Starting phenix.real_space_refine on Mon Mar 18 01:48:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0n_20608/03_2024/6u0n_20608_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0n_20608/03_2024/6u0n_20608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0n_20608/03_2024/6u0n_20608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0n_20608/03_2024/6u0n_20608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0n_20608/03_2024/6u0n_20608_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0n_20608/03_2024/6u0n_20608_neut_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 118 5.16 5 C 12153 2.51 5 N 3304 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 47": "OD1" <-> "OD2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "E ASP 10": "OD1" <-> "OD2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F GLU 77": "OE1" <-> "OE2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 32": "OD1" <-> "OD2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 46": "OE1" <-> "OE2" Residue "P PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 85": "OD1" <-> "OD2" Residue "P TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "Q PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 585": "NH1" <-> "NH2" Residue "Y ARG 588": "NH1" <-> "NH2" Residue "Z PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19322 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2774 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 4 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2724 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 341} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 763 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 967 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYS:plan-2': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 28 Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 985 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYS:plan-2': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 786 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 790 Chain: "P" Number of atoms: 987 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 981 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'TYS:plan-2': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 132, 981 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'TYS:plan-2': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 997 Chain: "Q" Number of atoms: 792 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 786 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 110, 786 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 796 Chain: "X" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 991 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "Y" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "Z" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 927 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 55 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER L 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER L 70 " occ=0.50 residue: pdb=" N ACYS P 92 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS P 92 " occ=0.50 residue: pdb=" N ASER Q 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER Q 70 " occ=0.50 Time building chain proxies: 11.66, per 1000 atoms: 0.60 Number of scatterers: 19322 At special positions: 0 Unit cell: (146.923, 149.037, 167.006, 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 118 16.00 O 3747 8.00 N 3304 7.00 C 12153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS X 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS Y 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS Z 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG ACYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG BCYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.02 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 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN N 4 " - " MAN N 5 " " MAN O 4 " - " MAN O 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 363 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 88 " " NAG A 610 " - " ASN A 234 " " NAG B 601 " - " ASN B 448 " " NAG B 602 " - " ASN B 386 " " NAG B 603 " - " ASN B 88 " " NAG B 604 " - " ASN B 392 " " NAG B 610 " - " ASN B 276 " " NAG B 611 " - " ASN B 295 " " NAG B 612 " - " ASN B 332 " " NAG B 613 " - " ASN B 363 " " NAG B 614 " - " ASN B 339 " " NAG C 606 " - " ASN C 276 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 332 " " NAG C 609 " - " ASN C 363 " " NAG C 610 " - " ASN C 339 " " NAG C 611 " - " ASN C 448 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 88 " " NAG C 614 " - " ASN C 392 " " NAG G 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 386 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN B 262 " " NAG O 1 " - " ASN C 262 " Time building additional restraints: 7.50 Conformation dependent library (CDL) restraints added in 4.4 seconds 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4586 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 41 sheets defined 12.5% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.596A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.720A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.789A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.812A pdb=" N TRP B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 69' Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 335 through 349 removed outlier: 3.503A pdb=" N ASN B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 477 through 480 No H-bonds generated for 'chain 'B' and resid 477 through 480' Processing helix chain 'C' and resid 102 through 108 removed outlier: 4.272A pdb=" N ASP C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 352 removed outlier: 4.031A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'D' and resid 59 through 64 removed outlier: 3.738A pdb=" N TRP D 62 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 64 removed outlier: 3.509A pdb=" N TRP E 62 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP E 63 " --> pdb=" O SER E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 64 removed outlier: 3.573A pdb=" N TRP F 62 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 97 through 100 Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'P' and resid 84 through 86 No H-bonds generated for 'chain 'P' and resid 84 through 86' Processing helix chain 'P' and resid 97 through 99 No H-bonds generated for 'chain 'P' and resid 97 through 99' Processing helix chain 'Q' and resid 80 through 82 No H-bonds generated for 'chain 'Q' and resid 80 through 82' Processing helix chain 'X' and resid 517 through 523 removed outlier: 4.168A pdb=" N LEU X 523 " --> pdb=" O PHE X 519 " (cutoff:3.500A) Processing helix chain 'X' and resid 530 through 534 Processing helix chain 'X' and resid 537 through 544 removed outlier: 3.843A pdb=" N ARG X 542 " --> pdb=" O THR X 538 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN X 543 " --> pdb=" O VAL X 539 " (cutoff:3.500A) Processing helix chain 'X' and resid 570 through 573 No H-bonds generated for 'chain 'X' and resid 570 through 573' Processing helix chain 'X' and resid 579 through 593 removed outlier: 3.564A pdb=" N TYR X 586 " --> pdb=" O ALA X 582 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG X 588 " --> pdb=" O GLU X 584 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP X 589 " --> pdb=" O ARG X 585 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN X 590 " --> pdb=" O TYR X 586 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU X 592 " --> pdb=" O ARG X 588 " (cutoff:3.500A) Processing helix chain 'X' and resid 619 through 621 No H-bonds generated for 'chain 'X' and resid 619 through 621' Processing helix chain 'X' and resid 628 through 632 removed outlier: 4.005A pdb=" N ASP X 632 " --> pdb=" O TRP X 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 628 through 632' Processing helix chain 'X' and resid 641 through 650 removed outlier: 3.595A pdb=" N GLU X 647 " --> pdb=" O TYR X 643 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU X 648 " --> pdb=" O GLY X 644 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN X 650 " --> pdb=" O LEU X 646 " (cutoff:3.500A) Processing helix chain 'Y' and resid 530 through 536 removed outlier: 3.706A pdb=" N SER Y 534 " --> pdb=" O MET Y 530 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET Y 535 " --> pdb=" O GLY Y 531 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR Y 536 " --> pdb=" O ALA Y 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 530 through 536' Processing helix chain 'Y' and resid 539 through 542 No H-bonds generated for 'chain 'Y' and resid 539 through 542' Processing helix chain 'Y' and resid 570 through 573 No H-bonds generated for 'chain 'Y' and resid 570 through 573' Processing helix chain 'Y' and resid 577 through 587 removed outlier: 3.504A pdb=" N LEU Y 581 " --> pdb=" O GLN Y 577 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA Y 582 " --> pdb=" O ALA Y 578 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Y 583 " --> pdb=" O ARG Y 579 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR Y 586 " --> pdb=" O ALA Y 582 " (cutoff:3.500A) Processing helix chain 'Y' and resid 590 through 595 Processing helix chain 'Y' and resid 621 through 624 No H-bonds generated for 'chain 'Y' and resid 621 through 624' Processing helix chain 'Y' and resid 628 through 634 removed outlier: 3.549A pdb=" N GLU Y 634 " --> pdb=" O GLN Y 630 " (cutoff:3.500A) Processing helix chain 'Y' and resid 639 through 657 removed outlier: 3.638A pdb=" N GLY Y 644 " --> pdb=" O GLN Y 640 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU Y 645 " --> pdb=" O ILE Y 641 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Y 646 " --> pdb=" O ILE Y 642 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU Y 648 " --> pdb=" O GLY Y 644 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Y 650 " --> pdb=" O LEU Y 646 " (cutoff:3.500A) Processing helix chain 'Z' and resid 530 through 533 No H-bonds generated for 'chain 'Z' and resid 530 through 533' Processing helix chain 'Z' and resid 564 through 574 removed outlier: 3.746A pdb=" N LEU Z 568 " --> pdb=" O HIS Z 564 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR Z 569 " --> pdb=" O LEU Z 565 " (cutoff:3.500A) Processing helix chain 'Z' and resid 577 through 595 removed outlier: 3.809A pdb=" N LEU Z 581 " --> pdb=" O GLN Z 577 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR Z 586 " --> pdb=" O ALA Z 582 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN Z 591 " --> pdb=" O LEU Z 587 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU Z 592 " --> pdb=" O ARG Z 588 " (cutoff:3.500A) Processing helix chain 'Z' and resid 628 through 637 removed outlier: 5.533A pdb=" N ASN Z 637 " --> pdb=" O LYS Z 633 " (cutoff:3.500A) Processing helix chain 'Z' and resid 639 through 653 removed outlier: 4.023A pdb=" N GLY Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU Z 645 " --> pdb=" O ILE Z 641 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN Z 650 " --> pdb=" O LEU Z 646 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN Z 653 " --> pdb=" O SER Z 649 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 83 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.760A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 120 through 123 removed outlier: 3.663A pdb=" N GLN A 432 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 284 through 287 Processing sheet with id= E, first strand: chain 'A' and resid 443 through 449 removed outlier: 3.742A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.860A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.591A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 196 through 202 removed outlier: 3.571A pdb=" N THR B 123 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 121 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 120 " --> pdb=" O MET B 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 432 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 488 through 490 Processing sheet with id= K, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.713A pdb=" N ARG B 273 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 467 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ALA B 362 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 447 through 449 removed outlier: 3.521A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 375 through 377 Processing sheet with id= N, first strand: chain 'C' and resid 37 through 40 Processing sheet with id= O, first strand: chain 'C' and resid 83 through 86 removed outlier: 4.874A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.679A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.777A pdb=" N GLN C 432 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 284 through 286 Processing sheet with id= S, first strand: chain 'C' and resid 443 through 449 removed outlier: 4.107A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 298 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 359 through 361 removed outlier: 3.601A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.801A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 2 through 5 removed outlier: 4.230A pdb=" N LYS D 2 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 94 " --> pdb=" O LYS D 2 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 27 through 29 removed outlier: 3.869A pdb=" N TRP D 28 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 37 " --> pdb=" O TRP D 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.616A pdb=" N LYS E 2 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS E 84 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 2 through 5 Processing sheet with id= Z, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= AA, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.766A pdb=" N GLU H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN H 95 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 67 through 72 Processing sheet with id= AC, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.572A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 10 through 12 Processing sheet with id= AE, first strand: chain 'I' and resid 89 through 96 removed outlier: 6.512A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY I 50 " --> pdb=" O HIS I 58 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.474A pdb=" N LYS J 103 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA J 13 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR J 105 " --> pdb=" O ALA J 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'J' and resid 19 through 23 removed outlier: 3.580A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE J 75 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 95B through 98 removed outlier: 3.507A pdb=" N THR J 90 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 19 through 24 Processing sheet with id= AJ, first strand: chain 'L' and resid 95B through 98 removed outlier: 3.508A pdb=" N ALA L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 4 through 6 removed outlier: 3.631A pdb=" N VAL P 20 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.912A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA P 40 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU P 45 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Q' and resid 10 through 12 removed outlier: 5.766A pdb=" N LYS Q 103 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'Q' and resid 95B through 97 removed outlier: 3.551A pdb=" N TYR Q 36 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE Q 48 " --> pdb=" O TRP Q 35 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN Q 37 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Q' and resid 62 through 67 373 hydrogen bonds defined for protein. 976 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: 5.60 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6124 1.34 - 1.46: 4779 1.46 - 1.58: 8670 1.58 - 1.70: 6 1.70 - 1.82: 145 Bond restraints: 19724 Sorted by residual: bond pdb=" O3 TYS P 100F" pdb=" S TYS P 100F" ideal model delta sigma weight residual 1.458 1.633 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" O1 TYS I 100F" pdb=" S TYS I 100F" ideal model delta sigma weight residual 1.462 1.634 -0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" O2 TYS I 100I" pdb=" S TYS I 100I" ideal model delta sigma weight residual 1.461 1.632 -0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" O1 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.462 1.632 -0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" O3 TYS P 100I" pdb=" S TYS P 100I" ideal model delta sigma weight residual 1.458 1.627 -0.169 2.00e-02 2.50e+03 7.16e+01 ... (remaining 19719 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.14: 349 105.14 - 112.42: 10498 112.42 - 119.69: 6357 119.69 - 126.97: 9327 126.97 - 134.25: 327 Bond angle restraints: 26858 Sorted by residual: angle pdb=" C GLU J 50 " pdb=" N ASN J 51 " pdb=" CA ASN J 51 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C GLU Q 50 " pdb=" N ASN Q 51 " pdb=" CA ASN Q 51 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLU L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N SER C 56 " pdb=" CA SER C 56 " pdb=" C SER C 56 " ideal model delta sigma weight residual 111.02 116.22 -5.20 1.25e+00 6.40e-01 1.73e+01 angle pdb=" C LYS C 335 " pdb=" N ALA C 336 " pdb=" CA ALA C 336 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 ... (remaining 26853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 11314 21.85 - 43.70: 786 43.70 - 65.54: 87 65.54 - 87.39: 38 87.39 - 109.24: 14 Dihedral angle restraints: 12239 sinusoidal: 5119 harmonic: 7120 Sorted by residual: dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS X 605 " pdb=" CB CYS X 605 " ideal model delta sinusoidal sigma weight residual -86.00 -12.87 -73.13 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS Z 605 " pdb=" CB CYS Z 605 " ideal model delta sinusoidal sigma weight residual -86.00 -18.96 -67.04 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS B 378 " pdb=" SG CYS B 378 " pdb=" SG CYS B 445 " pdb=" CB CYS B 445 " ideal model delta sinusoidal sigma weight residual -86.00 -139.10 53.10 1 1.00e+01 1.00e-02 3.84e+01 ... (remaining 12236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3142 0.141 - 0.282: 48 0.282 - 0.423: 5 0.423 - 0.564: 1 0.564 - 0.705: 2 Chirality restraints: 3198 Sorted by residual: chirality pdb=" C1 NAG B 613 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 613 " pdb=" O5 NAG B 613 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 NAG C 609 " pdb=" ND2 ASN C 363 " pdb=" C2 NAG C 609 " pdb=" O5 NAG C 609 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 88 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.96e+00 ... (remaining 3195 not shown) Planarity restraints: 3375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 448 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C ASN B 448 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN B 448 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 449 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 75 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO C 76 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 243 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C SER A 243 " 0.045 2.00e-02 2.50e+03 pdb=" O SER A 243 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 244 " -0.015 2.00e-02 2.50e+03 ... (remaining 3372 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4102 2.77 - 3.31: 16591 3.31 - 3.84: 31262 3.84 - 4.37: 35557 4.37 - 4.90: 62421 Nonbonded interactions: 149933 Sorted by model distance: nonbonded pdb=" O LYS B 229 " pdb=" OG SER B 241 " model vdw 2.242 2.440 nonbonded pdb=" O SER C 56 " pdb=" OG SER C 56 " model vdw 2.283 2.440 nonbonded pdb=" O LEU B 369 " pdb=" OG1 THR B 373 " model vdw 2.306 2.440 nonbonded pdb=" O SER E 23 " pdb=" OG SER E 23 " model vdw 2.326 2.440 nonbonded pdb=" OG1 THR A 37 " pdb=" O ALA A 497 " model vdw 2.328 2.440 ... (remaining 149928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 46 or (resid 47 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 61 or (resid 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 77 or (r \ esid 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or \ (resid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 t \ hrough 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) \ or resid 93 through 124 or (resid 125 and (name N or name CA or name C or name O \ or name CB )) or resid 126 or (resid 127 and (name N or name CA or name C or na \ me O or name CB )) or (resid 194 through 195 and (name N or name CA or name C or \ name O or name CB )) or resid 196 through 206 or (resid 207 through 208 and (na \ me N or name CA or name C or name O or name CB )) or resid 209 through 229 or (r \ esid 230 through 232 and (name N or name CA or name C or name O or name CB )) or \ resid 233 through 349 or (resid 350 and (name N or name CA or name C or name O \ or name CB )) or resid 351 through 397 or (resid 412 and (name N or name CA or n \ ame C or name O or name CB )) or resid 413 through 458 or resid 460 through 465 \ or (resid 466 through 467 and (name N or name CA or name C or name O or name CB \ )) or resid 468 through 491 or (resid 492 and (name N or name CA or name C or na \ me O or name CB )) or resid 493 through 499 or (resid 500 and (name N or name CA \ or name C or name O or name CB )) or resid 501 through 502 or resid 603 through \ 610)) selection = (chain 'B' and (resid 35 through 56 or (resid 57 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 61 or (resid 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 96 or (r \ esid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 thr \ ough 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) \ or resid 118 through 124 or (resid 125 and (name N or name CA or name C or name \ O or name CB )) or resid 126 through 127 or (resid 194 through 195 and (name N o \ r name CA or name C or name O or name CB )) or resid 196 through 202 or (resid 2 \ 03 through 204 and (name N or name CA or name C or name O or name CB )) or resid \ 205 through 206 or (resid 207 through 208 and (name N or name CA or name C or n \ ame O or name CB )) or resid 209 through 231 or (resid 232 and (name N or name C \ A or name C or name O or name CB )) or resid 233 through 300 or resid 325 throug \ h 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) or \ resid 359 through 369 or (resid 370 and (name N or name CA or name C or name O o \ r name CB )) or resid 371 through 395 or (resid 396 and (name N or name CA or na \ me C or name O or name CB )) or resid 397 through 439 or (resid 440 and (name N \ or name CA or name C or name O or name CB )) or resid 441 through 456 or (resid \ 457 and (name N or name CA or name C or name O or name CB )) or resid 458 or res \ id 463 through 464 or (resid 465 and (name N or name CA or name C or name O or n \ ame CB or name OG1)) or (resid 466 through 467 and (name N or name CA or name C \ or name O or name CB )) or resid 468 through 491 or (resid 492 and (name N or na \ me CA or name C or name O or name CB )) or resid 493 through 499 or (resid 500 a \ nd (name N or name CA or name C or name O or name CB )) or resid 501 through 502 \ or resid 602 through 612)) selection = (chain 'C' and (resid 35 through 56 or (resid 57 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 91 or (resid 92 and (na \ me N or name CA or name C or name O or name CB )) or resid 93 through 116 or (re \ sid 117 and (name N or name CA or name C or name O or name CB )) or resid 118 th \ rough 229 or (resid 230 through 232 and (name N or name CA or name C or name O o \ r name CB )) or resid 233 through 300 or resid 325 through 349 or (resid 350 and \ (name N or name CA or name C or name O or name CB )) or resid 351 through 357 o \ r (resid 358 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 59 through 397 or (resid 412 and (name N or name CA or name C or name O or name \ CB )) or resid 413 through 439 or (resid 440 and (name N or name CA or name C or \ name O or name CB )) or resid 441 through 458 or resid 460 through 465 or (resi \ d 466 through 467 and (name N or name CA or name C or name O or name CB )) or re \ sid 468 through 502 or resid 607 through 612)) } ncs_group { reference = (chain 'D' and (resid 1 through 20 or (resid 21 through 22 and (name N or name C \ A or name C or name O or name CB or name CG or name CD )) or resid 23 through 86 \ or (resid 87 and (name N or name CA or name C or name O or name CB )) or resid \ 88 through 90 or (resid 91 and (name N or name CA or name C or name O or name CB \ )) or resid 92 through 97)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 20 or (resid 21 through 22 and (name N or name C \ A or name C or name O or name CB or name CG or name CD )) or resid 23 through 86 \ or (resid 87 and (name N or name CA or name C or name O or name CB )) or resid \ 88 through 90 or (resid 91 and (name N or name CA or name C or name O or name CB \ )) or resid 92 through 97)) } ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = (chain 'H' and (resid 2 through 91 or resid 93 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 112)) selection = (chain 'I' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 or (resid 12 through 13 and (name N or name \ CA or name C or name O or name CB )) or resid 14 through 18 or (resid 19 and (na \ me N or name CA or name C or name O or name CB )) or resid 20 through 91 or resi \ d 93 through 100Q or (resid 101 and (name N or name CA or name C or name O or na \ me CB )) or resid 102 through 112)) selection = (chain 'P' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 91 or resid 93 through 100O or (res \ id 100P and (name N or name CA or name C or name O or name CB )) or resid 100Q o \ r (resid 101 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 02 through 104 or (resid 105 and (name N or name CA or name C or name O or name \ CB )) or resid 106 through 112)) } ncs_group { reference = (chain 'J' and (resid 2 through 51 or (resid 52 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 59 or (resid 60 through \ 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through \ 69 or resid 71 through 107)) selection = (chain 'L' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 69 or resid 71 through 107)) selection = (chain 'Q' and (resid 2 through 51 or (resid 52 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 59 or (resid 60 through \ 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through \ 69 or resid 71 through 107)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'X' and (resid 521 through 528 or (resid 529 and (name N or name CA or na \ me C or name O or name CB )) or resid 530 through 539 or (resid 540 and (name N \ or name CA or name C or name O or name CB )) or (resid 542 and (name N or name C \ A or name C or name O or name CB )) or (resid 560 through 563 and (name N or nam \ e CA or name C or name O or name CB )) or resid 564 through 600 or (resid 601 an \ d (name N or name CA or name C or name O or name CB )) or resid 602 through 606 \ or (resid 607 and (name N or name CA or name C or name O or name CB )) or resid \ 608 through 616 or (resid 617 and (name N or name CA or name C or name O or name \ CB )) or resid 618 through 629 or (resid 630 and (name N or name CA or name C o \ r name O or name CB )) or resid 631 through 632 or (resid 633 and (name N or nam \ e CA or name C or name O or name CB )) or resid 634 through 636 or (resid 637 an \ d (name N or name CA or name C or name O or name CB )) or resid 638 through 639 \ or (resid 640 through 641 and (name N or name CA or name C or name O or name CB \ )) or resid 642 through 647 or (resid 648 and (name N or name CA or name C or na \ me O or name CB )) or resid 649 through 650 or (resid 651 and (name N or name CA \ or name C or name O or name CB )) or resid 652 through 653)) selection = (chain 'Y' and (resid 521 through 528 or (resid 529 and (name N or name CA or na \ me C or name O or name CB )) or resid 530 through 540 or resid 542 or (resid 560 \ through 563 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 64 through 606 or (resid 607 and (name N or name CA or name C or name O or name \ CB )) or resid 608 through 629 or (resid 630 and (name N or name CA or name C or \ name O or name CB )) or resid 631 through 632 or (resid 633 and (name N or name \ CA or name C or name O or name CB )) or resid 634 through 639 or (resid 640 thr \ ough 641 and (name N or name CA or name C or name O or name CB )) or resid 642 t \ hrough 649 or (resid 650 through 651 and (name N or name CA or name C or name O \ or name CB )) or resid 652 or (resid 653 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'Z' and (resid 521 through 557 or resid 560 through 600 or (resid 601 and \ (name N or name CA or name C or name O or name CB )) or resid 602 through 616 o \ r (resid 617 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 18 through 636 or (resid 637 and (name N or name CA or name C or name O or name \ CB )) or resid 638 through 649 or (resid 650 through 651 and (name N or name CA \ or name C or name O or name CB )) or resid 652 through 653)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.410 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 53.840 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.008 0.175 19724 Z= 0.507 Angle : 0.908 10.493 26858 Z= 0.471 Chirality : 0.059 0.705 3198 Planarity : 0.006 0.066 3346 Dihedral : 15.218 109.240 7539 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.58 % Favored : 90.34 % Rotamer: Outliers : 0.56 % Allowed : 6.51 % Favored : 92.93 % 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: -5.29 (0.13), residues: 2420 helix: -4.82 (0.08), residues: 401 sheet: -2.85 (0.17), residues: 736 loop : -3.51 (0.13), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 614 HIS 0.007 0.001 HIS A 352 PHE 0.021 0.002 PHE A 376 TYR 0.019 0.002 TYR B 484 ARG 0.005 0.000 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 444 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8648 (mttt) cc_final: 0.8250 (mttp) REVERT: A 62 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7964 (mm-30) REVERT: A 479 TRP cc_start: 0.7378 (m-10) cc_final: 0.7023 (m-10) REVERT: B 340 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7841 (tp30) REVERT: B 377 ASN cc_start: 0.7613 (t0) cc_final: 0.7323 (t0) REVERT: D 89 GLN cc_start: 0.9021 (mt0) cc_final: 0.8364 (mp10) REVERT: F 70 ILE cc_start: 0.8945 (mm) cc_final: 0.8739 (mm) REVERT: F 94 GLN cc_start: 0.8795 (pt0) cc_final: 0.8563 (pm20) REVERT: H 79 TYR cc_start: 0.7890 (m-80) cc_final: 0.7624 (m-10) REVERT: I 10 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8070 (mm-30) REVERT: J 21 ILE cc_start: 0.9191 (mm) cc_final: 0.8973 (mp) REVERT: J 92 ASP cc_start: 0.8236 (t0) cc_final: 0.7605 (p0) REVERT: L 45 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8802 (tttt) REVERT: L 90 THR cc_start: 0.8044 (t) cc_final: 0.7576 (m) REVERT: L 95 LEU cc_start: 0.9257 (mp) cc_final: 0.8841 (tp) REVERT: P 38 ARG cc_start: 0.6821 (ptt180) cc_final: 0.6398 (ptm-80) REVERT: P 61 GLN cc_start: 0.8644 (tp40) cc_final: 0.8303 (tp-100) REVERT: P 66 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8170 (ptm160) REVERT: P 82 ARG cc_start: 0.7052 (ptt-90) cc_final: 0.6771 (mpt180) REVERT: P 82 LEU cc_start: 0.8655 (mt) cc_final: 0.7086 (mp) REVERT: P 101 ASP cc_start: 0.8675 (t70) cc_final: 0.8367 (t0) outliers start: 11 outliers final: 6 residues processed: 452 average time/residue: 0.3142 time to fit residues: 215.1925 Evaluate side-chains 359 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 353 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 67 ASN A 279 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 287 GLN C 72 HIS C 258 GLN C 280 ASN C 422 GLN D 33 GLN E 27 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN F 32 ASN I 6 GLN I 58 HIS I 95 ASN J 37 GLN L 31 ASN L 37 GLN ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 ASN Q 37 GLN X 590 GLN X 625 ASN Y 562 GLN Y 564 HIS Y 590 GLN Y 652 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 19724 Z= 0.457 Angle : 0.717 9.090 26858 Z= 0.368 Chirality : 0.050 0.562 3198 Planarity : 0.005 0.060 3346 Dihedral : 10.099 81.310 3517 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.08 % Allowed : 16.10 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.14), residues: 2420 helix: -3.97 (0.15), residues: 376 sheet: -2.48 (0.18), residues: 774 loop : -3.14 (0.14), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 479 HIS 0.011 0.001 HIS E 27 PHE 0.023 0.002 PHE Q 62 TYR 0.024 0.002 TYR J 87 ARG 0.011 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 366 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8568 (mttt) cc_final: 0.8325 (mttp) REVERT: A 62 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 340 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7346 (tp30) REVERT: B 377 ASN cc_start: 0.7582 (t0) cc_final: 0.7360 (t0) REVERT: D 89 GLN cc_start: 0.8871 (mt0) cc_final: 0.8377 (mp10) REVERT: F 94 GLN cc_start: 0.8794 (pt0) cc_final: 0.8389 (pm20) REVERT: H 4 LEU cc_start: 0.8091 (mt) cc_final: 0.7800 (tp) REVERT: H 69 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8331 (mm) REVERT: I 3 GLN cc_start: 0.8777 (pp30) cc_final: 0.8520 (pm20) REVERT: I 10 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8088 (mm-30) REVERT: I 13 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8266 (mmtt) REVERT: I 23 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7893 (tm-30) REVERT: J 92 ASP cc_start: 0.8280 (t0) cc_final: 0.7589 (p0) REVERT: J 103 LYS cc_start: 0.8806 (tptt) cc_final: 0.8600 (tptt) REVERT: L 32 ASP cc_start: 0.7737 (p0) cc_final: 0.7481 (p0) REVERT: L 36 TYR cc_start: 0.7580 (m-80) cc_final: 0.7180 (m-80) REVERT: L 45 LYS cc_start: 0.9019 (ttpt) cc_final: 0.8764 (tttt) REVERT: L 90 THR cc_start: 0.8456 (t) cc_final: 0.8026 (m) REVERT: L 95 LEU cc_start: 0.9317 (mp) cc_final: 0.8891 (tp) REVERT: L 103 LYS cc_start: 0.8705 (mppt) cc_final: 0.8259 (mppt) REVERT: P 64 ARG cc_start: 0.7388 (mtt-85) cc_final: 0.7103 (mtt-85) REVERT: P 66 ARG cc_start: 0.8557 (mtp180) cc_final: 0.8322 (ptm160) REVERT: P 82 ARG cc_start: 0.7111 (ptt-90) cc_final: 0.6722 (mpt180) REVERT: P 101 ASP cc_start: 0.8683 (t70) cc_final: 0.8409 (t0) REVERT: Q 66 LYS cc_start: 0.9216 (ttpp) cc_final: 0.8843 (ttmm) REVERT: Q 72 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7650 (p) outliers start: 61 outliers final: 38 residues processed: 400 average time/residue: 0.2989 time to fit residues: 185.9212 Evaluate side-chains 378 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 338 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 595 ILE Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain X residue 618 ASN Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 221 optimal weight: 0.0050 chunk 238 optimal weight: 9.9990 chunk 196 optimal weight: 0.7980 chunk 219 optimal weight: 0.0570 chunk 75 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 overall best weight: 0.7514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN C 216 HIS ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN L 37 GLN P 23 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19724 Z= 0.197 Angle : 0.592 8.847 26858 Z= 0.301 Chirality : 0.047 0.550 3198 Planarity : 0.004 0.064 3346 Dihedral : 8.739 71.631 3514 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.13 % Allowed : 18.88 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.15), residues: 2420 helix: -3.25 (0.19), residues: 374 sheet: -2.07 (0.19), residues: 719 loop : -2.92 (0.15), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 614 HIS 0.006 0.001 HIS I 81 PHE 0.012 0.001 PHE P 63 TYR 0.014 0.001 TYR B 484 ARG 0.005 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 368 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8516 (mttt) cc_final: 0.8268 (mttp) REVERT: A 62 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 340 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7201 (tp30) REVERT: B 377 ASN cc_start: 0.7509 (t0) cc_final: 0.7253 (t0) REVERT: C 91 GLU cc_start: 0.7397 (tp30) cc_final: 0.7004 (tp30) REVERT: C 92 GLU cc_start: 0.7665 (tp30) cc_final: 0.7358 (tp30) REVERT: D 89 GLN cc_start: 0.8788 (mt0) cc_final: 0.8254 (mp10) REVERT: F 32 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7578 (t0) REVERT: H 4 LEU cc_start: 0.8176 (mt) cc_final: 0.7918 (tp) REVERT: I 10 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8034 (mm-30) REVERT: I 23 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7850 (tm-30) REVERT: J 92 ASP cc_start: 0.8157 (t0) cc_final: 0.7460 (p0) REVERT: L 32 ASP cc_start: 0.7629 (p0) cc_final: 0.7382 (p0) REVERT: L 36 TYR cc_start: 0.7676 (m-80) cc_final: 0.7289 (m-80) REVERT: L 45 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8642 (tttt) REVERT: L 90 THR cc_start: 0.8286 (t) cc_final: 0.7779 (m) REVERT: L 95 LEU cc_start: 0.9285 (mp) cc_final: 0.8894 (tp) REVERT: P 61 GLN cc_start: 0.8324 (tp-100) cc_final: 0.8091 (tp-100) REVERT: P 66 ARG cc_start: 0.8564 (mtp180) cc_final: 0.8254 (ptm160) REVERT: P 82 ARG cc_start: 0.7155 (ptt-90) cc_final: 0.6738 (mpt180) REVERT: P 101 ASP cc_start: 0.8623 (t70) cc_final: 0.8385 (t0) REVERT: Q 66 LYS cc_start: 0.9185 (ttpp) cc_final: 0.8847 (ttmm) REVERT: Q 72 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7734 (p) outliers start: 62 outliers final: 38 residues processed: 402 average time/residue: 0.2757 time to fit residues: 175.5373 Evaluate side-chains 380 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 340 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain X residue 618 ASN Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain Z residue 652 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 148 optimal weight: 0.0770 chunk 221 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN H 39 GLN I 6 GLN J 30 ASN L 31 ASN L 38 GLN P 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19724 Z= 0.337 Angle : 0.639 8.853 26858 Z= 0.323 Chirality : 0.048 0.532 3198 Planarity : 0.004 0.059 3346 Dihedral : 8.108 73.644 3514 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.04 % Allowed : 20.49 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.15), residues: 2420 helix: -2.79 (0.22), residues: 376 sheet: -1.97 (0.19), residues: 723 loop : -2.76 (0.15), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 479 HIS 0.006 0.001 HIS I 81 PHE 0.014 0.001 PHE A 53 TYR 0.017 0.002 TYR J 49 ARG 0.003 0.000 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 357 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7904 (mm-30) REVERT: B 340 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7298 (tp30) REVERT: B 377 ASN cc_start: 0.7584 (t0) cc_final: 0.7299 (t0) REVERT: C 92 GLU cc_start: 0.7723 (tp30) cc_final: 0.7504 (tp30) REVERT: D 89 GLN cc_start: 0.8837 (mt0) cc_final: 0.7886 (mp10) REVERT: I 10 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8045 (mm-30) REVERT: I 23 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7839 (tm-30) REVERT: J 17 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6639 (mp10) REVERT: J 92 ASP cc_start: 0.8197 (t0) cc_final: 0.7526 (p0) REVERT: L 32 ASP cc_start: 0.7765 (p0) cc_final: 0.7476 (p0) REVERT: L 36 TYR cc_start: 0.7842 (m-80) cc_final: 0.7452 (m-80) REVERT: L 45 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8736 (tttt) REVERT: L 90 THR cc_start: 0.8412 (t) cc_final: 0.7981 (m) REVERT: P 66 ARG cc_start: 0.8597 (mtp180) cc_final: 0.8304 (ptm160) REVERT: P 101 ASP cc_start: 0.8688 (t70) cc_final: 0.8402 (t0) REVERT: Q 61 ARG cc_start: 0.7006 (ptm-80) cc_final: 0.6362 (ptm-80) REVERT: Q 66 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8852 (ttmm) REVERT: Q 72 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7693 (p) outliers start: 80 outliers final: 59 residues processed: 404 average time/residue: 0.2842 time to fit residues: 180.8212 Evaluate side-chains 403 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 342 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain P residue 19 LYS Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 543 ASN Chi-restraints excluded: chain X residue 595 ILE Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain X residue 618 ASN Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 162 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN D 33 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN I 6 GLN L 31 ASN P 23 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19724 Z= 0.296 Angle : 0.617 8.950 26858 Z= 0.311 Chirality : 0.048 0.533 3198 Planarity : 0.004 0.063 3346 Dihedral : 7.515 73.269 3514 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 4.09 % Allowed : 22.01 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.16), residues: 2420 helix: -2.60 (0.23), residues: 375 sheet: -1.84 (0.19), residues: 740 loop : -2.63 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 479 HIS 0.005 0.001 HIS I 81 PHE 0.013 0.001 PHE A 53 TYR 0.023 0.001 TYR L 49 ARG 0.004 0.000 ARG P 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 359 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7279 (tp30) REVERT: B 377 ASN cc_start: 0.7592 (t0) cc_final: 0.7330 (t0) REVERT: C 91 GLU cc_start: 0.7180 (tp30) cc_final: 0.6905 (tp30) REVERT: C 92 GLU cc_start: 0.7686 (tp30) cc_final: 0.7320 (tp30) REVERT: D 89 GLN cc_start: 0.8504 (mt0) cc_final: 0.8077 (mp10) REVERT: F 94 GLN cc_start: 0.8609 (pt0) cc_final: 0.8142 (pm20) REVERT: I 10 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8062 (mm-30) REVERT: I 23 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7842 (tm-30) REVERT: J 92 ASP cc_start: 0.8195 (t0) cc_final: 0.7519 (p0) REVERT: L 36 TYR cc_start: 0.7931 (m-80) cc_final: 0.7534 (m-80) REVERT: L 45 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8789 (tttt) REVERT: L 90 THR cc_start: 0.8458 (t) cc_final: 0.8012 (m) REVERT: L 95 LEU cc_start: 0.9344 (mp) cc_final: 0.8860 (tp) REVERT: P 62 LYS cc_start: 0.8523 (pttm) cc_final: 0.8236 (pttp) REVERT: P 64 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7563 (ptp90) REVERT: P 101 ASP cc_start: 0.8694 (t70) cc_final: 0.8448 (t0) REVERT: Q 61 ARG cc_start: 0.6879 (ptm-80) cc_final: 0.6314 (ptm-80) REVERT: Q 66 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8856 (ttmm) REVERT: Q 72 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7563 (p) REVERT: X 633 LYS cc_start: 0.8876 (mppt) cc_final: 0.8579 (mptt) outliers start: 81 outliers final: 66 residues processed: 404 average time/residue: 0.2875 time to fit residues: 185.1647 Evaluate side-chains 405 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 337 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain P residue 19 LYS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 64 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 604 CYS Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain Z residue 652 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 235 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 283 ASN E 25 GLN E 40 GLN J 30 ASN P 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19724 Z= 0.234 Angle : 0.589 8.728 26858 Z= 0.296 Chirality : 0.047 0.526 3198 Planarity : 0.004 0.060 3346 Dihedral : 6.857 72.557 3514 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.64 % Allowed : 22.16 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.16), residues: 2420 helix: -2.30 (0.24), residues: 378 sheet: -1.62 (0.19), residues: 740 loop : -2.56 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 479 HIS 0.005 0.001 HIS I 81 PHE 0.011 0.001 PHE A 53 TYR 0.020 0.001 TYR B 435 ARG 0.008 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 351 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8327 (mtpp) cc_final: 0.8115 (mttp) REVERT: B 340 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7248 (tp30) REVERT: B 377 ASN cc_start: 0.7625 (t0) cc_final: 0.7357 (t0) REVERT: C 91 GLU cc_start: 0.7134 (tp30) cc_final: 0.6886 (tp30) REVERT: C 92 GLU cc_start: 0.7669 (tp30) cc_final: 0.7306 (tp30) REVERT: D 89 GLN cc_start: 0.8841 (mt0) cc_final: 0.8191 (mp10) REVERT: F 94 GLN cc_start: 0.8611 (pt0) cc_final: 0.8148 (pm20) REVERT: I 10 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8068 (mm-30) REVERT: I 23 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7790 (tm-30) REVERT: J 92 ASP cc_start: 0.8213 (t0) cc_final: 0.7568 (p0) REVERT: L 36 TYR cc_start: 0.7901 (m-80) cc_final: 0.7515 (m-80) REVERT: L 45 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8810 (tttt) REVERT: L 90 THR cc_start: 0.8461 (t) cc_final: 0.8025 (m) REVERT: L 95 LEU cc_start: 0.9337 (mp) cc_final: 0.8862 (tp) REVERT: P 101 ASP cc_start: 0.8656 (t70) cc_final: 0.8420 (t0) REVERT: Q 66 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8870 (ttmm) REVERT: Q 72 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7584 (p) REVERT: X 633 LYS cc_start: 0.8884 (mppt) cc_final: 0.8592 (mptt) REVERT: Z 585 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7889 (mtt180) outliers start: 92 outliers final: 68 residues processed: 401 average time/residue: 0.2840 time to fit residues: 179.8580 Evaluate side-chains 411 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 341 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain P residue 19 LYS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 64 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 543 ASN Chi-restraints excluded: chain X residue 599 SER Chi-restraints excluded: chain X residue 604 CYS Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain X residue 618 ASN Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 585 ARG Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 0.0370 chunk 171 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 131 optimal weight: 0.0970 chunk 234 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19724 Z= 0.187 Angle : 0.560 8.649 26858 Z= 0.282 Chirality : 0.046 0.511 3198 Planarity : 0.004 0.059 3346 Dihedral : 6.294 71.803 3514 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.14 % Allowed : 23.12 % Favored : 72.74 % 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: -3.10 (0.16), residues: 2420 helix: -1.99 (0.25), residues: 370 sheet: -1.39 (0.20), residues: 731 loop : -2.52 (0.15), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 571 HIS 0.004 0.001 HIS I 81 PHE 0.010 0.001 PHE B 382 TYR 0.023 0.001 TYR L 49 ARG 0.004 0.000 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 358 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 GLU cc_start: 0.7983 (tp30) cc_final: 0.7627 (tp30) REVERT: B 340 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7180 (tp30) REVERT: B 377 ASN cc_start: 0.7748 (t0) cc_final: 0.7440 (t0) REVERT: C 92 GLU cc_start: 0.7691 (tp30) cc_final: 0.7248 (tp30) REVERT: D 89 GLN cc_start: 0.8834 (mt0) cc_final: 0.8281 (mp10) REVERT: F 94 GLN cc_start: 0.8553 (pt0) cc_final: 0.8149 (pm20) REVERT: I 10 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8101 (mm-30) REVERT: I 23 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7719 (tm-30) REVERT: J 86 TYR cc_start: 0.8651 (m-80) cc_final: 0.7967 (m-10) REVERT: J 92 ASP cc_start: 0.8186 (t0) cc_final: 0.7580 (p0) REVERT: L 32 ASP cc_start: 0.7587 (p0) cc_final: 0.7277 (p0) REVERT: L 36 TYR cc_start: 0.7925 (m-80) cc_final: 0.7532 (m-80) REVERT: L 45 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8741 (tttt) REVERT: L 90 THR cc_start: 0.8408 (t) cc_final: 0.7967 (m) REVERT: L 95 LEU cc_start: 0.9285 (mp) cc_final: 0.8844 (tp) REVERT: P 64 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7523 (ptp90) REVERT: P 101 ASP cc_start: 0.8603 (t70) cc_final: 0.8399 (t0) REVERT: Q 72 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7583 (p) REVERT: X 633 LYS cc_start: 0.8880 (mppt) cc_final: 0.8584 (mptt) REVERT: Z 585 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7904 (mtt180) outliers start: 82 outliers final: 68 residues processed: 405 average time/residue: 0.3067 time to fit residues: 197.9819 Evaluate side-chains 420 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 349 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 ASN Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain P residue 19 LYS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 64 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 543 ASN Chi-restraints excluded: chain X residue 599 SER Chi-restraints excluded: chain X residue 604 CYS Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain X residue 618 ASN Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 585 ARG Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 148 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19724 Z= 0.296 Angle : 0.607 8.480 26858 Z= 0.304 Chirality : 0.047 0.510 3198 Planarity : 0.004 0.055 3346 Dihedral : 6.388 73.859 3514 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.09 % Allowed : 23.47 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.16), residues: 2420 helix: -1.86 (0.25), residues: 374 sheet: -1.40 (0.20), residues: 731 loop : -2.48 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 479 HIS 0.005 0.001 HIS I 81 PHE 0.012 0.001 PHE A 53 TYR 0.016 0.001 TYR B 435 ARG 0.004 0.000 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 351 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7293 (tp30) REVERT: B 377 ASN cc_start: 0.7763 (t0) cc_final: 0.7481 (t0) REVERT: D 89 GLN cc_start: 0.8868 (mt0) cc_final: 0.8164 (mp10) REVERT: F 77 GLU cc_start: 0.8967 (pm20) cc_final: 0.8661 (pm20) REVERT: F 94 GLN cc_start: 0.8558 (pt0) cc_final: 0.8149 (pm20) REVERT: I 10 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8074 (mm-30) REVERT: I 23 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7567 (tm-30) REVERT: J 86 TYR cc_start: 0.8760 (m-80) cc_final: 0.8061 (m-10) REVERT: J 92 ASP cc_start: 0.8202 (t0) cc_final: 0.7566 (p0) REVERT: L 45 LYS cc_start: 0.9131 (ttpt) cc_final: 0.8881 (tttt) REVERT: L 90 THR cc_start: 0.8461 (t) cc_final: 0.8029 (m) REVERT: L 95 LEU cc_start: 0.9299 (mp) cc_final: 0.8841 (tp) REVERT: P 101 ASP cc_start: 0.8648 (t70) cc_final: 0.8425 (t0) REVERT: Q 72 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7583 (p) REVERT: X 633 LYS cc_start: 0.8968 (mppt) cc_final: 0.8578 (mptt) REVERT: Z 585 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7919 (mtt180) outliers start: 81 outliers final: 69 residues processed: 401 average time/residue: 0.2779 time to fit residues: 176.5893 Evaluate side-chains 413 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 342 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 LYS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 64 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 543 ASN Chi-restraints excluded: chain X residue 599 SER Chi-restraints excluded: chain X residue 604 CYS Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain X residue 618 ASN Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 585 ARG Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 217 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19724 Z= 0.200 Angle : 0.580 10.606 26858 Z= 0.290 Chirality : 0.046 0.509 3198 Planarity : 0.004 0.057 3346 Dihedral : 6.093 72.465 3514 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.14 % Allowed : 23.62 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.16), residues: 2420 helix: -1.63 (0.26), residues: 370 sheet: -1.27 (0.20), residues: 733 loop : -2.42 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 571 HIS 0.005 0.001 HIS I 81 PHE 0.009 0.001 PHE B 53 TYR 0.024 0.001 TYR L 49 ARG 0.004 0.000 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 351 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8601 (mttt) cc_final: 0.8322 (mttm) REVERT: B 340 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7180 (tp30) REVERT: B 377 ASN cc_start: 0.7782 (t0) cc_final: 0.7474 (t0) REVERT: C 92 GLU cc_start: 0.7786 (tp30) cc_final: 0.7403 (tp30) REVERT: D 89 GLN cc_start: 0.8876 (mt0) cc_final: 0.8171 (mp10) REVERT: F 77 GLU cc_start: 0.8941 (pm20) cc_final: 0.8650 (pm20) REVERT: F 94 GLN cc_start: 0.8582 (pt0) cc_final: 0.8176 (pm20) REVERT: I 10 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8082 (mm-30) REVERT: I 23 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7573 (tm-30) REVERT: J 86 TYR cc_start: 0.8702 (m-80) cc_final: 0.8114 (m-10) REVERT: J 92 ASP cc_start: 0.8184 (t0) cc_final: 0.7567 (p0) REVERT: L 45 LYS cc_start: 0.9163 (ttpt) cc_final: 0.8842 (tttt) REVERT: L 90 THR cc_start: 0.8395 (t) cc_final: 0.7967 (m) REVERT: L 95 LEU cc_start: 0.9281 (mp) cc_final: 0.8831 (tp) REVERT: Q 66 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8889 (ttmm) REVERT: Q 72 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7585 (p) REVERT: X 633 LYS cc_start: 0.8944 (mppt) cc_final: 0.8550 (mptt) REVERT: Z 585 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7928 (mtt180) outliers start: 82 outliers final: 74 residues processed: 400 average time/residue: 0.2767 time to fit residues: 176.2694 Evaluate side-chains 421 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 345 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 ASN Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain P residue 19 LYS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 64 ARG Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 543 ASN Chi-restraints excluded: chain X residue 599 SER Chi-restraints excluded: chain X residue 604 CYS Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain X residue 618 ASN Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 585 ARG Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.0006 > 50: distance: 69 - 76: 31.512 distance: 76 - 77: 45.557 distance: 77 - 80: 37.104 distance: 78 - 79: 52.134 distance: 78 - 84: 22.054 distance: 80 - 81: 6.253 distance: 81 - 82: 38.140 distance: 81 - 83: 38.597 distance: 84 - 85: 12.397 distance: 85 - 86: 5.645 distance: 85 - 88: 35.591 distance: 86 - 87: 16.613 distance: 86 - 92: 14.805 distance: 88 - 89: 31.593 distance: 89 - 90: 29.406 distance: 89 - 91: 34.274 distance: 92 - 93: 29.576 distance: 93 - 96: 10.742 distance: 94 - 95: 9.459 distance: 94 - 101: 32.198 distance: 96 - 97: 7.027 distance: 97 - 98: 14.299 distance: 98 - 99: 16.790 distance: 99 - 100: 19.594 distance: 101 - 102: 33.168 distance: 102 - 103: 9.501 distance: 102 - 105: 13.499 distance: 103 - 104: 33.442 distance: 103 - 109: 12.998 distance: 105 - 106: 35.363 distance: 106 - 107: 52.131 distance: 109 - 110: 11.071 distance: 110 - 111: 40.568 distance: 110 - 113: 21.814 distance: 111 - 112: 22.668 distance: 111 - 116: 10.021 distance: 113 - 114: 9.155 distance: 113 - 115: 9.246 distance: 116 - 117: 23.812 distance: 117 - 118: 25.809 distance: 117 - 120: 29.386 distance: 118 - 119: 13.445 distance: 118 - 123: 38.321 distance: 120 - 121: 23.518 distance: 120 - 122: 19.539 distance: 123 - 124: 56.303 distance: 124 - 125: 20.813 distance: 124 - 127: 16.119 distance: 125 - 126: 32.421 distance: 125 - 137: 45.184 distance: 127 - 128: 13.304 distance: 128 - 129: 17.116 distance: 128 - 130: 12.802 distance: 129 - 131: 7.104 distance: 130 - 132: 11.818 distance: 130 - 133: 7.462 distance: 131 - 132: 16.145 distance: 132 - 134: 9.911 distance: 133 - 135: 7.523 distance: 134 - 136: 8.314 distance: 135 - 136: 9.091 distance: 137 - 138: 37.992 distance: 138 - 139: 7.961 distance: 139 - 140: 28.541 distance: 139 - 141: 49.737 distance: 141 - 142: 11.104 distance: 142 - 143: 16.186 distance: 142 - 145: 29.153 distance: 143 - 144: 14.561 distance: 143 - 149: 21.716 distance: 145 - 146: 14.322 distance: 145 - 147: 33.474 distance: 146 - 148: 34.722 distance: 149 - 150: 21.485 distance: 150 - 151: 14.302 distance: 150 - 153: 12.472 distance: 151 - 152: 15.416 distance: 151 - 158: 25.874 distance: 153 - 154: 30.426 distance: 154 - 155: 32.872 distance: 155 - 156: 49.709 distance: 156 - 157: 5.140