 average time/residue: 1.8346 time to fit residues: 1582.1452 Evaluate side-chains 704 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 667 time to evaluate : 4.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 252 LYS Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain w residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 4.9990 chunk 410 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 456 optimal weight: 0.9980 chunk 379 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 36 ASN B 115 GLN C 123 ASN C 156 GLN D 36 ASN E 96 GLN F 36 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN J 36 ASN K 96 GLN L 36 ASN M 96 GLN N 36 ASN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38584 Z= 0.202 Angle : 0.588 5.804 52312 Z= 0.312 Chirality : 0.043 0.186 5576 Planarity : 0.004 0.032 6856 Dihedral : 5.421 43.006 5345 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.69 % Allowed : 8.31 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.12), residues: 4760 helix: 1.26 (0.12), residues: 1904 sheet: -0.40 (0.19), residues: 656 loop : 0.47 (0.14), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 368 HIS 0.011 0.002 HIS I 153 PHE 0.034 0.002 PHE I 345 TYR 0.013 0.002 TYR F 32 ARG 0.004 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 700 time to evaluate : 4.294 Fit side-chains revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8740 (mt) cc_final: 0.8489 (mt) REVERT: C 305 ARG cc_start: 0.7672 (tpt170) cc_final: 0.7281 (tpp80) REVERT: E 305 ARG cc_start: 0.7712 (tpt170) cc_final: 0.7271 (tpp80) REVERT: F 66 LEU cc_start: 0.8768 (mt) cc_final: 0.8541 (mt) REVERT: G 305 ARG cc_start: 0.7695 (tpt170) cc_final: 0.7306 (tpp80) REVERT: G 375 MET cc_start: 0.7982 (tpp) cc_final: 0.7762 (tpp) REVERT: I 305 ARG cc_start: 0.7678 (tpt170) cc_final: 0.7238 (tpp80) REVERT: I 375 MET cc_start: 0.7956 (tpp) cc_final: 0.7739 (tpp) REVERT: K 305 ARG cc_start: 0.7695 (tpt170) cc_final: 0.7306 (mmp-170) REVERT: M 305 ARG cc_start: 0.7648 (tpt170) cc_final: 0.7130 (tpp80) REVERT: O 305 ARG cc_start: 0.7625 (tpt170) cc_final: 0.7128 (tpp80) outliers start: 27 outliers final: 20 residues processed: 723 average time/residue: 1.8215 time to fit residues: 1549.4945 Evaluate side-chains 694 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 674 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain F residue 137 LYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 252 LYS Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 258 optimal weight: 20.0000 chunk 384 optimal weight: 9.9990 chunk 255 optimal weight: 3.9990 chunk 454 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 156 GLN B 36 ASN C 123 ASN D 36 ASN D 115 GLN E 96 GLN E 123 ASN E 156 GLN E 401 GLN F 36 ASN G 96 GLN G 123 ASN G 156 GLN H 36 ASN I 96 GLN I 123 ASN I 156 GLN I 401 GLN J 36 ASN K 123 ASN K 156 GLN L 36 ASN M 96 GLN M 123 ASN M 156 GLN N 36 ASN O 123 ASN O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 38584 Z= 0.293 Angle : 0.661 6.497 52312 Z= 0.352 Chirality : 0.046 0.212 5576 Planarity : 0.005 0.034 6856 Dihedral : 5.571 42.311 5345 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.98 % Allowed : 8.18 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 4760 helix: 1.18 (0.12), residues: 1904 sheet: -0.36 (0.18), residues: 744 loop : 0.50 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 368 HIS 0.015 0.003 HIS A 153 PHE 0.034 0.003 PHE I 345 TYR 0.017 0.003 TYR N 32 ARG 0.006 0.001 ARG G 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 691 time to evaluate : 4.443 Fit side-chains revert: symmetry clash REVERT: C 305 ARG cc_start: 0.7675 (tpt170) cc_final: 0.7283 (tpp80) REVERT: E 305 ARG cc_start: 0.7709 (tpt170) cc_final: 0.7278 (tpp80) REVERT: G 305 ARG cc_start: 0.7711 (tpt170) cc_final: 0.7326 (tpp80) REVERT: I 305 ARG cc_start: 0.7678 (tpt170) cc_final: 0.7249 (tpp80) REVERT: K 305 ARG cc_start: 0.7701 (tpt170) cc_final: 0.7262 (tpp80) REVERT: M 305 ARG cc_start: 0.7661 (tpt170) cc_final: 0.7205 (tpp80) REVERT: O 305 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7116 (tpp80) outliers start: 38 outliers final: 30 residues processed: 725 average time/residue: 1.7922 time to fit residues: 1534.9673 Evaluate side-chains 707 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 677 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain F residue 137 LYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 252 LYS Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 252 LYS Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 309 optimal weight: 0.4980 chunk 224 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 357 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 156 GLN B 36 ASN C 123 ASN C 156 GLN D 36 ASN E 96 GLN E 156 GLN E 401 GLN F 36 ASN G 96 GLN G 156 GLN H 36 ASN I 96 GLN I 156 GLN I 401 GLN J 36 ASN K 123 ASN K 156 GLN K 401 GLN L 36 ASN M 96 GLN M 156 GLN N 36 ASN O 123 ASN O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 401 GLN P 36 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38584 Z= 0.229 Angle : 0.602 6.129 52312 Z= 0.320 Chirality : 0.044 0.196 5576 Planarity : 0.004 0.031 6856 Dihedral : 5.323 41.178 5345 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.85 % Allowed : 8.41 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.12), residues: 4760 helix: 1.31 (0.12), residues: 1904 sheet: -0.29 (0.18), residues: 736 loop : 0.54 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 368 HIS 0.012 0.002 HIS O 153 PHE 0.034 0.003 PHE G 345 TYR 0.016 0.002 TYR N 32 ARG 0.005 0.001 ARG O 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 681 time to evaluate : 4.416 Fit side-chains revert: symmetry clash REVERT: C 305 ARG cc_start: 0.7672 (tpt170) cc_final: 0.7250 (tpp80) REVERT: E 305 ARG cc_start: 0.7694 (tpt170) cc_final: 0.7186 (mmp-170) REVERT: F 66 LEU cc_start: 0.8764 (mt) cc_final: 0.8541 (mt) REVERT: G 305 ARG cc_start: 0.7691 (tpt170) cc_final: 0.7158 (mmp-170) REVERT: G 349 MET cc_start: 0.8802 (mtp) cc_final: 0.8495 (mtp) REVERT: I 305 ARG cc_start: 0.7668 (tpt170) cc_final: 0.7171 (tpp80) REVERT: K 305 ARG cc_start: 0.7700 (tpt170) cc_final: 0.7193 (tpp80) REVERT: M 305 ARG cc_start: 0.7643 (tpt170) cc_final: 0.7187 (tpp80) REVERT: O 305 ARG cc_start: 0.7622 (tpt170) cc_final: 0.7127 (tpp80) outliers start: 33 outliers final: 25 residues processed: 710 average time/residue: 1.8441 time to fit residues: 1541.9041 Evaluate side-chains 696 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 671 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 252 LYS Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain w residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 7.9990 chunk 435 optimal weight: 5.9990 chunk 397 optimal weight: 5.9990 chunk 423 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 383 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 chunk 422 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN B 36 ASN C 156 GLN D 36 ASN E 96 GLN E 123 ASN E 156 GLN E 401 GLN F 36 ASN G 96 GLN G 123 ASN G 156 GLN H 36 ASN I 96 GLN I 156 GLN I 401 GLN J 36 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN L 36 ASN M 96 GLN M 156 GLN N 36 ASN O 123 ASN O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38584 Z= 0.293 Angle : 0.663 6.473 52312 Z= 0.353 Chirality : 0.046 0.211 5576 Planarity : 0.005 0.033 6856 Dihedral : 5.498 40.778 5345 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.80 % Allowed : 8.64 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 4760 helix: 1.19 (0.12), residues: 1904 sheet: -0.43 (0.18), residues: 744 loop : 0.51 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 368 HIS 0.015 0.003 HIS A 153 PHE 0.036 0.003 PHE O 345 TYR 0.018 0.003 TYR F 32 ARG 0.006 0.001 ARG O 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 684 time to evaluate : 4.235 Fit side-chains revert: symmetry clash REVERT: C 305 ARG cc_start: 0.7674 (tpt170) cc_final: 0.7245 (tpp80) REVERT: E 305 ARG cc_start: 0.7711 (tpt170) cc_final: 0.7273 (tpp80) REVERT: E 349 MET cc_start: 0.8972 (mtp) cc_final: 0.8766 (mtp) REVERT: G 305 ARG cc_start: 0.7701 (tpt170) cc_final: 0.7280 (tpp80) REVERT: I 305 ARG cc_start: 0.7669 (tpt170) cc_final: 0.7176 (tpp80) REVERT: K 305 ARG cc_start: 0.7699 (tpt170) cc_final: 0.7253 (tpp80) REVERT: M 305 ARG cc_start: 0.7667 (tpt170) cc_final: 0.7214 (tpp80) REVERT: O 305 ARG cc_start: 0.7628 (tpt170) cc_final: 0.7187 (tpp80) outliers start: 31 outliers final: 30 residues processed: 713 average time/residue: 1.7856 time to fit residues: 1501.1401 Evaluate side-chains 705 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 675 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 252 LYS Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain w residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 3.9990 chunk 448 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 chunk 470 optimal weight: 7.9990 chunk 432 optimal weight: 8.9990 chunk 374 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 156 GLN B 36 ASN C 156 GLN D 36 ASN D 115 GLN E 156 GLN E 401 GLN F 36 ASN G 96 GLN G 123 ASN G 156 GLN H 36 ASN H 115 GLN I 156 GLN J 36 ASN K 123 ASN K 156 GLN L 36 ASN M 123 ASN M 156 GLN M 401 GLN N 36 ASN O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38584 Z= 0.289 Angle : 0.657 6.322 52312 Z= 0.349 Chirality : 0.046 0.210 5576 Planarity : 0.005 0.032 6856 Dihedral : 5.472 41.486 5345 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.80 % Allowed : 8.64 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 4760 helix: 1.18 (0.11), residues: 1904 sheet: -0.44 (0.18), residues: 744 loop : 0.52 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 368 HIS 0.014 0.002 HIS A 153 PHE 0.038 0.003 PHE O 345 TYR 0.021 0.002 TYR L 32 ARG 0.006 0.001 ARG O 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 672 time to evaluate : 4.133 Fit side-chains revert: symmetry clash REVERT: C 305 ARG cc_start: 0.7672 (tpt170) cc_final: 0.7246 (tpp80) REVERT: E 305 ARG cc_start: 0.7709 (tpt170) cc_final: 0.7278 (tpp80) REVERT: G 305 ARG cc_start: 0.7705 (tpt170) cc_final: 0.7280 (tpp80) REVERT: I 305 ARG cc_start: 0.7671 (tpt170) cc_final: 0.7177 (tpp80) REVERT: K 305 ARG cc_start: 0.7699 (tpt170) cc_final: 0.7197 (tpp80) REVERT: M 305 ARG cc_start: 0.7666 (tpt170) cc_final: 0.7211 (tpp80) REVERT: O 305 ARG cc_start: 0.7628 (tpt170) cc_final: 0.7189 (tpp80) outliers start: 31 outliers final: 29 residues processed: 700 average time/residue: 1.7989 time to fit residues: 1485.1774 Evaluate side-chains 701 residues out of total 3976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 672 time to evaluate : 4.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain O residue 252 LYS Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain w residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 3.9990 chunk 398 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 345 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 375 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 156 GLN B 36 ASN C 156 GLN D 36 ASN E 156 GLN E 401 GLN F 36 ASN G 123 ASN G 156 GLN G 401 GLN H 36 ASN I 156 GLN J 36 ASN K 123 ASN K 156 GLN L 36 ASN M 123 ASN M 156 GLN N 36 ASN O 123 ASN O 156 GLN ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.156271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.113842 restraints weight = 25667.907| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 0.98 r_work: 0.2937 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38584 Z= 0.222 Angle : 0.601 6.086 52312 Z= 0.318 Chirality : 0.044 0.194 5576 Planarity : 0.004 0.031 6856 Dihedral : 5.253 39.672 5345 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.77 % Allowed : 8.51 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.12), residues: 4760 helix: 1.33 (0.12), residues: 1904 sheet: -0.34 (0.18), residues: 736 loop : 0.57 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 368 HIS 0.012 0.002 HIS A 153 PHE 0.035 0.003 PHE A 345 TYR 0.019 0.002 TYR F 32 ARG 0.004 0.000 ARG G 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20527.40 seconds wall clock time: 360 minutes 59.97 seconds (21659.97 seconds total)