Starting phenix.real_space_refine on Mon Feb 19 16:53:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7t_31781/02_2024/7v7t_31781.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7t_31781/02_2024/7v7t_31781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7t_31781/02_2024/7v7t_31781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7t_31781/02_2024/7v7t_31781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7t_31781/02_2024/7v7t_31781.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7t_31781/02_2024/7v7t_31781.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.054 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 108 5.16 5 C 16060 2.51 5 N 4116 2.21 5 O 5006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "B PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 977": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25290 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 13.69, per 1000 atoms: 0.54 Number of scatterers: 25290 At special positions: 0 Unit cell: (141.9, 145.2, 198, 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 108 16.00 O 5006 8.00 N 4116 7.00 C 16060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.02 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 341 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 614 " " NAG J 1 " - " ASN A 707 " " NAG K 1 " - " ASN A 715 " " NAG L 1 " - " ASN A 799 " " NAG M 1 " - " ASN A1072 " " NAG N 1 " - " ASN A1096 " " NAG O 1 " - " ASN A1132 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 163 " " NAG R 1 " - " ASN B 280 " " NAG S 1 " - " ASN B 341 " " NAG T 1 " - " ASN B 614 " " NAG U 1 " - " ASN B 707 " " NAG V 1 " - " ASN B 715 " " NAG W 1 " - " ASN B 799 " " NAG X 1 " - " ASN B1072 " " NAG Y 1 " - " ASN B1096 " " NAG Z 1 " - " ASN B1132 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 163 " " NAG c 1 " - " ASN C 232 " " NAG d 1 " - " ASN C 280 " " NAG e 1 " - " ASN C 329 " " NAG f 1 " - " ASN C 614 " " NAG g 1 " - " ASN C 707 " " NAG h 1 " - " ASN C 715 " " NAG i 1 " - " ASN C 799 " " NAG j 1 " - " ASN C1072 " " NAG k 1 " - " ASN C1096 " " NAG l 1 " - " ASN C1132 " Time building additional restraints: 10.64 Conformation dependent library (CDL) restraints added in 4.9 seconds 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 47 sheets defined 24.6% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.320A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.833A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 757 through 781 removed outlier: 4.094A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.511A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.560A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.294A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.506A pdb=" N GLN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.557A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.329A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 4.004A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.872A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.068A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.780A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.635A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.616A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.002A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.643A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 982 removed outlier: 3.652A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.311A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.728A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 removed outlier: 3.536A pdb=" N PHE C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C 341 " --> pdb=" O GLY C 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 336 through 341' Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.528A pdb=" N TRP C 351 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.161A pdb=" N ASN C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 753 removed outlier: 3.913A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 removed outlier: 4.326A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.516A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 882 Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.885A pdb=" N TYR C 902 " --> pdb=" O MET C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 939 removed outlier: 4.296A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.578A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.891A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.827A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.742A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 574 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.868A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.221A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.562A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.721A pdb=" N ASN A 540 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 7.248A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 571 through 574 removed outlier: 3.676A pdb=" N ALA A 573 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.012A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.914A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.550A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.587A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.710A pdb=" N ILE A 786 " --> pdb=" O ASN C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 4.633A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.841A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.066A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.346A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.532A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.480A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC8, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.372A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AD1, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AD2, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.079A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 699 through 701 removed outlier: 7.111A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.080A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.535A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD7, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.106A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.691A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.023A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.222A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 309 through 317 removed outlier: 6.962A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE4, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE5, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE6, first strand: chain 'C' and resid 652 through 653 removed outlier: 5.822A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.602A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.531A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AF2, first strand: chain 'C' and resid 1092 through 1095 989 hydrogen bonds defined for protein. 2712 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: 11.06 Time building geometry restraints manager: 11.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7980 1.34 - 1.46: 6447 1.46 - 1.58: 11278 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25837 Sorted by residual: bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.79e+00 bond pdb=" C1 NAG d 2 " pdb=" O5 NAG d 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.76e+00 ... (remaining 25832 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.02: 570 106.02 - 113.01: 14299 113.01 - 120.01: 8458 120.01 - 127.00: 11608 127.00 - 133.99: 222 Bond angle restraints: 35157 Sorted by residual: angle pdb=" N THR C 616 " pdb=" CA THR C 616 " pdb=" C THR C 616 " ideal model delta sigma weight residual 114.56 109.19 5.37 1.27e+00 6.20e-01 1.79e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.58 -3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" N PRO A 559 " pdb=" CA PRO A 559 " pdb=" C PRO A 559 " ideal model delta sigma weight residual 112.47 118.90 -6.43 2.06e+00 2.36e-01 9.76e+00 angle pdb=" C ASN A 232 " pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 120.49 124.53 -4.04 1.38e+00 5.25e-01 8.55e+00 angle pdb=" N PRO C 559 " pdb=" CA PRO C 559 " pdb=" C PRO C 559 " ideal model delta sigma weight residual 112.47 118.18 -5.71 2.06e+00 2.36e-01 7.69e+00 ... (remaining 35152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.64: 15192 20.64 - 41.27: 1065 41.27 - 61.91: 176 61.91 - 82.54: 40 82.54 - 103.18: 15 Dihedral angle restraints: 16488 sinusoidal: 7498 harmonic: 8990 Sorted by residual: dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual -86.00 1.73 -87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS C1080 " pdb=" SG CYS C1080 " pdb=" SG CYS C1124 " pdb=" CB CYS C1124 " ideal model delta sinusoidal sigma weight residual 93.00 7.49 85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -169.91 83.91 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 16485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 4217 0.151 - 0.303: 17 0.303 - 0.454: 1 0.454 - 0.606: 0 0.606 - 0.757: 1 Chirality restraints: 4236 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 4233 not shown) Planarity restraints: 4493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 983 " -0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO C 984 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 984 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1137 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO A1138 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1138 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1138 " -0.027 5.00e-02 4.00e+02 ... (remaining 4490 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 724 2.70 - 3.25: 24287 3.25 - 3.80: 38354 3.80 - 4.35: 47416 4.35 - 4.90: 82148 Nonbonded interactions: 192929 Sorted by model distance: nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.149 2.440 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.174 2.440 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE2 GLU B 189 " model vdw 2.216 2.440 nonbonded pdb=" OE1 GLN A 802 " pdb=" O6 NAG L 1 " model vdw 2.219 2.440 ... (remaining 192924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 1144 or resid 2001 through 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 1144 or resid 2001 thr \ ough 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.400 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 70.640 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.410 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: 0.000 Load rotamer database and sin/cos tables:14.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 0.049 25837 Z= 0.244 Angle : 0.589 8.652 35157 Z= 0.289 Chirality : 0.048 0.757 4236 Planarity : 0.004 0.061 4445 Dihedral : 13.854 103.181 10580 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3041 helix: 2.20 (0.21), residues: 667 sheet: 0.59 (0.19), residues: 715 loop : -1.08 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 434 HIS 0.002 0.000 HIS C1062 PHE 0.026 0.001 PHE A 904 TYR 0.017 0.001 TYR A 871 ARG 0.005 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8927 (mp) cc_final: 0.8594 (tp) REVERT: B 52 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 81 ASN cc_start: 0.8399 (m-40) cc_final: 0.8111 (p0) REVERT: B 133 PHE cc_start: 0.8642 (m-80) cc_final: 0.8394 (m-80) REVERT: B 419 TYR cc_start: 0.9050 (m-10) cc_final: 0.8529 (m-10) REVERT: C 64 TRP cc_start: 0.7204 (t60) cc_final: 0.6652 (t60) REVERT: C 133 PHE cc_start: 0.8058 (m-80) cc_final: 0.7706 (m-80) REVERT: C 195 ILE cc_start: 0.8650 (tp) cc_final: 0.8405 (tp) REVERT: C 1000 GLN cc_start: 0.8061 (tp40) cc_final: 0.7702 (tp-100) outliers start: 0 outliers final: 2 residues processed: 171 average time/residue: 1.1851 time to fit residues: 239.6109 Evaluate side-chains 102 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1015 GLU Chi-restraints excluded: chain C residue 866 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 1.9990 chunk 232 optimal weight: 0.0980 chunk 129 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 240 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 899 GLN C 115 GLN C 604 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25837 Z= 0.271 Angle : 0.581 9.321 35157 Z= 0.293 Chirality : 0.046 0.340 4236 Planarity : 0.004 0.066 4445 Dihedral : 8.246 179.520 5060 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.83 % Favored : 95.07 % Rotamer: Outliers : 0.81 % Allowed : 8.11 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3041 helix: 2.14 (0.21), residues: 667 sheet: 0.57 (0.19), residues: 727 loop : -1.10 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS B1086 PHE 0.025 0.001 PHE A 904 TYR 0.021 0.001 TYR C1065 ARG 0.029 0.001 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8986 (mp) cc_final: 0.8612 (tp) REVERT: A 975 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8314 (tt) REVERT: B 115 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8054 (tp-100) REVERT: B 133 PHE cc_start: 0.8593 (m-80) cc_final: 0.8387 (m-80) REVERT: B 240 LEU cc_start: 0.8184 (mp) cc_final: 0.7597 (tp) REVERT: C 307 GLU cc_start: 0.7398 (mp0) cc_final: 0.7190 (mp0) REVERT: C 332 ASN cc_start: 0.8801 (t0) cc_final: 0.8601 (p0) REVERT: C 771 GLU cc_start: 0.7861 (tp30) cc_final: 0.7607 (tt0) REVERT: C 772 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7578 (mp-120) REVERT: C 1000 GLN cc_start: 0.8102 (tp40) cc_final: 0.7692 (tp-100) outliers start: 22 outliers final: 11 residues processed: 120 average time/residue: 1.0993 time to fit residues: 159.8596 Evaluate side-chains 107 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 232 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 248 optimal weight: 40.0000 chunk 276 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 802 GLN C 899 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25837 Z= 0.204 Angle : 0.538 9.441 35157 Z= 0.270 Chirality : 0.045 0.341 4236 Planarity : 0.004 0.058 4445 Dihedral : 7.143 83.642 5054 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 1.67 % Allowed : 10.73 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3041 helix: 2.28 (0.21), residues: 659 sheet: 0.64 (0.19), residues: 727 loop : -1.07 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 434 HIS 0.004 0.001 HIS C1099 PHE 0.017 0.001 PHE C1119 TYR 0.018 0.001 TYR C1065 ARG 0.006 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 103 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.8008 (t) REVERT: A 240 LEU cc_start: 0.8978 (mp) cc_final: 0.8597 (tp) REVERT: B 133 PHE cc_start: 0.8609 (m-80) cc_final: 0.8397 (m-80) REVERT: B 240 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7719 (tp) REVERT: B 422 LYS cc_start: 0.8606 (tptp) cc_final: 0.8371 (tppp) REVERT: C 307 GLU cc_start: 0.7407 (mp0) cc_final: 0.7190 (mp0) REVERT: C 332 ASN cc_start: 0.8796 (t0) cc_final: 0.8588 (p0) REVERT: C 771 GLU cc_start: 0.7773 (tp30) cc_final: 0.7531 (tt0) REVERT: C 772 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7545 (mp-120) REVERT: C 1000 GLN cc_start: 0.8111 (tp40) cc_final: 0.7597 (tp-100) outliers start: 45 outliers final: 18 residues processed: 136 average time/residue: 0.9378 time to fit residues: 158.4394 Evaluate side-chains 113 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 0.1980 chunk 209 optimal weight: 5.9990 chunk 144 optimal weight: 0.2980 chunk 30 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 802 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25837 Z= 0.202 Angle : 0.536 9.594 35157 Z= 0.268 Chirality : 0.044 0.345 4236 Planarity : 0.004 0.054 4445 Dihedral : 6.663 78.443 5054 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 1.81 % Allowed : 12.84 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3041 helix: 2.32 (0.21), residues: 665 sheet: 0.69 (0.19), residues: 719 loop : -1.07 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 PHE 0.020 0.001 PHE C 133 TYR 0.018 0.001 TYR B1065 ARG 0.004 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 98 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7937 (t) REVERT: A 240 LEU cc_start: 0.8967 (mp) cc_final: 0.8502 (tp) REVERT: A 738 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8001 (ttt) REVERT: A 1027 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8048 (ttp) REVERT: B 115 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7949 (tp-100) REVERT: B 240 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7691 (tp) REVERT: B 422 LYS cc_start: 0.8638 (tptp) cc_final: 0.8412 (tppp) REVERT: C 332 ASN cc_start: 0.8825 (t0) cc_final: 0.8625 (p0) REVERT: C 771 GLU cc_start: 0.7813 (tp30) cc_final: 0.7568 (tt0) REVERT: C 772 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7540 (mp-120) REVERT: C 982 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8530 (pp) REVERT: C 1000 GLN cc_start: 0.8091 (tp40) cc_final: 0.7548 (tp-100) outliers start: 49 outliers final: 19 residues processed: 134 average time/residue: 0.9197 time to fit residues: 154.4485 Evaluate side-chains 118 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 30.0000 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 205 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 GLN B1009 GLN C 802 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25837 Z= 0.417 Angle : 0.629 9.660 35157 Z= 0.318 Chirality : 0.048 0.340 4236 Planarity : 0.004 0.054 4445 Dihedral : 6.746 74.365 5054 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 2.07 % Allowed : 14.62 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3041 helix: 2.04 (0.21), residues: 671 sheet: 0.44 (0.19), residues: 723 loop : -1.22 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 884 HIS 0.007 0.001 HIS B1086 PHE 0.030 0.002 PHE C1119 TYR 0.025 0.001 TYR C1065 ARG 0.008 0.000 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 94 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7947 (t) REVERT: A 240 LEU cc_start: 0.8961 (mp) cc_final: 0.8489 (tp) REVERT: A 738 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7868 (ttt) REVERT: B 115 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7865 (tp-100) REVERT: B 240 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7804 (tp) REVERT: B 422 LYS cc_start: 0.8552 (tptp) cc_final: 0.8314 (tppp) REVERT: C 225 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7120 (t) REVERT: C 332 ASN cc_start: 0.8794 (t0) cc_final: 0.8571 (p0) REVERT: C 772 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7731 (mp-120) REVERT: C 1000 GLN cc_start: 0.8251 (tp40) cc_final: 0.7988 (tm-30) outliers start: 56 outliers final: 27 residues processed: 137 average time/residue: 0.9412 time to fit residues: 160.5007 Evaluate side-chains 126 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 246 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 802 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25837 Z= 0.184 Angle : 0.538 9.549 35157 Z= 0.269 Chirality : 0.045 0.349 4236 Planarity : 0.004 0.051 4445 Dihedral : 6.260 69.646 5054 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 1.70 % Allowed : 15.77 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3041 helix: 2.32 (0.21), residues: 663 sheet: 0.56 (0.19), residues: 729 loop : -1.17 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 PHE 0.026 0.001 PHE C 133 TYR 0.017 0.001 TYR C1065 ARG 0.003 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 104 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8107 (m-10) cc_final: 0.7678 (m-80) REVERT: A 225 VAL cc_start: 0.8143 (t) cc_final: 0.7935 (t) REVERT: A 240 LEU cc_start: 0.8914 (mp) cc_final: 0.8451 (tp) REVERT: A 738 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7886 (ttt) REVERT: B 115 GLN cc_start: 0.8285 (tp-100) cc_final: 0.7892 (tp-100) REVERT: B 133 PHE cc_start: 0.8550 (m-80) cc_final: 0.8148 (m-10) REVERT: B 240 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7806 (tp) REVERT: B 422 LYS cc_start: 0.8629 (tptp) cc_final: 0.8409 (tppp) REVERT: C 332 ASN cc_start: 0.8795 (t0) cc_final: 0.8590 (p0) REVERT: C 772 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7551 (mp-120) REVERT: C 1000 GLN cc_start: 0.8195 (tp40) cc_final: 0.7666 (tp-100) outliers start: 46 outliers final: 24 residues processed: 142 average time/residue: 1.1147 time to fit residues: 193.4437 Evaluate side-chains 120 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 0.6980 chunk 33 optimal weight: 30.0000 chunk 169 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 250 optimal weight: 20.0000 chunk 165 optimal weight: 0.8980 chunk 295 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25837 Z= 0.202 Angle : 0.551 9.634 35157 Z= 0.275 Chirality : 0.045 0.347 4236 Planarity : 0.004 0.049 4445 Dihedral : 6.073 64.962 5054 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 1.67 % Allowed : 16.03 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3041 helix: 2.39 (0.21), residues: 658 sheet: 0.61 (0.19), residues: 720 loop : -1.14 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 884 HIS 0.003 0.001 HIS B1086 PHE 0.017 0.001 PHE B 390 TYR 0.018 0.001 TYR B1065 ARG 0.003 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 94 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8091 (m-10) cc_final: 0.7657 (m-80) REVERT: A 240 LEU cc_start: 0.8924 (mp) cc_final: 0.8494 (tp) REVERT: A 738 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7897 (ttt) REVERT: B 115 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7788 (tp40) REVERT: B 133 PHE cc_start: 0.8609 (m-80) cc_final: 0.8146 (m-10) REVERT: B 135 PHE cc_start: 0.7567 (m-80) cc_final: 0.7358 (m-80) REVERT: B 240 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7830 (tp) REVERT: B 422 LYS cc_start: 0.8659 (tptp) cc_final: 0.8443 (tppp) REVERT: C 332 ASN cc_start: 0.8801 (t0) cc_final: 0.8596 (p0) REVERT: C 772 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7502 (mp-120) REVERT: C 1000 GLN cc_start: 0.8181 (tp40) cc_final: 0.7922 (tm-30) outliers start: 45 outliers final: 30 residues processed: 131 average time/residue: 1.0758 time to fit residues: 179.0717 Evaluate side-chains 125 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25837 Z= 0.272 Angle : 0.580 9.633 35157 Z= 0.289 Chirality : 0.046 0.344 4236 Planarity : 0.004 0.049 4445 Dihedral : 6.054 60.004 5054 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 1.78 % Allowed : 16.28 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3041 helix: 2.31 (0.21), residues: 658 sheet: 0.57 (0.19), residues: 715 loop : -1.15 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 884 HIS 0.005 0.001 HIS B1086 PHE 0.027 0.001 PHE C 133 TYR 0.020 0.001 TYR C1065 ARG 0.004 0.000 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 93 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8114 (m-10) cc_final: 0.7671 (m-80) REVERT: A 240 LEU cc_start: 0.8962 (mp) cc_final: 0.8526 (tp) REVERT: A 738 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7901 (ttt) REVERT: B 115 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7902 (tp40) REVERT: B 133 PHE cc_start: 0.8621 (m-80) cc_final: 0.8202 (m-10) REVERT: B 240 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7833 (tp) REVERT: B 422 LYS cc_start: 0.8661 (tptp) cc_final: 0.8443 (tppp) REVERT: C 332 ASN cc_start: 0.8800 (t0) cc_final: 0.8592 (p0) REVERT: C 772 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7620 (mp-120) REVERT: C 1000 GLN cc_start: 0.8232 (tp40) cc_final: 0.7971 (tm-30) outliers start: 48 outliers final: 32 residues processed: 131 average time/residue: 0.9477 time to fit residues: 155.0930 Evaluate side-chains 127 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 854 ASN Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 3.9990 chunk 283 optimal weight: 0.5980 chunk 258 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 chunk 260 optimal weight: 0.5980 chunk 274 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25837 Z= 0.218 Angle : 0.559 9.613 35157 Z= 0.279 Chirality : 0.045 0.343 4236 Planarity : 0.004 0.049 4445 Dihedral : 5.866 56.254 5054 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Rotamer: Outliers : 1.89 % Allowed : 16.32 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3041 helix: 2.37 (0.21), residues: 659 sheet: 0.60 (0.19), residues: 717 loop : -1.13 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 PHE 0.018 0.001 PHE B1119 TYR 0.018 0.001 TYR C1065 ARG 0.005 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 95 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8105 (m-10) cc_final: 0.7814 (m-80) REVERT: A 225 VAL cc_start: 0.8182 (t) cc_final: 0.7969 (t) REVERT: A 240 LEU cc_start: 0.8945 (mp) cc_final: 0.8543 (tp) REVERT: A 738 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8004 (ttt) REVERT: B 115 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7786 (tp40) REVERT: B 133 PHE cc_start: 0.8594 (m-80) cc_final: 0.8144 (m-10) REVERT: B 240 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7904 (tp) REVERT: B 422 LYS cc_start: 0.8707 (tptp) cc_final: 0.8497 (tppp) REVERT: B 1037 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8830 (mtp180) REVERT: C 332 ASN cc_start: 0.8806 (t0) cc_final: 0.8598 (p0) REVERT: C 772 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7526 (mp-120) REVERT: C 1000 GLN cc_start: 0.8202 (tp40) cc_final: 0.7943 (tm-30) outliers start: 51 outliers final: 36 residues processed: 138 average time/residue: 1.0279 time to fit residues: 176.2748 Evaluate side-chains 134 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 305 optimal weight: 0.1980 chunk 281 optimal weight: 2.9990 chunk 243 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25837 Z= 0.247 Angle : 0.572 9.644 35157 Z= 0.286 Chirality : 0.046 0.341 4236 Planarity : 0.004 0.049 4445 Dihedral : 5.789 56.843 5054 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 1.63 % Allowed : 16.80 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3041 helix: 2.33 (0.21), residues: 659 sheet: 0.57 (0.19), residues: 707 loop : -1.15 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 884 HIS 0.004 0.001 HIS B1086 PHE 0.025 0.001 PHE C 133 TYR 0.019 0.001 TYR C1065 ARG 0.004 0.000 ARG C 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 95 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8100 (m-10) cc_final: 0.7811 (m-80) REVERT: A 240 LEU cc_start: 0.8948 (mp) cc_final: 0.8563 (tp) REVERT: A 738 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8018 (ttt) REVERT: B 115 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7833 (tp40) REVERT: B 133 PHE cc_start: 0.8610 (m-80) cc_final: 0.8141 (m-10) REVERT: B 240 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7908 (tp) REVERT: B 422 LYS cc_start: 0.8710 (tptp) cc_final: 0.8498 (tppp) REVERT: B 1037 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8835 (mtp180) REVERT: C 332 ASN cc_start: 0.8806 (t0) cc_final: 0.8599 (p0) REVERT: C 772 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7616 (mp-120) REVERT: C 1000 GLN cc_start: 0.8227 (tp40) cc_final: 0.7965 (tm-30) outliers start: 44 outliers final: 35 residues processed: 132 average time/residue: 0.9923 time to fit residues: 161.0927 Evaluate side-chains 129 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 90 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 824 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 224 optimal weight: 0.0270 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 250 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 overall best weight: 1.0442 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.146251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.090088 restraints weight = 48610.930| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.31 r_work: 0.2994 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25837 Z= 0.197 Angle : 0.554 9.691 35157 Z= 0.277 Chirality : 0.045 0.341 4236 Planarity : 0.004 0.049 4445 Dihedral : 5.603 56.077 5054 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 1.63 % Allowed : 16.91 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3041 helix: 2.45 (0.21), residues: 653 sheet: 0.64 (0.19), residues: 708 loop : -1.12 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 64 HIS 0.003 0.001 HIS B1086 PHE 0.016 0.001 PHE A1119 TYR 0.017 0.001 TYR C1065 ARG 0.005 0.000 ARG B 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5497.95 seconds wall clock time: 101 minutes 15.27 seconds (6075.27 seconds total)