Starting phenix.real_space_refine on Mon Sep 14 00:50:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yem_72855/09_2026/9yem_72855.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yem_72855/09_2026/9yem_72855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yem_72855/09_2026/9yem_72855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yem_72855/09_2026/9yem_72855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yem_72855/09_2026/9yem_72855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yem_72855/09_2026/9yem_72855.map" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.014 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 168 5.16 5 C 16281 2.51 5 N 4425 2.21 5 O 5358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26232 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "N" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "D" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "H" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "J" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "Q" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: 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: "Y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: 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: "b" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "c" Number of atoms: 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: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "j" 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: "l" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "t" 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "I" 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: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.26, per 1000 atoms: 0.24 Number of scatterers: 26232 At special positions: 0 Unit cell: (187.359, 200.355, 127.794, 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 168 16.00 O 5358 8.00 N 4425 7.00 C 16281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, 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=2.03 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 K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 98 " - pdb=" SG CYS K 100C" distance=2.03 Simple disulfide: pdb=" SG CYS K 100 " - pdb=" SG CYS M 100 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 98 " - pdb=" SG CYS M 100C" distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS D 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 100C" distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 100C" distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 605 " - pdb=" SG CYS J 501 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.04 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 433 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 98 " - pdb=" SG CYS O 100C" distance=2.03 Simple disulfide: pdb=" SG CYS O 100 " - pdb=" SG CYS Q 100 " distance=2.05 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100C" distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 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 ALPHA1-2 " MAN T 4 " - " MAN T 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN b 5 " - " MAN b 6 " " MAN b 8 " - " MAN b 9 " " MAN d 4 " - " MAN d 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN l 5 " - " MAN l 6 " " MAN l 8 " - " MAN l 9 " " MAN n 4 " - " MAN n 5 " " MAN s 5 " - " MAN s 6 " " MAN s 8 " - " MAN s 9 " " MAN v 5 " - " MAN v 6 " " MAN v 8 " - " MAN v 9 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 8 " " MAN Y 4 " - " MAN Y 7 " " BMA b 3 " - " MAN b 8 " " MAN b 4 " - " MAN b 7 " " BMA d 3 " - " MAN d 4 " " BMA i 3 " - " MAN i 8 " " MAN i 4 " - " MAN i 7 " " BMA l 3 " - " MAN l 8 " " MAN l 4 " - " MAN l 7 " " BMA n 3 " - " MAN n 4 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 7 " " BMA v 3 " - " MAN v 8 " " MAN v 4 " - " MAN v 7 " ALPHA1-6 " BMA T 3 " - " MAN T 6 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " " BMA b 3 " - " MAN b 4 " " MAN b 4 " - " MAN b 5 " " BMA d 3 " - " MAN d 6 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 5 " " BMA l 3 " - " MAN l 4 " " MAN l 4 " - " MAN l 5 " " BMA n 3 " - " MAN n 6 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " " BMA v 3 " - " MAN v 4 " " MAN v 4 " - " MAN v 5 " BETA1-4 " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " 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 b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " 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 i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " 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 q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " 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-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 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 197 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 355 " " NAG C 607 " - " ASN C 392 " " NAG C 608 " - " ASN C 137 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 133 " " NAG D 603 " - " ASN D 197 " " NAG D 604 " - " ASN D 234 " " NAG D 605 " - " ASN D 339 " " NAG D 606 " - " ASN D 355 " " NAG D 607 " - " ASN D 392 " " NAG D 608 " - " ASN D 137 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG I 703 " - " ASN I 618 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 133 " " NAG J 603 " - " ASN J 197 " " NAG J 604 " - " ASN J 234 " " NAG J 605 " - " ASN J 339 " " NAG J 606 " - " ASN J 355 " " NAG J 607 " - " ASN J 392 " " NAG J 608 " - " ASN J 137 " " NAG S 1 " - " ASN C 160 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 276 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 332 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN C 301 " " NAG b 1 " - " ASN C 295 " " NAG c 1 " - " ASN D 160 " " NAG d 1 " - " ASN D 262 " " NAG e 1 " - " ASN D 276 " " NAG f 1 " - " ASN D 363 " " NAG g 1 " - " ASN D 386 " " NAG h 1 " - " ASN D 448 " " NAG i 1 " - " ASN D 332 " " NAG j 1 " - " ASN D 156 " " NAG k 1 " - " ASN D 301 " " NAG l 1 " - " ASN D 295 " " NAG m 1 " - " ASN J 160 " " NAG n 1 " - " ASN J 262 " " NAG o 1 " - " ASN J 276 " " NAG p 1 " - " ASN J 363 " " NAG q 1 " - " ASN J 386 " " NAG r 1 " - " ASN J 448 " " NAG s 1 " - " ASN J 332 " " NAG t 1 " - " ASN J 156 " " NAG u 1 " - " ASN J 301 " " NAG v 1 " - " ASN J 295 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5730 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 48 sheets defined 19.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 569 through 596 removed outlier: 4.188A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.267A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 662 removed outlier: 3.827A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.708A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.405A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.975A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.201A 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 387 through 391 removed outlier: 3.708A pdb=" N PHE C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.531A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 4.174A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 63 through 67 removed outlier: 3.885A pdb=" N PHE K 67 " --> pdb=" O LYS K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 86 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 84 removed outlier: 3.682A pdb=" N ALA N 84 " --> pdb=" O GLU N 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.908A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.506A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 removed outlier: 4.106A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 637 removed outlier: 4.337A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.931A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 64 removed outlier: 3.700A pdb=" N TYR D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.225A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 335 through 354 removed outlier: 3.956A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.508A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.652A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 460 through 463 removed outlier: 4.188A pdb=" N SER D 463 " --> pdb=" O SER D 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 460 through 463' Processing helix chain 'D' and resid 475 through 483 removed outlier: 4.179A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 61 through 67 removed outlier: 4.000A pdb=" N LYS E 64 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY E 65 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE E 67 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 537 through 543 Processing helix chain 'I' and resid 571 through 595 Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 627 through 636 removed outlier: 4.249A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 663 removed outlier: 3.570A pdb=" N ILE I 642 " --> pdb=" O TYR I 638 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR I 643 " --> pdb=" O THR I 639 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY I 644 " --> pdb=" O GLN I 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 64 removed outlier: 3.704A pdb=" N TYR J 61 " --> pdb=" O ASP J 57 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 117 removed outlier: 4.307A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 127 removed outlier: 3.773A pdb=" N VAL J 127 " --> pdb=" O PRO J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 353 removed outlier: 3.841A pdb=" N LYS J 351 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.529A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 390 Processing helix chain 'J' and resid 425 through 429 removed outlier: 3.524A pdb=" N ARG J 429 " --> pdb=" O MET J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 463 removed outlier: 4.203A pdb=" N SER J 463 " --> pdb=" O SER J 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 460 through 463' Processing helix chain 'J' and resid 475 through 484 removed outlier: 4.161A pdb=" N TRP J 479 " --> pdb=" O MET J 475 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 83 through 86 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.583A pdb=" N SER P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 30 No H-bonds generated for 'chain 'Q' and resid 28 through 30' Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 73 through 75 No H-bonds generated for 'chain 'Q' and resid 73 through 75' Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.400A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.820A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.728A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.279A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 256 through 257 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 256 through 257 current: chain 'C' and resid 284 through 308 removed outlier: 7.140A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'K' and resid 3 through 8 removed outlier: 3.777A pdb=" N HIS K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER K 70 " --> pdb=" O SER K 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100C through 100D Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.557A pdb=" N GLN L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100C through 100D Processing sheet with id=AB5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.702A pdb=" N ILE N 11 " --> pdb=" O GLN N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 53 through 54 removed outlier: 5.416A pdb=" N ARG N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN N 37 " --> pdb=" O ARG N 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.374A pdb=" N CYS B 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N TYR D 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR B 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL D 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL B 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.837A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 75 through 76 removed outlier: 3.641A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 92 through 94 Processing sheet with id=AC3, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AC4, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.187A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 256 through 257 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 256 through 257 current: chain 'D' and resid 284 through 302 removed outlier: 7.221A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 330 through 334 current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 Processing sheet with id=AC6, first strand: chain 'D' and resid 304 through 307 Processing sheet with id=AC7, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 59 current: chain 'E' and resid 100C through 100D Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AD2, first strand: chain 'F' and resid 53 through 54 removed outlier: 5.645A pdb=" N ARG F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN F 37 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.100A pdb=" N LEU G 20 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100C through 100D Processing sheet with id=AD5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 5.837A pdb=" N GLN H 37 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 603 through 609 removed outlier: 8.405A pdb=" N CYS I 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR J 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR I 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL J 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL I 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.900A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 75 through 76 removed outlier: 3.664A pdb=" N VAL J 75 " --> pdb=" O CYS J 54 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 92 through 94 Processing sheet with id=AE2, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=AE3, first strand: chain 'J' and resid 201 through 203 removed outlier: 6.170A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 256 through 257 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 256 through 257 current: chain 'J' and resid 284 through 307 removed outlier: 6.855A pdb=" N ASN J 301 " --> pdb=" O ILE J 322 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE J 322 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 317 through 323 current: chain 'J' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 381 through 385 current: chain 'J' and resid 465 through 470 Processing sheet with id=AE5, first strand: chain 'O' and resid 3 through 8 Processing sheet with id=AE6, first strand: chain 'O' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 10 through 12 current: chain 'O' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100C through 100D Processing sheet with id=AE7, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.158A pdb=" N ILE P 11 " --> pdb=" O GLN P 105 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 3 through 6 removed outlier: 3.671A pdb=" N LEU Q 20 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 12 current: chain 'Q' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 57 through 59 current: chain 'Q' and resid 100C through 100D Processing sheet with id=AF2, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.377A pdb=" N ILE R 11 " --> pdb=" O GLN R 105 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN R 37 " --> pdb=" O ARG R 46 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) 707 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.29 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8300 1.35 - 1.48: 7023 1.48 - 1.61: 11182 1.61 - 1.74: 0 1.74 - 1.87: 222 Bond restraints: 26727 Sorted by residual: bond pdb=" N ASP N 1 " pdb=" CA ASP N 1 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.77e+00 bond pdb=" N ASP H 1 " pdb=" CA ASP H 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.32e+00 bond pdb=" CB CYS O 100 " pdb=" SG CYS O 100 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.14e+00 bond pdb=" N ASP R 1 " pdb=" CA ASP R 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 ... (remaining 26722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 35140 1.80 - 3.60: 1003 3.60 - 5.41: 110 5.41 - 7.21: 16 7.21 - 9.01: 4 Bond angle restraints: 36273 Sorted by residual: angle pdb=" CA THR R 26 " pdb=" C THR R 26 " pdb=" N GLN R 27 " ideal model delta sigma weight residual 116.84 124.78 -7.94 1.71e+00 3.42e-01 2.16e+01 angle pdb=" N ASP D 141 " pdb=" CA ASP D 141 " pdb=" C ASP D 141 " ideal model delta sigma weight residual 114.75 109.17 5.58 1.26e+00 6.30e-01 1.96e+01 angle pdb=" C GLN Q 81 " pdb=" N MET Q 82 " pdb=" CA MET Q 82 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C CYS Q 100 " pdb=" CA CYS Q 100 " pdb=" CB CYS Q 100 " ideal model delta sigma weight residual 110.84 104.13 6.71 1.66e+00 3.63e-01 1.63e+01 angle pdb=" CA ARG G 19 " pdb=" CB ARG G 19 " pdb=" CG ARG G 19 " ideal model delta sigma weight residual 114.10 121.96 -7.86 2.00e+00 2.50e-01 1.54e+01 ... (remaining 36268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 16137 17.88 - 35.76: 1287 35.76 - 53.64: 349 53.64 - 71.51: 101 71.51 - 89.39: 42 Dihedral angle restraints: 17916 sinusoidal: 9009 harmonic: 8907 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -137.23 51.23 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -135.30 49.30 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS O 100 " pdb=" SG CYS O 100 " pdb=" SG CYS Q 100 " pdb=" CB CYS Q 100 " ideal model delta sinusoidal sigma weight residual -86.00 -36.98 -49.02 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 17913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3458 0.042 - 0.085: 706 0.085 - 0.127: 297 0.127 - 0.170: 57 0.170 - 0.212: 9 Chirality restraints: 4527 Sorted by residual: chirality pdb=" C1 NAG J 607 " pdb=" ND2 ASN J 392 " pdb=" C2 NAG J 607 " pdb=" O5 NAG J 607 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C3 MAN b 4 " pdb=" C2 MAN b 4 " pdb=" C4 MAN b 4 " pdb=" O3 MAN b 4 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA MET F 4 " pdb=" N MET F 4 " pdb=" C MET F 4 " pdb=" CB MET F 4 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 4524 not shown) Planarity restraints: 4509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG M 83 " -0.233 9.50e-02 1.11e+02 1.05e-01 7.12e+00 pdb=" NE ARG M 83 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG M 83 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG M 83 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG M 83 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 83 " -0.159 9.50e-02 1.11e+02 7.12e-02 3.19e+00 pdb=" NE ARG G 83 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG G 83 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG G 83 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 83 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 94 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO L 95 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.025 5.00e-02 4.00e+02 ... (remaining 4506 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 12085 2.92 - 3.41: 26640 3.41 - 3.91: 41770 3.91 - 4.40: 47750 4.40 - 4.90: 78575 Nonbonded interactions: 206820 Sorted by model distance: nonbonded pdb=" O PRO H 40 " pdb=" OE2 GLU H 42 " model vdw 2.419 3.040 nonbonded pdb=" O THR P 97 " pdb=" OG1 THR P 97 " model vdw 2.433 3.040 nonbonded pdb=" O ARG F 96 " pdb=" OG1 THR F 97 " model vdw 2.446 3.040 nonbonded pdb=" O ARG G 54 " pdb=" OG SER G 55 " model vdw 2.453 3.040 nonbonded pdb=" O LEU I 581 " pdb=" OE2 GLU I 584 " model vdw 2.458 3.040 ... (remaining 206815 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 'u' } ncs_group { reference = chain 'T' selection = chain 'd' selection = chain 'n' } ncs_group { reference = chain 'Y' selection = chain 'b' selection = chain 'i' selection = chain 'l' selection = chain 's' selection = chain 'v' } ncs_group { reference = chain 'Z' selection = chain 'j' selection = chain 't' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.350 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.120 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.003 0.058 26934 Z= 0.163 Angle : 0.779 9.679 36837 Z= 0.407 Chirality : 0.044 0.212 4527 Planarity : 0.005 0.105 4446 Dihedral : 14.464 89.392 12015 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.51 % Favored : 94.29 % Rotamer: Outliers : 1.40 % Allowed : 12.46 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3066 helix: -0.14 (0.25), residues: 435 sheet: -0.98 (0.16), residues: 891 loop : -1.63 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 83 TYR 0.021 0.001 TYR F 94 PHE 0.020 0.001 PHE F 98 TRP 0.020 0.001 TRP B 571 HIS 0.012 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (26727) covalent geometry : angle 0.71897 / 0.40 (36273) SS BOND : bond 0.00417 / 0.29 ( 57) SS BOND : angle 1.02876 / 0.67 ( 114) hydrogen bonds : bond 0.13469 / 8.61 ( 707) hydrogen bonds : angle 6.86390 / 4.91 ( 1812) link_ALPHA1-2 : bond 0.01243 / 0.72 ( 15) link_ALPHA1-2 : angle 3.29228 / 2.21 ( 45) link_ALPHA1-3 : bond 0.01151 / 0.66 ( 15) link_ALPHA1-3 : angle 2.53012 / 1.61 ( 45) link_ALPHA1-6 : bond 0.00964 / 0.58 ( 15) link_ALPHA1-6 : angle 2.38687 / 1.47 ( 45) link_BETA1-4 : bond 0.00531 / 0.31 ( 42) link_BETA1-4 : angle 2.40227 / 1.75 ( 126) link_NAG-ASN : bond 0.00558 / 0.36 ( 63) link_NAG-ASN : angle 3.03900 / 2.09 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 434 MET cc_start: 0.9453 (tmm) cc_final: 0.9213 (tmm) REVERT: K 11 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6383 (tt) REVERT: K 43 ARG cc_start: 0.7773 (ptm160) cc_final: 0.7075 (ptt-90) REVERT: K 75 ARG cc_start: 0.9345 (ptp-170) cc_final: 0.9135 (ptp-110) REVERT: K 82 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.4694 (ppp) REVERT: K 82 ASN cc_start: 0.8056 (t0) cc_final: 0.7640 (t0) REVERT: M 29 PHE cc_start: 0.8501 (t80) cc_final: 0.7220 (t80) REVERT: M 34 MET cc_start: 0.8119 (mmm) cc_final: 0.7606 (mmm) REVERT: N 2 ILE cc_start: 0.7856 (mm) cc_final: 0.7532 (tp) REVERT: N 36 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6235 (m-80) REVERT: D 434 MET cc_start: 0.9270 (tmm) cc_final: 0.8653 (tmm) REVERT: E 43 ARG cc_start: 0.7747 (ptm160) cc_final: 0.7163 (pmt170) REVERT: E 100 ASP cc_start: 0.7835 (m-30) cc_final: 0.7604 (p0) REVERT: G 29 PHE cc_start: 0.8218 (t80) cc_final: 0.7064 (t80) REVERT: G 103 TRP cc_start: 0.4723 (OUTLIER) cc_final: 0.3460 (m-10) REVERT: J 153 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: O 43 ARG cc_start: 0.7595 (ptm160) cc_final: 0.6945 (pmt170) REVERT: P 94 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7199 (t80) REVERT: Q 29 PHE cc_start: 0.7689 (t80) cc_final: 0.7187 (t80) REVERT: Q 73 ASN cc_start: 0.9524 (m-40) cc_final: 0.8924 (m-40) outliers start: 38 outliers final: 20 residues processed: 223 average time/residue: 0.2291 time to fit residues: 76.1410 Evaluate side-chains 170 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain P residue 94 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 374 HIS C 411 ASN K 82AASN L 93 ASN M 76 ASN M 82BASN N 37 GLN D 114 GLN D 280 ASN D 374 HIS F 38 GLN F 93 ASN G 76 ASN J 280 ASN J 374 HIS P 38 GLN P 93 ASN Q 76 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.056949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.038672 restraints weight = 168279.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040029 restraints weight = 82760.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040878 restraints weight = 55717.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.041343 restraints weight = 44057.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.041700 restraints weight = 38508.184| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26934 Z= 0.128 Angle : 0.732 11.935 36837 Z= 0.347 Chirality : 0.047 0.376 4527 Planarity : 0.004 0.047 4446 Dihedral : 9.504 82.713 6441 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 2.25 % Allowed : 12.79 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3066 helix: 0.50 (0.26), residues: 429 sheet: -0.68 (0.17), residues: 909 loop : -1.44 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 83 TYR 0.026 0.002 TYR H 94 PHE 0.023 0.002 PHE L 98 TRP 0.014 0.001 TRP G 103 HIS 0.010 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (26727) covalent geometry : angle 0.67401 / 0.33 (36273) SS BOND : bond 0.00311 / 0.19 ( 57) SS BOND : angle 0.82554 / 0.53 ( 114) hydrogen bonds : bond 0.04187 / 2.77 ( 707) hydrogen bonds : angle 5.82399 / 4.16 ( 1812) link_ALPHA1-2 : bond 0.00780 / 0.46 ( 15) link_ALPHA1-2 : angle 2.15789 / 1.36 ( 45) link_ALPHA1-3 : bond 0.01021 / 0.58 ( 15) link_ALPHA1-3 : angle 2.23763 / 1.39 ( 45) link_ALPHA1-6 : bond 0.00490 / 0.30 ( 15) link_ALPHA1-6 : angle 1.96565 / 1.18 ( 45) link_BETA1-4 : bond 0.00453 / 0.26 ( 42) link_BETA1-4 : angle 1.99400 / 1.44 ( 126) link_NAG-ASN : bond 0.00661 / 0.43 ( 63) link_NAG-ASN : angle 3.31999 / 2.31 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 1.034 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: C 271 MET cc_start: 0.8150 (mmm) cc_final: 0.7939 (mmm) REVERT: C 434 MET cc_start: 0.9497 (tmm) cc_final: 0.9070 (tmm) REVERT: K 11 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6643 (tt) REVERT: K 43 ARG cc_start: 0.7891 (ptm160) cc_final: 0.7134 (ptt-90) REVERT: K 82 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.5407 (ppp) REVERT: M 29 PHE cc_start: 0.8157 (t80) cc_final: 0.6793 (t80) REVERT: M 34 MET cc_start: 0.8203 (mmm) cc_final: 0.7737 (mmm) REVERT: N 36 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: B 589 ASP cc_start: 0.9057 (m-30) cc_final: 0.8803 (t0) REVERT: D 434 MET cc_start: 0.9262 (tmm) cc_final: 0.8857 (tmm) REVERT: E 43 ARG cc_start: 0.7933 (ptm160) cc_final: 0.7293 (pmt170) REVERT: E 100 ASP cc_start: 0.7715 (m-30) cc_final: 0.7408 (m-30) REVERT: G 29 PHE cc_start: 0.7909 (t80) cc_final: 0.6742 (t80) REVERT: G 103 TRP cc_start: 0.4851 (OUTLIER) cc_final: 0.3589 (m100) REVERT: I 530 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7194 (ttm) REVERT: I 654 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8800 (tm-30) REVERT: J 452 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8964 (tt) REVERT: O 4 LEU cc_start: 0.8954 (mm) cc_final: 0.8689 (tp) REVERT: O 43 ARG cc_start: 0.7712 (ptm160) cc_final: 0.6804 (ptt-90) REVERT: O 100 ASP cc_start: 0.7774 (p0) cc_final: 0.7570 (p0) REVERT: P 94 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.7049 (t80) REVERT: Q 29 PHE cc_start: 0.7368 (t80) cc_final: 0.6729 (t80) REVERT: Q 73 ASN cc_start: 0.9521 (m-40) cc_final: 0.8845 (m-40) REVERT: R 36 PHE cc_start: 0.6873 (m-80) cc_final: 0.6115 (m-10) outliers start: 61 outliers final: 31 residues processed: 219 average time/residue: 0.1929 time to fit residues: 66.5210 Evaluate side-chains 183 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain I residue 530 MET Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain P residue 94 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 95 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 282 optimal weight: 40.0000 chunk 73 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 72 HIS D 66 HIS D 72 HIS G 46 GLN H 37 GLN J 72 HIS J 280 ASN Q 46 GLN R 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.055572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.037341 restraints weight = 171088.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.038638 restraints weight = 87272.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.039456 restraints weight = 59642.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.039968 restraints weight = 47786.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040233 restraints weight = 41841.542| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 26934 Z= 0.275 Angle : 0.814 11.584 36837 Z= 0.384 Chirality : 0.048 0.306 4527 Planarity : 0.004 0.053 4446 Dihedral : 9.485 85.916 6425 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.56 % Favored : 93.25 % Rotamer: Outliers : 3.50 % Allowed : 14.05 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.15), residues: 3066 helix: 0.50 (0.26), residues: 426 sheet: -0.78 (0.16), residues: 1023 loop : -1.48 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG O 54 TYR 0.027 0.002 TYR N 94 PHE 0.020 0.002 PHE L 36 TRP 0.016 0.002 TRP D 96 HIS 0.011 0.002 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.27 (26727) covalent geometry : angle 0.75822 / 0.37 (36273) SS BOND : bond 0.00469 / 0.29 ( 57) SS BOND : angle 1.07403 / 0.70 ( 114) hydrogen bonds : bond 0.04435 / 2.95 ( 707) hydrogen bonds : angle 5.93528 / 4.23 ( 1812) link_ALPHA1-2 : bond 0.00490 / 0.30 ( 15) link_ALPHA1-2 : angle 2.15340 / 1.37 ( 45) link_ALPHA1-3 : bond 0.00916 / 0.53 ( 15) link_ALPHA1-3 : angle 2.65076 / 1.67 ( 45) link_ALPHA1-6 : bond 0.00605 / 0.35 ( 15) link_ALPHA1-6 : angle 2.26993 / 1.40 ( 45) link_BETA1-4 : bond 0.00348 / 0.22 ( 42) link_BETA1-4 : angle 2.01708 / 1.44 ( 126) link_NAG-ASN : bond 0.00656 / 0.42 ( 63) link_NAG-ASN : angle 3.36441 / 2.36 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 150 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 TYR cc_start: 0.8769 (m-10) cc_final: 0.8525 (m-10) REVERT: K 43 ARG cc_start: 0.7894 (ptm160) cc_final: 0.7537 (ptt-90) REVERT: K 82 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.5793 (ppp) REVERT: M 29 PHE cc_start: 0.8185 (t80) cc_final: 0.7903 (m-80) REVERT: M 34 MET cc_start: 0.8279 (mmm) cc_final: 0.8053 (mmm) REVERT: N 36 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: B 589 ASP cc_start: 0.9088 (m-30) cc_final: 0.8850 (t0) REVERT: D 434 MET cc_start: 0.9284 (tmm) cc_final: 0.8641 (tmm) REVERT: E 43 ARG cc_start: 0.7844 (ptm160) cc_final: 0.7263 (pmt170) REVERT: G 29 PHE cc_start: 0.7895 (t80) cc_final: 0.6823 (t80) REVERT: G 103 TRP cc_start: 0.4825 (OUTLIER) cc_final: 0.3481 (m100) REVERT: I 543 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8817 (t0) REVERT: I 654 GLU cc_start: 0.9314 (tm-30) cc_final: 0.8886 (tm-30) REVERT: J 161 MET cc_start: 0.9039 (tpp) cc_final: 0.8546 (tpt) REVERT: O 4 LEU cc_start: 0.8958 (mm) cc_final: 0.8700 (tp) REVERT: O 34 MET cc_start: 0.8298 (mmm) cc_final: 0.8077 (mmm) REVERT: O 43 ARG cc_start: 0.7640 (ptm160) cc_final: 0.6798 (ptt-90) REVERT: P 32 ARG cc_start: 0.9408 (mtt180) cc_final: 0.9171 (mtp180) REVERT: Q 29 PHE cc_start: 0.7430 (t80) cc_final: 0.7090 (t80) REVERT: R 36 PHE cc_start: 0.6873 (m-80) cc_final: 0.6095 (m-10) outliers start: 95 outliers final: 60 residues processed: 226 average time/residue: 0.1906 time to fit residues: 68.7589 Evaluate side-chains 200 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 136 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain I residue 543 ASN Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 100 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 5 optimal weight: 0.3980 chunk 161 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 195 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.056909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038574 restraints weight = 166810.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039952 restraints weight = 82815.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.040808 restraints weight = 55778.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.041282 restraints weight = 44238.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.041638 restraints weight = 38730.218| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26934 Z= 0.124 Angle : 0.698 12.136 36837 Z= 0.331 Chirality : 0.046 0.342 4527 Planarity : 0.004 0.052 4446 Dihedral : 8.747 89.211 6421 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 2.84 % Allowed : 15.30 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 3066 helix: 0.84 (0.27), residues: 426 sheet: -0.57 (0.16), residues: 999 loop : -1.35 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG M 83 TYR 0.022 0.002 TYR H 49 PHE 0.019 0.001 PHE L 98 TRP 0.015 0.001 TRP G 103 HIS 0.010 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (26727) covalent geometry : angle 0.64536 / 0.32 (36273) SS BOND : bond 0.00324 / 0.20 ( 57) SS BOND : angle 1.18532 / 0.80 ( 114) hydrogen bonds : bond 0.03743 / 2.49 ( 707) hydrogen bonds : angle 5.54239 / 3.96 ( 1812) link_ALPHA1-2 : bond 0.00741 / 0.44 ( 15) link_ALPHA1-2 : angle 1.93362 / 1.20 ( 45) link_ALPHA1-3 : bond 0.01059 / 0.61 ( 15) link_ALPHA1-3 : angle 2.19144 / 1.36 ( 45) link_ALPHA1-6 : bond 0.00582 / 0.36 ( 15) link_ALPHA1-6 : angle 2.01227 / 1.22 ( 45) link_BETA1-4 : bond 0.00390 / 0.22 ( 42) link_BETA1-4 : angle 1.74968 / 1.26 ( 126) link_NAG-ASN : bond 0.00682 / 0.46 ( 63) link_NAG-ASN : angle 3.04436 / 2.11 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 159 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8535 (t0) REVERT: A 638 TYR cc_start: 0.8720 (m-80) cc_final: 0.8386 (m-10) REVERT: C 434 MET cc_start: 0.9433 (tmm) cc_final: 0.9093 (tmm) REVERT: K 43 ARG cc_start: 0.7806 (ptm160) cc_final: 0.7026 (ptt-90) REVERT: K 82 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.5672 (ppp) REVERT: K 82 ASN cc_start: 0.6983 (t0) cc_final: 0.6037 (p0) REVERT: M 29 PHE cc_start: 0.8050 (t80) cc_final: 0.7830 (t80) REVERT: M 82 MET cc_start: 0.3400 (ttt) cc_final: 0.2711 (ptt) REVERT: N 36 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: B 543 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8591 (t0) REVERT: B 589 ASP cc_start: 0.9038 (m-30) cc_final: 0.8785 (t0) REVERT: E 43 ARG cc_start: 0.7801 (ptm160) cc_final: 0.7132 (pmt170) REVERT: G 29 PHE cc_start: 0.7686 (t80) cc_final: 0.6603 (t80) REVERT: G 103 TRP cc_start: 0.4826 (OUTLIER) cc_final: 0.3496 (m100) REVERT: H 49 TYR cc_start: 0.8739 (p90) cc_final: 0.8447 (p90) REVERT: I 543 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8671 (t0) REVERT: I 638 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8879 (m-10) REVERT: I 654 GLU cc_start: 0.9294 (tm-30) cc_final: 0.8893 (tm-30) REVERT: J 161 MET cc_start: 0.9037 (tpp) cc_final: 0.8634 (tpt) REVERT: J 434 MET cc_start: 0.9261 (tmm) cc_final: 0.8888 (tmm) REVERT: J 452 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8911 (tt) REVERT: O 4 LEU cc_start: 0.8892 (mm) cc_final: 0.8667 (tp) REVERT: O 43 ARG cc_start: 0.7563 (ptm160) cc_final: 0.6748 (ptt-90) REVERT: Q 29 PHE cc_start: 0.7140 (t80) cc_final: 0.6501 (t80) REVERT: Q 73 ASN cc_start: 0.9501 (m-40) cc_final: 0.8798 (m-40) REVERT: R 36 PHE cc_start: 0.6939 (m-80) cc_final: 0.6120 (m-10) outliers start: 77 outliers final: 48 residues processed: 223 average time/residue: 0.1824 time to fit residues: 65.7765 Evaluate side-chains 201 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 103 TRP Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain I residue 543 ASN Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 638 TYR Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain Q residue 28 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 106 optimal weight: 4.9990 chunk 287 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 291 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 ASN ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN J 280 ASN R 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.054530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.036381 restraints weight = 170454.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.037692 restraints weight = 84622.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.038481 restraints weight = 57425.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.038910 restraints weight = 45709.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.039268 restraints weight = 40270.390| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 26934 Z= 0.400 Angle : 0.932 11.070 36837 Z= 0.437 Chirality : 0.050 0.322 4527 Planarity : 0.005 0.080 4446 Dihedral : 9.537 62.873 6418 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.70 % Favored : 92.14 % Rotamer: Outliers : 3.98 % Allowed : 16.04 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 3066 helix: 0.22 (0.26), residues: 426 sheet: -0.84 (0.16), residues: 1032 loop : -1.56 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 83 TYR 0.026 0.003 TYR N 94 PHE 0.026 0.003 PHE F 36 TRP 0.018 0.002 TRP D 479 HIS 0.013 0.002 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00889 / 0.40 (26727) covalent geometry : angle 0.88098 / 0.43 (36273) SS BOND : bond 0.00659 / 0.44 ( 57) SS BOND : angle 1.53337 / 1.00 ( 114) hydrogen bonds : bond 0.04742 / 3.16 ( 707) hydrogen bonds : angle 6.13032 / 4.37 ( 1812) link_ALPHA1-2 : bond 0.00378 / 0.24 ( 15) link_ALPHA1-2 : angle 2.20968 / 1.40 ( 45) link_ALPHA1-3 : bond 0.00848 / 0.49 ( 15) link_ALPHA1-3 : angle 3.03467 / 1.93 ( 45) link_ALPHA1-6 : bond 0.00757 / 0.43 ( 15) link_ALPHA1-6 : angle 2.58260 / 1.66 ( 45) link_BETA1-4 : bond 0.00494 / 0.33 ( 42) link_BETA1-4 : angle 2.05585 / 1.46 ( 126) link_NAG-ASN : bond 0.00834 / 0.53 ( 63) link_NAG-ASN : angle 3.32145 / 2.32 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 136 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7960 (ttm) cc_final: 0.7572 (mtp) REVERT: C 432 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8503 (mp10) REVERT: K 43 ARG cc_start: 0.8005 (ptm160) cc_final: 0.7382 (ptt-90) REVERT: K 82 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.5873 (ppp) REVERT: M 34 MET cc_start: 0.8432 (mmm) cc_final: 0.8066 (mmm) REVERT: N 36 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6155 (m-80) REVERT: B 652 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8831 (pp30) REVERT: E 43 ARG cc_start: 0.7866 (ptm160) cc_final: 0.7038 (ptt-90) REVERT: E 82 MET cc_start: 0.2446 (ttt) cc_final: 0.2223 (tpp) REVERT: G 29 PHE cc_start: 0.7735 (t80) cc_final: 0.6701 (t80) REVERT: G 103 TRP cc_start: 0.4995 (OUTLIER) cc_final: 0.3409 (m100) REVERT: H 49 TYR cc_start: 0.8742 (p90) cc_final: 0.8338 (p90) REVERT: I 654 GLU cc_start: 0.9397 (tm-30) cc_final: 0.8958 (tm-30) REVERT: J 125 LEU cc_start: 0.9633 (mt) cc_final: 0.9429 (mt) REVERT: J 434 MET cc_start: 0.9201 (tmm) cc_final: 0.8958 (tmm) REVERT: J 452 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8853 (tt) REVERT: O 4 LEU cc_start: 0.8998 (mm) cc_final: 0.8752 (tp) REVERT: O 43 ARG cc_start: 0.7751 (ptm160) cc_final: 0.6875 (ptt-90) REVERT: Q 29 PHE cc_start: 0.7228 (t80) cc_final: 0.6503 (t80) REVERT: R 4 MET cc_start: 0.5979 (tpp) cc_final: 0.5762 (tpp) REVERT: R 36 PHE cc_start: 0.6902 (m-80) cc_final: 0.6109 (m-10) outliers start: 108 outliers final: 80 residues processed: 228 average time/residue: 0.1820 time to fit residues: 67.2450 Evaluate side-chains 214 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 128 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 36 PHE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 100 CYS Chi-restraints excluded: chain M residue 103 TRP Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 543 ASN Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain R residue 37 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 170 optimal weight: 0.0010 chunk 183 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 281 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS I 656 ASN J 280 ASN ** R 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.056586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.038123 restraints weight = 166044.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.039507 restraints weight = 80279.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.040372 restraints weight = 53669.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.040918 restraints weight = 42259.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041180 restraints weight = 36590.454| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26934 Z= 0.121 Angle : 0.698 11.789 36837 Z= 0.331 Chirality : 0.046 0.332 4527 Planarity : 0.004 0.069 4446 Dihedral : 8.637 59.858 6418 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 2.88 % Allowed : 17.33 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 3066 helix: 0.68 (0.26), residues: 429 sheet: -0.72 (0.16), residues: 1035 loop : -1.36 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 75 TYR 0.030 0.002 TYR N 94 PHE 0.018 0.001 PHE L 98 TRP 0.014 0.001 TRP G 103 HIS 0.012 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (26727) covalent geometry : angle 0.64958 / 0.32 (36273) SS BOND : bond 0.00314 / 0.18 ( 57) SS BOND : angle 1.10552 / 0.75 ( 114) hydrogen bonds : bond 0.03682 / 2.45 ( 707) hydrogen bonds : angle 5.53534 / 3.94 ( 1812) link_ALPHA1-2 : bond 0.00736 / 0.43 ( 15) link_ALPHA1-2 : angle 1.88241 / 1.17 ( 45) link_ALPHA1-3 : bond 0.01080 / 0.62 ( 15) link_ALPHA1-3 : angle 2.12854 / 1.32 ( 45) link_ALPHA1-6 : bond 0.00631 / 0.38 ( 15) link_ALPHA1-6 : angle 2.04485 / 1.26 ( 45) link_BETA1-4 : bond 0.00353 / 0.21 ( 42) link_BETA1-4 : angle 1.66920 / 1.20 ( 126) link_NAG-ASN : bond 0.00585 / 0.39 ( 63) link_NAG-ASN : angle 2.89164 / 2.00 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 155 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8573 (t0) REVERT: C 434 MET cc_start: 0.8597 (tmm) cc_final: 0.7433 (tmm) REVERT: K 43 ARG cc_start: 0.7833 (ptm160) cc_final: 0.7125 (ptt-90) REVERT: K 82 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.5990 (ppp) REVERT: M 82 MET cc_start: 0.3359 (ttt) cc_final: 0.2815 (ptt) REVERT: N 36 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6297 (m-80) REVERT: B 543 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8626 (t0) REVERT: B 589 ASP cc_start: 0.9156 (m-30) cc_final: 0.8835 (t0) REVERT: D 195 ASN cc_start: 0.8589 (p0) cc_final: 0.8370 (p0) REVERT: E 43 ARG cc_start: 0.7759 (ptm160) cc_final: 0.6945 (ptt-90) REVERT: E 75 ARG cc_start: 0.9413 (ptp-170) cc_final: 0.9023 (ptp90) REVERT: E 105 GLN cc_start: 0.7268 (mp10) cc_final: 0.6935 (pm20) REVERT: G 29 PHE cc_start: 0.7545 (t80) cc_final: 0.6509 (t80) REVERT: G 103 TRP cc_start: 0.4912 (OUTLIER) cc_final: 0.3653 (m100) REVERT: H 49 TYR cc_start: 0.8690 (p90) cc_final: 0.8392 (p90) REVERT: I 543 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8807 (t0) REVERT: I 626 MET cc_start: 0.7997 (ttm) cc_final: 0.7776 (mtp) REVERT: I 638 TYR cc_start: 0.9161 (m-80) cc_final: 0.8942 (m-10) REVERT: I 654 GLU cc_start: 0.9366 (tm-30) cc_final: 0.8869 (tm-30) REVERT: I 655 LYS cc_start: 0.9661 (tppt) cc_final: 0.9352 (tptp) REVERT: J 161 MET cc_start: 0.8691 (tpt) cc_final: 0.8295 (tpt) REVERT: J 452 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8927 (tt) REVERT: O 34 MET cc_start: 0.8878 (mmm) cc_final: 0.8651 (mmm) REVERT: O 43 ARG cc_start: 0.7635 (ptm160) cc_final: 0.6767 (ptt-90) REVERT: O 100 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6910 (p0) REVERT: O 100 ASP cc_start: 0.7733 (p0) cc_final: 0.7148 (p0) REVERT: Q 29 PHE cc_start: 0.6958 (t80) cc_final: 0.6503 (t80) REVERT: Q 73 ASN cc_start: 0.9463 (m-40) cc_final: 0.8728 (m-40) REVERT: R 36 PHE cc_start: 0.6984 (m-80) cc_final: 0.6182 (m-10) outliers start: 78 outliers final: 56 residues processed: 216 average time/residue: 0.1878 time to fit residues: 65.1294 Evaluate side-chains 205 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 141 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 36 PHE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 543 ASN Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 37 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 191 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 276 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 155 optimal weight: 0.0670 chunk 238 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 3 HIS ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.056279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.037975 restraints weight = 166525.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.039364 restraints weight = 81433.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.040232 restraints weight = 54465.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040736 restraints weight = 42807.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.041093 restraints weight = 37236.822| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26934 Z= 0.149 Angle : 0.691 11.271 36837 Z= 0.325 Chirality : 0.045 0.293 4527 Planarity : 0.004 0.079 4446 Dihedral : 8.326 59.629 6418 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.97 % Favored : 93.87 % Rotamer: Outliers : 3.17 % Allowed : 17.33 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.15), residues: 3066 helix: 0.74 (0.26), residues: 429 sheet: -0.56 (0.16), residues: 993 loop : -1.32 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 75 TYR 0.028 0.002 TYR H 94 PHE 0.015 0.001 PHE L 98 TRP 0.015 0.001 TRP G 103 HIS 0.010 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (26727) covalent geometry : angle 0.64263 / 0.31 (36273) SS BOND : bond 0.00301 / 0.19 ( 57) SS BOND : angle 1.13020 / 0.76 ( 114) hydrogen bonds : bond 0.03571 / 2.39 ( 707) hydrogen bonds : angle 5.45464 / 3.88 ( 1812) link_ALPHA1-2 : bond 0.00568 / 0.34 ( 15) link_ALPHA1-2 : angle 1.83795 / 1.15 ( 45) link_ALPHA1-3 : bond 0.01003 / 0.57 ( 15) link_ALPHA1-3 : angle 2.26060 / 1.41 ( 45) link_ALPHA1-6 : bond 0.00550 / 0.34 ( 15) link_ALPHA1-6 : angle 2.03953 / 1.26 ( 45) link_BETA1-4 : bond 0.00290 / 0.17 ( 42) link_BETA1-4 : angle 1.66724 / 1.20 ( 126) link_NAG-ASN : bond 0.00541 / 0.36 ( 63) link_NAG-ASN : angle 2.83643 / 1.97 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 148 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8610 (t0) REVERT: K 43 ARG cc_start: 0.7873 (ptm160) cc_final: 0.7142 (ptt-90) REVERT: K 82 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.5999 (ppp) REVERT: M 34 MET cc_start: 0.8277 (mmm) cc_final: 0.8013 (mmm) REVERT: M 82 MET cc_start: 0.3540 (ttt) cc_final: 0.2861 (ptm) REVERT: N 36 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6297 (m-80) REVERT: B 543 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8591 (t0) REVERT: B 589 ASP cc_start: 0.9172 (m-30) cc_final: 0.8848 (t0) REVERT: E 43 ARG cc_start: 0.7868 (ptm160) cc_final: 0.6991 (ptt-90) REVERT: E 75 ARG cc_start: 0.9396 (ptp-170) cc_final: 0.8990 (ptp90) REVERT: E 105 GLN cc_start: 0.7308 (mp10) cc_final: 0.6989 (pm20) REVERT: G 29 PHE cc_start: 0.7584 (t80) cc_final: 0.6553 (t80) REVERT: G 103 TRP cc_start: 0.4922 (OUTLIER) cc_final: 0.3625 (m100) REVERT: H 49 TYR cc_start: 0.8673 (p90) cc_final: 0.8421 (p90) REVERT: I 543 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8804 (t0) REVERT: I 626 MET cc_start: 0.8015 (ttm) cc_final: 0.7799 (mtp) REVERT: I 638 TYR cc_start: 0.9152 (m-80) cc_final: 0.8946 (m-10) REVERT: J 452 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8891 (tt) REVERT: O 4 LEU cc_start: 0.8900 (mm) cc_final: 0.8637 (tp) REVERT: O 34 MET cc_start: 0.8936 (mmm) cc_final: 0.8717 (mmm) REVERT: O 43 ARG cc_start: 0.7609 (ptm160) cc_final: 0.6719 (ptt-90) REVERT: P 98 PHE cc_start: 0.4748 (OUTLIER) cc_final: 0.3440 (m-80) REVERT: Q 29 PHE cc_start: 0.7108 (t80) cc_final: 0.6647 (t80) REVERT: Q 73 ASN cc_start: 0.9457 (m-40) cc_final: 0.8700 (m-40) REVERT: R 36 PHE cc_start: 0.7020 (m-80) cc_final: 0.6204 (m-10) outliers start: 86 outliers final: 63 residues processed: 211 average time/residue: 0.1788 time to fit residues: 61.2455 Evaluate side-chains 213 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 36 PHE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 543 ASN Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 37 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 99 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 231 optimal weight: 0.4980 chunk 219 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 175 optimal weight: 0.5980 chunk 75 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.056361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.037972 restraints weight = 167386.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.039313 restraints weight = 81183.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.040167 restraints weight = 54299.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.040706 restraints weight = 42802.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.041022 restraints weight = 37175.368| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26934 Z= 0.147 Angle : 0.683 11.156 36837 Z= 0.322 Chirality : 0.045 0.286 4527 Planarity : 0.004 0.060 4446 Dihedral : 8.137 59.127 6417 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.90 % Favored : 93.93 % Rotamer: Outliers : 2.95 % Allowed : 17.59 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.15), residues: 3066 helix: 0.78 (0.26), residues: 429 sheet: -0.59 (0.16), residues: 1011 loop : -1.30 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 75 TYR 0.023 0.002 TYR H 94 PHE 0.014 0.001 PHE L 98 TRP 0.014 0.001 TRP G 103 HIS 0.010 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (26727) covalent geometry : angle 0.63747 / 0.31 (36273) SS BOND : bond 0.00288 / 0.18 ( 57) SS BOND : angle 1.02547 / 0.69 ( 114) hydrogen bonds : bond 0.03515 / 2.34 ( 707) hydrogen bonds : angle 5.40791 / 3.85 ( 1812) link_ALPHA1-2 : bond 0.00577 / 0.34 ( 15) link_ALPHA1-2 : angle 1.75524 / 1.10 ( 45) link_ALPHA1-3 : bond 0.00987 / 0.56 ( 15) link_ALPHA1-3 : angle 2.18731 / 1.37 ( 45) link_ALPHA1-6 : bond 0.00571 / 0.35 ( 15) link_ALPHA1-6 : angle 2.01598 / 1.25 ( 45) link_BETA1-4 : bond 0.00295 / 0.18 ( 42) link_BETA1-4 : angle 1.61781 / 1.16 ( 126) link_NAG-ASN : bond 0.00513 / 0.34 ( 63) link_NAG-ASN : angle 2.79719 / 1.95 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 146 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8631 (t0) REVERT: C 432 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8405 (mp10) REVERT: K 43 ARG cc_start: 0.7944 (ptm160) cc_final: 0.7240 (ptt-90) REVERT: K 82 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.5847 (ppp) REVERT: K 82 ASN cc_start: 0.6903 (t0) cc_final: 0.5878 (p0) REVERT: M 34 MET cc_start: 0.8277 (mmm) cc_final: 0.8064 (mmm) REVERT: M 82 MET cc_start: 0.3496 (ttt) cc_final: 0.2879 (ptm) REVERT: N 36 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6241 (m-80) REVERT: B 535 MET cc_start: 0.8697 (mtm) cc_final: 0.8384 (pmm) REVERT: B 543 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8616 (t0) REVERT: B 589 ASP cc_start: 0.9171 (m-30) cc_final: 0.8845 (t0) REVERT: B 626 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7407 (mtp) REVERT: E 43 ARG cc_start: 0.7819 (ptm160) cc_final: 0.6934 (ptt-90) REVERT: E 75 ARG cc_start: 0.9397 (ptp-170) cc_final: 0.9003 (ptp90) REVERT: E 105 GLN cc_start: 0.7246 (mp10) cc_final: 0.6941 (pm20) REVERT: G 29 PHE cc_start: 0.7465 (t80) cc_final: 0.6477 (t80) REVERT: G 103 TRP cc_start: 0.4903 (OUTLIER) cc_final: 0.3761 (m100) REVERT: H 49 TYR cc_start: 0.8654 (p90) cc_final: 0.8418 (p90) REVERT: I 543 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8794 (t0) REVERT: I 638 TYR cc_start: 0.9133 (m-80) cc_final: 0.8920 (m-10) REVERT: J 161 MET cc_start: 0.9105 (tpp) cc_final: 0.8319 (tpt) REVERT: J 452 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8902 (tt) REVERT: O 4 LEU cc_start: 0.8919 (mm) cc_final: 0.8651 (tp) REVERT: O 34 MET cc_start: 0.8932 (mmm) cc_final: 0.8724 (mmm) REVERT: O 43 ARG cc_start: 0.7616 (ptm160) cc_final: 0.6721 (ptt-90) REVERT: P 98 PHE cc_start: 0.4755 (OUTLIER) cc_final: 0.3358 (m-80) REVERT: Q 29 PHE cc_start: 0.7002 (t80) cc_final: 0.6585 (t80) REVERT: Q 73 ASN cc_start: 0.9443 (m-40) cc_final: 0.8698 (m-40) REVERT: R 36 PHE cc_start: 0.6954 (m-80) cc_final: 0.6156 (m-10) outliers start: 80 outliers final: 68 residues processed: 204 average time/residue: 0.1695 time to fit residues: 56.4029 Evaluate side-chains 217 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 139 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 36 PHE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 543 ASN Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain R residue 37 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 94 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 287 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.055584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.037429 restraints weight = 169050.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.038741 restraints weight = 85186.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.039501 restraints weight = 58186.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.040059 restraints weight = 46720.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040349 restraints weight = 40671.793| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26934 Z= 0.273 Angle : 0.786 12.524 36837 Z= 0.369 Chirality : 0.047 0.250 4527 Planarity : 0.004 0.065 4446 Dihedral : 8.678 59.654 6417 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.92 % Rotamer: Outliers : 3.39 % Allowed : 17.33 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 3066 helix: 0.59 (0.26), residues: 429 sheet: -0.70 (0.16), residues: 993 loop : -1.33 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 75 TYR 0.038 0.002 TYR N 94 PHE 0.025 0.002 PHE M 58 TRP 0.016 0.002 TRP D 479 HIS 0.010 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.27 (26727) covalent geometry : angle 0.73955 / 0.36 (36273) SS BOND : bond 0.00401 / 0.25 ( 57) SS BOND : angle 1.32080 / 0.86 ( 114) hydrogen bonds : bond 0.04047 / 2.70 ( 707) hydrogen bonds : angle 5.70667 / 4.05 ( 1812) link_ALPHA1-2 : bond 0.00382 / 0.24 ( 15) link_ALPHA1-2 : angle 1.91591 / 1.21 ( 45) link_ALPHA1-3 : bond 0.00828 / 0.47 ( 15) link_ALPHA1-3 : angle 2.57851 / 1.63 ( 45) link_ALPHA1-6 : bond 0.00627 / 0.38 ( 15) link_ALPHA1-6 : angle 2.17094 / 1.37 ( 45) link_BETA1-4 : bond 0.00327 / 0.21 ( 42) link_BETA1-4 : angle 1.77593 / 1.26 ( 126) link_NAG-ASN : bond 0.00613 / 0.40 ( 63) link_NAG-ASN : angle 2.93513 / 2.05 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 133 time to evaluate : 1.031 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 543 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8785 (m-40) REVERT: C 432 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: K 43 ARG cc_start: 0.7784 (ptm160) cc_final: 0.7095 (ptt-90) REVERT: K 82 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.5922 (ppp) REVERT: K 82 ASN cc_start: 0.6930 (t0) cc_final: 0.5906 (p0) REVERT: K 107 THR cc_start: 0.6286 (OUTLIER) cc_final: 0.6029 (p) REVERT: M 82 MET cc_start: 0.3561 (ttt) cc_final: 0.3026 (ptm) REVERT: N 36 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: B 543 ASN cc_start: 0.9275 (OUTLIER) cc_final: 0.8654 (t0) REVERT: B 626 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7376 (mtp) REVERT: E 43 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7001 (ptt-90) REVERT: E 105 GLN cc_start: 0.7414 (mp10) cc_final: 0.7193 (pm20) REVERT: G 29 PHE cc_start: 0.7759 (t80) cc_final: 0.6619 (t80) REVERT: G 103 TRP cc_start: 0.4846 (OUTLIER) cc_final: 0.3662 (m100) REVERT: H 49 TYR cc_start: 0.8692 (p90) cc_final: 0.8400 (p90) REVERT: J 161 MET cc_start: 0.9111 (tpp) cc_final: 0.8276 (tpt) REVERT: J 452 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8911 (tt) REVERT: O 43 ARG cc_start: 0.7590 (ptm160) cc_final: 0.6702 (ptt-90) REVERT: P 98 PHE cc_start: 0.4729 (OUTLIER) cc_final: 0.3660 (m-80) REVERT: Q 29 PHE cc_start: 0.7190 (t80) cc_final: 0.6926 (t80) REVERT: Q 73 ASN cc_start: 0.9469 (m-40) cc_final: 0.8757 (m110) REVERT: R 36 PHE cc_start: 0.7067 (m-80) cc_final: 0.6250 (m-10) outliers start: 92 outliers final: 73 residues processed: 203 average time/residue: 0.1675 time to fit residues: 55.9225 Evaluate side-chains 215 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 132 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 36 PHE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 543 ASN Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain R residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 153 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 249 optimal weight: 0.1980 chunk 86 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 290 optimal weight: 0.6980 chunk 195 optimal weight: 20.0000 chunk 278 optimal weight: 20.0000 chunk 224 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.056853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038404 restraints weight = 165423.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.039820 restraints weight = 80649.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040715 restraints weight = 53672.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.041257 restraints weight = 42286.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.041518 restraints weight = 36575.310| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.002 0.034 26934 Z= 0.113 Angle : 0.676 11.847 36837 Z= 0.318 Chirality : 0.045 0.295 4527 Planarity : 0.004 0.054 4446 Dihedral : 7.981 59.574 6417 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 2.58 % Allowed : 18.22 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 3066 helix: 0.82 (0.26), residues: 429 sheet: -0.51 (0.17), residues: 945 loop : -1.24 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 75 TYR 0.033 0.002 TYR N 94 PHE 0.021 0.001 PHE M 58 TRP 0.013 0.001 TRP G 103 HIS 0.010 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (26727) covalent geometry : angle 0.63314 / 0.31 (36273) SS BOND : bond 0.00254 / 0.15 ( 57) SS BOND : angle 0.91043 / 0.59 ( 114) hydrogen bonds : bond 0.03424 / 2.27 ( 707) hydrogen bonds : angle 5.31370 / 3.77 ( 1812) link_ALPHA1-2 : bond 0.00688 / 0.39 ( 15) link_ALPHA1-2 : angle 1.67532 / 1.05 ( 45) link_ALPHA1-3 : bond 0.01057 / 0.59 ( 15) link_ALPHA1-3 : angle 2.02177 / 1.26 ( 45) link_ALPHA1-6 : bond 0.00643 / 0.38 ( 15) link_ALPHA1-6 : angle 1.98719 / 1.24 ( 45) link_BETA1-4 : bond 0.00354 / 0.21 ( 42) link_BETA1-4 : angle 1.56392 / 1.12 ( 126) link_NAG-ASN : bond 0.00630 / 0.38 ( 63) link_NAG-ASN : angle 2.71104 / 1.89 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 157 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8545 (t0) REVERT: C 432 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: K 43 ARG cc_start: 0.7753 (ptm160) cc_final: 0.7044 (ptt-90) REVERT: K 82 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.5728 (ppp) REVERT: K 82 ASN cc_start: 0.6958 (t0) cc_final: 0.5954 (p0) REVERT: M 82 MET cc_start: 0.3393 (ttt) cc_final: 0.2881 (ptm) REVERT: N 36 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6331 (m-80) REVERT: B 589 ASP cc_start: 0.9160 (m-30) cc_final: 0.8802 (t0) REVERT: B 626 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7617 (mtp) REVERT: E 43 ARG cc_start: 0.7817 (ptm160) cc_final: 0.7003 (ptt-90) REVERT: E 75 ARG cc_start: 0.9409 (ptp-170) cc_final: 0.9028 (ptp90) REVERT: G 29 PHE cc_start: 0.7426 (t80) cc_final: 0.6501 (t80) REVERT: G 103 TRP cc_start: 0.4808 (OUTLIER) cc_final: 0.4038 (m100) REVERT: I 543 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8787 (m-40) REVERT: I 638 TYR cc_start: 0.9076 (m-80) cc_final: 0.8825 (m-10) REVERT: I 654 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9198 (tm-30) REVERT: J 161 MET cc_start: 0.9187 (tpp) cc_final: 0.8446 (tpt) REVERT: J 452 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8934 (tt) REVERT: O 43 ARG cc_start: 0.7616 (ptm160) cc_final: 0.6715 (ptt-90) REVERT: O 100 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6793 (p0) REVERT: P 98 PHE cc_start: 0.4722 (OUTLIER) cc_final: 0.3384 (m-80) REVERT: Q 29 PHE cc_start: 0.6845 (t80) cc_final: 0.6525 (t80) REVERT: Q 73 ASN cc_start: 0.9443 (m-40) cc_final: 0.8696 (m-40) REVERT: R 36 PHE cc_start: 0.7023 (m-80) cc_final: 0.6267 (m-10) outliers start: 70 outliers final: 52 residues processed: 209 average time/residue: 0.1752 time to fit residues: 59.7410 Evaluate side-chains 203 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 141 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 36 PHE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 543 ASN Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 663 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain R residue 37 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 236 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 266 optimal weight: 0.9980 chunk 264 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 285 optimal weight: 0.0050 chunk 271 optimal weight: 9.9990 chunk 132 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 overall best weight: 1.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.056664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.038493 restraints weight = 165616.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039861 restraints weight = 82155.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.040732 restraints weight = 55198.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041220 restraints weight = 43562.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.041585 restraints weight = 37971.443| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26934 Z= 0.140 Angle : 0.682 11.526 36837 Z= 0.321 Chirality : 0.045 0.267 4527 Planarity : 0.004 0.056 4446 Dihedral : 7.882 59.022 6417 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.84 % Favored : 94.10 % Rotamer: Outliers : 2.54 % Allowed : 18.14 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 3066 helix: 0.83 (0.26), residues: 429 sheet: -0.56 (0.16), residues: 1005 loop : -1.21 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 542 TYR 0.038 0.002 TYR H 94 PHE 0.023 0.001 PHE M 58 TRP 0.016 0.001 TRP B 623 HIS 0.010 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (26727) covalent geometry : angle 0.63815 / 0.31 (36273) SS BOND : bond 0.00295 / 0.18 ( 57) SS BOND : angle 1.03225 / 0.68 ( 114) hydrogen bonds : bond 0.03437 / 2.28 ( 707) hydrogen bonds : angle 5.30510 / 3.76 ( 1812) link_ALPHA1-2 : bond 0.00546 / 0.32 ( 15) link_ALPHA1-2 : angle 1.71268 / 1.07 ( 45) link_ALPHA1-3 : bond 0.00971 / 0.54 ( 15) link_ALPHA1-3 : angle 2.14788 / 1.35 ( 45) link_ALPHA1-6 : bond 0.00570 / 0.35 ( 15) link_ALPHA1-6 : angle 1.97688 / 1.23 ( 45) link_BETA1-4 : bond 0.00295 / 0.18 ( 42) link_BETA1-4 : angle 1.58712 / 1.14 ( 126) link_NAG-ASN : bond 0.00517 / 0.33 ( 63) link_NAG-ASN : angle 2.74516 / 1.90 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5059.24 seconds wall clock time: 88 minutes 39.15 seconds (5319.15 seconds total)