Starting phenix.real_space_refine on Wed Nov 20 00:32:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/11_2024/8fis_29209.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/11_2024/8fis_29209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/11_2024/8fis_29209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/11_2024/8fis_29209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/11_2024/8fis_29209.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fis_29209/11_2024/8fis_29209.cif" } resolution = 3.18 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= 0.005 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 12660 2.51 5 N 3332 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20356 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "C" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3562 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "G" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "J" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1143 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1828 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" 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: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" 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: "c" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" 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: "i" 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" 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: "p" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "q" 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: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" 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: "t" 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: "u" 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: "v" 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: "w" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.27, per 1000 atoms: 0.70 Number of scatterers: 20356 At special positions: 0 Unit cell: (154.869, 134.292, 145.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 4230 8.00 N 3332 7.00 C 12660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.08 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100Q" distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L1023 " - pdb=" SG CYS L1088 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA c 3 " - " MAN c 4 " " BMA p 3 " - " MAN p 4 " " BMA w 3 " - " MAN w 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 5 " " BMA e 3 " - " MAN e 4 " " BMA r 3 " - " MAN r 4 " " BMA w 3 " - " MAN w 5 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 618 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 355 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 462 " " NAG D 1 " - " ASN C 197 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 618 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 339 " " NAG F 603 " - " ASN F 355 " " NAG F 604 " - " ASN F 137 " " NAG F 605 " - " ASN F 462 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 276 " " NAG G 604 " - " ASN G 339 " " NAG G 605 " - " ASN G 355 " " NAG G 606 " - " ASN G 137 " " NAG G 607 " - " ASN G 462 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 295 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 392 " " NAG S 1 " - " ASN C 160 " " NAG T 1 " - " ASN C 363 " " NAG U 1 " - " ASN C 133 " " NAG V 1 " - " ASN C 276 " " NAG W 1 " - " ASN C 88 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN F 156 " " NAG a 1 " - " ASN F 197 " " NAG b 1 " - " ASN F 234 " " NAG c 1 " - " ASN F 262 " " NAG d 1 " - " ASN F 295 " " NAG e 1 " - " ASN F 301 " " NAG f 1 " - " ASN F 332 " " NAG g 1 " - " ASN F 386 " " NAG h 1 " - " ASN F 392 " " NAG i 1 " - " ASN F 448 " " NAG j 1 " - " ASN F 160 " " NAG k 1 " - " ASN F 363 " " NAG l 1 " - " ASN F 133 " " NAG m 1 " - " ASN F 276 " " NAG n 1 " - " ASN G 197 " " NAG o 1 " - " ASN G 234 " " NAG p 1 " - " ASN G 262 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 301 " " NAG s 1 " - " ASN G 332 " " NAG t 1 " - " ASN G 386 " " NAG u 1 " - " ASN G 392 " " NAG v 1 " - " ASN G 448 " " NAG w 1 " - " ASN G 160 " " NAG x 1 " - " ASN G 363 " " NAG y 1 " - " ASN G 156 " Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 2.6 seconds 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4336 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 40 sheets defined 21.3% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.465A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.881A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 596 removed outlier: 3.737A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.371A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.935A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.847A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 661 removed outlier: 3.572A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.806A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 removed outlier: 3.639A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.796A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.541A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 116 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.670A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.692A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 527 removed outlier: 4.195A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.648A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 578 " --> pdb=" O LYS E 574 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.270A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 625 removed outlier: 3.740A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 removed outlier: 3.661A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 655 removed outlier: 3.542A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 660 removed outlier: 3.763A pdb=" N ASP E 659 " --> pdb=" O ASN E 656 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU E 660 " --> pdb=" O GLU E 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 656 through 660' Processing helix chain 'F' and resid 58 through 65 removed outlier: 4.375A pdb=" N GLU F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 115 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 139 through 151 removed outlier: 3.543A pdb=" N ARG F 151 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.021A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.791A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 61 removed outlier: 3.919A pdb=" N ALA G 60 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 117 removed outlier: 3.673A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.817A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.679A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.790A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.509A pdb=" N GLN J 31 " --> pdb=" O ILE J 28 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.518A pdb=" N LYS J 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 100C through 100E No H-bonds generated for 'chain 'J' and resid 100C through 100E' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.904A pdb=" N GLN I 31 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.673A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 100C through 100E No H-bonds generated for 'chain 'I' and resid 100C through 100E' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.655A pdb=" N GLN L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 32' Processing helix chain 'L' and resid 83 through 87 removed outlier: 4.002A pdb=" N THR L 87 " --> pdb=" O PRO L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1079 through 1083 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.833A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.716A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP G 35 " --> pdb=" O THR G 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.778A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.796A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.832A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.205A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 removed outlier: 17.654A pdb=" N PHE C 288 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 17.775A pdb=" N THR C 455 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 17.430A pdb=" N THR C 290 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 13.365A pdb=" N ILE C 453 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N VAL C 292 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY C 451 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE C 294 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 449 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N CYS C 296 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER C 447 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ARG C 298 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N CYS C 445 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN C 300 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE C 443 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'E' and resid 603 through 604 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.263A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.907A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.719A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'F' and resid 271 through 274 removed outlier: 7.343A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 271 through 274 removed outlier: 11.480A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.477A pdb=" N PHE F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 12.119A pdb=" N ILE F 453 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 301 through 312 removed outlier: 6.558A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 423 through 425 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.164A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 86 " --> pdb=" O VAL G 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.726A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.249A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 181 through 183 removed outlier: 4.623A pdb=" N LYS G 171 " --> pdb=" O GLU H 100B" (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLU H 100B" --> pdb=" O LYS G 171 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS H 100A" --> pdb=" O SER H 100T" (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER H 100T" --> pdb=" O CYS H 100A" (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU H 100C" --> pdb=" O ALA H 100R" (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.566A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 315 through 323 removed outlier: 6.692A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.131A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 423 through 425 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.645A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 34 " --> pdb=" O MET J 51 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.645A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 34 " --> pdb=" O MET J 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.640A pdb=" N ILE I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.718A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.650A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS H 22 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.513A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.645A pdb=" N VAL L 5 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 57 through 59 removed outlier: 5.599A pdb=" N PHE L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG L 38 " --> pdb=" O PHE L 47 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR L 102 " --> pdb=" O ARG L 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 57 through 59 removed outlier: 5.599A pdb=" N PHE L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG L 38 " --> pdb=" O PHE L 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 1009 through 1013 removed outlier: 3.659A pdb=" N ALA L1013 " --> pdb=" O ILE L1105 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP L1035 " --> pdb=" O LEU L1047 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 1009 through 1013 removed outlier: 3.659A pdb=" N ALA L1013 " --> pdb=" O ILE L1105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL L1097 " --> pdb=" O THR L1090 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 1019 through 1024 666 hydrogen bonds defined for protein. 1779 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: 8.25 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3406 1.32 - 1.45: 5958 1.45 - 1.58: 11196 1.58 - 1.71: 2 1.71 - 1.83: 180 Bond restraints: 20742 Sorted by residual: bond pdb=" O3 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.458 1.634 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" O1 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.462 1.634 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" OH TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.679 1.534 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" CA SER G 199 " pdb=" CB SER G 199 " ideal model delta sigma weight residual 1.537 1.452 0.084 1.45e-02 4.76e+03 3.38e+01 ... (remaining 20737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 26938 1.86 - 3.72: 911 3.72 - 5.58: 226 5.58 - 7.45: 53 7.45 - 9.31: 5 Bond angle restraints: 28133 Sorted by residual: angle pdb=" N MET C 150 " pdb=" CA MET C 150 " pdb=" C MET C 150 " ideal model delta sigma weight residual 112.92 103.97 8.95 1.23e+00 6.61e-01 5.30e+01 angle pdb=" N ILE A 641 " pdb=" CA ILE A 641 " pdb=" C ILE A 641 " ideal model delta sigma weight residual 112.96 106.20 6.76 1.00e+00 1.00e+00 4.57e+01 angle pdb=" C PRO G 118 " pdb=" CA PRO G 118 " pdb=" CB PRO G 118 " ideal model delta sigma weight residual 111.56 102.93 8.63 1.65e+00 3.67e-01 2.74e+01 angle pdb=" CA THR C 139 " pdb=" C THR C 139 " pdb=" O THR C 139 " ideal model delta sigma weight residual 122.01 116.96 5.05 1.05e+00 9.07e-01 2.31e+01 angle pdb=" N ASP C 141 " pdb=" CA ASP C 141 " pdb=" C ASP C 141 " ideal model delta sigma weight residual 113.97 107.90 6.07 1.28e+00 6.10e-01 2.25e+01 ... (remaining 28128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 12816 22.64 - 45.28: 967 45.28 - 67.91: 223 67.91 - 90.55: 140 90.55 - 113.19: 76 Dihedral angle restraints: 14222 sinusoidal: 7470 harmonic: 6752 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual -86.00 -170.73 84.73 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -147.46 61.46 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -142.77 56.77 1 1.00e+01 1.00e-02 4.34e+01 ... (remaining 14219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3485 0.143 - 0.286: 42 0.286 - 0.429: 1 0.429 - 0.573: 0 0.573 - 0.716: 2 Chirality restraints: 3530 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN F 160 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 160 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" C1 NAG G 606 " pdb=" ND2 ASN G 137 " pdb=" C2 NAG G 606 " pdb=" O5 NAG G 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 3527 not shown) Planarity restraints: 3473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 151 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.59e+00 pdb=" NE ARG C 151 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 151 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 151 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 151 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 205 " 0.044 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO C 206 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 173 " -0.013 2.00e-02 2.50e+03 1.45e-02 4.20e+00 pdb=" CG TYR F 173 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 173 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR F 173 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR F 173 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 173 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 173 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 173 " -0.001 2.00e-02 2.50e+03 ... (remaining 3470 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 432 2.67 - 3.23: 18730 3.23 - 3.78: 29220 3.78 - 4.34: 41923 4.34 - 4.90: 68342 Nonbonded interactions: 158647 Sorted by model distance: nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.110 3.040 nonbonded pdb=" O ASN G 355 " pdb=" OG SER G 397 " model vdw 2.117 3.040 nonbonded pdb=" O ASN F 478 " pdb=" OG SER F 481 " model vdw 2.179 3.040 nonbonded pdb=" O LEU B 629 " pdb=" NZ LYS B 633 " model vdw 2.205 3.120 nonbonded pdb=" OG1 THR E 606 " pdb=" O VAL F 36 " model vdw 2.213 3.040 ... (remaining 158642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 520 through 546 or resid 569 through 664 or resid 701 thro \ ugh 703)) selection = (chain 'B' and (resid 520 through 546 or resid 569 through 664 or resid 701 thro \ ugh 703)) selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 32 through 185 or resid 188 through 505 or resid 601 throu \ gh 604)) selection = (chain 'F' and (resid 32 through 505 or resid 601 through 604)) selection = (chain 'G' and (resid 32 through 505 or resid 601 through 604)) } ncs_group { reference = chain 'D' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'x' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'c' selection = chain 'e' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'w' selection = chain 'y' } 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: 4.620 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: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 51.050 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.200 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.006 0.176 20742 Z= 0.338 Angle : 0.827 9.308 28133 Z= 0.384 Chirality : 0.055 0.716 3530 Planarity : 0.004 0.111 3407 Dihedral : 19.549 113.189 9766 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.25 % Allowed : 9.68 % Favored : 90.07 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2315 helix: -0.93 (0.26), residues: 377 sheet: 0.39 (0.22), residues: 597 loop : -0.98 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 69 HIS 0.011 0.001 HIS F 374 PHE 0.014 0.001 PHE G 288 TYR 0.035 0.001 TYR F 173 ARG 0.011 0.000 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 364 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 367 average time/residue: 0.3781 time to fit residues: 204.3497 Evaluate side-chains 223 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 50.0000 chunk 176 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 630 GLN C 80 ASN C 103 GLN C 195 ASN E 575 GLN E 630 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 432 GLN G 33 ASN G 66 HIS G 80 ASN G 478 ASN J 3 GLN I 73 ASN H 39 GLN H 52AHIS L1037 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20742 Z= 0.250 Angle : 0.710 16.611 28133 Z= 0.348 Chirality : 0.048 0.407 3530 Planarity : 0.004 0.050 3407 Dihedral : 14.488 81.742 5442 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 2.31 % Allowed : 13.37 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2315 helix: 0.04 (0.26), residues: 373 sheet: 0.63 (0.22), residues: 566 loop : -1.05 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 69 HIS 0.005 0.001 HIS G 105 PHE 0.018 0.002 PHE G 288 TYR 0.023 0.001 TYR B 638 ARG 0.006 0.001 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 624 ASP cc_start: 0.7339 (t0) cc_final: 0.7067 (t0) REVERT: C 217 TYR cc_start: 0.8018 (m-80) cc_final: 0.7576 (m-80) REVERT: F 475 MET cc_start: 0.7178 (mmt) cc_final: 0.6872 (mmt) REVERT: J 82 MET cc_start: 0.7800 (mmm) cc_final: 0.7564 (tpp) REVERT: I 24 LEU cc_start: 0.8652 (tt) cc_final: 0.8407 (tp) REVERT: H 94 LYS cc_start: 0.7772 (pttt) cc_final: 0.7558 (ptmt) outliers start: 47 outliers final: 20 residues processed: 281 average time/residue: 0.3426 time to fit residues: 149.4910 Evaluate side-chains 228 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 176 optimal weight: 0.4980 chunk 144 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 chunk 188 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 HIS G 33 ASN G 114 GLN J 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20742 Z= 0.379 Angle : 0.712 11.526 28133 Z= 0.348 Chirality : 0.049 0.401 3530 Planarity : 0.004 0.051 3407 Dihedral : 12.015 72.083 5441 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 3.19 % Allowed : 14.35 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2315 helix: 0.15 (0.27), residues: 385 sheet: 0.39 (0.21), residues: 598 loop : -1.08 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 69 HIS 0.004 0.001 HIS G 105 PHE 0.028 0.002 PHE F 288 TYR 0.023 0.001 TYR B 638 ARG 0.005 0.001 ARG J 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 624 ASP cc_start: 0.7446 (t0) cc_final: 0.7040 (t0) REVERT: C 217 TYR cc_start: 0.8109 (m-80) cc_final: 0.7656 (m-80) REVERT: C 374 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.6724 (p-80) REVERT: C 416 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8066 (pp) REVERT: C 434 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7986 (ptp) REVERT: F 374 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.6615 (p-80) REVERT: F 475 MET cc_start: 0.7406 (mmt) cc_final: 0.7008 (mmt) REVERT: H 94 LYS cc_start: 0.7867 (pttt) cc_final: 0.7634 (pttm) outliers start: 65 outliers final: 35 residues processed: 268 average time/residue: 0.3419 time to fit residues: 143.0595 Evaluate side-chains 232 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 258 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 209 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 225 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 201 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20742 Z= 0.203 Angle : 0.630 10.989 28133 Z= 0.308 Chirality : 0.047 0.407 3530 Planarity : 0.003 0.048 3407 Dihedral : 9.824 63.735 5441 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 2.51 % Allowed : 15.38 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2315 helix: 0.25 (0.26), residues: 398 sheet: 0.46 (0.21), residues: 613 loop : -1.11 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 96 HIS 0.006 0.001 HIS F 66 PHE 0.018 0.002 PHE I 62 TYR 0.025 0.001 TYR B 638 ARG 0.006 0.000 ARG H 100U *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7819 (ttm) cc_final: 0.7405 (ttm) REVERT: C 217 TYR cc_start: 0.8048 (m-80) cc_final: 0.7663 (m-80) REVERT: C 374 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.6734 (p-80) REVERT: F 374 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.6367 (p-80) REVERT: F 475 MET cc_start: 0.7268 (mmt) cc_final: 0.6888 (mmt) REVERT: H 95 ASP cc_start: 0.6954 (m-30) cc_final: 0.6623 (m-30) REVERT: H 100 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7295 (mt-10) outliers start: 51 outliers final: 28 residues processed: 250 average time/residue: 0.3176 time to fit residues: 124.7237 Evaluate side-chains 224 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN I 100CASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20742 Z= 0.224 Angle : 0.623 10.197 28133 Z= 0.306 Chirality : 0.046 0.400 3530 Planarity : 0.003 0.049 3407 Dihedral : 8.635 59.042 5441 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 2.95 % Allowed : 15.58 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2315 helix: 0.39 (0.27), residues: 396 sheet: 0.44 (0.21), residues: 597 loop : -1.15 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 36 HIS 0.007 0.001 HIS H 52A PHE 0.014 0.001 PHE G 288 TYR 0.023 0.001 TYR B 638 ARG 0.006 0.000 ARG H 100U *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5621 (tp) REVERT: C 150 MET cc_start: 0.8100 (mmm) cc_final: 0.7844 (tpp) REVERT: C 217 TYR cc_start: 0.8060 (m-80) cc_final: 0.7675 (m-80) REVERT: C 374 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.6682 (p-80) REVERT: F 374 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.6299 (p-80) outliers start: 60 outliers final: 36 residues processed: 257 average time/residue: 0.3326 time to fit residues: 134.8761 Evaluate side-chains 238 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 0.4980 chunk 202 optimal weight: 9.9990 chunk 44 optimal weight: 0.0670 chunk 132 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 66 HIS ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN H 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20742 Z= 0.174 Angle : 0.595 9.739 28133 Z= 0.294 Chirality : 0.045 0.398 3530 Planarity : 0.003 0.048 3407 Dihedral : 7.799 58.961 5441 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 3.14 % Allowed : 15.53 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2315 helix: 0.55 (0.27), residues: 395 sheet: 0.51 (0.21), residues: 615 loop : -1.07 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 69 HIS 0.005 0.001 HIS F 66 PHE 0.016 0.001 PHE I 67 TYR 0.020 0.001 TYR B 638 ARG 0.008 0.000 ARG H 100U *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5733 (tp) REVERT: C 150 MET cc_start: 0.8121 (mmm) cc_final: 0.7880 (tpp) REVERT: C 217 TYR cc_start: 0.8054 (m-80) cc_final: 0.7700 (m-80) REVERT: C 374 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.6560 (p-80) REVERT: F 374 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.6108 (p-80) REVERT: J 82 MET cc_start: 0.7341 (mtp) cc_final: 0.6883 (mtp) outliers start: 64 outliers final: 41 residues processed: 255 average time/residue: 0.3312 time to fit residues: 133.7547 Evaluate side-chains 243 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 224 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN I 100CASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20742 Z= 0.270 Angle : 0.627 10.272 28133 Z= 0.309 Chirality : 0.045 0.389 3530 Planarity : 0.003 0.048 3407 Dihedral : 7.334 59.705 5441 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 3.19 % Allowed : 15.68 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2315 helix: 0.61 (0.27), residues: 393 sheet: 0.51 (0.21), residues: 588 loop : -1.14 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 36 HIS 0.004 0.001 HIS G 105 PHE 0.020 0.002 PHE G 288 TYR 0.018 0.001 TYR B 638 ARG 0.007 0.000 ARG H 100U *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5792 (tp) REVERT: C 150 MET cc_start: 0.8083 (mmm) cc_final: 0.7710 (tpt) REVERT: C 374 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.6616 (p-80) REVERT: F 217 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.6620 (t80) REVERT: F 374 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.6321 (p-80) outliers start: 65 outliers final: 47 residues processed: 253 average time/residue: 0.3232 time to fit residues: 128.4523 Evaluate side-chains 245 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 134 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 153 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20742 Z= 0.177 Angle : 0.591 10.247 28133 Z= 0.293 Chirality : 0.044 0.387 3530 Planarity : 0.003 0.047 3407 Dihedral : 6.958 58.879 5441 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 2.65 % Allowed : 16.36 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2315 helix: 0.72 (0.27), residues: 395 sheet: 0.64 (0.21), residues: 578 loop : -1.10 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 36 HIS 0.005 0.001 HIS H 52A PHE 0.018 0.001 PHE I 17 TYR 0.018 0.001 TYR B 638 ARG 0.005 0.000 ARG J 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5752 (tp) REVERT: B 626 MET cc_start: 0.7497 (ttm) cc_final: 0.6965 (ttm) REVERT: C 150 MET cc_start: 0.8021 (mmm) cc_final: 0.7673 (tpt) REVERT: C 217 TYR cc_start: 0.7985 (m-80) cc_final: 0.7649 (m-80) REVERT: C 374 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.6468 (p-80) REVERT: F 374 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.6119 (p-80) REVERT: J 82 MET cc_start: 0.7146 (mtp) cc_final: 0.6912 (mtp) REVERT: H 52 HIS cc_start: 0.6374 (p-80) cc_final: 0.6063 (p-80) outliers start: 54 outliers final: 44 residues processed: 253 average time/residue: 0.3141 time to fit residues: 124.9909 Evaluate side-chains 249 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 1069 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 8.9990 chunk 215 optimal weight: 0.7980 chunk 196 optimal weight: 10.0000 chunk 209 optimal weight: 0.0270 chunk 125 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 164 optimal weight: 0.0270 chunk 64 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 197 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 478 ASN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20742 Z= 0.167 Angle : 0.585 11.049 28133 Z= 0.290 Chirality : 0.043 0.386 3530 Planarity : 0.003 0.047 3407 Dihedral : 6.707 59.096 5441 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 2.56 % Allowed : 16.86 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2315 helix: 0.92 (0.28), residues: 384 sheet: 0.69 (0.21), residues: 584 loop : -1.06 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 36 HIS 0.004 0.001 HIS C 72 PHE 0.018 0.001 PHE I 17 TYR 0.018 0.001 TYR B 638 ARG 0.007 0.000 ARG J 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5798 (tp) REVERT: B 626 MET cc_start: 0.7548 (ttm) cc_final: 0.7115 (ttm) REVERT: C 150 MET cc_start: 0.8000 (mmm) cc_final: 0.7699 (tpt) REVERT: C 374 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.6359 (p-80) REVERT: F 374 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.6115 (p-80) REVERT: J 82 MET cc_start: 0.7175 (mtp) cc_final: 0.6777 (mtp) outliers start: 52 outliers final: 44 residues processed: 251 average time/residue: 0.3175 time to fit residues: 125.5439 Evaluate side-chains 246 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 0.7980 chunk 221 optimal weight: 10.0000 chunk 135 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 232 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20742 Z= 0.201 Angle : 0.586 10.466 28133 Z= 0.291 Chirality : 0.044 0.377 3530 Planarity : 0.003 0.047 3407 Dihedral : 6.602 59.644 5441 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 2.65 % Allowed : 16.81 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2315 helix: 0.94 (0.28), residues: 383 sheet: 0.65 (0.21), residues: 576 loop : -1.04 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 36 HIS 0.003 0.001 HIS C 72 PHE 0.018 0.001 PHE I 17 TYR 0.017 0.001 TYR B 638 ARG 0.011 0.000 ARG H 100U ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5816 (tp) REVERT: B 626 MET cc_start: 0.7598 (ttm) cc_final: 0.7107 (ttm) REVERT: C 150 MET cc_start: 0.8022 (mmm) cc_final: 0.7717 (tpt) REVERT: C 374 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.6357 (p-80) REVERT: F 374 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.6159 (p-80) REVERT: J 82 MET cc_start: 0.7213 (mtp) cc_final: 0.6860 (mtp) REVERT: J 85 GLU cc_start: 0.7764 (pm20) cc_final: 0.7549 (pm20) REVERT: H 52 HIS cc_start: 0.6174 (p-80) cc_final: 0.5956 (p-80) outliers start: 54 outliers final: 47 residues processed: 246 average time/residue: 0.3123 time to fit residues: 122.2407 Evaluate side-chains 250 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 chunk 170 optimal weight: 0.0770 chunk 27 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 77 optimal weight: 0.0670 chunk 190 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.082544 restraints weight = 38289.992| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.38 r_work: 0.3049 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20742 Z= 0.139 Angle : 0.560 10.174 28133 Z= 0.279 Chirality : 0.043 0.368 3530 Planarity : 0.003 0.048 3407 Dihedral : 6.326 57.954 5441 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.97 % Favored : 94.99 % Rotamer: Outliers : 2.21 % Allowed : 17.20 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2315 helix: 1.06 (0.28), residues: 379 sheet: 0.75 (0.21), residues: 592 loop : -0.97 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 69 HIS 0.004 0.001 HIS C 72 PHE 0.019 0.001 PHE I 17 TYR 0.016 0.001 TYR B 638 ARG 0.007 0.000 ARG H 100U Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4336.55 seconds wall clock time: 80 minutes 31.91 seconds (4831.91 seconds total)