Starting phenix.real_space_refine on Mon Feb 19 16:59:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7v_31783/02_2024/7v7v_31783.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7v_31783/02_2024/7v7v_31783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7v_31783/02_2024/7v7v_31783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7v_31783/02_2024/7v7v_31783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7v_31783/02_2024/7v7v_31783.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7v_31783/02_2024/7v7v_31783.pdb" } resolution = 3.1 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= 0.055 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 16068 2.51 5 N 4117 2.21 5 O 5011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1090": "OE1" <-> "OE2" Residue "B GLU 1015": "OE1" <-> "OE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 25304 Number of models: 1 Model: "" Number of chains: 42 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: "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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.78, per 1000 atoms: 0.51 Number of scatterers: 25304 At special positions: 0 Unit cell: (139.7, 148.5, 200.2, 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 5011 8.00 N 4117 7.00 C 16068 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=2.03 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=2.03 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 m 1 " - " NAG m 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 601 " " NAG C2003 " - " 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 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 10.00 Conformation dependent library (CDL) restraints added in 4.3 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: 59 helices and 46 sheets defined 24.4% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.686A pdb=" N GLU A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.324A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.860A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) 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 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 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: 4.313A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 938 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.670A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.149A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.843A 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 362 through 369 removed outlier: 4.112A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.151A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) 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 753 removed outlier: 4.141A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.677A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.529A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.568A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.937A 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: 3.509A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.705A 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 removed outlier: 3.528A pdb=" N GLN B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) 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 980 removed outlier: 3.550A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.383A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.767A 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 Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.568A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (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: 3.884A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 removed outlier: 4.462A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 882 Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 939 removed outlier: 4.306A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.421A 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: 3.565A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.834A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.540A 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 26 through 30 removed outlier: 7.756A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.907A 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: 6.837A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.040A 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: 7.238A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.533A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 317 removed outlier: 3.539A pdb=" N THR A 313 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.505A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 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 652 through 653 removed outlier: 6.181A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.797A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.613A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.544A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.886A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.021A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.255A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.316A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 321 through 326 removed outlier: 5.032A pdb=" N ASN B 538 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY B 564 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC7, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.369A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AD1, first strand: chain 'B' and resid 652 through 653 removed outlier: 5.933A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.988A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.057A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.412A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.976A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.045A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.769A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.099A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.196A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N VAL C 126 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N GLU C 167 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N ILE C 128 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR C 165 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL C 130 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASN C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU C 132 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA C 161 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN C 134 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.100A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.198A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.565A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.513A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1118 through 1123 removed outlier: 4.552A pdb=" N ALA C1085 " --> pdb=" O SER C1121 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1092 through 1095 1001 hydrogen bonds defined for protein. 2751 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: 11.85 Time building geometry restraints manager: 10.79 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: 7983 1.34 - 1.46: 6432 1.46 - 1.58: 11304 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25851 Sorted by residual: bond pdb=" C1 NAG A2002 " pdb=" O5 NAG A2002 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 ... (remaining 25846 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 680 106.59 - 113.44: 14451 113.44 - 120.29: 8671 120.29 - 127.13: 11163 127.13 - 133.98: 211 Bond angle restraints: 35176 Sorted by residual: angle pdb=" C GLU B 482 " pdb=" CA GLU B 482 " pdb=" CB GLU B 482 " ideal model delta sigma weight residual 116.63 110.28 6.35 1.16e+00 7.43e-01 3.00e+01 angle pdb=" N VAL A 157 " pdb=" CA VAL A 157 " pdb=" C VAL A 157 " ideal model delta sigma weight residual 113.39 108.70 4.69 1.47e+00 4.63e-01 1.02e+01 angle pdb=" CA GLU B 482 " pdb=" C GLU B 482 " pdb=" N GLY B 483 " ideal model delta sigma weight residual 119.63 117.05 2.58 8.10e-01 1.52e+00 1.02e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.52 -3.82 1.22e+00 6.72e-01 9.79e+00 angle pdb=" N PRO C 559 " pdb=" CA PRO C 559 " pdb=" C PRO C 559 " ideal model delta sigma weight residual 112.47 118.08 -5.61 2.06e+00 2.36e-01 7.42e+00 ... (remaining 35171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 15484 23.43 - 46.87: 862 46.87 - 70.30: 118 70.30 - 93.74: 29 93.74 - 117.17: 16 Dihedral angle restraints: 16509 sinusoidal: 7519 harmonic: 8990 Sorted by residual: 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 -173.03 87.03 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sinusoidal sigma weight residual -86.00 -6.10 -79.90 1 1.00e+01 1.00e-02 7.92e+01 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 -7.14 -78.86 1 1.00e+01 1.00e-02 7.74e+01 ... (remaining 16506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4218 0.136 - 0.272: 22 0.272 - 0.409: 0 0.409 - 0.545: 0 0.545 - 0.681: 1 Chirality restraints: 4241 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 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PRO C 559 " pdb=" N PRO C 559 " pdb=" C PRO C 559 " pdb=" CB PRO C 559 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA PRO A 559 " pdb=" N PRO A 559 " pdb=" C PRO A 559 " pdb=" CB PRO A 559 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 4238 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.032 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 984 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 983 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO C 984 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 984 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO C 985 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 985 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 985 " -0.026 5.00e-02 4.00e+02 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 655 2.70 - 3.25: 24049 3.25 - 3.80: 38256 3.80 - 4.35: 47620 4.35 - 4.90: 82054 Nonbonded interactions: 192634 Sorted by model distance: nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.145 2.440 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.154 2.440 nonbonded pdb=" OG1 THR C 124 " pdb=" OD1 ASN C 125 " model vdw 2.170 2.440 nonbonded pdb=" O ASN A 437 " pdb=" OG SER A 441 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.212 2.440 ... (remaining 192629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1144 or resid 2001 through 2003)) selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 1144 or resid 2001 through 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 1144 or resid 2001 thr \ ough 2003)) } 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' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.030 Extract box with map and model: 13.150 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 67.300 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 0.080 25851 Z= 0.247 Angle : 0.582 7.885 35176 Z= 0.281 Chirality : 0.047 0.681 4241 Planarity : 0.003 0.048 4446 Dihedral : 14.230 117.173 10601 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.39 (0.16), residues: 3041 helix: 2.40 (0.22), residues: 668 sheet: 0.82 (0.19), residues: 716 loop : -0.94 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 884 HIS 0.001 0.000 HIS A1062 PHE 0.016 0.001 PHE B 904 TYR 0.016 0.001 TYR B1065 ARG 0.002 0.000 ARG A1037 *********************** 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 212 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7196 (t80) cc_final: 0.6880 (t80) REVERT: A 644 ARG cc_start: 0.7396 (tpp-160) cc_final: 0.7144 (tpm170) REVERT: A 757 PHE cc_start: 0.7975 (p90) cc_final: 0.7160 (p90) REVERT: A 771 GLU cc_start: 0.8243 (tt0) cc_final: 0.7956 (tt0) REVERT: B 52 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 129 LYS cc_start: 0.6971 (mmmm) cc_final: 0.6752 (mttt) REVERT: B 133 PHE cc_start: 0.7998 (m-80) cc_final: 0.7652 (m-80) REVERT: B 140 PHE cc_start: 0.7371 (p90) cc_final: 0.7114 (p90) REVERT: B 240 LEU cc_start: 0.7653 (mm) cc_final: 0.7439 (mp) REVERT: B 243 HIS cc_start: 0.4393 (p-80) cc_final: 0.3916 (p-80) REVERT: B 416 ILE cc_start: 0.8892 (pt) cc_final: 0.8593 (pt) REVERT: B 451 TYR cc_start: 0.7849 (p90) cc_final: 0.6971 (p90) REVERT: B 506 TYR cc_start: 0.8137 (m-80) cc_final: 0.7765 (m-80) REVERT: B 659 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6962 (tm-30) REVERT: B 876 LEU cc_start: 0.8997 (tp) cc_final: 0.8598 (mt) REVERT: B 955 GLN cc_start: 0.8523 (tt0) cc_final: 0.8308 (tt0) REVERT: C 363 TYR cc_start: 0.9060 (m-80) cc_final: 0.8779 (m-80) REVERT: C 572 ASP cc_start: 0.7309 (m-30) cc_final: 0.6847 (m-30) REVERT: C 979 LEU cc_start: 0.9193 (mt) cc_final: 0.8988 (mt) REVERT: C 1140 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8489 (mm-40) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3689 time to fit residues: 123.5836 Evaluate side-chains 119 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 240 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 179 optimal weight: 0.2980 chunk 278 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 760 GLN B 899 GLN B 976 ASN C 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25851 Z= 0.263 Angle : 0.581 10.284 35176 Z= 0.288 Chirality : 0.046 0.268 4241 Planarity : 0.004 0.076 4446 Dihedral : 9.036 112.811 5075 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Rotamer: Outliers : 0.67 % Allowed : 6.14 % Favored : 93.19 % 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: 0.26 (0.15), residues: 3041 helix: 2.25 (0.21), residues: 685 sheet: 0.72 (0.19), residues: 710 loop : -1.02 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.003 0.001 HIS A1046 PHE 0.021 0.001 PHE C 904 TYR 0.022 0.001 TYR A1065 ARG 0.006 0.000 ARG A1037 *********************** 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 139 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7249 (t80) cc_final: 0.7015 (t80) REVERT: A 235 ARG cc_start: 0.8448 (mtm110) cc_final: 0.7949 (mtm-85) REVERT: A 644 ARG cc_start: 0.7443 (tpp-160) cc_final: 0.7174 (tpm170) REVERT: A 757 PHE cc_start: 0.8188 (p90) cc_final: 0.7880 (p90) REVERT: A 771 GLU cc_start: 0.8326 (tt0) cc_final: 0.7960 (tt0) REVERT: A 1048 MET cc_start: 0.8684 (ptm) cc_final: 0.8385 (ptp) REVERT: B 52 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8353 (tm-30) REVERT: B 129 LYS cc_start: 0.7002 (mmmm) cc_final: 0.6760 (mttt) REVERT: B 133 PHE cc_start: 0.7820 (m-80) cc_final: 0.7539 (m-80) REVERT: B 140 PHE cc_start: 0.7437 (p90) cc_final: 0.7174 (p90) REVERT: B 404 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: B 451 TYR cc_start: 0.7905 (p90) cc_final: 0.6918 (p90) REVERT: B 506 TYR cc_start: 0.8141 (m-80) cc_final: 0.7722 (m-80) REVERT: B 659 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7085 (tm-30) REVERT: B 955 GLN cc_start: 0.8513 (tt0) cc_final: 0.8292 (tt0) REVERT: C 140 PHE cc_start: 0.7612 (p90) cc_final: 0.7380 (p90) REVERT: C 363 TYR cc_start: 0.9049 (m-80) cc_final: 0.8760 (m-80) REVERT: C 372 PHE cc_start: 0.7861 (m-80) cc_final: 0.7595 (m-80) REVERT: C 572 ASP cc_start: 0.7350 (m-30) cc_final: 0.7004 (m-30) outliers start: 18 outliers final: 13 residues processed: 135 average time/residue: 0.3813 time to fit residues: 81.5478 Evaluate side-chains 125 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 865 ASP 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: 2.9990 chunk 232 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 301 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 GLN B 976 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25851 Z= 0.270 Angle : 0.571 13.768 35176 Z= 0.283 Chirality : 0.046 0.259 4241 Planarity : 0.004 0.048 4446 Dihedral : 8.479 111.933 5075 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 1.07 % Allowed : 9.44 % Favored : 89.49 % 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: 0.19 (0.15), residues: 3041 helix: 2.20 (0.21), residues: 675 sheet: 0.67 (0.19), residues: 705 loop : -1.05 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 884 HIS 0.004 0.001 HIS A1086 PHE 0.021 0.001 PHE C 904 TYR 0.021 0.001 TYR A1065 ARG 0.007 0.000 ARG B 344 *********************** 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 141 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8456 (mtm110) cc_final: 0.7685 (mtm-85) REVERT: A 757 PHE cc_start: 0.8184 (p90) cc_final: 0.7874 (p90) REVERT: B 52 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8350 (tm-30) REVERT: B 133 PHE cc_start: 0.7941 (m-80) cc_final: 0.7739 (m-80) REVERT: B 140 PHE cc_start: 0.7558 (p90) cc_final: 0.7225 (p90) REVERT: B 404 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: B 451 TYR cc_start: 0.7863 (p90) cc_final: 0.6828 (p90) REVERT: B 506 TYR cc_start: 0.7999 (m-80) cc_final: 0.7627 (m-80) REVERT: B 659 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7140 (tm-30) REVERT: B 955 GLN cc_start: 0.8572 (tt0) cc_final: 0.8332 (tt0) REVERT: C 140 PHE cc_start: 0.7683 (p90) cc_final: 0.7409 (p90) REVERT: C 171 GLN cc_start: 0.7261 (tm-30) cc_final: 0.6920 (tm-30) REVERT: C 363 TYR cc_start: 0.9098 (m-80) cc_final: 0.8799 (m-80) REVERT: C 372 PHE cc_start: 0.7913 (m-80) cc_final: 0.7641 (m-80) REVERT: C 572 ASP cc_start: 0.7397 (m-30) cc_final: 0.7061 (m-30) outliers start: 29 outliers final: 21 residues processed: 134 average time/residue: 0.3663 time to fit residues: 80.7358 Evaluate side-chains 123 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 865 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 0.0000 chunk 209 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 187 optimal weight: 0.4980 chunk 280 optimal weight: 0.7980 chunk 296 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 392 ASN B 976 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25851 Z= 0.199 Angle : 0.544 11.897 35176 Z= 0.267 Chirality : 0.045 0.259 4241 Planarity : 0.004 0.047 4446 Dihedral : 7.966 109.352 5075 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 1.52 % Allowed : 10.99 % Favored : 87.49 % 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: 0.26 (0.15), residues: 3041 helix: 2.23 (0.21), residues: 678 sheet: 0.74 (0.19), residues: 698 loop : -1.00 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 884 HIS 0.002 0.001 HIS B1046 PHE 0.019 0.001 PHE B 166 TYR 0.018 0.001 TYR B1065 ARG 0.003 0.000 ARG B 401 *********************** 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 149 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8491 (mtm110) cc_final: 0.7998 (mtm-85) REVERT: A 757 PHE cc_start: 0.8171 (p90) cc_final: 0.7814 (p90) REVERT: B 52 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 81 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7991 (p0) REVERT: B 133 PHE cc_start: 0.7970 (m-80) cc_final: 0.7723 (m-10) REVERT: B 140 PHE cc_start: 0.7423 (p90) cc_final: 0.6970 (p90) REVERT: B 240 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7483 (tp) REVERT: B 404 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: B 451 TYR cc_start: 0.7825 (p90) cc_final: 0.6887 (p90) REVERT: B 506 TYR cc_start: 0.8048 (m-80) cc_final: 0.7736 (m-80) REVERT: B 955 GLN cc_start: 0.8560 (tt0) cc_final: 0.8319 (tt0) REVERT: C 140 PHE cc_start: 0.7709 (p90) cc_final: 0.7460 (p90) REVERT: C 171 GLN cc_start: 0.7277 (tm-30) cc_final: 0.7061 (tm-30) REVERT: C 363 TYR cc_start: 0.9072 (m-80) cc_final: 0.8773 (m-80) REVERT: C 372 PHE cc_start: 0.7958 (m-80) cc_final: 0.7672 (m-80) REVERT: C 572 ASP cc_start: 0.7429 (m-30) cc_final: 0.7016 (m-30) outliers start: 41 outliers final: 24 residues processed: 141 average time/residue: 0.3352 time to fit residues: 78.3281 Evaluate side-chains 128 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 865 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 0.4980 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 220 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 266 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 976 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25851 Z= 0.215 Angle : 0.549 11.706 35176 Z= 0.269 Chirality : 0.045 0.261 4241 Planarity : 0.004 0.047 4446 Dihedral : 7.723 107.195 5075 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 1.81 % Allowed : 11.92 % Favored : 86.27 % 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: 0.26 (0.15), residues: 3041 helix: 2.27 (0.21), residues: 672 sheet: 0.76 (0.19), residues: 692 loop : -1.01 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 884 HIS 0.002 0.001 HIS B1046 PHE 0.018 0.001 PHE B1119 TYR 0.019 0.001 TYR A1065 ARG 0.003 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 157 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 108 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7978 (m-80) cc_final: 0.6997 (m-80) REVERT: A 235 ARG cc_start: 0.8493 (mtm110) cc_final: 0.8012 (mtm-85) REVERT: A 757 PHE cc_start: 0.8187 (p90) cc_final: 0.7880 (p90) REVERT: B 52 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8336 (tm-30) REVERT: B 133 PHE cc_start: 0.7979 (m-80) cc_final: 0.7710 (m-10) REVERT: B 140 PHE cc_start: 0.7424 (p90) cc_final: 0.6977 (p90) REVERT: B 233 ILE cc_start: 0.7803 (mm) cc_final: 0.7592 (mm) REVERT: B 404 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: B 451 TYR cc_start: 0.7880 (p90) cc_final: 0.6980 (p90) REVERT: B 506 TYR cc_start: 0.8054 (m-80) cc_final: 0.7721 (m-80) REVERT: B 955 GLN cc_start: 0.8588 (tt0) cc_final: 0.8339 (tt0) REVERT: C 140 PHE cc_start: 0.7734 (p90) cc_final: 0.7475 (p90) REVERT: C 171 GLN cc_start: 0.7359 (tm-30) cc_final: 0.7051 (tm-30) REVERT: C 363 TYR cc_start: 0.9067 (m-80) cc_final: 0.8768 (m-80) REVERT: C 372 PHE cc_start: 0.7977 (m-80) cc_final: 0.7728 (m-80) REVERT: C 558 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8984 (mp) REVERT: C 572 ASP cc_start: 0.7438 (m-30) cc_final: 0.7008 (m-30) outliers start: 49 outliers final: 34 residues processed: 149 average time/residue: 0.3770 time to fit residues: 94.0221 Evaluate side-chains 139 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 103 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 551 THR 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 227 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 865 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 0.0050 chunk 267 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 297 optimal weight: 0.0000 chunk 246 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN B 976 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25851 Z= 0.138 Angle : 0.522 11.947 35176 Z= 0.252 Chirality : 0.043 0.258 4241 Planarity : 0.003 0.047 4446 Dihedral : 6.859 93.981 5075 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 1.59 % Allowed : 12.58 % Favored : 85.83 % 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: 0.42 (0.15), residues: 3041 helix: 2.50 (0.21), residues: 660 sheet: 0.79 (0.19), residues: 716 loop : -0.92 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 884 HIS 0.002 0.000 HIS B1086 PHE 0.018 0.001 PHE B 390 TYR 0.016 0.001 TYR B1065 ARG 0.003 0.000 ARG B 401 *********************** 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 163 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7898 (m-80) cc_final: 0.6940 (m-80) REVERT: A 235 ARG cc_start: 0.8467 (mtm110) cc_final: 0.8006 (mtm-85) REVERT: A 738 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8102 (tpp) REVERT: A 757 PHE cc_start: 0.8162 (p90) cc_final: 0.7803 (p90) REVERT: B 52 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8307 (tm-30) REVERT: B 133 PHE cc_start: 0.7991 (m-80) cc_final: 0.7519 (m-10) REVERT: B 140 PHE cc_start: 0.7319 (p90) cc_final: 0.6841 (p90) REVERT: B 404 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: B 451 TYR cc_start: 0.7847 (p90) cc_final: 0.6981 (p90) REVERT: B 659 GLU cc_start: 0.7307 (tm-30) cc_final: 0.7086 (tm-30) REVERT: B 738 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8357 (tpt) REVERT: B 955 GLN cc_start: 0.8524 (tt0) cc_final: 0.8278 (tt0) REVERT: C 363 TYR cc_start: 0.9036 (m-80) cc_final: 0.8728 (m-80) REVERT: C 372 PHE cc_start: 0.8004 (m-80) cc_final: 0.7738 (m-80) REVERT: C 558 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9029 (mp) REVERT: C 572 ASP cc_start: 0.7496 (m-30) cc_final: 0.7044 (m-30) outliers start: 43 outliers final: 33 residues processed: 155 average time/residue: 0.3188 time to fit residues: 83.5832 Evaluate side-chains 137 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 588 CYS 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 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 652 GLU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 865 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 295 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 136 optimal weight: 0.0030 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25851 Z= 0.181 Angle : 0.543 11.971 35176 Z= 0.264 Chirality : 0.044 0.259 4241 Planarity : 0.004 0.057 4446 Dihedral : 6.682 88.011 5075 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 1.85 % Allowed : 12.95 % Favored : 85.20 % 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: 0.43 (0.15), residues: 3041 helix: 2.51 (0.21), residues: 665 sheet: 0.89 (0.20), residues: 682 loop : -0.94 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 884 HIS 0.002 0.001 HIS A1062 PHE 0.017 0.001 PHE B 390 TYR 0.018 0.001 TYR B1065 ARG 0.004 0.000 ARG B 401 *********************** 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 155 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 105 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7949 (m-80) cc_final: 0.6990 (m-80) REVERT: A 235 ARG cc_start: 0.8459 (mtm110) cc_final: 0.8027 (mtm-85) REVERT: A 738 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8175 (tpp) REVERT: A 757 PHE cc_start: 0.8128 (p90) cc_final: 0.7821 (p90) REVERT: B 52 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8305 (tm-30) REVERT: B 133 PHE cc_start: 0.8013 (m-80) cc_final: 0.7561 (m-80) REVERT: B 140 PHE cc_start: 0.7345 (p90) cc_final: 0.6868 (p90) REVERT: B 404 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: B 451 TYR cc_start: 0.7788 (p90) cc_final: 0.6844 (p90) REVERT: B 659 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7098 (tm-30) REVERT: B 738 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8382 (tpt) REVERT: B 955 GLN cc_start: 0.8564 (tt0) cc_final: 0.8315 (tt0) REVERT: B 1037 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8310 (mtp180) REVERT: C 64 TRP cc_start: 0.8139 (t60) cc_final: 0.7740 (t60) REVERT: C 363 TYR cc_start: 0.9021 (m-80) cc_final: 0.8684 (m-80) REVERT: C 372 PHE cc_start: 0.7977 (m-80) cc_final: 0.7717 (m-80) REVERT: C 558 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8945 (mp) REVERT: C 572 ASP cc_start: 0.7498 (m-30) cc_final: 0.7054 (m-30) outliers start: 50 outliers final: 38 residues processed: 146 average time/residue: 0.3696 time to fit residues: 91.8573 Evaluate side-chains 146 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 103 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 588 CYS 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 316 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 865 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 232 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN B 976 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25851 Z= 0.156 Angle : 0.533 12.183 35176 Z= 0.257 Chirality : 0.044 0.259 4241 Planarity : 0.003 0.055 4446 Dihedral : 6.431 83.595 5075 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 1.85 % Allowed : 13.18 % Favored : 84.97 % 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: 0.44 (0.15), residues: 3041 helix: 2.54 (0.21), residues: 665 sheet: 0.83 (0.19), residues: 700 loop : -0.93 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 884 HIS 0.002 0.000 HIS A1086 PHE 0.017 0.001 PHE B 390 TYR 0.017 0.001 TYR B1065 ARG 0.002 0.000 ARG B 401 *********************** 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 163 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 113 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7977 (m-80) cc_final: 0.6999 (m-80) REVERT: A 235 ARG cc_start: 0.8456 (mtm110) cc_final: 0.8034 (mtm-85) REVERT: A 738 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8143 (tpp) REVERT: A 757 PHE cc_start: 0.8127 (p90) cc_final: 0.7799 (p90) REVERT: B 52 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8302 (tm-30) REVERT: B 133 PHE cc_start: 0.8040 (m-80) cc_final: 0.7535 (m-10) REVERT: B 140 PHE cc_start: 0.7273 (p90) cc_final: 0.6829 (p90) REVERT: B 404 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: B 451 TYR cc_start: 0.7785 (p90) cc_final: 0.6884 (p90) REVERT: B 659 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7143 (tm-30) REVERT: B 738 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8386 (tpt) REVERT: B 955 GLN cc_start: 0.8514 (tt0) cc_final: 0.8264 (tt0) REVERT: B 1037 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8333 (mtp180) REVERT: C 64 TRP cc_start: 0.8156 (t60) cc_final: 0.7734 (t60) REVERT: C 363 TYR cc_start: 0.9027 (m-80) cc_final: 0.8693 (m-80) REVERT: C 372 PHE cc_start: 0.7992 (m-80) cc_final: 0.7733 (m-80) REVERT: C 558 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8913 (mp) REVERT: C 572 ASP cc_start: 0.7498 (m-30) cc_final: 0.7027 (m-30) REVERT: C 803 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8754 (mt) outliers start: 50 outliers final: 40 residues processed: 153 average time/residue: 0.3260 time to fit residues: 83.1378 Evaluate side-chains 152 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 106 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 588 CYS 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 227 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 865 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 258 optimal weight: 0.6980 chunk 275 optimal weight: 0.0050 chunk 165 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 216 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 chunk 260 optimal weight: 0.8980 chunk 274 optimal weight: 0.4980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25851 Z= 0.143 Angle : 0.525 12.267 35176 Z= 0.253 Chirality : 0.043 0.258 4241 Planarity : 0.003 0.053 4446 Dihedral : 6.233 82.764 5075 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 1.70 % Allowed : 13.43 % Favored : 84.86 % 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: 0.48 (0.15), residues: 3041 helix: 2.57 (0.21), residues: 666 sheet: 0.84 (0.19), residues: 707 loop : -0.90 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 884 HIS 0.001 0.000 HIS B1086 PHE 0.016 0.001 PHE B 390 TYR 0.023 0.001 TYR C 493 ARG 0.003 0.000 ARG A 981 *********************** 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 158 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 112 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7964 (m-80) cc_final: 0.6997 (m-80) REVERT: A 235 ARG cc_start: 0.8451 (mtm110) cc_final: 0.8034 (mtm-85) REVERT: A 639 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7763 (p0) REVERT: A 738 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8104 (tpp) REVERT: A 757 PHE cc_start: 0.8104 (p90) cc_final: 0.7817 (p90) REVERT: B 52 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8298 (tm-30) REVERT: B 133 PHE cc_start: 0.8048 (m-80) cc_final: 0.7513 (m-10) REVERT: B 140 PHE cc_start: 0.7258 (p90) cc_final: 0.6822 (p90) REVERT: B 240 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7670 (tt) REVERT: B 404 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: B 451 TYR cc_start: 0.7717 (p90) cc_final: 0.6880 (p90) REVERT: B 659 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7102 (tm-30) REVERT: B 955 GLN cc_start: 0.8514 (tt0) cc_final: 0.8266 (tt0) REVERT: B 1037 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8334 (mtp180) REVERT: C 64 TRP cc_start: 0.8077 (t60) cc_final: 0.7656 (t60) REVERT: C 363 TYR cc_start: 0.9026 (m-80) cc_final: 0.8701 (m-80) REVERT: C 372 PHE cc_start: 0.7995 (m-80) cc_final: 0.7741 (m-80) REVERT: C 558 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8865 (mp) REVERT: C 572 ASP cc_start: 0.7459 (m-30) cc_final: 0.6968 (m-30) REVERT: C 803 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8799 (mt) outliers start: 46 outliers final: 37 residues processed: 150 average time/residue: 0.3442 time to fit residues: 86.0069 Evaluate side-chains 153 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 109 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 639 ASN 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 316 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 865 ASP 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: 4.9990 chunk 177 optimal weight: 0.0170 chunk 138 optimal weight: 0.9990 chunk 202 optimal weight: 0.0040 chunk 305 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 243 optimal weight: 0.0000 chunk 25 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN B 976 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25851 Z= 0.127 Angle : 0.519 12.346 35176 Z= 0.250 Chirality : 0.043 0.258 4241 Planarity : 0.003 0.054 4446 Dihedral : 6.023 81.753 5075 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 1.48 % Allowed : 13.69 % Favored : 84.83 % 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: 0.56 (0.15), residues: 3041 helix: 2.60 (0.21), residues: 667 sheet: 0.93 (0.19), residues: 704 loop : -0.86 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 434 HIS 0.001 0.000 HIS B1086 PHE 0.016 0.001 PHE B 390 TYR 0.021 0.001 TYR C 493 ARG 0.003 0.000 ARG B 401 ********************** 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 153 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 113 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7942 (m-80) cc_final: 0.6994 (m-80) REVERT: A 168 TYR cc_start: 0.7160 (t80) cc_final: 0.6895 (t80) REVERT: A 235 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7994 (mtm-85) REVERT: A 639 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7751 (p0) REVERT: A 738 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8024 (tpp) REVERT: A 757 PHE cc_start: 0.8030 (p90) cc_final: 0.7716 (p90) REVERT: B 52 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8247 (tm-30) REVERT: B 133 PHE cc_start: 0.8077 (m-80) cc_final: 0.7533 (m-10) REVERT: B 140 PHE cc_start: 0.7253 (p90) cc_final: 0.6832 (p90) REVERT: B 240 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 243 HIS cc_start: 0.4196 (p-80) cc_final: 0.3655 (p-80) REVERT: B 404 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: B 451 TYR cc_start: 0.7588 (p90) cc_final: 0.6766 (p90) REVERT: B 659 GLU cc_start: 0.7309 (tm-30) cc_final: 0.7029 (tm-30) REVERT: B 955 GLN cc_start: 0.8511 (tt0) cc_final: 0.8261 (tt0) REVERT: B 1037 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8345 (mtp180) REVERT: C 64 TRP cc_start: 0.8022 (t60) cc_final: 0.7626 (t60) REVERT: C 363 TYR cc_start: 0.9015 (m-80) cc_final: 0.8699 (m-80) REVERT: C 372 PHE cc_start: 0.7998 (m-80) cc_final: 0.7748 (m-80) REVERT: C 558 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8928 (mp) REVERT: C 572 ASP cc_start: 0.7462 (m-30) cc_final: 0.6952 (m-30) REVERT: C 803 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8826 (mt) outliers start: 40 outliers final: 33 residues processed: 147 average time/residue: 0.3730 time to fit residues: 91.5730 Evaluate side-chains 152 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 112 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 639 ASN 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 404 GLU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 639 ASN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 865 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 35 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN C 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.132081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073852 restraints weight = 46278.965| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.16 r_work: 0.2869 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.079 25851 Z= 0.729 Angle : 0.797 13.260 35176 Z= 0.402 Chirality : 0.055 0.272 4241 Planarity : 0.005 0.062 4446 Dihedral : 7.077 83.514 5075 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 1.89 % Allowed : 13.73 % Favored : 84.38 % 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: -0.30 (0.15), residues: 3041 helix: 1.92 (0.20), residues: 673 sheet: 0.23 (0.20), residues: 628 loop : -1.29 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 884 HIS 0.011 0.002 HIS A1046 PHE 0.024 0.003 PHE B1119 TYR 0.038 0.002 TYR A1065 ARG 0.013 0.001 ARG A1037 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5104.27 seconds wall clock time: 94 minutes 5.47 seconds (5645.47 seconds total)