Starting phenix.real_space_refine on Mon Feb 19 18:49:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7g_31770/02_2024/7v7g_31770.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7g_31770/02_2024/7v7g_31770.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/7v7g_31770/02_2024/7v7g_31770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7g_31770/02_2024/7v7g_31770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7g_31770/02_2024/7v7g_31770.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7g_31770/02_2024/7v7g_31770.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= -0.001 sd= 0.037 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 111 5.16 5 C 16179 2.51 5 N 4134 2.21 5 O 5037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "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: 25461 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} 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: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" 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 Time building chain proxies: 13.28, per 1000 atoms: 0.52 Number of scatterers: 25461 At special positions: 0 Unit cell: (141.9, 149.6, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5037 8.00 N 4134 7.00 C 16179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=1, 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 343 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 165 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 343 " " NAG B2005 " - " ASN B 603 " " NAG B2006 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 234 " " NAG C2003 " - " ASN C 331 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 709 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 709 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 343 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.35 Conformation dependent library (CDL) restraints added in 4.7 seconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5832 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 51 sheets defined 24.4% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.727A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.516A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.930A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.015A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.654A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.067A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.699A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.724A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.520A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.919A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.950A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.546A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.615A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.813A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.506A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.533A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.562A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.595A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.989A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.639A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.834A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.153A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.971A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.601A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.587A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.468A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.881A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.295A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.839A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.550A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.550A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 143 through 144 removed outlier: 5.382A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.511A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.741A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.654A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.967A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.751A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.502A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.598A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.796A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.035A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.777A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.578A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.213A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.699A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.887A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.527A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.640A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.000A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.369A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.549A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.824A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.826A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.556A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 135 removed outlier: 7.030A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.248A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.325A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.118A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.514A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.920A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2694 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: 11.30 Time building geometry restraints manager: 11.86 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: 8015 1.34 - 1.46: 6076 1.46 - 1.58: 11790 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26019 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.41e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C1 NAG A2002 " pdb=" O5 NAG A2002 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 ... (remaining 26014 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.27: 671 106.27 - 113.20: 14432 113.20 - 120.14: 8639 120.14 - 127.07: 11452 127.07 - 134.00: 218 Bond angle restraints: 35412 Sorted by residual: angle pdb=" N ASN C 164 " pdb=" CA ASN C 164 " pdb=" C ASN C 164 " ideal model delta sigma weight residual 108.19 112.87 -4.68 1.29e+00 6.01e-01 1.32e+01 angle pdb=" N GLN C1002 " pdb=" CA GLN C1002 " pdb=" CB GLN C1002 " ideal model delta sigma weight residual 110.12 115.17 -5.05 1.47e+00 4.63e-01 1.18e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.65 -3.95 1.22e+00 6.72e-01 1.05e+01 angle pdb=" C ASN C 164 " pdb=" N ASN C 165 " pdb=" CA ASN C 165 " ideal model delta sigma weight residual 121.97 126.79 -4.82 1.73e+00 3.34e-01 7.76e+00 angle pdb=" CA LEU C 560 " pdb=" CB LEU C 560 " pdb=" CG LEU C 560 " ideal model delta sigma weight residual 116.30 125.91 -9.61 3.50e+00 8.16e-02 7.54e+00 ... (remaining 35407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 14916 18.05 - 36.11: 1279 36.11 - 54.16: 253 54.16 - 72.22: 60 72.22 - 90.27: 22 Dihedral angle restraints: 16530 sinusoidal: 7467 harmonic: 9063 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 -176.73 -90.27 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -166.29 80.29 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -162.93 76.93 1 1.00e+01 1.00e-02 7.43e+01 ... (remaining 16527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 4249 0.191 - 0.381: 4 0.381 - 0.572: 1 0.572 - 0.763: 1 0.763 - 0.953: 2 Chirality restraints: 4257 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 4254 not shown) Planarity restraints: 4524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO B 987 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.039 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO C 295 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 173 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO B 174 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " 0.029 5.00e-02 4.00e+02 ... (remaining 4521 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1047 2.71 - 3.26: 25458 3.26 - 3.81: 40025 3.81 - 4.35: 47227 4.35 - 4.90: 81878 Nonbonded interactions: 195635 Sorted by model distance: nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.168 2.440 nonbonded pdb=" OE2 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.180 2.520 nonbonded pdb=" OG1 THR C 393 " pdb=" OE2 GLU C 516 " model vdw 2.198 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OD1 ASN C 914 " model vdw 2.200 2.440 nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 2.215 2.440 ... (remaining 195630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 1146 or resid 2001 through 2004)) selection = (chain 'C' and (resid 14 through 1146 or resid 2001 through 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 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: 0.040 Extract box with map and model: 13.150 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 69.490 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.470 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 0.047 26019 Z= 0.274 Angle : 0.621 9.613 35412 Z= 0.309 Chirality : 0.052 0.953 4257 Planarity : 0.004 0.066 4476 Dihedral : 13.604 89.455 10590 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 0.04 % Allowed : 0.22 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3066 helix: 2.04 (0.21), residues: 661 sheet: 0.51 (0.19), residues: 716 loop : -1.30 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 353 HIS 0.002 0.000 HIS C1088 PHE 0.028 0.001 PHE C 906 TYR 0.020 0.001 TYR B 636 ARG 0.004 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4437 (pmm) cc_final: 0.4165 (pmm) REVERT: A 360 ASN cc_start: 0.9045 (m-40) cc_final: 0.8682 (p0) REVERT: A 773 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6242 (tm-30) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.3991 time to fit residues: 51.4892 Evaluate side-chains 48 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 chunk 147 optimal weight: 50.0000 chunk 180 optimal weight: 4.9990 chunk 280 optimal weight: 5.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 804 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 26019 Z= 0.401 Angle : 0.644 11.532 35412 Z= 0.324 Chirality : 0.049 0.616 4257 Planarity : 0.004 0.064 4476 Dihedral : 7.313 82.092 5040 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.49 % Favored : 93.44 % Rotamer: Outliers : 0.15 % Allowed : 7.06 % Favored : 92.80 % 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: -0.37 (0.15), residues: 3066 helix: 1.64 (0.21), residues: 694 sheet: 0.23 (0.19), residues: 763 loop : -1.38 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1102 HIS 0.004 0.001 HIS B1048 PHE 0.029 0.002 PHE A 906 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 2.755 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4511 (pmm) cc_final: 0.4278 (pmm) REVERT: A 773 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6244 (tm-30) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 0.3530 time to fit residues: 37.4610 Evaluate side-chains 53 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 303 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 278 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 804 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26019 Z= 0.193 Angle : 0.539 9.430 35412 Z= 0.271 Chirality : 0.046 0.552 4257 Planarity : 0.004 0.062 4476 Dihedral : 6.657 79.792 5040 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 0.66 % Allowed : 9.81 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3066 helix: 1.93 (0.21), residues: 688 sheet: 0.46 (0.19), residues: 723 loop : -1.32 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.002 0.000 HIS A1088 PHE 0.016 0.001 PHE A 133 TYR 0.015 0.001 TYR C1067 ARG 0.006 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 2.699 Fit side-chains REVERT: A 153 MET cc_start: 0.4441 (pmm) cc_final: 0.4154 (pmm) REVERT: A 773 GLU cc_start: 0.6480 (tm-30) cc_final: 0.6136 (tm-30) REVERT: C 81 ASN cc_start: 0.6347 (OUTLIER) cc_final: 0.5807 (p0) outliers start: 18 outliers final: 8 residues processed: 76 average time/residue: 0.3722 time to fit residues: 51.5091 Evaluate side-chains 60 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 40.0000 chunk 267 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A1002 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 81 ASN C 394 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26019 Z= 0.354 Angle : 0.604 9.732 35412 Z= 0.303 Chirality : 0.047 0.595 4257 Planarity : 0.004 0.062 4476 Dihedral : 6.554 67.976 5040 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.56 % Favored : 93.38 % Rotamer: Outliers : 1.21 % Allowed : 11.80 % Favored : 86.99 % 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: -0.29 (0.15), residues: 3066 helix: 1.80 (0.21), residues: 689 sheet: 0.21 (0.19), residues: 768 loop : -1.33 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.004 0.001 HIS B1048 PHE 0.020 0.002 PHE A 906 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 50 time to evaluate : 2.931 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4530 (pmm) cc_final: 0.4248 (pmm) REVERT: A 773 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6308 (tm-30) REVERT: B 878 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8850 (tt) REVERT: C 81 ASN cc_start: 0.6219 (OUTLIER) cc_final: 0.5677 (p0) REVERT: C 651 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9127 (mt) outliers start: 33 outliers final: 18 residues processed: 80 average time/residue: 0.3175 time to fit residues: 45.9696 Evaluate side-chains 69 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 48 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 254 optimal weight: 6.9990 chunk 206 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26019 Z= 0.355 Angle : 0.606 9.399 35412 Z= 0.303 Chirality : 0.047 0.591 4257 Planarity : 0.004 0.061 4476 Dihedral : 6.543 61.076 5040 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 1.76 % Allowed : 12.97 % Favored : 85.26 % 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: -0.36 (0.15), residues: 3066 helix: 1.79 (0.21), residues: 683 sheet: 0.15 (0.19), residues: 757 loop : -1.38 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.003 0.001 HIS B1088 PHE 0.018 0.001 PHE C1121 TYR 0.017 0.001 TYR B1067 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 51 time to evaluate : 2.868 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4461 (pmm) cc_final: 0.4194 (pmm) REVERT: A 560 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8835 (mp) REVERT: B 878 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8853 (tt) REVERT: C 81 ASN cc_start: 0.6277 (OUTLIER) cc_final: 0.5895 (p0) REVERT: C 142 ASP cc_start: 0.4654 (OUTLIER) cc_final: 0.4081 (m-30) REVERT: C 651 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9111 (mt) outliers start: 48 outliers final: 22 residues processed: 98 average time/residue: 0.2866 time to fit residues: 51.2529 Evaluate side-chains 73 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 46 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1101 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B1005 GLN C 81 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26019 Z= 0.181 Angle : 0.549 10.345 35412 Z= 0.272 Chirality : 0.046 0.545 4257 Planarity : 0.004 0.061 4476 Dihedral : 6.245 57.725 5040 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 1.58 % Allowed : 14.04 % 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: -0.18 (0.15), residues: 3066 helix: 2.01 (0.21), residues: 683 sheet: 0.37 (0.19), residues: 719 loop : -1.32 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.002 0.000 HIS C1088 PHE 0.013 0.001 PHE A1121 TYR 0.015 0.001 TYR C1067 ARG 0.002 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 57 time to evaluate : 2.877 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4416 (pmm) cc_final: 0.4136 (pmm) REVERT: A 360 ASN cc_start: 0.9185 (m110) cc_final: 0.8714 (p0) REVERT: A 560 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8838 (mp) REVERT: B 878 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8798 (tt) REVERT: C 81 ASN cc_start: 0.6475 (OUTLIER) cc_final: 0.5930 (p0) REVERT: C 142 ASP cc_start: 0.4621 (OUTLIER) cc_final: 0.4045 (m-30) outliers start: 43 outliers final: 24 residues processed: 98 average time/residue: 0.2954 time to fit residues: 52.8985 Evaluate side-chains 77 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 49 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1101 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 297 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26019 Z= 0.348 Angle : 0.607 9.384 35412 Z= 0.302 Chirality : 0.047 0.596 4257 Planarity : 0.004 0.060 4476 Dihedral : 6.333 59.667 5040 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.39 % Favored : 93.54 % Rotamer: Outliers : 1.51 % Allowed : 14.92 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3066 helix: 1.92 (0.21), residues: 678 sheet: 0.22 (0.19), residues: 747 loop : -1.37 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.003 0.001 HIS B1048 PHE 0.024 0.002 PHE B 133 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 50 time to evaluate : 2.779 Fit side-chains REVERT: A 153 MET cc_start: 0.4563 (pmm) cc_final: 0.4303 (pmm) REVERT: A 560 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8821 (mp) REVERT: A 1002 GLN cc_start: 0.7509 (tp-100) cc_final: 0.7260 (tp-100) REVERT: B 878 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8839 (tt) REVERT: C 142 ASP cc_start: 0.4656 (OUTLIER) cc_final: 0.4064 (m-30) REVERT: C 244 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6125 (pp) REVERT: C 651 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9051 (mt) outliers start: 41 outliers final: 27 residues processed: 90 average time/residue: 0.2900 time to fit residues: 47.8253 Evaluate side-chains 79 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 47 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1101 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 147 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 234 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26019 Z= 0.177 Angle : 0.536 9.425 35412 Z= 0.266 Chirality : 0.045 0.540 4257 Planarity : 0.004 0.061 4476 Dihedral : 6.000 57.985 5040 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 1.21 % Allowed : 15.33 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3066 helix: 2.04 (0.21), residues: 685 sheet: 0.43 (0.19), residues: 719 loop : -1.33 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.002 0.000 HIS C1088 PHE 0.018 0.001 PHE B 133 TYR 0.015 0.001 TYR C1067 ARG 0.002 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 58 time to evaluate : 3.053 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4371 (pmm) cc_final: 0.4087 (pmm) REVERT: A 360 ASN cc_start: 0.9181 (m110) cc_final: 0.8768 (p0) REVERT: A 560 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8795 (mp) REVERT: B 878 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8803 (tt) REVERT: C 142 ASP cc_start: 0.4620 (OUTLIER) cc_final: 0.4025 (m-30) REVERT: C 244 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6092 (pp) outliers start: 33 outliers final: 27 residues processed: 89 average time/residue: 0.3222 time to fit residues: 52.3311 Evaluate side-chains 83 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 52 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 277 optimal weight: 0.0020 chunk 167 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 217 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 250 optimal weight: 4.9990 chunk 262 optimal weight: 0.6980 chunk 276 optimal weight: 4.9990 overall best weight: 1.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 0.003 0.038 26019 Z= 0.221 Angle : 0.551 9.840 35412 Z= 0.274 Chirality : 0.046 0.560 4257 Planarity : 0.004 0.060 4476 Dihedral : 5.883 57.973 5040 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 1.36 % Allowed : 15.29 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3066 helix: 2.08 (0.21), residues: 679 sheet: 0.40 (0.19), residues: 717 loop : -1.33 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.002 0.000 HIS C1088 PHE 0.018 0.001 PHE C 456 TYR 0.015 0.001 TYR B1067 ARG 0.010 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 55 time to evaluate : 2.900 Fit side-chains REVERT: A 153 MET cc_start: 0.4510 (pmm) cc_final: 0.4235 (pmm) REVERT: A 360 ASN cc_start: 0.9192 (m110) cc_final: 0.8794 (p0) REVERT: A 560 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8795 (mp) REVERT: B 878 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8817 (tt) REVERT: C 142 ASP cc_start: 0.4608 (OUTLIER) cc_final: 0.4013 (m-30) REVERT: C 153 MET cc_start: 0.0255 (ttt) cc_final: -0.0002 (tpp) REVERT: C 244 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6131 (pp) outliers start: 37 outliers final: 27 residues processed: 90 average time/residue: 0.3054 time to fit residues: 50.6604 Evaluate side-chains 83 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 52 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1101 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 0.0470 chunk 150 optimal weight: 20.0000 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26019 Z= 0.161 Angle : 0.534 11.294 35412 Z= 0.266 Chirality : 0.045 0.534 4257 Planarity : 0.004 0.086 4476 Dihedral : 5.695 57.563 5040 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 1.10 % Allowed : 15.62 % Favored : 83.28 % 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: -0.06 (0.15), residues: 3066 helix: 2.11 (0.21), residues: 687 sheet: 0.46 (0.19), residues: 733 loop : -1.27 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 353 HIS 0.002 0.000 HIS A 207 PHE 0.018 0.001 PHE A 392 TYR 0.015 0.001 TYR C1067 ARG 0.020 0.000 ARG C 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 55 time to evaluate : 2.787 Fit side-chains REVERT: A 153 MET cc_start: 0.4499 (pmm) cc_final: 0.4163 (pmm) REVERT: A 360 ASN cc_start: 0.9169 (m110) cc_final: 0.8767 (p0) REVERT: A 560 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8802 (mp) REVERT: A 985 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6631 (t0) REVERT: B 878 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8795 (tt) REVERT: C 142 ASP cc_start: 0.4660 (OUTLIER) cc_final: 0.4040 (m-30) REVERT: C 153 MET cc_start: 0.0045 (ttt) cc_final: -0.0188 (tpp) REVERT: C 244 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6128 (pp) REVERT: C 360 ASN cc_start: 0.9004 (t0) cc_final: 0.8548 (m-40) REVERT: C 742 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9018 (mt) outliers start: 30 outliers final: 23 residues processed: 83 average time/residue: 0.2953 time to fit residues: 45.3449 Evaluate side-chains 82 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 53 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1101 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 75 optimal weight: 0.0570 chunk 226 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 68 optimal weight: 0.9980 chunk 245 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 overall best weight: 2.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.080154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.051098 restraints weight = 108567.906| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.30 r_work: 0.2893 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26019 Z= 0.290 Angle : 0.580 10.074 35412 Z= 0.291 Chirality : 0.046 0.570 4257 Planarity : 0.004 0.098 4476 Dihedral : 5.832 58.599 5040 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.26 % Favored : 93.67 % Rotamer: Outliers : 1.21 % Allowed : 15.62 % Favored : 83.17 % 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: -0.17 (0.15), residues: 3066 helix: 2.01 (0.21), residues: 683 sheet: 0.35 (0.19), residues: 741 loop : -1.31 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 353 HIS 0.003 0.001 HIS B1048 PHE 0.017 0.001 PHE C1121 TYR 0.017 0.001 TYR B1067 ARG 0.022 0.000 ARG C 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4332.41 seconds wall clock time: 80 minutes 44.39 seconds (4844.39 seconds total)