Starting phenix.real_space_refine on Sun Aug 24 07:32:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lpn_23480/08_2025/7lpn_23480.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lpn_23480/08_2025/7lpn_23480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lpn_23480/08_2025/7lpn_23480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lpn_23480/08_2025/7lpn_23480.map" model { file = "/net/cci-nas-00/data/ceres_data/7lpn_23480/08_2025/7lpn_23480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lpn_23480/08_2025/7lpn_23480.cif" } resolution = 3.61 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= 0.016 sd= 0.107 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 123 5.16 5 C 11094 2.51 5 N 2961 2.21 5 O 3609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17787 Number of models: 1 Model: "" Number of chains: 42 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 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: "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: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "Z" 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: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.50, per 1000 atoms: 0.25 Number of scatterers: 17787 At special positions: 0 Unit cell: (130.442, 132.563, 120.897, 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 123 16.00 O 3609 8.00 N 2961 7.00 C 11094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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 G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 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=2.04 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 D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA a 3 " - " MAN a 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA f 3 " - " MAN f 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG 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 R 2 " - " BMA R 3 " " 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 W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 137 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 363 " " NAG C 609 " - " ASN C 160 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 276 " " NAG F 604 " - " ASN F 339 " " NAG F 605 " - " ASN F 355 " " NAG F 606 " - " ASN F 137 " " NAG F 607 " - " ASN F 448 " " NAG F 608 " - " ASN F 363 " " NAG F 609 " - " ASN F 160 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 276 " " NAG G 604 " - " ASN G 339 " " NAG G 605 " - " ASN G 355 " " NAG G 606 " - " ASN G 137 " " NAG G 607 " - " ASN G 448 " " NAG G 608 " - " ASN G 363 " " NAG G 609 " - " ASN G 160 " " NAG J 1 " - " ASN G 156 " " NAG K 1 " - " ASN G 197 " " NAG L 1 " - " ASN G 234 " " NAG M 1 " - " ASN G 295 " " NAG N 1 " - " ASN G 301 " " NAG O 1 " - " ASN G 332 " " NAG P 1 " - " ASN G 386 " " NAG Q 1 " - " ASN G 392 " " NAG R 1 " - " ASN G 262 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 234 " " NAG V 1 " - " ASN C 295 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 386 " " NAG Z 1 " - " ASN C 392 " " NAG a 1 " - " ASN C 262 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 197 " " NAG d 1 " - " ASN F 234 " " NAG e 1 " - " ASN F 295 " " NAG f 1 " - " ASN F 301 " " NAG g 1 " - " ASN F 332 " " NAG h 1 " - " ASN F 386 " " NAG i 1 " - " ASN F 392 " " NAG j 1 " - " ASN F 262 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 750.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3852 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 36 sheets defined 21.2% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.643A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.877A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.003A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.645A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 641 through 661 removed outlier: 3.654A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.552A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.733A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100C through 100E No H-bonds generated for 'chain 'H' and resid 100C through 100E' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.686A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 Processing helix chain 'A' and resid 611 through 616 removed outlier: 3.960A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.587A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.668A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 661 removed outlier: 3.587A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 4.188A pdb=" N GLU C 62 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.671A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.218A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.710A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 4.184A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.970A pdb=" N GLN D 31 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 100C through 100E No H-bonds generated for 'chain 'D' and resid 100C through 100E' Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 538 through 543 removed outlier: 3.828A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 595 Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.148A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 removed outlier: 3.544A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 637 removed outlier: 3.644A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 661 Processing helix chain 'F' and resid 99 through 115 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.669A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 481 removed outlier: 4.085A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.701A pdb=" N GLN I 31 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 100C through 100E No H-bonds generated for 'chain 'I' and resid 100C through 100E' Processing sheet with id=AA1, first strand: chain 'B' and resid 604 through 609 removed outlier: 3.525A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.693A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.729A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.777A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.777A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'G' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.061A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET H 34 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.061A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.861A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.230A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.656A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.683A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.415A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.000A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.135A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.520A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 360 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.674A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 423 through 425 Processing sheet with id=AC4, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.502A pdb=" N VAL D 5 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR D 110 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 89 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET D 34 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR D 110 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 604 through 609 removed outlier: 3.511A pdb=" N CYS E 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL F 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.744A pdb=" N LYS F 487 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.710A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AD2, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.548A pdb=" N ARG F 273 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.548A pdb=" N ARG F 273 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.691A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.503A pdb=" N VAL I 5 " --> pdb=" O GLU I 23 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.775A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET I 34 " --> pdb=" O MET I 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.775A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET I 34 " --> pdb=" O MET I 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1431 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: 2.93 Time building geometry restraints manager: 2.27 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: 5580 1.35 - 1.47: 4613 1.47 - 1.59: 7765 1.59 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 18126 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" N GLU I 1 " pdb=" CA GLU I 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N GLU D 1 " pdb=" CA GLU D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 18121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 23917 1.89 - 3.77: 527 3.77 - 5.66: 103 5.66 - 7.54: 20 7.54 - 9.43: 3 Bond angle restraints: 24570 Sorted by residual: angle pdb=" N SER I 97 " pdb=" CA SER I 97 " pdb=" C SER I 97 " ideal model delta sigma weight residual 107.49 113.32 -5.83 1.74e+00 3.30e-01 1.12e+01 angle pdb=" CA LEU F 494 " pdb=" CB LEU F 494 " pdb=" CG LEU F 494 " ideal model delta sigma weight residual 116.30 125.73 -9.43 3.50e+00 8.16e-02 7.25e+00 angle pdb=" CA CYS F 54 " pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " ideal model delta sigma weight residual 114.40 120.55 -6.15 2.30e+00 1.89e-01 7.14e+00 angle pdb=" N LEU A 544 " pdb=" CA LEU A 544 " pdb=" C LEU A 544 " ideal model delta sigma weight residual 114.04 110.77 3.27 1.24e+00 6.50e-01 6.97e+00 angle pdb=" CA LEU G 494 " pdb=" CB LEU G 494 " pdb=" CG LEU G 494 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 ... (remaining 24565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 11128 22.04 - 44.07: 860 44.07 - 66.11: 130 66.11 - 88.15: 83 88.15 - 110.19: 48 Dihedral angle restraints: 12249 sinusoidal: 6270 harmonic: 5979 Sorted by residual: dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual -86.00 -26.75 -59.25 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -141.73 55.73 1 1.00e+01 1.00e-02 4.19e+01 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 -141.35 55.35 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 12246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2517 0.055 - 0.109: 367 0.109 - 0.164: 129 0.164 - 0.219: 5 0.219 - 0.273: 12 Chirality restraints: 3030 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3027 not shown) Planarity restraints: 3063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 571 " -0.014 2.00e-02 2.50e+03 1.03e-02 2.67e+00 pdb=" CG TRP A 571 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 571 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 571 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 571 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 571 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 571 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 571 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 571 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 571 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 69 " -0.011 2.00e-02 2.50e+03 9.12e-03 2.08e+00 pdb=" CG TRP G 69 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP G 69 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP G 69 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 69 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 69 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 69 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 69 " -0.013 2.00e-02 2.50e+03 8.76e-03 1.92e+00 pdb=" CG TRP C 69 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP C 69 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP C 69 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 69 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 69 " -0.003 2.00e-02 2.50e+03 ... (remaining 3060 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 386 2.66 - 3.22: 16864 3.22 - 3.78: 24668 3.78 - 4.34: 33616 4.34 - 4.90: 55177 Nonbonded interactions: 130711 Sorted by model distance: nonbonded pdb=" O3 NAG Q 1 " pdb=" O5 NAG Q 2 " model vdw 2.103 3.040 nonbonded pdb=" O3 NAG Z 1 " pdb=" O5 NAG Z 2 " model vdw 2.112 3.040 nonbonded pdb=" O3 NAG i 1 " pdb=" O5 NAG i 2 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR G 163 " pdb=" OE1 GLU G 164 " model vdw 2.135 3.040 nonbonded pdb=" OG SER F 460 " pdb=" OD1 ASN F 462 " model vdw 2.145 3.040 ... (remaining 130706 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 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'S' selection = chain 'T' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'W' selection = chain 'a' selection = chain 'f' selection = chain 'j' } 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.180 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.004 0.039 18270 Z= 0.215 Angle : 0.678 9.426 24963 Z= 0.293 Chirality : 0.049 0.273 3030 Planarity : 0.002 0.024 3003 Dihedral : 17.479 110.186 8280 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.80 (0.19), residues: 2040 helix: 1.20 (0.32), residues: 342 sheet: -0.51 (0.25), residues: 459 loop : -1.05 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 105 TYR 0.004 0.001 TYR C 486 PHE 0.009 0.001 PHE C 288 TRP 0.028 0.001 TRP A 571 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00431 (18126) covalent geometry : angle 0.66062 (24570) SS BOND : bond 0.00317 ( 39) SS BOND : angle 0.85378 ( 78) hydrogen bonds : bond 0.26944 ( 504) hydrogen bonds : angle 8.76505 ( 1431) link_ALPHA1-3 : bond 0.00406 ( 3) link_ALPHA1-3 : angle 1.59405 ( 9) link_ALPHA1-6 : bond 0.00475 ( 3) link_ALPHA1-6 : angle 1.48740 ( 9) link_BETA1-4 : bond 0.00534 ( 39) link_BETA1-4 : angle 1.91199 ( 117) link_NAG-ASN : bond 0.00158 ( 60) link_NAG-ASN : angle 1.08685 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: B 543 ASN cc_start: 0.8910 (t0) cc_final: 0.8623 (t0) REVERT: B 647 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8097 (tm-30) REVERT: G 195 ASN cc_start: 0.8149 (p0) cc_final: 0.7834 (p0) REVERT: A 543 ASN cc_start: 0.8850 (t0) cc_final: 0.8477 (t0) REVERT: A 584 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8354 (tm-30) REVERT: A 647 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 648 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 654 GLU cc_start: 0.8654 (tp30) cc_final: 0.8408 (tp30) REVERT: D 44 GLU cc_start: 0.8400 (mp0) cc_final: 0.8176 (mp0) REVERT: E 543 ASN cc_start: 0.8689 (t0) cc_final: 0.8295 (t0) REVERT: E 584 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8282 (tm-30) REVERT: E 647 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7850 (tm-30) REVERT: E 648 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8590 (mm-30) REVERT: F 434 MET cc_start: 0.8500 (ttm) cc_final: 0.8227 (ttm) REVERT: I 44 GLU cc_start: 0.8415 (mp0) cc_final: 0.8179 (mp0) REVERT: I 82 MET cc_start: 0.8466 (mmp) cc_final: 0.8014 (mmp) outliers start: 4 outliers final: 3 residues processed: 192 average time/residue: 0.1201 time to fit residues: 36.0919 Evaluate side-chains 138 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain I residue 68 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 GLN A 616 ASN C 103 GLN F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.079226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.058948 restraints weight = 48099.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.061390 restraints weight = 25277.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.063017 restraints weight = 17367.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064082 restraints weight = 13809.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064711 restraints weight = 11943.175| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18270 Z= 0.178 Angle : 0.661 12.494 24963 Z= 0.318 Chirality : 0.045 0.178 3030 Planarity : 0.003 0.035 3003 Dihedral : 13.525 75.239 4401 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.55 % Allowed : 7.38 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.99 (0.19), residues: 2040 helix: 0.90 (0.29), residues: 363 sheet: -0.51 (0.25), residues: 438 loop : -1.22 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 273 TYR 0.010 0.001 TYR C 173 PHE 0.024 0.002 PHE D 17 TRP 0.023 0.001 TRP A 571 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00405 (18126) covalent geometry : angle 0.62830 (24570) SS BOND : bond 0.00307 ( 39) SS BOND : angle 0.98045 ( 78) hydrogen bonds : bond 0.05546 ( 504) hydrogen bonds : angle 6.19672 ( 1431) link_ALPHA1-3 : bond 0.00852 ( 3) link_ALPHA1-3 : angle 2.18760 ( 9) link_ALPHA1-6 : bond 0.00827 ( 3) link_ALPHA1-6 : angle 1.41489 ( 9) link_BETA1-4 : bond 0.00639 ( 39) link_BETA1-4 : angle 2.45236 ( 117) link_NAG-ASN : bond 0.00270 ( 60) link_NAG-ASN : angle 1.41514 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.557 Fit side-chains REVERT: B 543 ASN cc_start: 0.8950 (t0) cc_final: 0.8446 (t0) REVERT: B 584 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 647 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 654 GLU cc_start: 0.9203 (tp30) cc_final: 0.8964 (tp30) REVERT: G 271 MET cc_start: 0.7693 (mmm) cc_final: 0.7486 (mmm) REVERT: A 543 ASN cc_start: 0.8944 (t0) cc_final: 0.8397 (t0) REVERT: A 584 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7933 (tm-30) REVERT: A 647 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 648 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8781 (mm-30) REVERT: A 654 GLU cc_start: 0.8931 (tp30) cc_final: 0.8723 (tp30) REVERT: D 44 GLU cc_start: 0.8504 (mp0) cc_final: 0.8268 (mp0) REVERT: E 543 ASN cc_start: 0.8818 (t0) cc_final: 0.8248 (t0) REVERT: E 647 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8282 (tm-30) REVERT: E 648 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8817 (mm-30) REVERT: F 426 MET cc_start: 0.8543 (ptm) cc_final: 0.8285 (ptm) REVERT: F 434 MET cc_start: 0.8437 (ttm) cc_final: 0.8103 (ttm) REVERT: I 44 GLU cc_start: 0.8509 (mp0) cc_final: 0.8252 (mp0) REVERT: I 82 MET cc_start: 0.8291 (mmp) cc_final: 0.7634 (mmp) outliers start: 10 outliers final: 6 residues processed: 149 average time/residue: 0.1109 time to fit residues: 26.1004 Evaluate side-chains 135 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain F residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 14 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.077437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.056957 restraints weight = 49483.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.059386 restraints weight = 26127.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.060966 restraints weight = 18078.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.061997 restraints weight = 14505.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.062653 restraints weight = 12632.818| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 18270 Z= 0.245 Angle : 0.686 12.247 24963 Z= 0.330 Chirality : 0.047 0.200 3030 Planarity : 0.003 0.032 3003 Dihedral : 10.609 56.997 4398 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.94 % Allowed : 10.58 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.15 (0.18), residues: 2040 helix: 0.81 (0.29), residues: 363 sheet: -0.55 (0.24), residues: 465 loop : -1.38 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 617 TYR 0.020 0.001 TYR H 100G PHE 0.022 0.002 PHE C 288 TRP 0.018 0.002 TRP A 571 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00565 (18126) covalent geometry : angle 0.65553 (24570) SS BOND : bond 0.00433 ( 39) SS BOND : angle 1.25792 ( 78) hydrogen bonds : bond 0.05057 ( 504) hydrogen bonds : angle 5.69277 ( 1431) link_ALPHA1-3 : bond 0.00937 ( 3) link_ALPHA1-3 : angle 1.71011 ( 9) link_ALPHA1-6 : bond 0.01114 ( 3) link_ALPHA1-6 : angle 1.26824 ( 9) link_BETA1-4 : bond 0.00554 ( 39) link_BETA1-4 : angle 2.21842 ( 117) link_NAG-ASN : bond 0.00335 ( 60) link_NAG-ASN : angle 1.58997 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.554 Fit side-chains REVERT: B 543 ASN cc_start: 0.8941 (t0) cc_final: 0.8394 (t0) REVERT: B 584 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 647 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 654 GLU cc_start: 0.9211 (tp30) cc_final: 0.8997 (tp30) REVERT: H 51 MET cc_start: 0.8026 (tpt) cc_final: 0.7781 (tpt) REVERT: H 72 ASP cc_start: 0.7217 (t0) cc_final: 0.6958 (t0) REVERT: A 543 ASN cc_start: 0.8945 (t0) cc_final: 0.8410 (t0) REVERT: A 584 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 647 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 648 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8723 (mm-30) REVERT: A 654 GLU cc_start: 0.9014 (tp30) cc_final: 0.8782 (tp30) REVERT: C 210 PHE cc_start: 0.9284 (m-10) cc_final: 0.9059 (m-10) REVERT: D 13 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7953 (tm-30) REVERT: D 44 GLU cc_start: 0.8406 (mp0) cc_final: 0.8169 (mp0) REVERT: D 72 ASP cc_start: 0.7172 (t0) cc_final: 0.6938 (t0) REVERT: E 543 ASN cc_start: 0.8849 (t0) cc_final: 0.8233 (t0) REVERT: E 584 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7867 (tm-30) REVERT: E 647 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8414 (tm-30) REVERT: F 434 MET cc_start: 0.8455 (ttm) cc_final: 0.8245 (ttm) REVERT: I 44 GLU cc_start: 0.8537 (mp0) cc_final: 0.8285 (mp0) REVERT: I 82 MET cc_start: 0.8635 (mmp) cc_final: 0.7917 (mmp) outliers start: 17 outliers final: 8 residues processed: 147 average time/residue: 0.1126 time to fit residues: 26.4463 Evaluate side-chains 131 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.081101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.061508 restraints weight = 48629.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.064682 restraints weight = 29366.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.066766 restraints weight = 18421.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066650 restraints weight = 14248.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.066811 restraints weight = 14404.005| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18270 Z= 0.114 Angle : 0.584 12.354 24963 Z= 0.278 Chirality : 0.044 0.178 3030 Planarity : 0.003 0.033 3003 Dihedral : 8.508 54.964 4398 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.49 % Allowed : 11.74 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.97 (0.18), residues: 2040 helix: 1.05 (0.29), residues: 363 sheet: -0.37 (0.24), residues: 459 loop : -1.32 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.026 0.001 TYR D 100G PHE 0.026 0.001 PHE D 17 TRP 0.019 0.001 TRP A 571 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00251 (18126) covalent geometry : angle 0.55714 (24570) SS BOND : bond 0.00194 ( 39) SS BOND : angle 0.75547 ( 78) hydrogen bonds : bond 0.03789 ( 504) hydrogen bonds : angle 5.14581 ( 1431) link_ALPHA1-3 : bond 0.01304 ( 3) link_ALPHA1-3 : angle 1.32376 ( 9) link_ALPHA1-6 : bond 0.00945 ( 3) link_ALPHA1-6 : angle 1.32637 ( 9) link_BETA1-4 : bond 0.00523 ( 39) link_BETA1-4 : angle 2.03148 ( 117) link_NAG-ASN : bond 0.00203 ( 60) link_NAG-ASN : angle 1.37461 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.454 Fit side-chains REVERT: B 543 ASN cc_start: 0.8604 (t0) cc_final: 0.8254 (t0) REVERT: B 584 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8027 (tm-30) REVERT: B 647 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 654 GLU cc_start: 0.9146 (tp30) cc_final: 0.8894 (tp30) REVERT: A 543 ASN cc_start: 0.8667 (t0) cc_final: 0.8254 (t0) REVERT: A 574 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8276 (ptmt) REVERT: A 584 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 633 LYS cc_start: 0.9158 (mttp) cc_final: 0.8889 (mptt) REVERT: A 647 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 648 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8452 (mm-30) REVERT: C 47 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: C 161 MET cc_start: 0.8401 (tpp) cc_final: 0.8123 (tpp) REVERT: C 210 PHE cc_start: 0.8903 (m-10) cc_final: 0.8660 (m-10) REVERT: D 44 GLU cc_start: 0.8234 (mp0) cc_final: 0.8027 (mp0) REVERT: E 543 ASN cc_start: 0.8563 (t0) cc_final: 0.8085 (t0) REVERT: E 584 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8132 (tm-30) REVERT: E 647 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8086 (tm-30) REVERT: F 47 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: I 82 MET cc_start: 0.8771 (mmp) cc_final: 0.8290 (mmp) REVERT: I 82 LEU cc_start: 0.8955 (mm) cc_final: 0.8729 (mm) outliers start: 27 outliers final: 15 residues processed: 165 average time/residue: 0.1100 time to fit residues: 28.9097 Evaluate side-chains 145 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 149 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 85 optimal weight: 0.0770 chunk 62 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.061930 restraints weight = 48525.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.065111 restraints weight = 29447.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067150 restraints weight = 18473.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.067049 restraints weight = 14470.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067243 restraints weight = 14463.990| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18270 Z= 0.110 Angle : 0.571 11.804 24963 Z= 0.272 Chirality : 0.044 0.172 3030 Planarity : 0.003 0.041 3003 Dihedral : 7.513 55.755 4398 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.98 % Allowed : 13.00 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.87 (0.18), residues: 2040 helix: 1.25 (0.29), residues: 360 sheet: -0.27 (0.24), residues: 477 loop : -1.32 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.026 0.001 TYR H 100G PHE 0.028 0.001 PHE H 17 TRP 0.026 0.001 TRP A 571 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00247 (18126) covalent geometry : angle 0.54515 (24570) SS BOND : bond 0.00257 ( 39) SS BOND : angle 0.74152 ( 78) hydrogen bonds : bond 0.03541 ( 504) hydrogen bonds : angle 4.97044 ( 1431) link_ALPHA1-3 : bond 0.01211 ( 3) link_ALPHA1-3 : angle 1.20098 ( 9) link_ALPHA1-6 : bond 0.00906 ( 3) link_ALPHA1-6 : angle 1.30301 ( 9) link_BETA1-4 : bond 0.00499 ( 39) link_BETA1-4 : angle 1.94015 ( 117) link_NAG-ASN : bond 0.00210 ( 60) link_NAG-ASN : angle 1.34032 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.589 Fit side-chains REVERT: B 543 ASN cc_start: 0.8571 (t0) cc_final: 0.8242 (t0) REVERT: B 584 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7820 (tm-30) REVERT: B 588 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7762 (ttm170) REVERT: B 647 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7988 (tm-30) REVERT: B 654 GLU cc_start: 0.9102 (tp30) cc_final: 0.8845 (tp30) REVERT: H 105 ARG cc_start: 0.8290 (mmm160) cc_final: 0.8013 (mmm160) REVERT: A 543 ASN cc_start: 0.8598 (t0) cc_final: 0.8192 (t0) REVERT: A 574 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8340 (ptpt) REVERT: A 584 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 647 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 648 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8380 (mm-30) REVERT: C 47 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: C 210 PHE cc_start: 0.8864 (m-10) cc_final: 0.8637 (m-10) REVERT: D 30 ASN cc_start: 0.8916 (p0) cc_final: 0.8680 (p0) REVERT: D 44 GLU cc_start: 0.8208 (mp0) cc_final: 0.8006 (mp0) REVERT: E 543 ASN cc_start: 0.8521 (t0) cc_final: 0.8117 (t0) REVERT: E 647 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8064 (tm-30) REVERT: F 475 MET cc_start: 0.8452 (tpp) cc_final: 0.8215 (tpp) REVERT: I 82 MET cc_start: 0.8688 (mmp) cc_final: 0.8013 (mmp) outliers start: 36 outliers final: 20 residues processed: 174 average time/residue: 0.1092 time to fit residues: 30.3698 Evaluate side-chains 153 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 204 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.080462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.060897 restraints weight = 48317.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064086 restraints weight = 29323.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.065716 restraints weight = 18511.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065849 restraints weight = 14948.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066045 restraints weight = 14799.914| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18270 Z= 0.151 Angle : 0.600 13.809 24963 Z= 0.285 Chirality : 0.044 0.179 3030 Planarity : 0.003 0.046 3003 Dihedral : 7.075 56.124 4398 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.93 % Allowed : 13.66 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.83 (0.18), residues: 2040 helix: 1.27 (0.29), residues: 360 sheet: -0.20 (0.24), residues: 477 loop : -1.31 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.017 0.001 TYR D 100G PHE 0.023 0.002 PHE H 17 TRP 0.033 0.001 TRP A 571 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00350 (18126) covalent geometry : angle 0.57409 (24570) SS BOND : bond 0.00477 ( 39) SS BOND : angle 1.18185 ( 78) hydrogen bonds : bond 0.03603 ( 504) hydrogen bonds : angle 4.90431 ( 1431) link_ALPHA1-3 : bond 0.01112 ( 3) link_ALPHA1-3 : angle 1.18256 ( 9) link_ALPHA1-6 : bond 0.00846 ( 3) link_ALPHA1-6 : angle 1.27263 ( 9) link_BETA1-4 : bond 0.00492 ( 39) link_BETA1-4 : angle 1.85943 ( 117) link_NAG-ASN : bond 0.00222 ( 60) link_NAG-ASN : angle 1.38420 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.618 Fit side-chains REVERT: B 543 ASN cc_start: 0.8621 (t0) cc_final: 0.8275 (t0) REVERT: B 584 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 588 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7851 (ttm170) REVERT: B 647 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 654 GLU cc_start: 0.9116 (tp30) cc_final: 0.8873 (tp30) REVERT: A 543 ASN cc_start: 0.8673 (t0) cc_final: 0.8299 (t0) REVERT: A 571 TRP cc_start: 0.3781 (t60) cc_final: 0.3547 (t60) REVERT: A 574 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8257 (ptmt) REVERT: A 584 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 647 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 648 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8290 (mm-30) REVERT: C 47 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: C 210 PHE cc_start: 0.8932 (m-10) cc_final: 0.8707 (m-10) REVERT: D 44 GLU cc_start: 0.8250 (mp0) cc_final: 0.8039 (mp0) REVERT: E 543 ASN cc_start: 0.8572 (t0) cc_final: 0.8141 (t0) REVERT: E 584 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8184 (tm-30) REVERT: E 647 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8072 (tm-30) REVERT: F 125 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9154 (tt) REVERT: F 475 MET cc_start: 0.8555 (tpp) cc_final: 0.8303 (tpp) REVERT: I 82 MET cc_start: 0.8670 (mmp) cc_final: 0.8116 (mmp) REVERT: I 82 LEU cc_start: 0.9014 (mm) cc_final: 0.8627 (mm) outliers start: 35 outliers final: 26 residues processed: 166 average time/residue: 0.1075 time to fit residues: 28.2444 Evaluate side-chains 158 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 135 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 5 optimal weight: 0.0040 chunk 160 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN F 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.081526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.061970 restraints weight = 48647.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065231 restraints weight = 29243.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067239 restraints weight = 18295.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067145 restraints weight = 14216.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067322 restraints weight = 14366.506| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18270 Z= 0.111 Angle : 0.579 14.712 24963 Z= 0.274 Chirality : 0.043 0.169 3030 Planarity : 0.003 0.039 3003 Dihedral : 6.608 56.639 4398 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.04 % Allowed : 14.05 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.68 (0.19), residues: 2040 helix: 1.43 (0.29), residues: 363 sheet: -0.08 (0.24), residues: 480 loop : -1.25 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.016 0.001 TYR D 100G PHE 0.021 0.001 PHE H 17 TRP 0.033 0.001 TRP A 571 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00251 (18126) covalent geometry : angle 0.55542 (24570) SS BOND : bond 0.00173 ( 39) SS BOND : angle 0.95279 ( 78) hydrogen bonds : bond 0.03304 ( 504) hydrogen bonds : angle 4.74877 ( 1431) link_ALPHA1-3 : bond 0.01097 ( 3) link_ALPHA1-3 : angle 1.08668 ( 9) link_ALPHA1-6 : bond 0.00730 ( 3) link_ALPHA1-6 : angle 1.22305 ( 9) link_BETA1-4 : bond 0.00479 ( 39) link_BETA1-4 : angle 1.76636 ( 117) link_NAG-ASN : bond 0.00189 ( 60) link_NAG-ASN : angle 1.32379 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.505 Fit side-chains REVERT: B 543 ASN cc_start: 0.8646 (t0) cc_final: 0.8297 (t0) REVERT: B 584 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 588 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7710 (ttm170) REVERT: B 647 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 654 GLU cc_start: 0.9086 (tp30) cc_final: 0.8832 (tp30) REVERT: H 51 MET cc_start: 0.8500 (tpt) cc_final: 0.8139 (tpp) REVERT: A 543 ASN cc_start: 0.8627 (t0) cc_final: 0.8216 (t0) REVERT: A 574 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8252 (ptmt) REVERT: A 584 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 647 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 648 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8290 (mm-30) REVERT: C 47 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: D 30 ASN cc_start: 0.8926 (p0) cc_final: 0.8650 (p0) REVERT: D 44 GLU cc_start: 0.8229 (mp0) cc_final: 0.8012 (mp0) REVERT: E 543 ASN cc_start: 0.8543 (t0) cc_final: 0.8109 (t0) REVERT: E 584 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8078 (tm-30) REVERT: F 47 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: F 125 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9156 (tt) REVERT: F 374 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7268 (p-80) REVERT: I 82 MET cc_start: 0.8715 (mmp) cc_final: 0.8152 (mmp) REVERT: I 82 LEU cc_start: 0.9039 (mm) cc_final: 0.8641 (mm) outliers start: 37 outliers final: 23 residues processed: 179 average time/residue: 0.1033 time to fit residues: 29.6837 Evaluate side-chains 156 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 169 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.061619 restraints weight = 48539.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.064863 restraints weight = 29181.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066871 restraints weight = 18257.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066847 restraints weight = 14356.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067004 restraints weight = 14227.315| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18270 Z= 0.127 Angle : 0.590 13.778 24963 Z= 0.280 Chirality : 0.043 0.174 3030 Planarity : 0.003 0.035 3003 Dihedral : 6.425 56.833 4398 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.98 % Allowed : 14.77 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.69 (0.18), residues: 2040 helix: 1.42 (0.29), residues: 363 sheet: -0.14 (0.23), residues: 495 loop : -1.24 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.006 0.001 TYR H 100G PHE 0.020 0.001 PHE H 17 TRP 0.028 0.001 TRP A 571 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00292 (18126) covalent geometry : angle 0.56804 (24570) SS BOND : bond 0.00203 ( 39) SS BOND : angle 0.95033 ( 78) hydrogen bonds : bond 0.03352 ( 504) hydrogen bonds : angle 4.71620 ( 1431) link_ALPHA1-3 : bond 0.01009 ( 3) link_ALPHA1-3 : angle 1.13309 ( 9) link_ALPHA1-6 : bond 0.00717 ( 3) link_ALPHA1-6 : angle 1.19450 ( 9) link_BETA1-4 : bond 0.00493 ( 39) link_BETA1-4 : angle 1.75271 ( 117) link_NAG-ASN : bond 0.00200 ( 60) link_NAG-ASN : angle 1.33685 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.473 Fit side-chains REVERT: B 543 ASN cc_start: 0.8660 (t0) cc_final: 0.8304 (t0) REVERT: B 584 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 588 ARG cc_start: 0.8211 (tpp80) cc_final: 0.7713 (ttm170) REVERT: B 647 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8081 (tm-30) REVERT: H 51 MET cc_start: 0.8505 (tpt) cc_final: 0.8153 (tpp) REVERT: H 83 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8725 (mmtm) REVERT: A 543 ASN cc_start: 0.8631 (t0) cc_final: 0.8263 (t0) REVERT: A 574 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8292 (ptmt) REVERT: A 584 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 647 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7820 (tm-30) REVERT: A 648 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8408 (mm-30) REVERT: C 47 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: D 30 ASN cc_start: 0.8919 (p0) cc_final: 0.8666 (p0) REVERT: D 44 GLU cc_start: 0.8230 (mp0) cc_final: 0.8017 (mp0) REVERT: E 543 ASN cc_start: 0.8550 (t0) cc_final: 0.8113 (t0) REVERT: E 584 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8072 (tm-30) REVERT: E 626 MET cc_start: 0.8838 (mtp) cc_final: 0.8630 (ttm) REVERT: E 647 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7848 (tm-30) REVERT: F 47 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: F 125 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9157 (tt) REVERT: F 288 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.8169 (p90) REVERT: F 374 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.7408 (p-80) REVERT: I 82 MET cc_start: 0.8743 (mmp) cc_final: 0.8157 (mmp) REVERT: I 82 LEU cc_start: 0.9033 (mm) cc_final: 0.8624 (mm) outliers start: 36 outliers final: 27 residues processed: 170 average time/residue: 0.1160 time to fit residues: 31.1048 Evaluate side-chains 164 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 28 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 151 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.059456 restraints weight = 48908.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.062636 restraints weight = 29838.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064154 restraints weight = 18904.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064215 restraints weight = 15498.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.064423 restraints weight = 15407.846| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18270 Z= 0.222 Angle : 0.663 13.681 24963 Z= 0.318 Chirality : 0.044 0.193 3030 Planarity : 0.003 0.032 3003 Dihedral : 6.614 56.551 4398 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.15 % Allowed : 14.99 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.87 (0.18), residues: 2040 helix: 1.28 (0.28), residues: 363 sheet: -0.39 (0.23), residues: 513 loop : -1.31 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.007 0.001 TYR I 32 PHE 0.029 0.002 PHE H 17 TRP 0.025 0.002 TRP C 479 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00518 (18126) covalent geometry : angle 0.63917 (24570) SS BOND : bond 0.00384 ( 39) SS BOND : angle 1.30635 ( 78) hydrogen bonds : bond 0.03871 ( 504) hydrogen bonds : angle 4.93257 ( 1431) link_ALPHA1-3 : bond 0.00884 ( 3) link_ALPHA1-3 : angle 1.23032 ( 9) link_ALPHA1-6 : bond 0.00742 ( 3) link_ALPHA1-6 : angle 1.17841 ( 9) link_BETA1-4 : bond 0.00484 ( 39) link_BETA1-4 : angle 1.79480 ( 117) link_NAG-ASN : bond 0.00300 ( 60) link_NAG-ASN : angle 1.49965 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.535 Fit side-chains REVERT: B 543 ASN cc_start: 0.8623 (t0) cc_final: 0.8299 (t0) REVERT: B 584 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 588 ARG cc_start: 0.8197 (tpp80) cc_final: 0.7735 (ttm170) REVERT: B 647 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8075 (tm-30) REVERT: H 83 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8680 (mmtt) REVERT: A 543 ASN cc_start: 0.8629 (t0) cc_final: 0.8244 (t0) REVERT: A 574 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8316 (ptmt) REVERT: A 584 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 647 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 648 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8345 (mm-30) REVERT: D 44 GLU cc_start: 0.8176 (mp0) cc_final: 0.7970 (mp0) REVERT: E 543 ASN cc_start: 0.8582 (t0) cc_final: 0.8163 (t0) REVERT: E 584 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8128 (tm-30) REVERT: F 125 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9161 (tt) REVERT: F 475 MET cc_start: 0.8678 (tpp) cc_final: 0.8264 (tpp) REVERT: I 82 MET cc_start: 0.8818 (mmp) cc_final: 0.8165 (mmp) outliers start: 39 outliers final: 30 residues processed: 169 average time/residue: 0.1010 time to fit residues: 27.3472 Evaluate side-chains 164 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 202 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 156 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN C 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.080331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060846 restraints weight = 48259.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064035 restraints weight = 29267.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.065980 restraints weight = 18446.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.065914 restraints weight = 14448.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066080 restraints weight = 14503.153| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18270 Z= 0.130 Angle : 0.610 13.992 24963 Z= 0.290 Chirality : 0.043 0.175 3030 Planarity : 0.003 0.033 3003 Dihedral : 6.450 56.659 4398 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.98 % Allowed : 15.32 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.73 (0.18), residues: 2040 helix: 1.43 (0.29), residues: 363 sheet: -0.17 (0.23), residues: 495 loop : -1.28 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 105 TYR 0.006 0.001 TYR A 638 PHE 0.029 0.001 PHE H 17 TRP 0.027 0.001 TRP A 571 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00302 (18126) covalent geometry : angle 0.58804 (24570) SS BOND : bond 0.00205 ( 39) SS BOND : angle 0.96726 ( 78) hydrogen bonds : bond 0.03474 ( 504) hydrogen bonds : angle 4.76779 ( 1431) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 1.12974 ( 9) link_ALPHA1-6 : bond 0.00691 ( 3) link_ALPHA1-6 : angle 1.17368 ( 9) link_BETA1-4 : bond 0.00482 ( 39) link_BETA1-4 : angle 1.73753 ( 117) link_NAG-ASN : bond 0.00193 ( 60) link_NAG-ASN : angle 1.38002 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.426 Fit side-chains REVERT: B 535 MET cc_start: 0.8915 (mmm) cc_final: 0.8699 (mpp) REVERT: B 543 ASN cc_start: 0.8656 (t0) cc_final: 0.8302 (t0) REVERT: B 584 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 588 ARG cc_start: 0.8213 (tpp80) cc_final: 0.7748 (ttm170) REVERT: B 647 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8064 (tm-30) REVERT: H 83 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8670 (mmtt) REVERT: A 543 ASN cc_start: 0.8606 (t0) cc_final: 0.8180 (t0) REVERT: A 574 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8283 (ptpt) REVERT: A 584 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 647 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 648 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8397 (mm-30) REVERT: C 47 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: C 475 MET cc_start: 0.8655 (tpp) cc_final: 0.8413 (tpp) REVERT: D 44 GLU cc_start: 0.8251 (mp0) cc_final: 0.8022 (mp0) REVERT: E 543 ASN cc_start: 0.8556 (t0) cc_final: 0.8124 (t0) REVERT: E 584 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8102 (tm-30) REVERT: F 125 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9191 (tt) REVERT: I 82 MET cc_start: 0.8753 (mmp) cc_final: 0.8158 (mmp) outliers start: 36 outliers final: 32 residues processed: 167 average time/residue: 0.1089 time to fit residues: 28.5831 Evaluate side-chains 165 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 19 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 0.0770 chunk 164 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.080488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.060955 restraints weight = 48762.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.064147 restraints weight = 29454.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.065733 restraints weight = 18570.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.065805 restraints weight = 15054.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066048 restraints weight = 14956.004| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18270 Z= 0.130 Angle : 0.612 13.683 24963 Z= 0.291 Chirality : 0.043 0.190 3030 Planarity : 0.003 0.032 3003 Dihedral : 6.392 56.774 4398 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.98 % Allowed : 15.32 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.71 (0.18), residues: 2040 helix: 1.43 (0.29), residues: 363 sheet: -0.15 (0.23), residues: 495 loop : -1.27 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.007 0.001 TYR A 638 PHE 0.028 0.001 PHE H 17 TRP 0.034 0.001 TRP A 571 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00301 (18126) covalent geometry : angle 0.59038 (24570) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.03338 ( 78) hydrogen bonds : bond 0.03423 ( 504) hydrogen bonds : angle 4.75285 ( 1431) link_ALPHA1-3 : bond 0.00932 ( 3) link_ALPHA1-3 : angle 1.14524 ( 9) link_ALPHA1-6 : bond 0.00687 ( 3) link_ALPHA1-6 : angle 1.16483 ( 9) link_BETA1-4 : bond 0.00489 ( 39) link_BETA1-4 : angle 1.72991 ( 117) link_NAG-ASN : bond 0.00192 ( 60) link_NAG-ASN : angle 1.36470 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.73 seconds wall clock time: 36 minutes 24.06 seconds (2184.06 seconds total)