Starting phenix.real_space_refine on Sat Feb 17 19:19:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0l_20605/02_2024/6u0l_20605_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0l_20605/02_2024/6u0l_20605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0l_20605/02_2024/6u0l_20605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0l_20605/02_2024/6u0l_20605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0l_20605/02_2024/6u0l_20605_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u0l_20605/02_2024/6u0l_20605_neut_updated.pdb" } resolution = 3.3 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= 0.004 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 120 5.16 5 C 12319 2.51 5 N 3336 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" 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 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 101": "OD1" <-> "OD2" 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 ASP 85": "OD1" <-> "OD2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 101": "OD1" <-> "OD2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J ASP 82": "OD1" <-> "OD2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 85": "OD1" <-> "OD2" Residue "P TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 100": "OD1" <-> "OD2" Residue "Q ASP 60": "OD1" <-> "OD2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 85": "OD1" <-> "OD2" Residue "Q TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "X ASP 624": "OD1" <-> "OD2" Residue "X GLU 634": "OE1" <-> "OE2" Residue "X TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 624": "OD1" <-> "OD2" Residue "Z PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 542": "NH1" <-> "NH2" Residue "Z ASP 624": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19611 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2791 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2814 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 998 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'TYS:plan-2': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'TYS:plan-2': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1008 Chain: "I" Number of atoms: 998 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'TYS:plan-2': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'TYS:plan-2': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1008 Chain: "J" Number of atoms: 812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} bond proxies already assigned to first conformer: 803 Chain: "L" Number of atoms: 806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} bond proxies already assigned to first conformer: 810 Chain: "P" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'TYS:plan-2': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 Chain: "Q" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 984 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "Y" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Z" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 46 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: 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: "M" 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: "N" 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: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" 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: "S" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "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 Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS H 92 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 92 " occ=0.50 residue: pdb=" N ACYS I 92 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 92 " occ=0.50 residue: pdb=" N ASER J 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER J 70 " occ=0.50 residue: pdb=" N ACYS J 88 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 88 " occ=0.50 residue: pdb=" N ASER L 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER L 70 " occ=0.50 residue: pdb=" C1 NAG B 604 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG B 604 " occ=0.69 Time building chain proxies: 12.36, per 1000 atoms: 0.63 Number of scatterers: 19611 At special positions: 0 Unit cell: (149.037, 150.094, 154.322, 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 120 16.00 O 3836 8.00 N 3336 7.00 C 12319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS Y 605 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 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 ACYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG BCYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG ACYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG BCYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG ACYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG BCYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS 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=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.02 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 K 4 " - " MAN K 5 " " MAN O 4 " - " MAN O 5 " " MAN S 4 " - " MAN S 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA O 3 " - " MAN O 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG A 601 " - " ASN A 363 " " NAG A 604 " - " ASN A 448 " " NAG A 612 " - " ASN A 339 " " NAG A 613 " - " ASN A 88 " " NAG A 614 " - " ASN A 234 " " NAG A 615 " - " ASN A 355 " " NAG B 601 " - " ASN B 339 " " NAG B 604 " - " ASN B 234 " " NAG B 605 " - " ASN B 448 " " NAG B 615 " - " ASN B 332 " " NAG B 616 " - " ASN B 363 " " NAG C 601 " - " ASN C 448 " " NAG C 607 " - " ASN C 276 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 332 " " NAG C 610 " - " ASN C 339 " " NAG C 611 " - " ASN C 386 " " NAG C 612 " - " ASN C 88 " " NAG C 613 " - " ASN C 363 " " NAG C 614 " - " ASN C 392 " " NAG G 1 " - " ASN A 386 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN B 386 " " NAG O 1 " - " ASN B 262 " " NAG R 1 " - " ASN B 276 " " NAG S 1 " - " ASN C 262 " " NAG X 701 " - " ASN X 637 " Time building additional restraints: 8.10 Conformation dependent library (CDL) restraints added in 4.6 seconds 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 42 sheets defined 15.6% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.678A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.748A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.731A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.999A pdb=" N THR B 71 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 104 No H-bonds generated for 'chain 'B' and resid 101 through 104' Processing helix chain 'B' and resid 106 through 114 removed outlier: 4.014A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 475 through 478 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.819A pdb=" N TRP C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.611A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.798A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'D' and resid 59 through 64 removed outlier: 3.531A pdb=" N TRP D 62 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 64 removed outlier: 3.531A pdb=" N TRP E 62 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP E 63 " --> pdb=" O SER E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 64 removed outlier: 3.530A pdb=" N TRP F 62 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 100A through 100C No H-bonds generated for 'chain 'H' and resid 100A through 100C' 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 97 through 100 removed outlier: 3.548A pdb=" N VAL I 100 " --> pdb=" O ILE I 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 97 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 '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: 4.509A pdb=" N LEU X 523 " --> pdb=" O PHE X 519 " (cutoff:3.500A) Processing helix chain 'X' and resid 530 through 535 Processing helix chain 'X' and resid 537 through 543 removed outlier: 3.873A pdb=" N ALA X 541 " --> pdb=" O LEU X 537 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG X 542 " --> pdb=" O THR X 538 " (cutoff:3.500A) Processing helix chain 'X' and resid 561 through 576 removed outlier: 3.682A pdb=" N LEU X 568 " --> pdb=" O HIS X 564 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TRP X 571 " --> pdb=" O LYS X 567 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY X 572 " --> pdb=" O LEU X 568 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE X 573 " --> pdb=" O THR X 569 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN X 575 " --> pdb=" O TRP X 571 " (cutoff:3.500A) Processing helix chain 'X' and resid 579 through 590 removed outlier: 3.645A pdb=" N ARG X 588 " --> pdb=" O GLU X 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP X 589 " --> pdb=" O ARG X 585 " (cutoff:3.500A) Processing helix chain 'X' and resid 592 through 596 removed outlier: 3.676A pdb=" N TRP X 596 " --> pdb=" O LEU X 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 592 through 596' Processing helix chain 'X' and resid 619 through 623 Processing helix chain 'X' and resid 628 through 635 removed outlier: 3.644A pdb=" N GLU X 634 " --> pdb=" O GLN X 630 " (cutoff:3.500A) Processing helix chain 'X' and resid 639 through 652 removed outlier: 3.566A pdb=" N LEU X 645 " --> pdb=" O ILE X 641 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU X 647 " --> pdb=" O TYR X 643 " (cutoff:3.500A) Processing helix chain 'Y' and resid 515 through 525 removed outlier: 3.677A pdb=" N PHE Y 519 " --> pdb=" O GLY Y 516 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU Y 520 " --> pdb=" O ALA Y 517 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE Y 522 " --> pdb=" O PHE Y 519 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY Y 524 " --> pdb=" O GLY Y 521 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA Y 525 " --> pdb=" O PHE Y 522 " (cutoff:3.500A) Processing helix chain 'Y' and resid 530 through 543 removed outlier: 3.519A pdb=" N MET Y 535 " --> pdb=" O GLY Y 531 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR Y 538 " --> pdb=" O SER Y 534 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL Y 539 " --> pdb=" O MET Y 535 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG Y 542 " --> pdb=" O THR Y 538 " (cutoff:3.500A) Processing helix chain 'Y' and resid 562 through 565 No H-bonds generated for 'chain 'Y' and resid 562 through 565' Processing helix chain 'Y' and resid 570 through 595 removed outlier: 3.512A pdb=" N LYS Y 574 " --> pdb=" O VAL Y 570 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN Y 575 " --> pdb=" O TRP Y 571 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA Y 578 " --> pdb=" O LYS Y 574 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL Y 580 " --> pdb=" O LEU Y 576 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU Y 581 " --> pdb=" O GLN Y 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR Y 586 " --> pdb=" O ALA Y 582 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU Y 592 " --> pdb=" O ARG Y 588 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY Y 594 " --> pdb=" O GLN Y 590 " (cutoff:3.500A) Processing helix chain 'Y' and resid 628 through 635 removed outlier: 3.768A pdb=" N ASP Y 632 " --> pdb=" O TRP Y 628 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS Y 633 " --> pdb=" O LEU Y 629 " (cutoff:3.500A) Processing helix chain 'Y' and resid 639 through 652 removed outlier: 3.583A pdb=" N TYR Y 643 " --> pdb=" O THR Y 639 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN Y 650 " --> pdb=" O LEU Y 646 " (cutoff:3.500A) Processing helix chain 'Z' and resid 530 through 540 Processing helix chain 'Z' and resid 565 through 596 removed outlier: 4.366A pdb=" N GLN Z 575 " --> pdb=" O TRP Z 571 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG Z 579 " --> pdb=" O GLN Z 575 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR Z 586 " --> pdb=" O ALA Z 582 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN Z 591 " --> pdb=" O LEU Z 587 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU Z 592 " --> pdb=" O ARG Z 588 " (cutoff:3.500A) Processing helix chain 'Z' and resid 628 through 634 removed outlier: 3.571A pdb=" N ASP Z 632 " --> pdb=" O LEU Z 629 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS Z 633 " --> pdb=" O GLN Z 630 " (cutoff:3.500A) Processing helix chain 'Z' and resid 639 through 656 removed outlier: 3.831A pdb=" N GLN Z 650 " --> pdb=" O LEU Z 646 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN Z 653 " --> pdb=" O SER Z 649 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS Z 655 " --> pdb=" O ASN Z 651 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.637A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 120 through 124 Processing sheet with id= D, first strand: chain 'A' and resid 284 through 286 Processing sheet with id= E, first strand: chain 'A' and resid 447 through 449 Processing sheet with id= F, first strand: chain 'A' and resid 382 through 384 removed outlier: 4.468A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 35 through 40 removed outlier: 3.719A pdb=" N ALA B 497 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'B' and resid 83 through 85 Processing sheet with id= J, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.739A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 120 through 123 Processing sheet with id= L, first strand: chain 'B' and resid 223 through 225 Processing sheet with id= M, first strand: chain 'B' and resid 284 through 287 Processing sheet with id= N, first strand: chain 'B' and resid 443 through 449 removed outlier: 4.242A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 447 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 382 through 384 removed outlier: 4.629A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 54 through 56 Processing sheet with id= Q, first strand: chain 'C' and resid 91 through 93 Processing sheet with id= R, first strand: chain 'C' and resid 197 through 202 removed outlier: 3.678A pdb=" N VAL C 120 " --> pdb=" O MET C 434 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 223 through 225 Processing sheet with id= T, first strand: chain 'C' and resid 271 through 273 Processing sheet with id= U, first strand: chain 'C' and resid 443 through 447 removed outlier: 3.742A pdb=" N ILE C 294 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.536A pdb=" N ASN D 30 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS D 35 " --> pdb=" O ASN D 30 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 12 through 17 removed outlier: 3.630A pdb=" N VAL D 12 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS D 16 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 2 through 5 removed outlier: 6.536A pdb=" N ASN E 30 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS E 35 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 12 through 17 removed outlier: 3.630A pdb=" N VAL E 12 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS E 16 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.536A pdb=" N ASN F 30 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS F 35 " --> pdb=" O ASN F 30 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 12 through 17 removed outlier: 3.629A pdb=" N VAL F 12 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N CYS F 16 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.745A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.527A pdb=" N ASN H 95 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 4 through 6 Processing sheet with id= AE, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.538A pdb=" N ASN I 95 " --> pdb=" O ALA I 33 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.000A pdb=" N LYS J 103 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ALA J 13 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 6.104A 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 18 through 24 Processing sheet with id= AH, first strand: chain 'J' and resid 85 through 88 removed outlier: 5.679A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 90 through 92 Processing sheet with id= AJ, first strand: chain 'L' and resid 18 through 24 Processing sheet with id= AK, first strand: chain 'L' and resid 95B through 97 removed outlier: 5.774A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.765A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA P 40 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU P 45 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'P' and resid 18 through 23 Processing sheet with id= AN, first strand: chain 'Q' and resid 10 through 13 removed outlier: 6.327A pdb=" N LYS Q 103 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA Q 13 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR Q 105 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id= AP, first strand: chain 'Q' and resid 95B through 98 removed outlier: 5.894A pdb=" N GLN Q 37 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1360 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: 6.42 Time building geometry restraints manager: 8.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6267 1.34 - 1.48: 5419 1.48 - 1.62: 8179 1.62 - 1.76: 10 1.76 - 1.89: 143 Bond restraints: 20018 Sorted by residual: bond pdb=" O1 TYS I 100F" pdb=" S TYS I 100F" ideal model delta sigma weight residual 1.462 1.635 -0.173 2.00e-02 2.50e+03 7.48e+01 bond pdb=" O3 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.458 1.631 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" O1 TYS P 100F" pdb=" S TYS P 100F" ideal model delta sigma weight residual 1.462 1.632 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" O2 TYS P 100I" pdb=" S TYS P 100I" ideal model delta sigma weight residual 1.461 1.627 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" O3 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.458 1.624 -0.166 2.00e-02 2.50e+03 6.86e+01 ... (remaining 20013 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.46: 377 105.46 - 112.65: 11005 112.65 - 119.84: 6424 119.84 - 127.03: 9137 127.03 - 134.21: 309 Bond angle restraints: 27252 Sorted by residual: angle pdb=" N ARG X 542 " pdb=" CA ARG X 542 " pdb=" C ARG X 542 " ideal model delta sigma weight residual 113.43 105.11 8.32 1.26e+00 6.30e-01 4.36e+01 angle pdb=" C GLU L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 132.96 -11.42 1.91e+00 2.74e-01 3.58e+01 angle pdb=" N LEU X 544 " pdb=" CA LEU X 544 " pdb=" C LEU X 544 " ideal model delta sigma weight residual 108.99 117.15 -8.16 1.57e+00 4.06e-01 2.70e+01 angle pdb=" CA GLU L 50 " pdb=" CB GLU L 50 " pdb=" CG GLU L 50 " ideal model delta sigma weight residual 114.10 124.22 -10.12 2.00e+00 2.50e-01 2.56e+01 angle pdb=" C TYR H 100O" pdb=" N ASP H 100P" pdb=" CA ASP H 100P" ideal model delta sigma weight residual 122.46 129.42 -6.96 1.41e+00 5.03e-01 2.44e+01 ... (remaining 27247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 11391 21.34 - 42.68: 868 42.68 - 64.02: 153 64.02 - 85.36: 45 85.36 - 106.71: 16 Dihedral angle restraints: 12473 sinusoidal: 5311 harmonic: 7162 Sorted by residual: 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 -1.26 -84.74 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CA ILE A 277 " pdb=" C ILE A 277 " pdb=" N THR A 278 " pdb=" CA THR A 278 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ALA B 336 " pdb=" C ALA B 336 " pdb=" N THR B 337 " pdb=" CA THR B 337 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 12470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.220: 3216 0.220 - 0.439: 18 0.439 - 0.659: 2 0.659 - 0.878: 0 0.878 - 1.098: 2 Chirality restraints: 3238 Sorted by residual: chirality pdb=" C1 NAG C 611 " pdb=" ND2 ASN C 386 " pdb=" C2 NAG C 611 " pdb=" O5 NAG C 611 " both_signs ideal model delta sigma weight residual False -2.40 -1.30 -1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" C1 NAG B 605 " pdb=" ND2 ASN B 448 " pdb=" C2 NAG B 605 " pdb=" O5 NAG B 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" C1 NAG B 616 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 616 " pdb=" O5 NAG B 616 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 3235 not shown) Planarity restraints: 3430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 102 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C VAL P 102 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL P 102 " 0.021 2.00e-02 2.50e+03 pdb=" N TRP P 103 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 102 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" C VAL I 102 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL I 102 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP I 103 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 614 " -0.031 2.00e-02 2.50e+03 2.53e-02 8.02e+00 pdb=" C7 NAG C 614 " 0.008 2.00e-02 2.50e+03 pdb=" C8 NAG C 614 " -0.024 2.00e-02 2.50e+03 pdb=" N2 NAG C 614 " 0.040 2.00e-02 2.50e+03 pdb=" O7 NAG C 614 " 0.006 2.00e-02 2.50e+03 ... (remaining 3427 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 555 2.66 - 3.22: 17313 3.22 - 3.78: 29797 3.78 - 4.34: 39043 4.34 - 4.90: 66381 Nonbonded interactions: 153089 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.106 2.440 nonbonded pdb=" CB SER C 388 " pdb=" O7 NAG C 611 " model vdw 2.203 3.440 nonbonded pdb=" OD1 ASP P 72 " pdb=" OG SER P 74 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR B 37 " pdb=" OG1 THR B 499 " model vdw 2.292 2.440 nonbonded pdb=" OG SER B 334 " pdb=" OG1 THR B 337 " model vdw 2.299 2.440 ... (remaining 153084 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 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 86 or (r \ esid 87 and (name N or name CA or name C or name O or name CB )) or resid 88 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 126 or resid 194 through 202 or (resid 203 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 name O or name CB )) \ or resid 209 through 240 or (resid 241 and (name N or name CA or name C or name \ O or name CB )) or resid 242 through 251 or (resid 252 and (name N or name CA o \ r name C or name O or name CB )) or resid 253 through 266 or (resid 267 through \ 269 and (name N or name CA or name C or name O or name CB )) or resid 270 throug \ h 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 name C or name O o \ r name CB )) or resid 413 through 456 or (resid 457 and (name N or name CA or na \ me C or name O or name CB )) or resid 458 or (resid 460 and (name N or name CA o \ r name C or name O or name CB )) or resid 464 or (resid 465 and (name N or name \ CA or name C or name O or name CB or name OG1)) or (resid 466 and (name N or nam \ e CA or name C or name O or name CB )) or resid 467 through 501 or resid 604 thr \ ough 615)) selection = (chain 'B' and (resid 35 through 55 or (resid 56 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 79 or (resid 80 and (na \ me N or name CA or name C or name O or name CB )) or resid 81 through 89 or (res \ id 90 through 91 and (name N or name CA or name C or name O or name CB )) or res \ id 92 through 126 or resid 194 through 240 or (resid 241 and (name N or name CA \ or name C or name O or name CB )) or resid 242 through 245 or (resid 246 and (na \ me N or name CA or name C or name O or name CB )) or resid 247 through 349 or (r \ esid 350 and (name N or name CA or name C or name O or name CB )) or resid 351 t \ hrough 359 or (resid 360 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE )) or resid 361 through 397 or (resid 412 and (n \ ame N or name CA or name C or name O or name CB )) or resid 413 through 458 or ( \ resid 460 and (name N or name CA or name C or name O or name CB )) or resid 464 \ through 499 or (resid 500 and (name N or name CA or name C or name O or name CB \ )) or resid 501 or resid 601 through 616)) selection = (chain 'C' and (resid 35 through 45 or (resid 46 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 55 or (resid 56 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 (name N or name CA or name C or name O or name CB )) or res \ id 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or r \ esid 65 through 77 or (resid 78 and (name N or name CA or name C or name O or na \ me 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 through 89 or (resid 90 through 91 and (name N or name CA \ or name C or name O or name CB )) or resid 92 through 96 or (resid 97 and (name \ N or name CA or name C or name O or name CB )) or resid 98 through 116 or (resi \ d 117 and (name N or name CA or name C or name O or name CB )) or resid 118 thro \ ugh 202 or (resid 203 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 nam \ e CA or name C or name O or name CB )) or resid 209 through 245 or (resid 246 an \ d (name N or name CA or name C or name O or name CB )) or resid 247 through 251 \ or (resid 252 and (name N or name CA or name C or name O or name CB )) or resid \ 253 through 266 or (resid 267 through 269 and (name N or name CA or name C or na \ me O or name CB )) or resid 270 through 300 or resid 325 through 359 or (resid 3 \ 60 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE )) or resid 361 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 456 or (resid 457 and (name N \ or name CA or name C or name O or name CB )) or resid 458 or resid 463 through 4 \ 64 or (resid 465 and (name N or name CA or name C or name O or name CB or name O \ G1)) or resid 466 through 473 or (resid 474 and (name N or name CA or name C or \ name O or name CB )) or resid 475 through 499 or (resid 500 and (name N or name \ CA or name C or name O or name CB )) or resid 501 or resid 610 through 614)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = (chain 'H' and (resid 2 through 91 or resid 93 through 112)) selection = (chain 'I' and (resid 2 through 91 or resid 93 through 112)) selection = (chain 'P' and (resid 2 through 91 or resid 93 through 112)) } ncs_group { reference = (chain 'J' and (resid 2 through 69 or resid 71 through 87 or resid 89 through 10 \ 7)) selection = (chain 'L' and (resid 2 through 69 or resid 71 through 87 or resid 89 through 10 \ 7)) selection = (chain 'Q' and (resid 2 through 69 or resid 71 through 87 or resid 89 through 10 \ 7)) } ncs_group { reference = chain 'K' selection = chain 'S' } ncs_group { reference = (chain 'X' and ((resid 519 and (name N or name CA or name C or name O or name CB \ )) or resid 520 through 522 or (resid 523 and (name N or name CA or name C or n \ ame O or name CB )) or resid 524 through 542 or (resid 563 and (name N or name C \ A or name C or name O or name CB )) or resid 564 or (resid 565 and (name N or na \ me CA or name C or name O or name CB )) or resid 566 through 600 or (resid 601 a \ nd (name N or name CA or name C or name O or name CB )) or resid 602 through 636 \ or (resid 637 and (name N or name CA or name C or name O or name CB )) or resid \ 638 through 647 or (resid 648 and (name N or name CA or name C or name O or nam \ e CB )) or resid 649 through 651 or (resid 652 through 654 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'Y' and ((resid 519 and (name N or name CA or name C or name O or name CB \ )) or resid 520 through 522 or (resid 523 and (name N or name CA or name C or n \ ame O or name CB )) or resid 524 through 539 or (resid 540 through 542 and (name \ N or name CA or name C or name O or name CB )) or resid 563 through 564 or (res \ id 565 and (name N or name CA or name C or name O or name CB )) or resid 566 thr \ ough 598 or (resid 599 and (name N or name CA or name C or name O or name CB )) \ or resid 600 or (resid 601 and (name N or name CA or name C or name O or name CB \ )) or resid 602 through 615 or (resid 616 through 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 or name O or name CB )) or resid 631 through 632 or (res \ id 633 and (name N or name CA or name C or name O or name CB )) or resid 634 thr \ ough 636 or (resid 637 and (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 nam \ e C or name O or name CB )) or resid 642 through 646 or (resid 647 through 648 a \ nd (name N or name CA or name C or name O or name CB )) or resid 649 through 650 \ or (resid 651 through 654 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'Z' and (resid 519 through 541 or (resid 542 through 563 and (name N or n \ ame CA or name C or name O or name CB )) or resid 564 through 598 or (resid 599 \ and (name N or name CA or name C or name O or name CB )) or resid 600 through 61 \ 5 or (resid 616 through 617 and (name N or name CA or name C or name O or name C \ B )) or resid 618 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 thro \ ugh 641 and (name N or name CA or name C or name O or name CB )) or resid 642 th \ rough 646 or (resid 647 through 648 and (name N or name CA or name C or name O o \ r name CB )) or resid 649 or (resid 650 through 654 and (name N or name CA or na \ me C or name O or name CB )))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 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: 10.320 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 57.510 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.173 20018 Z= 0.700 Angle : 1.057 13.176 27252 Z= 0.567 Chirality : 0.069 1.098 3238 Planarity : 0.007 0.064 3402 Dihedral : 15.944 106.706 7743 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.53 % Favored : 90.34 % Rotamer: Outliers : 2.41 % Allowed : 9.65 % Favored : 87.94 % Cbeta Deviations : 0.04 % 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: -5.02 (0.13), residues: 2438 helix: -4.72 (0.09), residues: 439 sheet: -2.62 (0.17), residues: 758 loop : -3.25 (0.13), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 45 HIS 0.008 0.002 HIS C 66 PHE 0.023 0.003 PHE B 376 TYR 0.025 0.003 TYR A 217 ARG 0.007 0.001 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 462 time to evaluate : 2.386 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: B 435 TYR cc_start: 0.8524 (m-80) cc_final: 0.8284 (m-80) REVERT: C 279 ASN cc_start: 0.7022 (t0) cc_final: 0.6761 (t0) REVERT: C 368 ASP cc_start: 0.7454 (t70) cc_final: 0.7172 (t0) REVERT: E 63 ASP cc_start: 0.7538 (t70) cc_final: 0.7068 (t0) REVERT: E 81 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7908 (m) REVERT: E 85 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7314 (mp0) REVERT: E 94 GLN cc_start: 0.7357 (pp30) cc_final: 0.7087 (tm-30) REVERT: F 63 ASP cc_start: 0.7790 (t70) cc_final: 0.7568 (t0) REVERT: H 63 PHE cc_start: 0.8261 (m-80) cc_final: 0.8035 (m-80) REVERT: H 91 TYR cc_start: 0.7401 (m-80) cc_final: 0.6742 (m-10) REVERT: J 95 LEU cc_start: 0.9203 (mm) cc_final: 0.8968 (mm) REVERT: L 32 ASP cc_start: 0.8592 (p0) cc_final: 0.8204 (p0) REVERT: L 54 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7479 (mtm-85) REVERT: L 78 LEU cc_start: 0.8666 (mm) cc_final: 0.7489 (tt) outliers start: 48 outliers final: 11 residues processed: 488 average time/residue: 0.3409 time to fit residues: 244.8328 Evaluate side-chains 341 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 329 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain Z residue 606 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 222 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 99 ASN A 295 ASN A 352 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 425 ASN A 440 GLN B 195 ASN B 279 ASN B 374 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 197 ASN C 258 GLN C 280 ASN C 287 GLN C 293 GLN C 478 ASN D 27 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN F 27 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 81 HIS L 30 ASN P 6 GLN P 12 ASN Q 7 GLN Q 37 GLN X 543 ASN X 590 GLN ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 618 ASN X 656 ASN Y 543 ASN Y 625 ASN Z 616 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20018 Z= 0.258 Angle : 0.665 9.912 27252 Z= 0.340 Chirality : 0.047 0.496 3238 Planarity : 0.005 0.059 3402 Dihedral : 9.777 75.996 3608 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.45 % Allowed : 17.18 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.15), residues: 2438 helix: -3.55 (0.16), residues: 417 sheet: -1.96 (0.19), residues: 761 loop : -2.82 (0.14), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 479 HIS 0.005 0.001 HIS C 216 PHE 0.015 0.001 PHE B 361 TYR 0.030 0.002 TYR L 49 ARG 0.008 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 374 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.7345 (mmt) cc_final: 0.6869 (mmt) REVERT: E 63 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7271 (t0) REVERT: E 90 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7131 (mmtm) REVERT: F 50 LYS cc_start: 0.7646 (mppt) cc_final: 0.7342 (mptt) REVERT: F 63 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7612 (t0) REVERT: F 76 ILE cc_start: 0.8749 (mm) cc_final: 0.8484 (tp) REVERT: H 53 ILE cc_start: 0.8743 (tp) cc_final: 0.8323 (tp) REVERT: H 63 PHE cc_start: 0.8183 (m-80) cc_final: 0.7831 (m-80) REVERT: H 91 TYR cc_start: 0.7277 (m-80) cc_final: 0.6764 (m-10) REVERT: J 37 GLN cc_start: 0.6847 (tp40) cc_final: 0.6611 (tp40) REVERT: L 54 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7334 (mtm-85) REVERT: P 13 LYS cc_start: 0.8056 (tptt) cc_final: 0.7784 (tptt) REVERT: Q 54 ARG cc_start: 0.7802 (ptp-110) cc_final: 0.7461 (ptp-110) outliers start: 68 outliers final: 47 residues processed: 413 average time/residue: 0.3130 time to fit residues: 196.5083 Evaluate side-chains 381 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 331 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain J residue 36 TYR Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 641 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 348 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS I 39 GLN I 81 HIS J 38 GLN L 30 ASN ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 20018 Z= 0.546 Angle : 0.793 12.100 27252 Z= 0.400 Chirality : 0.052 0.455 3238 Planarity : 0.005 0.072 3402 Dihedral : 9.567 64.913 3602 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 4.63 % Allowed : 19.20 % Favored : 76.17 % 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: -3.84 (0.15), residues: 2438 helix: -2.94 (0.19), residues: 426 sheet: -1.89 (0.19), residues: 757 loop : -2.84 (0.15), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 479 HIS 0.009 0.002 HIS D 27 PHE 0.022 0.003 PHE B 223 TYR 0.029 0.002 TYR L 49 ARG 0.008 0.001 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 345 time to evaluate : 2.105 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: D 80 ASP cc_start: 0.7213 (p0) cc_final: 0.6636 (p0) REVERT: E 27 HIS cc_start: 0.7115 (OUTLIER) cc_final: 0.6587 (m90) REVERT: E 63 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7319 (t0) REVERT: E 90 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7468 (mmtm) REVERT: F 50 LYS cc_start: 0.7822 (mppt) cc_final: 0.7583 (mptt) REVERT: F 63 ASP cc_start: 0.8040 (t70) cc_final: 0.7810 (t0) REVERT: F 76 ILE cc_start: 0.8861 (mm) cc_final: 0.8585 (tp) REVERT: H 53 ILE cc_start: 0.8793 (tp) cc_final: 0.8429 (tp) REVERT: H 63 PHE cc_start: 0.8227 (m-80) cc_final: 0.7851 (m-80) REVERT: I 23 GLN cc_start: 0.8311 (tp40) cc_final: 0.8103 (tp40) REVERT: L 52 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8341 (p0) REVERT: L 54 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7291 (mtm-85) REVERT: P 23 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7625 (tm-30) REVERT: Q 54 ARG cc_start: 0.7836 (ptp-110) cc_final: 0.7528 (ptp-110) outliers start: 92 outliers final: 62 residues processed: 399 average time/residue: 0.2994 time to fit residues: 183.0609 Evaluate side-chains 386 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 320 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 639 THR Chi-restraints excluded: chain Y residue 647 GLU Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 641 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS F 27 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS L 30 ASN P 12 ASN ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20018 Z= 0.208 Angle : 0.620 10.588 27252 Z= 0.312 Chirality : 0.046 0.427 3238 Planarity : 0.004 0.064 3402 Dihedral : 8.440 59.519 3602 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.33 % Allowed : 20.14 % Favored : 75.53 % 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: -3.43 (0.15), residues: 2438 helix: -2.39 (0.21), residues: 427 sheet: -1.69 (0.19), residues: 758 loop : -2.61 (0.15), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 28 HIS 0.006 0.001 HIS E 27 PHE 0.014 0.001 PHE D 26 TYR 0.032 0.002 TYR J 86 ARG 0.009 0.000 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 360 time to evaluate : 2.287 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: D 80 ASP cc_start: 0.7112 (p0) cc_final: 0.6478 (p0) REVERT: E 63 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7200 (t0) REVERT: F 50 LYS cc_start: 0.7735 (mppt) cc_final: 0.7462 (mptt) REVERT: H 53 ILE cc_start: 0.8756 (tp) cc_final: 0.8383 (tp) REVERT: H 63 PHE cc_start: 0.8161 (m-80) cc_final: 0.7936 (m-80) REVERT: I 10 GLU cc_start: 0.6486 (tp30) cc_final: 0.6135 (tp30) REVERT: L 54 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7325 (mtm-85) REVERT: L 66 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7559 (ttpp) REVERT: P 13 LYS cc_start: 0.8045 (tptt) cc_final: 0.7842 (tptt) REVERT: P 23 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7727 (tm-30) REVERT: X 625 ASN cc_start: 0.6905 (p0) cc_final: 0.6696 (p0) REVERT: Z 629 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8240 (mm) outliers start: 86 outliers final: 62 residues processed: 410 average time/residue: 0.3003 time to fit residues: 191.0693 Evaluate side-chains 400 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 336 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 626 MET Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 636 SER Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 440 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN I 81 HIS L 30 ASN ** P 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20018 Z= 0.318 Angle : 0.652 10.605 27252 Z= 0.326 Chirality : 0.047 0.405 3238 Planarity : 0.004 0.067 3402 Dihedral : 8.019 59.698 3602 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.58 % Allowed : 21.42 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.16), residues: 2438 helix: -2.18 (0.22), residues: 438 sheet: -1.61 (0.19), residues: 765 loop : -2.56 (0.15), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 479 HIS 0.005 0.001 HIS C 216 PHE 0.012 0.002 PHE B 223 TYR 0.028 0.002 TYR J 86 ARG 0.010 0.001 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 349 time to evaluate : 2.261 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 91 GLU cc_start: 0.7502 (tp30) cc_final: 0.7160 (tp30) REVERT: D 80 ASP cc_start: 0.7193 (p0) cc_final: 0.6546 (p0) REVERT: E 63 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7258 (t0) REVERT: F 50 LYS cc_start: 0.7755 (mppt) cc_final: 0.7466 (mptt) REVERT: H 53 ILE cc_start: 0.8832 (tp) cc_final: 0.8482 (tp) REVERT: I 10 GLU cc_start: 0.6587 (tp30) cc_final: 0.6237 (tp30) REVERT: L 52 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8357 (p0) REVERT: L 54 ARG cc_start: 0.7629 (mtm110) cc_final: 0.7379 (mtm-85) REVERT: P 23 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7705 (tm-30) REVERT: Z 622 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8008 (tt) REVERT: Z 629 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8250 (mm) outliers start: 91 outliers final: 67 residues processed: 402 average time/residue: 0.3085 time to fit residues: 191.1962 Evaluate side-chains 400 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 329 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 570 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 636 SER Chi-restraints excluded: chain Y residue 639 THR Chi-restraints excluded: chain Y residue 647 GLU Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 622 ILE Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 chunk 196 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS I 81 HIS J 7 GLN L 30 ASN P 12 ASN P 81 HIS ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20018 Z= 0.205 Angle : 0.607 10.639 27252 Z= 0.302 Chirality : 0.046 0.389 3238 Planarity : 0.004 0.064 3402 Dihedral : 7.372 57.810 3599 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.23 % Allowed : 22.45 % Favored : 73.31 % 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: -3.08 (0.16), residues: 2438 helix: -1.89 (0.22), residues: 443 sheet: -1.44 (0.19), residues: 752 loop : -2.49 (0.15), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 479 HIS 0.004 0.001 HIS P 81 PHE 0.025 0.001 PHE F 67 TYR 0.031 0.001 TYR J 86 ARG 0.010 0.001 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 365 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 GLU cc_start: 0.7427 (tp30) cc_final: 0.7135 (tp30) REVERT: C 104 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7999 (ttt) REVERT: D 80 ASP cc_start: 0.7154 (p0) cc_final: 0.6516 (p0) REVERT: E 63 ASP cc_start: 0.7695 (t70) cc_final: 0.7216 (t0) REVERT: E 85 GLU cc_start: 0.7166 (mp0) cc_final: 0.6930 (mp0) REVERT: F 50 LYS cc_start: 0.7604 (mppt) cc_final: 0.7337 (mptt) REVERT: H 53 ILE cc_start: 0.8802 (tp) cc_final: 0.8455 (tp) REVERT: H 63 PHE cc_start: 0.8043 (m-80) cc_final: 0.7748 (m-80) REVERT: H 105 GLN cc_start: 0.8366 (pm20) cc_final: 0.8135 (pp30) REVERT: L 54 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7416 (mtm-85) REVERT: P 13 LYS cc_start: 0.7960 (tptt) cc_final: 0.7605 (tptt) REVERT: P 23 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7648 (tm-30) REVERT: P 46 GLU cc_start: 0.7133 (tt0) cc_final: 0.6905 (pt0) REVERT: Z 622 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7751 (tt) REVERT: Z 629 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8159 (mm) REVERT: Z 631 TRP cc_start: 0.7121 (OUTLIER) cc_final: 0.5797 (t60) outliers start: 84 outliers final: 69 residues processed: 411 average time/residue: 0.2905 time to fit residues: 185.4875 Evaluate side-chains 413 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 340 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 81 HIS Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 636 SER Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 622 ILE Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 173 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 236 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS I 81 HIS ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN L 31 ASN P 12 ASN ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20018 Z= 0.264 Angle : 0.633 10.852 27252 Z= 0.314 Chirality : 0.046 0.373 3238 Planarity : 0.004 0.065 3402 Dihedral : 8.138 117.193 3599 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.63 % Allowed : 22.65 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.16), residues: 2438 helix: -1.76 (0.23), residues: 443 sheet: -1.38 (0.19), residues: 779 loop : -2.52 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 35 HIS 0.018 0.001 HIS P 81 PHE 0.016 0.001 PHE Q 62 TYR 0.028 0.002 TYR J 86 ARG 0.012 0.001 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 352 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 GLU cc_start: 0.7457 (tp30) cc_final: 0.7174 (tp30) REVERT: B 347 LYS cc_start: 0.7710 (ttpp) cc_final: 0.7449 (ptmt) REVERT: E 63 ASP cc_start: 0.7740 (t70) cc_final: 0.7285 (t0) REVERT: E 85 GLU cc_start: 0.7200 (mp0) cc_final: 0.6969 (mp0) REVERT: F 50 LYS cc_start: 0.7648 (mppt) cc_final: 0.7397 (mptt) REVERT: F 87 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: F 94 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7152 (pm20) REVERT: H 53 ILE cc_start: 0.8820 (tp) cc_final: 0.8482 (tp) REVERT: H 64 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7546 (tpp80) REVERT: L 52 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8356 (p0) REVERT: L 54 ARG cc_start: 0.7643 (mtm110) cc_final: 0.7405 (mtm-85) REVERT: P 13 LYS cc_start: 0.7924 (tptt) cc_final: 0.7509 (tptt) REVERT: P 23 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7733 (tm-30) REVERT: P 45 LEU cc_start: 0.7735 (mt) cc_final: 0.7484 (mt) REVERT: X 530 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6613 (mtt) REVERT: Y 520 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8811 (tt) REVERT: Z 622 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7740 (tt) REVERT: Z 629 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8186 (mm) REVERT: Z 631 TRP cc_start: 0.7218 (OUTLIER) cc_final: 0.5941 (t60) outliers start: 92 outliers final: 70 residues processed: 405 average time/residue: 0.2897 time to fit residues: 182.5398 Evaluate side-chains 417 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 339 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 520 LEU Chi-restraints excluded: chain Y residue 570 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 636 SER Chi-restraints excluded: chain Y residue 639 THR Chi-restraints excluded: chain Y residue 647 GLU Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 622 ILE Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 440 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS I 81 HIS ** L 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN P 12 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20018 Z= 0.259 Angle : 0.635 10.924 27252 Z= 0.316 Chirality : 0.046 0.370 3238 Planarity : 0.004 0.065 3402 Dihedral : 8.047 116.217 3599 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.63 % Allowed : 22.94 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.16), residues: 2438 helix: -1.68 (0.23), residues: 445 sheet: -1.32 (0.19), residues: 750 loop : -2.49 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 479 HIS 0.006 0.001 HIS P 81 PHE 0.015 0.001 PHE F 67 TYR 0.033 0.002 TYR L 49 ARG 0.013 0.001 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 350 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 347 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7445 (ptmt) REVERT: C 104 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8059 (ttt) REVERT: E 63 ASP cc_start: 0.7712 (t70) cc_final: 0.7254 (t0) REVERT: F 50 LYS cc_start: 0.7635 (mppt) cc_final: 0.7415 (mptt) REVERT: F 87 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: H 53 ILE cc_start: 0.8817 (tp) cc_final: 0.8490 (tp) REVERT: H 64 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7492 (tpp80) REVERT: L 52 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8332 (p0) REVERT: L 54 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7435 (mtm-85) REVERT: P 13 LYS cc_start: 0.7908 (tptt) cc_final: 0.7481 (tptt) REVERT: P 23 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7720 (tm-30) REVERT: X 530 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6303 (mtt) REVERT: Y 520 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8823 (tt) REVERT: Z 622 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7723 (tt) REVERT: Z 629 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8225 (mm) REVERT: Z 631 TRP cc_start: 0.7234 (OUTLIER) cc_final: 0.6019 (t60) outliers start: 92 outliers final: 73 residues processed: 403 average time/residue: 0.2886 time to fit residues: 181.3842 Evaluate side-chains 416 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 335 time to evaluate : 2.271 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 520 LEU Chi-restraints excluded: chain Y residue 570 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 636 SER Chi-restraints excluded: chain Y residue 639 THR Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 622 ILE Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 440 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** L 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN P 12 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20018 Z= 0.311 Angle : 0.663 11.015 27252 Z= 0.330 Chirality : 0.047 0.376 3238 Planarity : 0.004 0.067 3402 Dihedral : 8.096 116.002 3599 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.58 % Allowed : 23.34 % Favored : 72.08 % 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: -2.93 (0.16), residues: 2438 helix: -1.65 (0.23), residues: 441 sheet: -1.31 (0.19), residues: 754 loop : -2.48 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 479 HIS 0.006 0.001 HIS P 81 PHE 0.025 0.002 PHE C 233 TYR 0.030 0.002 TYR L 49 ARG 0.014 0.001 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 340 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 GLU cc_start: 0.7440 (tp30) cc_final: 0.7128 (tp30) REVERT: B 347 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7472 (ptmt) REVERT: B 479 TRP cc_start: 0.7723 (m-90) cc_final: 0.7514 (m-90) REVERT: C 104 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8098 (ttt) REVERT: E 63 ASP cc_start: 0.7726 (t70) cc_final: 0.7278 (t0) REVERT: H 53 ILE cc_start: 0.8827 (tp) cc_final: 0.8515 (tp) REVERT: L 54 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7331 (mtm-85) REVERT: P 13 LYS cc_start: 0.7902 (tptt) cc_final: 0.7663 (tptt) REVERT: P 23 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7721 (tm-30) REVERT: X 530 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6661 (mtt) REVERT: Y 520 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8871 (tt) REVERT: Z 622 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7759 (tt) REVERT: Z 629 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8240 (mm) REVERT: Z 631 TRP cc_start: 0.7318 (OUTLIER) cc_final: 0.6130 (t60) outliers start: 91 outliers final: 78 residues processed: 392 average time/residue: 0.2843 time to fit residues: 174.5844 Evaluate side-chains 418 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 334 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain X residue 520 LEU Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 520 LEU Chi-restraints excluded: chain Y residue 570 VAL Chi-restraints excluded: chain Y residue 576 LEU Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 636 SER Chi-restraints excluded: chain Y residue 639 THR Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 536 THR Chi-restraints excluded: chain Z residue 622 ILE Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 161 optimal weight: 0.0870 chunk 244 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** L 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN P 12 ASN ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20018 Z= 0.319 Angle : 0.668 11.248 27252 Z= 0.334 Chirality : 0.047 0.377 3238 Planarity : 0.004 0.068 3402 Dihedral : 8.125 116.167 3599 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.43 % Allowed : 23.68 % Favored : 71.89 % 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: -2.89 (0.16), residues: 2438 helix: -1.63 (0.23), residues: 441 sheet: -1.31 (0.19), residues: 749 loop : -2.43 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 479 HIS 0.005 0.001 HIS P 81 PHE 0.021 0.002 PHE C 233 TYR 0.024 0.002 TYR J 87 ARG 0.015 0.001 ARG P 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 342 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 347 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7467 (ptmt) REVERT: C 104 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8061 (ttt) REVERT: E 63 ASP cc_start: 0.7718 (t70) cc_final: 0.7277 (t0) REVERT: H 53 ILE cc_start: 0.8829 (tp) cc_final: 0.8526 (tp) REVERT: L 54 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7550 (mtm-85) REVERT: P 13 LYS cc_start: 0.7906 (tptt) cc_final: 0.7373 (tptt) REVERT: P 23 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7700 (tm-30) REVERT: Q 54 ARG cc_start: 0.7869 (ptp-110) cc_final: 0.7663 (ptp-110) REVERT: X 530 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6665 (mtt) REVERT: Y 520 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8896 (tt) REVERT: Z 622 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7767 (tt) REVERT: Z 629 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8287 (mm) REVERT: Z 631 TRP cc_start: 0.7353 (OUTLIER) cc_final: 0.6184 (t60) outliers start: 88 outliers final: 74 residues processed: 392 average time/residue: 0.2876 time to fit residues: 176.1616 Evaluate side-chains 414 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 334 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain X residue 520 LEU Chi-restraints excluded: chain X residue 530 MET Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 520 LEU Chi-restraints excluded: chain Y residue 570 VAL Chi-restraints excluded: chain Y residue 576 LEU Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 636 SER Chi-restraints excluded: chain Y residue 639 THR Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 622 ILE Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** L 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 GLN ** X 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.133760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.096345 restraints weight = 107549.301| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 5.37 r_work: 0.3172 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20018 Z= 0.404 Angle : 0.714 11.647 27252 Z= 0.355 Chirality : 0.048 0.387 3238 Planarity : 0.004 0.068 3402 Dihedral : 8.304 116.001 3599 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.48 % Allowed : 23.54 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.97 (0.16), residues: 2438 helix: -1.74 (0.23), residues: 439 sheet: -1.34 (0.19), residues: 749 loop : -2.46 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 479 HIS 0.005 0.001 HIS C 216 PHE 0.018 0.002 PHE C 233 TYR 0.027 0.002 TYR L 49 ARG 0.015 0.001 ARG P 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4883.18 seconds wall clock time: 89 minutes 34.47 seconds (5374.47 seconds total)