Starting phenix.real_space_refine on Fri Dec 8 03:59:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/12_2023/7qtq_14145_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/12_2023/7qtq_14145.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/7qtq_14145/12_2023/7qtq_14145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/12_2023/7qtq_14145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/12_2023/7qtq_14145_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtq_14145/12_2023/7qtq_14145_trim_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= -0.014 sd= 1.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians I 8 10.91 5 S 202 5.16 5 C 17708 2.51 5 N 4934 2.21 5 O 5281 1.98 5 H 26821 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 296": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 342": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A ARG 592": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A ARG 651": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 656": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A GLU 662": "OE1" <-> "OE2" Residue "A ARG 667": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A ARG 931": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A ARG 964": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 979": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1007": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1008": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1078": "OE1" <-> "OE2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "A ARG 1116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1121": "OE1" <-> "OE2" Residue "A ARG 1254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1436": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1763": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1925": "OE1" <-> "OE2" Residue "A ARG 1953": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1980": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1996": "OE1" <-> "OE2" Residue "A ARG 1999": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 2010": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2038": "OE1" <-> "OE2" Residue "A ARG 2045": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2057": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 2133": "OE1" <-> "OE2" Residue "A ARG 2153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 2307": "OE1" <-> "OE2" Residue "A ARG 2378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2386": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 2427": "OE1" <-> "OE2" Residue "A ARG 2428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 2439": "OE1" <-> "OE2" Residue "A ARG 2494": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2498": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 2605": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 2641": "OE1" <-> "OE2" Residue "A GLU 2695": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B ARG 296": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 342": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 559": "OE1" <-> "OE2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "B ARG 592": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 644": "OE1" <-> "OE2" Residue "B ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 656": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B ARG 667": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 716": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 931": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 940": "OE1" <-> "OE2" Residue "B GLU 941": "OE1" <-> "OE2" Residue "B GLU 955": "OE1" <-> "OE2" Residue "B ARG 1007": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1008": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 1038": "OE1" <-> "OE2" Residue "B GLU 1078": "OE1" <-> "OE2" Residue "B GLU 1097": "OE1" <-> "OE2" Residue "B GLU 1113": "OE1" <-> "OE2" Residue "B ARG 1116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 1133": "OE1" <-> "OE2" Residue "B ARG 1254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1436": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1763": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 1918": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1925": "OE1" <-> "OE2" Residue "B ARG 1953": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1980": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1999": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2045": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 2055": "OE1" <-> "OE2" Residue "B ARG 2057": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2173": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2386": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 2427": "OE1" <-> "OE2" Residue "B ARG 2428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2494": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2498": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2532": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 2578": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 2581": "OE1" <-> "OE2" Residue "B ARG 2605": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 2641": "OE1" <-> "OE2" Residue "B GLU 2647": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 54954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 27326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1790, 27326 Unusual residues: {'T44': 1} Classifications: {'peptide': 1789, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 123, 'TRANS': 1663, None: 2} Not linked: pdbres="ASP A2572 " pdbres="T44 A2573 " Not linked: pdbres="T44 A2573 " pdbres="ALA A2574 " Chain breaks: 30 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'DHA:plan-1': 1, 'T44:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 27326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1789, 27326 Unusual residues: {'T44': 1} Classifications: {'peptide': 1788, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 123, 'TRANS': 1662, None: 2} Not linked: pdbres="ASP B2572 " pdbres="T44 B2573 " Not linked: pdbres="T44 B2573 " pdbres="ALA B2574 " Chain breaks: 30 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'DHA:plan-1': 1, 'T44:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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: "F" 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 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: 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 Time building chain proxies: 17.88, per 1000 atoms: 0.33 Number of scatterers: 54954 At special positions: 0 Unit cell: (207.9, 165.825, 122.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 8 52.95 S 202 16.00 O 5281 8.00 N 4934 7.00 C 17708 6.00 H 26821 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=78, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 52 " distance=2.02 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 92 " distance=2.02 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 120 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 138 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 297 " distance=1.99 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 319 " distance=1.67 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 408 " - pdb=" SG CYS A 607 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 686 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 702 " distance=2.02 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS A 725 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 773 " - pdb=" SG CYS A 898 " distance=2.04 Simple disulfide: pdb=" SG CYS A 900 " - pdb=" SG CYS A 921 " distance=2.04 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1031 " distance=1.99 Simple disulfide: pdb=" SG CYS A1042 " - pdb=" SG CYS A1049 " distance=2.03 Simple disulfide: pdb=" SG CYS A1051 " - pdb=" SG CYS A1073 " distance=2.03 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1108 " distance=2.02 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1145 " distance=2.03 Simple disulfide: pdb=" SG CYS A1245 " - pdb=" SG CYS A1281 " distance=2.03 Simple disulfide: pdb=" SG CYS A1441 " - pdb=" SG CYS A1461 " distance=2.00 Simple disulfide: pdb=" SG CYS A1894 " - pdb=" SG CYS A1920 " distance=2.04 Simple disulfide: pdb=" SG CYS A1898 " - pdb=" SG CYS A1905 " distance=2.03 Simple disulfide: pdb=" SG CYS A1929 " - pdb=" SG CYS A1940 " distance=2.03 Simple disulfide: pdb=" SG CYS A1997 " - pdb=" SG CYS A2025 " distance=2.02 Simple disulfide: pdb=" SG CYS A2001 " - pdb=" SG CYS A2007 " distance=2.04 Simple disulfide: pdb=" SG CYS A2006 " - pdb=" SG CYS A2077 " distance=2.03 Simple disulfide: pdb=" SG CYS A2130 " - pdb=" SG CYS A2154 " distance=2.03 Simple disulfide: pdb=" SG CYS A2134 " - pdb=" SG CYS A2140 " distance=2.03 Simple disulfide: pdb=" SG CYS A2163 " - pdb=" SG CYS A2172 " distance=2.03 Simple disulfide: pdb=" SG CYS A2264 " - pdb=" SG CYS A2281 " distance=2.02 Simple disulfide: pdb=" SG CYS A2442 " - pdb=" SG CYS A2453 " distance=2.03 Simple disulfide: pdb=" SG CYS A2591 " - pdb=" SG CYS A2715 " distance=2.04 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 70 " distance=2.02 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 120 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 138 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 319 " distance=2.02 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 408 " - pdb=" SG CYS B 607 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 686 " distance=2.02 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 702 " distance=2.02 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS B 725 " distance=2.03 Simple disulfide: pdb=" SG CYS B 729 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 773 " - pdb=" SG CYS B 898 " distance=2.03 Simple disulfide: pdb=" SG CYS B 900 " - pdb=" SG CYS B 921 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1031 " distance=2.02 Simple disulfide: pdb=" SG CYS B1042 " - pdb=" SG CYS B1049 " distance=2.03 Simple disulfide: pdb=" SG CYS B1051 " - pdb=" SG CYS B1073 " distance=2.02 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1145 " distance=2.03 Simple disulfide: pdb=" SG CYS B1245 " - pdb=" SG CYS B1281 " distance=2.03 Simple disulfide: pdb=" SG CYS B1441 " - pdb=" SG CYS B1461 " distance=2.02 Simple disulfide: pdb=" SG CYS B1894 " - pdb=" SG CYS B1920 " distance=2.03 Simple disulfide: pdb=" SG CYS B1898 " - pdb=" SG CYS B1905 " distance=2.03 Simple disulfide: pdb=" SG CYS B1929 " - pdb=" SG CYS B1940 " distance=2.03 Simple disulfide: pdb=" SG CYS B1997 " - pdb=" SG CYS B2025 " distance=2.02 Simple disulfide: pdb=" SG CYS B2001 " - pdb=" SG CYS B2007 " distance=2.03 Simple disulfide: pdb=" SG CYS B2006 " - pdb=" SG CYS B2077 " distance=2.03 Simple disulfide: pdb=" SG CYS B2130 " - pdb=" SG CYS B2154 " distance=2.03 Simple disulfide: pdb=" SG CYS B2134 " - pdb=" SG CYS B2140 " distance=2.03 Simple disulfide: pdb=" SG CYS B2163 " - pdb=" SG CYS B2172 " distance=2.03 Simple disulfide: pdb=" SG CYS B2264 " - pdb=" SG CYS B2281 " distance=2.02 Simple disulfide: pdb=" SG CYS B2442 " - pdb=" SG CYS B2453 " distance=2.03 Simple disulfide: pdb=" SG CYS B2591 " - pdb=" SG CYS B2715 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-4 " NAG C 2 " - " MAN C 3 " " NAG E 2 " - " MAN E 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2801 " - " ASN A2250 " " NAG A2802 " - " ASN A2295 " " NAG A2803 " - " ASN A2122 " " NAG A2804 " - " ASN A 947 " " NAG A2805 " - " ASN A 198 " " NAG A2806 " - " ASN A 495 " " NAG B2801 " - " ASN B 198 " " NAG B2802 " - " ASN B 495 " " NAG B2803 " - " ASN B2250 " " NAG B2804 " - " ASN B2295 " " NAG B2805 " - " ASN B2122 " " NAG B2806 " - " ASN B 947 " " NAG C 1 " - " ASN A2014 " " NAG D 1 " - " ASN A 483 " " NAG E 1 " - " ASN B2014 " " NAG F 1 " - " ASN B 483 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 32.91 Conformation dependent library (CDL) restraints added in 4.0 seconds 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6626 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 28 sheets defined 27.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.53 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 removed outlier: 4.112A pdb=" N GLN A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 4.053A pdb=" N GLN A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 removed outlier: 3.919A pdb=" N ARG A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 213 No H-bonds generated for 'chain 'A' and resid 210 through 213' Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 275 through 292 removed outlier: 3.871A pdb=" N PHE A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 removed outlier: 3.649A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 Processing helix chain 'A' and resid 423 through 426 No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.924A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.735A pdb=" N GLN A 467 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 470 " --> pdb=" O GLN A 467 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 471 " --> pdb=" O GLN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 557 through 571 Processing helix chain 'A' and resid 574 through 583 removed outlier: 4.018A pdb=" N LEU A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 603 removed outlier: 3.547A pdb=" N MET A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 672 Processing helix chain 'A' and resid 728 through 742 Processing helix chain 'A' and resid 926 through 948 removed outlier: 3.737A pdb=" N VAL A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 3.592A pdb=" N ALA A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 987 removed outlier: 3.646A pdb=" N LEU A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS A 985 " --> pdb=" O THR A 981 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 986 " --> pdb=" O PHE A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1007 Processing helix chain 'A' and resid 1078 through 1086 Processing helix chain 'A' and resid 1148 through 1152 Processing helix chain 'A' and resid 1318 through 1328 removed outlier: 4.239A pdb=" N ARG A1328 " --> pdb=" O GLU A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1864 No H-bonds generated for 'chain 'A' and resid 1862 through 1864' Processing helix chain 'A' and resid 1888 through 1901 removed outlier: 3.617A pdb=" N GLU A1901 " --> pdb=" O ARG A1897 " (cutoff:3.500A) Processing helix chain 'A' and resid 1937 through 1939 No H-bonds generated for 'chain 'A' and resid 1937 through 1939' Processing helix chain 'A' and resid 1990 through 2003 Processing helix chain 'A' and resid 2091 through 2093 No H-bonds generated for 'chain 'A' and resid 2091 through 2093' Processing helix chain 'A' and resid 2099 through 2101 No H-bonds generated for 'chain 'A' and resid 2099 through 2101' Processing helix chain 'A' and resid 2123 through 2136 Processing helix chain 'A' and resid 2320 through 2324 Processing helix chain 'A' and resid 2339 through 2342 No H-bonds generated for 'chain 'A' and resid 2339 through 2342' Processing helix chain 'A' and resid 2354 through 2357 No H-bonds generated for 'chain 'A' and resid 2354 through 2357' Processing helix chain 'A' and resid 2361 through 2369 Processing helix chain 'A' and resid 2388 through 2396 removed outlier: 4.133A pdb=" N HIS A2395 " --> pdb=" O ILE A2391 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A2396 " --> pdb=" O ALA A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2426 through 2440 Processing helix chain 'A' and resid 2447 through 2456 removed outlier: 3.607A pdb=" N SER A2452 " --> pdb=" O GLN A2448 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A2456 " --> pdb=" O SER A2452 " (cutoff:3.500A) Processing helix chain 'A' and resid 2459 through 2470 removed outlier: 3.708A pdb=" N GLN A2466 " --> pdb=" O LEU A2462 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2497 removed outlier: 3.903A pdb=" N GLN A2497 " --> pdb=" O ALA A2493 " (cutoff:3.500A) Processing helix chain 'A' and resid 2516 through 2519 No H-bonds generated for 'chain 'A' and resid 2516 through 2519' Processing helix chain 'A' and resid 2521 through 2530 Processing helix chain 'A' and resid 2538 through 2547 removed outlier: 3.907A pdb=" N ALA A2542 " --> pdb=" O PHE A2539 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A2543 " --> pdb=" O DHA A2540 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A2547 " --> pdb=" O GLN A2544 " (cutoff:3.500A) Processing helix chain 'A' and resid 2555 through 2564 Processing helix chain 'A' and resid 2576 through 2588 removed outlier: 3.936A pdb=" N GLN A2582 " --> pdb=" O ARG A2578 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A2583 " --> pdb=" O ALA A2579 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2602 removed outlier: 4.031A pdb=" N ALA A2597 " --> pdb=" O VAL A2593 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2636 No H-bonds generated for 'chain 'A' and resid 2634 through 2636' Processing helix chain 'A' and resid 2646 through 2665 Processing helix chain 'A' and resid 2712 through 2726 removed outlier: 3.915A pdb=" N ILE A2722 " --> pdb=" O TRP A2718 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN A2723 " --> pdb=" O SER A2719 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 95 through 104 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 275 through 292 removed outlier: 3.649A pdb=" N PHE B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 364 through 376 Processing helix chain 'B' and resid 413 through 416 No H-bonds generated for 'chain 'B' and resid 413 through 416' Processing helix chain 'B' and resid 423 through 426 No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 436 through 445 Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.577A pdb=" N LEU B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 470 removed outlier: 4.505A pdb=" N GLN B 467 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 470 " --> pdb=" O GLN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 557 through 571 Processing helix chain 'B' and resid 574 through 583 removed outlier: 4.116A pdb=" N LEU B 578 " --> pdb=" O PRO B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 603 Processing helix chain 'B' and resid 660 through 674 removed outlier: 3.547A pdb=" N GLY B 673 " --> pdb=" O GLN B 669 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 742 Processing helix chain 'B' and resid 926 through 948 removed outlier: 3.774A pdb=" N VAL B 932 " --> pdb=" O VAL B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 960 Processing helix chain 'B' and resid 991 through 1009 removed outlier: 3.625A pdb=" N LEU B1009 " --> pdb=" O TYR B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1086 Processing helix chain 'B' and resid 1148 through 1153 Processing helix chain 'B' and resid 1318 through 1328 removed outlier: 3.819A pdb=" N GLU B1324 " --> pdb=" O PHE B1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 1862 through 1864 No H-bonds generated for 'chain 'B' and resid 1862 through 1864' Processing helix chain 'B' and resid 1888 through 1899 Processing helix chain 'B' and resid 1937 through 1939 No H-bonds generated for 'chain 'B' and resid 1937 through 1939' Processing helix chain 'B' and resid 1990 through 2003 removed outlier: 3.598A pdb=" N PHE B1995 " --> pdb=" O SER B1991 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B2001 " --> pdb=" O CYS B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2091 through 2093 No H-bonds generated for 'chain 'B' and resid 2091 through 2093' Processing helix chain 'B' and resid 2123 through 2136 removed outlier: 3.636A pdb=" N ARG B2129 " --> pdb=" O ALA B2125 " (cutoff:3.500A) Processing helix chain 'B' and resid 2320 through 2324 Processing helix chain 'B' and resid 2339 through 2342 No H-bonds generated for 'chain 'B' and resid 2339 through 2342' Processing helix chain 'B' and resid 2354 through 2357 No H-bonds generated for 'chain 'B' and resid 2354 through 2357' Processing helix chain 'B' and resid 2361 through 2368 removed outlier: 3.658A pdb=" N VAL B2366 " --> pdb=" O ALA B2362 " (cutoff:3.500A) Processing helix chain 'B' and resid 2388 through 2395 removed outlier: 3.710A pdb=" N ILE B2394 " --> pdb=" O ASP B2390 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N HIS B2395 " --> pdb=" O ILE B2391 " (cutoff:3.500A) Processing helix chain 'B' and resid 2426 through 2440 removed outlier: 3.616A pdb=" N GLN B2431 " --> pdb=" O GLU B2427 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B2434 " --> pdb=" O ARG B2430 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B2436 " --> pdb=" O GLN B2432 " (cutoff:3.500A) Processing helix chain 'B' and resid 2447 through 2454 removed outlier: 3.597A pdb=" N CYS B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Processing helix chain 'B' and resid 2459 through 2469 removed outlier: 3.525A pdb=" N ALA B2465 " --> pdb=" O ILE B2461 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B2466 " --> pdb=" O LEU B2462 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B2467 " --> pdb=" O ASN B2463 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2492 through 2495 No H-bonds generated for 'chain 'B' and resid 2492 through 2495' Processing helix chain 'B' and resid 2516 through 2519 No H-bonds generated for 'chain 'B' and resid 2516 through 2519' Processing helix chain 'B' and resid 2521 through 2529 Processing helix chain 'B' and resid 2538 through 2545 removed outlier: 4.154A pdb=" N ALA B2542 " --> pdb=" O PHE B2539 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B2543 " --> pdb=" O DHA B2540 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B2545 " --> pdb=" O ALA B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2555 through 2563 Processing helix chain 'B' and resid 2576 through 2588 removed outlier: 3.930A pdb=" N GLN B2582 " --> pdb=" O ARG B2578 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B2583 " --> pdb=" O ALA B2579 " (cutoff:3.500A) Processing helix chain 'B' and resid 2592 through 2602 removed outlier: 3.888A pdb=" N ALA B2597 " --> pdb=" O VAL B2593 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B2601 " --> pdb=" O ALA B2597 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2636 No H-bonds generated for 'chain 'B' and resid 2634 through 2636' Processing helix chain 'B' and resid 2646 through 2665 removed outlier: 4.033A pdb=" N GLN B2657 " --> pdb=" O LEU B2653 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B2663 " --> pdb=" O PHE B2659 " (cutoff:3.500A) Processing helix chain 'B' and resid 2712 through 2719 removed outlier: 3.501A pdb=" N PHE B2717 " --> pdb=" O ALA B2713 " (cutoff:3.500A) Processing helix chain 'B' and resid 2721 through 2726 Processing sheet with id= A, first strand: chain 'A' and resid 192 through 194 Processing sheet with id= B, first strand: chain 'A' and resid 328 through 330 Processing sheet with id= C, first strand: chain 'A' and resid 629 through 631 Processing sheet with id= D, first strand: chain 'A' and resid 695 through 697 Processing sheet with id= E, first strand: chain 'A' and resid 1117 through 1120 Processing sheet with id= F, first strand: chain 'A' and resid 1289 through 1291 removed outlier: 4.044A pdb=" N THR A1289 " --> pdb=" O GLY A1440 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1865 through 1867 removed outlier: 6.453A pdb=" N LEU A1942 " --> pdb=" O ILE A1866 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 1907 through 1910 removed outlier: 3.768A pdb=" N TYR A1923 " --> pdb=" O LEU A1907 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1973 through 1975 Processing sheet with id= J, first strand: chain 'A' and resid 2010 through 2015 Processing sheet with id= K, first strand: chain 'A' and resid 2094 through 2096 Processing sheet with id= L, first strand: chain 'A' and resid 2200 through 2203 removed outlier: 5.652A pdb=" N GLY A2253 " --> pdb=" O GLN A2208 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU A2210 " --> pdb=" O GLY A2253 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TRP A2255 " --> pdb=" O LEU A2210 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2212 through 2217 removed outlier: 6.599A pdb=" N ARG A2409 " --> pdb=" O LEU A2382 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ALA A2384 " --> pdb=" O ARG A2409 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A2411 " --> pdb=" O ALA A2384 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A2507 " --> pdb=" O LEU A2412 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N PHE A2609 " --> pdb=" O ILE A2508 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N SER A2510 " --> pdb=" O PHE A2609 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A2611 " --> pdb=" O SER A2510 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 2696 through 2699 Processing sheet with id= O, first strand: chain 'B' and resid 192 through 194 Processing sheet with id= P, first strand: chain 'B' and resid 328 through 330 Processing sheet with id= Q, first strand: chain 'B' and resid 629 through 631 Processing sheet with id= R, first strand: chain 'B' and resid 695 through 697 Processing sheet with id= S, first strand: chain 'B' and resid 1117 through 1120 Processing sheet with id= T, first strand: chain 'B' and resid 1366 through 1371 removed outlier: 3.723A pdb=" N THR B1292 " --> pdb=" O TRP B1368 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR B1289 " --> pdb=" O GLY B1440 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 1865 through 1867 removed outlier: 6.287A pdb=" N LEU B1942 " --> pdb=" O ILE B1866 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'B' and resid 1973 through 1975 removed outlier: 3.526A pdb=" N LYS B1973 " --> pdb=" O THR B2035 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 2010 through 2015 Processing sheet with id= X, first strand: chain 'B' and resid 2094 through 2096 Processing sheet with id= Y, first strand: chain 'B' and resid 2200 through 2203 removed outlier: 5.762A pdb=" N GLY B2253 " --> pdb=" O GLN B2208 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU B2210 " --> pdb=" O GLY B2253 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TRP B2255 " --> pdb=" O LEU B2210 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 2212 through 2217 Processing sheet with id= AA, first strand: chain 'B' and resid 2381 through 2384 removed outlier: 6.498A pdb=" N ARG B2409 " --> pdb=" O LEU B2382 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ALA B2384 " --> pdb=" O ARG B2409 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B2411 " --> pdb=" O ALA B2384 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'B' and resid 2696 through 2698 656 hydrogen bonds defined for protein. 1857 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: 18.62 Time building geometry restraints manager: 34.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.68: 55354 1.68 - 2.52: 242 2.52 - 3.36: 1 3.36 - 4.20: 0 4.20 - 5.05: 1 Warning: very large bond lengths. Bond restraints: 55598 Sorted by residual: bond pdb=" CH2 TRP B1879 " pdb=" HH2 TRP B1879 " ideal model delta sigma weight residual 0.930 5.047 -4.117 2.00e-02 2.50e+03 4.24e+04 bond pdb=" CH2 TRP B2354 " pdb=" HH2 TRP B2354 " ideal model delta sigma weight residual 0.930 2.911 -1.981 2.00e-02 2.50e+03 9.81e+03 bond pdb=" CA DHA A2540 " pdb=" CB DHA A2540 " ideal model delta sigma weight residual 1.530 1.307 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CA DHA B2540 " pdb=" CB DHA B2540 " ideal model delta sigma weight residual 1.530 1.314 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C TRP B2354 " pdb=" O TRP B2354 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.17e-02 7.31e+03 2.19e+01 ... (remaining 55593 not shown) Histogram of bond angle deviations from ideal: 51.85 - 73.14: 1 73.14 - 94.43: 0 94.43 - 115.73: 69523 115.73 - 137.02: 30504 137.02 - 158.31: 1 Bond angle restraints: 100029 Sorted by residual: angle pdb=" CZ2 TRP B1879 " pdb=" CH2 TRP B1879 " pdb=" HH2 TRP B1879 " ideal model delta sigma weight residual 119.25 51.85 67.40 3.00e+00 1.11e-01 5.05e+02 angle pdb=" CZ3 TRP B1879 " pdb=" CH2 TRP B1879 " pdb=" HH2 TRP B1879 " ideal model delta sigma weight residual 119.25 158.31 -39.06 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C DHA A2540 " pdb=" CA DHA A2540 " pdb=" CB DHA A2540 " ideal model delta sigma weight residual 110.10 127.58 -17.48 1.90e+00 2.77e-01 8.46e+01 angle pdb=" C DHA B2540 " pdb=" CA DHA B2540 " pdb=" CB DHA B2540 " ideal model delta sigma weight residual 110.10 126.59 -16.49 1.90e+00 2.77e-01 7.53e+01 angle pdb=" N DHA B2540 " pdb=" CA DHA B2540 " pdb=" CB DHA B2540 " ideal model delta sigma weight residual 110.50 123.87 -13.37 1.70e+00 3.46e-01 6.18e+01 ... (remaining 100024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 24423 22.90 - 45.80: 1526 45.80 - 68.70: 214 68.70 - 91.60: 54 91.60 - 114.50: 1 Dihedral angle restraints: 26218 sinusoidal: 14135 harmonic: 12083 Sorted by residual: dihedral pdb=" C DHA A2540 " pdb=" N DHA A2540 " pdb=" CA DHA A2540 " pdb=" CB DHA A2540 " ideal model delta harmonic sigma weight residual -122.60 -179.89 57.29 0 2.50e+00 1.60e-01 5.25e+02 dihedral pdb=" CE3 TRP B1879 " pdb=" CZ3 TRP B1879 " pdb=" CH2 TRP B1879 " pdb=" HH2 TRP B1879 " ideal model delta harmonic sigma weight residual -180.00 -65.50 -114.50 0 5.00e+00 4.00e-02 5.24e+02 dihedral pdb=" N DHA A2540 " pdb=" C DHA A2540 " pdb=" CA DHA A2540 " pdb=" CB DHA A2540 " ideal model delta harmonic sigma weight residual 122.80 179.89 -57.09 0 2.50e+00 1.60e-01 5.21e+02 ... (remaining 26215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 4242 0.280 - 0.561: 9 0.561 - 0.841: 3 0.841 - 1.121: 0 1.121 - 1.402: 1 Chirality restraints: 4255 Sorted by residual: chirality pdb=" C1 MAN C 3 " pdb=" O4 NAG C 2 " pdb=" C2 MAN C 3 " pdb=" O5 MAN C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.08 0.32 2.00e-02 2.50e+03 2.50e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.01e+01 chirality pdb=" C1 MAN E 3 " pdb=" O4 NAG E 2 " pdb=" C2 MAN E 3 " pdb=" O5 MAN E 3 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.71e+01 ... (remaining 4252 not shown) Planarity restraints: 8391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1879 " -0.365 2.00e-02 2.50e+03 2.88e-01 3.33e+03 pdb=" CG TRP B1879 " -0.141 2.00e-02 2.50e+03 pdb=" CD1 TRP B1879 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B1879 " -0.031 2.00e-02 2.50e+03 pdb=" NE1 TRP B1879 " 0.192 2.00e-02 2.50e+03 pdb=" CE2 TRP B1879 " 0.167 2.00e-02 2.50e+03 pdb=" CE3 TRP B1879 " -0.100 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1879 " 0.305 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1879 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B1879 " 0.233 2.00e-02 2.50e+03 pdb=" HD1 TRP B1879 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 TRP B1879 " 0.306 2.00e-02 2.50e+03 pdb=" HE3 TRP B1879 " -0.244 2.00e-02 2.50e+03 pdb=" HZ2 TRP B1879 " 0.444 2.00e-02 2.50e+03 pdb=" HZ3 TRP B1879 " -0.011 2.00e-02 2.50e+03 pdb=" HH2 TRP B1879 " -0.776 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 565 " 0.129 2.00e-02 2.50e+03 1.37e-01 2.83e+02 pdb=" CD GLN A 565 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 565 " -0.122 2.00e-02 2.50e+03 pdb=" NE2 GLN A 565 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 565 " -0.200 2.00e-02 2.50e+03 pdb="HE22 GLN A 565 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 562 " -0.102 2.00e-02 2.50e+03 1.07e-01 1.72e+02 pdb=" CG ASN A 562 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 562 " 0.095 2.00e-02 2.50e+03 pdb=" ND2 ASN A 562 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 562 " 0.154 2.00e-02 2.50e+03 pdb="HD22 ASN A 562 " -0.160 2.00e-02 2.50e+03 ... (remaining 8388 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.25: 8172 2.25 - 2.93: 136824 2.93 - 3.61: 174011 3.61 - 4.28: 263627 4.28 - 4.96: 416107 Nonbonded interactions: 998741 Sorted by model distance: nonbonded pdb=" O SER B1989 " pdb=" H GLY B1993 " model vdw 1.573 1.850 nonbonded pdb=" O ALA B2538 " pdb=" H ALA B2542 " model vdw 1.603 1.850 nonbonded pdb=" O TYR A1966 " pdb="HH12 ARG B 169 " model vdw 1.620 1.850 nonbonded pdb=" O GLN A 761 " pdb="HE22 GLN A 772 " model vdw 1.621 1.850 nonbonded pdb=" O SER A1989 " pdb=" H GLY A1993 " model vdw 1.629 1.850 ... (remaining 998736 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 31 through 973 or resid 983 through 2250 or (resid 2251 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2 or name NE1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2 o \ r name H or name HA or name HB2 or name HB3 or name HD1 or name HE1 or name HE3 \ or name HZ2 or name HZ3)) or resid 2252 through 2727 or resid 2801 through 2806) \ ) selection = (chain 'B' and (resid 31 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name H or name HA )) or resid 197 through 314 or (resid 315 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2 or name CE1 or name CE2 or name CZ or name OH or name H or name HA or nam \ e HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2)) or resid 316 \ through 505 or (resid 549 and (name N or name CA or name C or name O or name HA \ 2 or name HA3)) or resid 550 through 637 or resid 646 through 2727 or resid 2801 \ through 2806)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 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: 0.590 Extract box with map and model: 26.760 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 134.000 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.220 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:2.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.223 28777 Z= 0.523 Angle : 0.842 17.476 38988 Z= 0.474 Chirality : 0.058 1.402 4255 Planarity : 0.006 0.073 5112 Dihedral : 15.095 87.829 10882 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 0.20 % Allowed : 0.70 % Favored : 99.11 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.81 % 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: -2.27 (0.14), residues: 3443 helix: -0.99 (0.15), residues: 1039 sheet: -2.29 (0.24), residues: 422 loop : -1.60 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B2251 HIS 0.022 0.001 HIS A 313 PHE 0.049 0.002 PHE A 602 TYR 0.016 0.002 TYR B2059 ARG 0.029 0.001 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 387 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 392 average time/residue: 0.8856 time to fit residues: 535.3378 Evaluate side-chains 315 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 313 time to evaluate : 3.153 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4750 time to fit residues: 5.8840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 279 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 208 optimal weight: 2.9990 chunk 324 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28777 Z= 0.206 Angle : 0.588 10.598 38988 Z= 0.296 Chirality : 0.040 0.312 4255 Planarity : 0.006 0.141 5112 Dihedral : 6.627 59.262 4292 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.43 % Allowed : 5.53 % Favored : 94.04 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 3443 helix: -0.48 (0.16), residues: 1053 sheet: -2.07 (0.24), residues: 423 loop : -1.49 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 899 HIS 0.004 0.001 HIS A 313 PHE 0.018 0.001 PHE B 579 TYR 0.014 0.001 TYR B 945 ARG 0.007 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 353 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 340 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 349 average time/residue: 0.9272 time to fit residues: 489.2808 Evaluate side-chains 324 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 312 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5796 time to fit residues: 16.8588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 269 optimal weight: 0.0980 chunk 220 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 1.9990 chunk 350 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 322 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28777 Z= 0.264 Angle : 0.569 10.738 38988 Z= 0.285 Chirality : 0.040 0.330 4255 Planarity : 0.005 0.141 5112 Dihedral : 6.298 60.000 4292 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.33 % Allowed : 7.06 % Favored : 92.61 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3443 helix: -0.21 (0.16), residues: 1046 sheet: -1.98 (0.25), residues: 415 loop : -1.46 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2562 HIS 0.004 0.001 HIS B 320 PHE 0.011 0.001 PHE A 494 TYR 0.013 0.001 TYR B2157 ARG 0.007 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 330 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 335 average time/residue: 0.9031 time to fit residues: 453.7725 Evaluate side-chains 314 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 306 time to evaluate : 3.201 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4859 time to fit residues: 11.4373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 218 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 345 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 308 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A2568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28777 Z= 0.238 Angle : 0.549 12.143 38988 Z= 0.274 Chirality : 0.040 0.288 4255 Planarity : 0.005 0.142 5112 Dihedral : 6.023 59.276 4292 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.33 % Allowed : 8.22 % Favored : 91.45 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3443 helix: -0.01 (0.16), residues: 1054 sheet: -1.92 (0.24), residues: 425 loop : -1.41 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 899 HIS 0.007 0.001 HIS A2568 PHE 0.011 0.001 PHE B2342 TYR 0.013 0.001 TYR B2157 ARG 0.009 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 322 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 327 average time/residue: 0.8995 time to fit residues: 441.6732 Evaluate side-chains 315 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 308 time to evaluate : 3.301 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4996 time to fit residues: 10.7078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 256 optimal weight: 0.0470 chunk 142 optimal weight: 0.9980 chunk 294 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 309 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1876 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28777 Z= 0.202 Angle : 0.531 11.266 38988 Z= 0.263 Chirality : 0.039 0.279 4255 Planarity : 0.005 0.142 5112 Dihedral : 5.795 59.249 4292 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.23 % Allowed : 9.24 % Favored : 90.52 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 3443 helix: 0.16 (0.16), residues: 1053 sheet: -1.81 (0.25), residues: 407 loop : -1.34 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2562 HIS 0.005 0.001 HIS B 320 PHE 0.015 0.001 PHE A 698 TYR 0.011 0.001 TYR A2157 ARG 0.009 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 326 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 330 average time/residue: 0.8868 time to fit residues: 444.0040 Evaluate side-chains 318 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 314 time to evaluate : 3.188 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4686 time to fit residues: 7.6772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 2.9990 chunk 310 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 345 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28777 Z= 0.261 Angle : 0.540 11.156 38988 Z= 0.269 Chirality : 0.039 0.275 4255 Planarity : 0.005 0.142 5112 Dihedral : 5.751 59.883 4292 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.40 % Allowed : 9.71 % Favored : 89.89 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 3443 helix: 0.27 (0.16), residues: 1050 sheet: -1.81 (0.25), residues: 407 loop : -1.33 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2562 HIS 0.005 0.001 HIS B 320 PHE 0.019 0.001 PHE A 566 TYR 0.013 0.001 TYR B2157 ARG 0.008 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 324 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 332 average time/residue: 0.8986 time to fit residues: 448.0181 Evaluate side-chains 312 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 305 time to evaluate : 3.271 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4735 time to fit residues: 10.5522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 196 optimal weight: 0.0570 chunk 252 optimal weight: 0.0670 chunk 195 optimal weight: 0.6980 chunk 290 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 344 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28777 Z= 0.177 Angle : 0.523 11.451 38988 Z= 0.258 Chirality : 0.039 0.262 4255 Planarity : 0.005 0.142 5112 Dihedral : 5.565 59.138 4292 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.27 % Allowed : 10.11 % Favored : 89.63 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 3443 helix: 0.42 (0.17), residues: 1052 sheet: -1.70 (0.26), residues: 407 loop : -1.23 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 899 HIS 0.005 0.001 HIS B 320 PHE 0.021 0.001 PHE B 570 TYR 0.012 0.001 TYR B2157 ARG 0.009 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 330 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 322 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 327 average time/residue: 0.9227 time to fit residues: 457.2741 Evaluate side-chains 310 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 307 time to evaluate : 3.205 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4876 time to fit residues: 6.9037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN A2432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 28777 Z= 0.493 Angle : 0.615 11.112 38988 Z= 0.313 Chirality : 0.043 0.288 4255 Planarity : 0.006 0.143 5112 Dihedral : 6.014 59.530 4292 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 0.43 % Allowed : 10.64 % Favored : 88.93 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3443 helix: 0.16 (0.16), residues: 1060 sheet: -1.87 (0.26), residues: 395 loop : -1.45 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B2251 HIS 0.007 0.001 HIS B 313 PHE 0.020 0.002 PHE B2342 TYR 0.016 0.002 TYR B2157 ARG 0.010 0.001 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 320 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 307 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 315 average time/residue: 0.9043 time to fit residues: 428.8722 Evaluate side-chains 305 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 296 time to evaluate : 3.204 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5058 time to fit residues: 12.5922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 0.1980 chunk 329 optimal weight: 0.8980 chunk 300 optimal weight: 0.9990 chunk 320 optimal weight: 0.7980 chunk 192 optimal weight: 0.0020 chunk 139 optimal weight: 0.3980 chunk 251 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 319 optimal weight: 0.0980 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28777 Z= 0.156 Angle : 0.530 11.593 38988 Z= 0.264 Chirality : 0.039 0.250 4255 Planarity : 0.006 0.142 5112 Dihedral : 5.581 57.098 4292 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.27 % Allowed : 11.07 % Favored : 88.67 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3443 helix: 0.44 (0.17), residues: 1053 sheet: -1.76 (0.26), residues: 407 loop : -1.23 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2562 HIS 0.005 0.001 HIS B 320 PHE 0.011 0.001 PHE B 214 TYR 0.012 0.001 TYR B2157 ARG 0.013 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 316 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 320 average time/residue: 0.9253 time to fit residues: 449.2279 Evaluate side-chains 313 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 307 time to evaluate : 3.177 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4885 time to fit residues: 9.7743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 0.5980 chunk 339 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 235 optimal weight: 0.3980 chunk 355 optimal weight: 0.6980 chunk 327 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 173 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN B2448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28777 Z= 0.193 Angle : 0.525 11.501 38988 Z= 0.259 Chirality : 0.039 0.259 4255 Planarity : 0.005 0.142 5112 Dihedral : 5.396 58.447 4292 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.10 % Allowed : 11.46 % Favored : 88.44 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3443 helix: 0.56 (0.17), residues: 1055 sheet: -1.70 (0.26), residues: 407 loop : -1.16 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2562 HIS 0.005 0.001 HIS B 320 PHE 0.016 0.001 PHE B 494 TYR 0.014 0.001 TYR A1923 ARG 0.012 0.000 ARG A 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 315 is missing expected H atoms. Skipping. Evaluate side-chains 317 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 314 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 317 average time/residue: 0.9403 time to fit residues: 449.0031 Evaluate side-chains 306 residues out of total 3019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 303 time to evaluate : 3.205 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.5440 time to fit residues: 7.1192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 0.1980 chunk 301 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 283 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 291 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.162290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114779 restraints weight = 85455.281| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.11 r_work: 0.3179 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28777 Z= 0.176 Angle : 0.519 11.574 38988 Z= 0.256 Chirality : 0.039 0.255 4255 Planarity : 0.005 0.142 5112 Dihedral : 5.264 59.512 4292 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.07 % Allowed : 11.80 % Favored : 88.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3443 helix: 0.64 (0.17), residues: 1059 sheet: -1.60 (0.26), residues: 399 loop : -1.12 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2562 HIS 0.004 0.001 HIS B 320 PHE 0.030 0.001 PHE B 494 TYR 0.023 0.001 TYR A1923 ARG 0.012 0.000 ARG A 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10771.60 seconds wall clock time: 187 minutes 12.70 seconds (11232.70 seconds total)