Starting phenix.real_space_refine on Mon Feb 19 20:17:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v79_31763/02_2024/7v79_31763.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v79_31763/02_2024/7v79_31763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v79_31763/02_2024/7v79_31763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v79_31763/02_2024/7v79_31763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v79_31763/02_2024/7v79_31763.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v79_31763/02_2024/7v79_31763.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.067 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 16341 2.51 5 N 4135 2.21 5 O 5090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "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: 25677 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8166 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 53, 'TRANS': 990} Chain breaks: 7 Chain: "C" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8158 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 53, 'TRANS': 989} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.41, per 1000 atoms: 0.56 Number of scatterers: 25677 At special positions: 0 Unit cell: (144.1, 147.4, 196.9, 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 5090 8.00 N 4135 7.00 C 16341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " 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=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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 291 " - pdb=" SG CYS B 301 " 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.02 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG A2005 " - " ASN A 20 " " NAG A2006 " - " ASN A 188 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 331 " " NAG B2005 " - " ASN B 603 " " NAG B2006 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 331 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG C2007 " - " ASN C 188 " " NAG D 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " 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 165 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 343 " " 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 B 20 " " NAG a 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 343 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 709 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " " NAG k 1 " - " ASN C1134 " Time building additional restraints: 11.06 Conformation dependent library (CDL) restraints added in 4.8 seconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5848 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 47 sheets defined 25.0% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 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 364 through 371 removed outlier: 4.430A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.831A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.324A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.575A 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 898 through 910 removed outlier: 4.203A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.623A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 982 removed outlier: 3.800A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.857A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.565A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.436A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.172A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.553A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.695A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.976A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.721A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.675A 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 898 through 908 removed outlier: 3.607A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.664A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.660A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) 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: 3.615A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.099A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.778A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (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 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.500A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.619A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.907A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.567A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 638 removed outlier: 4.025A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.550A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.546A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.850A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) 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 908 removed outlier: 3.781A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.828A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.605A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.028A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.088A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.613A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.148A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.651A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.755A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.165A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.932A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.097A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.610A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.572A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.759A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.852A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.575A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.572A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.585A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 326 through 328 removed outlier: 5.700A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.313A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.271A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.530A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.544A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.038A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.465A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.970A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.999A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.537A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.595A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.512A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.744A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.565A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.565A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.547A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 988 hydrogen bonds defined for protein. 2685 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: 11.36 Time building geometry restraints manager: 11.66 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: 8030 1.34 - 1.46: 6653 1.46 - 1.58: 11426 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26247 Sorted by residual: bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.44e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C1 NAG C2003 " pdb=" O5 NAG C2003 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 ... (remaining 26242 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.10: 585 106.10 - 113.08: 14625 113.08 - 120.05: 8720 120.05 - 127.02: 11569 127.02 - 134.00: 225 Bond angle restraints: 35724 Sorted by residual: angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.42 117.57 -6.15 1.42e+00 4.96e-01 1.88e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 108.14 113.62 -5.48 1.52e+00 4.33e-01 1.30e+01 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 112.06 117.74 -5.68 1.66e+00 3.63e-01 1.17e+01 angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 122.36 127.38 -5.02 1.60e+00 3.91e-01 9.86e+00 angle pdb=" C ARG C 102 " pdb=" N GLY C 103 " pdb=" CA GLY C 103 " ideal model delta sigma weight residual 122.67 119.46 3.21 1.10e+00 8.26e-01 8.51e+00 ... (remaining 35719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 15580 23.01 - 46.02: 910 46.02 - 69.04: 145 69.04 - 92.05: 41 92.05 - 115.06: 67 Dihedral angle restraints: 16743 sinusoidal: 7644 harmonic: 9099 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 173.73 -80.73 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -6.95 -79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -7.79 -78.21 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 16740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4242 0.122 - 0.243: 53 0.243 - 0.365: 6 0.365 - 0.486: 2 0.486 - 0.608: 1 Chirality restraints: 4304 Sorted by residual: chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 4301 not shown) Planarity restraints: 4542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A 82 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 987 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " -0.018 2.00e-02 2.50e+03 1.70e-02 5.06e+00 pdb=" CG PHE B 906 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " -0.001 2.00e-02 2.50e+03 ... (remaining 4539 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 406 2.66 - 3.22: 23896 3.22 - 3.78: 36977 3.78 - 4.34: 49031 4.34 - 4.90: 83072 Nonbonded interactions: 193382 Sorted by model distance: nonbonded pdb=" OD1 ASN A 125 " pdb=" O3 NAG A2002 " model vdw 2.099 2.440 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.125 2.440 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.151 2.440 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.169 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.175 2.440 ... (remaining 193377 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 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2006)) selection = (chain 'C' and (resid 14 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2006)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } 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: 5.390 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: 0.050 Extract box with map and model: 12.840 Check model and map are aligned: 0.420 Set scattering table: 0.200 Process input model: 72.420 Find NCS groups from input model: 2.140 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.006 0.063 26247 Z= 0.369 Angle : 0.656 8.019 35724 Z= 0.328 Chirality : 0.050 0.608 4304 Planarity : 0.004 0.087 4492 Dihedral : 16.277 115.059 10775 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.49 (0.15), residues: 3077 helix: 1.39 (0.21), residues: 680 sheet: 0.26 (0.19), residues: 756 loop : -1.41 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 886 HIS 0.004 0.001 HIS C1064 PHE 0.039 0.002 PHE B 906 TYR 0.023 0.001 TYR A 873 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4929 (pmm) cc_final: 0.3533 (tmm) REVERT: A 187 LYS cc_start: 0.7014 (mmmm) cc_final: 0.6801 (tptp) REVERT: A 210 ILE cc_start: 0.8373 (tp) cc_final: 0.8085 (tp) REVERT: A 224 GLU cc_start: 0.7489 (pp20) cc_final: 0.6894 (pp20) REVERT: A 241 LEU cc_start: 0.6761 (mt) cc_final: 0.6514 (mt) REVERT: A 309 GLU cc_start: 0.7613 (mp0) cc_final: 0.7331 (pm20) REVERT: A 529 LYS cc_start: 0.8435 (mmpt) cc_final: 0.8122 (mmmt) REVERT: A 663 ASP cc_start: 0.8346 (m-30) cc_final: 0.8125 (m-30) REVERT: A 675 GLN cc_start: 0.5109 (pp30) cc_final: 0.4884 (tm-30) REVERT: A 950 ASP cc_start: 0.7768 (m-30) cc_final: 0.7218 (m-30) REVERT: A 1092 GLU cc_start: 0.7659 (tp30) cc_final: 0.7454 (pt0) REVERT: B 41 LYS cc_start: 0.7728 (mttt) cc_final: 0.7430 (mttm) REVERT: B 101 ILE cc_start: 0.7432 (mm) cc_final: 0.7184 (mp) REVERT: B 314 GLN cc_start: 0.8702 (tt0) cc_final: 0.8222 (mt0) REVERT: B 461 LEU cc_start: 0.8118 (mt) cc_final: 0.7877 (mt) REVERT: B 950 ASP cc_start: 0.7757 (m-30) cc_final: 0.7386 (m-30) REVERT: B 969 ASN cc_start: 0.8003 (t0) cc_final: 0.7798 (t0) REVERT: B 988 GLU cc_start: 0.7284 (pm20) cc_final: 0.6961 (pm20) REVERT: B 1114 ILE cc_start: 0.8737 (mt) cc_final: 0.8482 (tt) REVERT: C 429 PHE cc_start: 0.8192 (t80) cc_final: 0.7822 (t80) REVERT: C 564 GLN cc_start: 0.7268 (mm110) cc_final: 0.6847 (mm-40) REVERT: C 740 MET cc_start: 0.7742 (tpt) cc_final: 0.7356 (mtt) REVERT: C 1002 GLN cc_start: 0.7610 (tp-100) cc_final: 0.7366 (mt0) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3647 time to fit residues: 139.0032 Evaluate side-chains 172 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 130 optimal weight: 0.0060 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 282 optimal weight: 0.0970 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 239 GLN C 394 ASN C 856 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26247 Z= 0.182 Angle : 0.577 11.104 35724 Z= 0.281 Chirality : 0.047 0.396 4304 Planarity : 0.004 0.061 4492 Dihedral : 12.545 103.287 5222 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.71 % Rotamer: Outliers : 0.70 % Allowed : 6.30 % Favored : 93.00 % 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: 3077 helix: 1.58 (0.21), residues: 676 sheet: 0.36 (0.19), residues: 735 loop : -1.35 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.005 0.001 HIS B1088 PHE 0.024 0.001 PHE B 238 TYR 0.027 0.001 TYR C 453 ARG 0.004 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4970 (pmm) cc_final: 0.3679 (tmm) REVERT: A 187 LYS cc_start: 0.6988 (mmmm) cc_final: 0.6777 (tptp) REVERT: A 210 ILE cc_start: 0.8373 (tp) cc_final: 0.8117 (tp) REVERT: A 224 GLU cc_start: 0.7308 (pp20) cc_final: 0.6803 (pp20) REVERT: A 234 ASN cc_start: 0.5726 (t0) cc_final: 0.5342 (t0) REVERT: A 241 LEU cc_start: 0.6428 (mt) cc_final: 0.6133 (mt) REVERT: A 309 GLU cc_start: 0.7612 (mp0) cc_final: 0.7336 (pm20) REVERT: A 334 ASN cc_start: 0.8967 (t0) cc_final: 0.8290 (t0) REVERT: A 529 LYS cc_start: 0.8380 (mmpt) cc_final: 0.8067 (mmmt) REVERT: A 646 ARG cc_start: 0.7414 (mtp85) cc_final: 0.7201 (ttm170) REVERT: A 663 ASP cc_start: 0.8289 (m-30) cc_final: 0.8050 (m-30) REVERT: A 754 LEU cc_start: 0.8138 (pp) cc_final: 0.7906 (mt) REVERT: A 878 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6836 (tt) REVERT: B 41 LYS cc_start: 0.7717 (mttt) cc_final: 0.7397 (mttm) REVERT: B 101 ILE cc_start: 0.7442 (mm) cc_final: 0.7219 (mp) REVERT: B 239 GLN cc_start: 0.7651 (mt0) cc_final: 0.7305 (tt0) REVERT: B 314 GLN cc_start: 0.8616 (tt0) cc_final: 0.8132 (mt0) REVERT: B 351 TYR cc_start: 0.7282 (p90) cc_final: 0.6634 (p90) REVERT: B 461 LEU cc_start: 0.8166 (mt) cc_final: 0.7943 (mt) REVERT: B 988 GLU cc_start: 0.7294 (pm20) cc_final: 0.7071 (pm20) REVERT: B 1114 ILE cc_start: 0.8696 (mt) cc_final: 0.8436 (tt) REVERT: C 32 PHE cc_start: 0.7361 (m-10) cc_final: 0.7144 (m-80) REVERT: C 508 TYR cc_start: 0.7210 (m-80) cc_final: 0.6765 (m-80) REVERT: C 740 MET cc_start: 0.7625 (tpt) cc_final: 0.7374 (mtt) REVERT: C 869 MET cc_start: 0.7975 (mtt) cc_final: 0.7767 (mtt) REVERT: C 950 ASP cc_start: 0.7971 (t70) cc_final: 0.7460 (m-30) REVERT: C 1017 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7168 (tt0) outliers start: 19 outliers final: 14 residues processed: 195 average time/residue: 0.3525 time to fit residues: 112.7146 Evaluate side-chains 183 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 856 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 chunk 192 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 305 optimal weight: 0.4980 chunk 251 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 234 ASN A 804 GLN A 935 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 901 GLN C1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 26247 Z= 0.388 Angle : 0.659 11.361 35724 Z= 0.326 Chirality : 0.050 0.444 4304 Planarity : 0.004 0.056 4492 Dihedral : 10.838 97.025 5222 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 1.50 % Allowed : 10.37 % Favored : 88.13 % 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: -0.62 (0.15), residues: 3077 helix: 1.22 (0.21), residues: 671 sheet: 0.16 (0.19), residues: 755 loop : -1.44 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 353 HIS 0.006 0.002 HIS C1088 PHE 0.032 0.002 PHE B 906 TYR 0.024 0.002 TYR C 453 ARG 0.009 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 174 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6583 (p90) cc_final: 0.5866 (p90) REVERT: A 153 MET cc_start: 0.4907 (pmm) cc_final: 0.3684 (tmm) REVERT: A 187 LYS cc_start: 0.7038 (mmmm) cc_final: 0.6804 (tptp) REVERT: A 210 ILE cc_start: 0.8520 (tp) cc_final: 0.8295 (tp) REVERT: A 224 GLU cc_start: 0.7265 (pp20) cc_final: 0.6686 (pp20) REVERT: A 241 LEU cc_start: 0.6524 (mt) cc_final: 0.6237 (mt) REVERT: A 334 ASN cc_start: 0.8992 (t0) cc_final: 0.8322 (t0) REVERT: A 529 LYS cc_start: 0.8361 (mmpt) cc_final: 0.8064 (mmmt) REVERT: A 754 LEU cc_start: 0.8182 (pp) cc_final: 0.7801 (mt) REVERT: A 817 PHE cc_start: 0.7788 (t80) cc_final: 0.7402 (t80) REVERT: A 878 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6747 (tt) REVERT: A 1132 ILE cc_start: 0.8360 (pt) cc_final: 0.8156 (pt) REVERT: B 41 LYS cc_start: 0.7774 (mttt) cc_final: 0.7443 (mttm) REVERT: B 101 ILE cc_start: 0.7557 (mm) cc_final: 0.7309 (mp) REVERT: B 351 TYR cc_start: 0.7448 (p90) cc_final: 0.6818 (p90) REVERT: B 461 LEU cc_start: 0.8154 (mt) cc_final: 0.7927 (mt) REVERT: B 988 GLU cc_start: 0.7178 (pm20) cc_final: 0.6900 (pm20) REVERT: B 1114 ILE cc_start: 0.8776 (mt) cc_final: 0.8463 (tt) REVERT: C 32 PHE cc_start: 0.7434 (m-10) cc_final: 0.7220 (m-80) REVERT: C 239 GLN cc_start: 0.6324 (tt0) cc_final: 0.6109 (tt0) REVERT: C 551 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6748 (m) REVERT: C 740 MET cc_start: 0.7974 (tpt) cc_final: 0.7618 (mtt) REVERT: C 950 ASP cc_start: 0.8102 (t70) cc_final: 0.7613 (m-30) outliers start: 41 outliers final: 28 residues processed: 204 average time/residue: 0.3398 time to fit residues: 116.4544 Evaluate side-chains 195 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26247 Z= 0.273 Angle : 0.594 11.735 35724 Z= 0.292 Chirality : 0.048 0.407 4304 Planarity : 0.004 0.053 4492 Dihedral : 9.881 91.088 5222 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 2.13 % Allowed : 11.69 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3077 helix: 1.40 (0.21), residues: 661 sheet: 0.18 (0.19), residues: 738 loop : -1.44 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.004 0.001 HIS C1088 PHE 0.024 0.002 PHE B1121 TYR 0.022 0.001 TYR C 453 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 167 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6592 (p90) cc_final: 0.5867 (p90) REVERT: A 153 MET cc_start: 0.4840 (pmm) cc_final: 0.3630 (tmm) REVERT: A 187 LYS cc_start: 0.7102 (mmmm) cc_final: 0.6858 (tptp) REVERT: A 210 ILE cc_start: 0.8559 (tp) cc_final: 0.8338 (tp) REVERT: A 212 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6576 (tt) REVERT: A 224 GLU cc_start: 0.7302 (pp20) cc_final: 0.6714 (pp20) REVERT: A 234 ASN cc_start: 0.5699 (t0) cc_final: 0.5470 (t0) REVERT: A 241 LEU cc_start: 0.6428 (mt) cc_final: 0.6140 (mt) REVERT: A 334 ASN cc_start: 0.9025 (t0) cc_final: 0.8382 (t0) REVERT: A 529 LYS cc_start: 0.8339 (mmpt) cc_final: 0.8043 (mmmt) REVERT: A 754 LEU cc_start: 0.8139 (pp) cc_final: 0.7895 (mt) REVERT: A 762 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: A 878 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6788 (tt) REVERT: A 996 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7957 (mp) REVERT: A 1132 ILE cc_start: 0.8424 (pt) cc_final: 0.8131 (pt) REVERT: B 41 LYS cc_start: 0.7770 (mttt) cc_final: 0.7529 (mttm) REVERT: B 101 ILE cc_start: 0.7594 (mm) cc_final: 0.7340 (mp) REVERT: B 212 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5369 (mp) REVERT: B 351 TYR cc_start: 0.7407 (p90) cc_final: 0.6842 (p90) REVERT: B 461 LEU cc_start: 0.8142 (mt) cc_final: 0.7898 (mt) REVERT: B 1114 ILE cc_start: 0.8700 (mt) cc_final: 0.8429 (tt) REVERT: C 32 PHE cc_start: 0.7430 (m-10) cc_final: 0.7187 (m-80) REVERT: C 239 GLN cc_start: 0.6285 (tt0) cc_final: 0.6071 (tt0) REVERT: C 465 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7833 (tm-30) REVERT: C 551 VAL cc_start: 0.6889 (OUTLIER) cc_final: 0.6654 (m) REVERT: C 740 MET cc_start: 0.8034 (tpt) cc_final: 0.7650 (mtt) REVERT: C 918 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: C 950 ASP cc_start: 0.8029 (t70) cc_final: 0.7583 (m-30) outliers start: 58 outliers final: 35 residues processed: 214 average time/residue: 0.3293 time to fit residues: 117.7499 Evaluate side-chains 206 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 26247 Z= 0.336 Angle : 0.627 11.791 35724 Z= 0.308 Chirality : 0.049 0.436 4304 Planarity : 0.004 0.051 4492 Dihedral : 9.145 82.632 5222 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.05 % Rotamer: Outliers : 2.97 % Allowed : 12.83 % Favored : 84.21 % 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: -0.67 (0.15), residues: 3077 helix: 1.29 (0.21), residues: 661 sheet: 0.17 (0.19), residues: 737 loop : -1.51 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.005 0.001 HIS C1088 PHE 0.027 0.002 PHE C1121 TYR 0.021 0.001 TYR C 453 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 172 time to evaluate : 2.912 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6615 (p90) cc_final: 0.5958 (p90) REVERT: A 153 MET cc_start: 0.4730 (pmm) cc_final: 0.3581 (tmm) REVERT: A 187 LYS cc_start: 0.7318 (mmmm) cc_final: 0.7037 (tptp) REVERT: A 210 ILE cc_start: 0.8585 (tp) cc_final: 0.8375 (tp) REVERT: A 224 GLU cc_start: 0.7409 (pp20) cc_final: 0.6728 (pp20) REVERT: A 234 ASN cc_start: 0.5990 (t0) cc_final: 0.5711 (t0) REVERT: A 241 LEU cc_start: 0.6459 (mt) cc_final: 0.6170 (mt) REVERT: A 334 ASN cc_start: 0.8988 (t0) cc_final: 0.8335 (t0) REVERT: A 529 LYS cc_start: 0.8325 (mmpt) cc_final: 0.8023 (mmmt) REVERT: A 563 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.5500 (mp10) REVERT: A 754 LEU cc_start: 0.8091 (pp) cc_final: 0.7736 (mt) REVERT: A 817 PHE cc_start: 0.7833 (t80) cc_final: 0.7568 (t80) REVERT: A 878 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6804 (tt) REVERT: A 984 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7370 (pp) REVERT: A 1132 ILE cc_start: 0.8522 (pt) cc_final: 0.8241 (pt) REVERT: B 41 LYS cc_start: 0.7725 (mttt) cc_final: 0.7505 (mttm) REVERT: B 101 ILE cc_start: 0.7613 (mm) cc_final: 0.7347 (mp) REVERT: B 212 LEU cc_start: 0.5705 (OUTLIER) cc_final: 0.5420 (mp) REVERT: B 351 TYR cc_start: 0.7379 (p90) cc_final: 0.6839 (p90) REVERT: B 461 LEU cc_start: 0.8133 (mt) cc_final: 0.7884 (mt) REVERT: B 950 ASP cc_start: 0.7990 (m-30) cc_final: 0.7745 (m-30) REVERT: B 1114 ILE cc_start: 0.8716 (mt) cc_final: 0.8412 (tt) REVERT: C 32 PHE cc_start: 0.7522 (m-10) cc_final: 0.7264 (m-80) REVERT: C 168 PHE cc_start: 0.7768 (t80) cc_final: 0.7545 (t80) REVERT: C 456 PHE cc_start: 0.8509 (m-80) cc_final: 0.8137 (m-80) REVERT: C 465 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 551 VAL cc_start: 0.6879 (OUTLIER) cc_final: 0.6655 (m) REVERT: C 569 ILE cc_start: 0.4964 (OUTLIER) cc_final: 0.4717 (mp) REVERT: C 740 MET cc_start: 0.8159 (tpt) cc_final: 0.7819 (mtt) REVERT: C 918 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: C 950 ASP cc_start: 0.8066 (t70) cc_final: 0.7611 (m-30) outliers start: 81 outliers final: 48 residues processed: 240 average time/residue: 0.3326 time to fit residues: 133.9772 Evaluate side-chains 220 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 165 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 0.8980 chunk 270 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 249 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26247 Z= 0.226 Angle : 0.573 10.534 35724 Z= 0.281 Chirality : 0.047 0.423 4304 Planarity : 0.004 0.051 4492 Dihedral : 8.535 79.754 5222 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.78 % Allowed : 13.56 % Favored : 83.66 % 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: -0.53 (0.15), residues: 3077 helix: 1.55 (0.21), residues: 648 sheet: 0.23 (0.19), residues: 738 loop : -1.45 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.003 0.001 HIS C1064 PHE 0.021 0.001 PHE B1121 TYR 0.019 0.001 TYR C 453 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 164 time to evaluate : 2.589 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6589 (p90) cc_final: 0.5882 (p90) REVERT: A 153 MET cc_start: 0.4718 (pmm) cc_final: 0.3582 (tmm) REVERT: A 187 LYS cc_start: 0.7341 (mmmm) cc_final: 0.7122 (tptp) REVERT: A 210 ILE cc_start: 0.8599 (tp) cc_final: 0.8390 (tp) REVERT: A 212 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6696 (tt) REVERT: A 234 ASN cc_start: 0.5795 (t0) cc_final: 0.5507 (t0) REVERT: A 241 LEU cc_start: 0.6358 (mt) cc_final: 0.6062 (mt) REVERT: A 244 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7182 (pp) REVERT: A 334 ASN cc_start: 0.9017 (t0) cc_final: 0.8383 (t0) REVERT: A 529 LYS cc_start: 0.8332 (mmpt) cc_final: 0.8041 (mmmt) REVERT: A 563 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.5497 (mp10) REVERT: A 754 LEU cc_start: 0.8090 (pp) cc_final: 0.7776 (mt) REVERT: A 984 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7412 (pp) REVERT: A 1132 ILE cc_start: 0.8478 (pt) cc_final: 0.8204 (pt) REVERT: B 41 LYS cc_start: 0.7732 (mttt) cc_final: 0.7520 (mttm) REVERT: B 101 ILE cc_start: 0.7616 (mm) cc_final: 0.7342 (mp) REVERT: B 212 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5428 (mp) REVERT: B 351 TYR cc_start: 0.7328 (p90) cc_final: 0.6803 (p90) REVERT: B 390 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7411 (mt) REVERT: B 461 LEU cc_start: 0.8240 (mt) cc_final: 0.7992 (mt) REVERT: B 569 ILE cc_start: 0.3677 (OUTLIER) cc_final: 0.3477 (mp) REVERT: B 703 ASN cc_start: 0.8001 (p0) cc_final: 0.7752 (p0) REVERT: B 988 GLU cc_start: 0.6999 (pm20) cc_final: 0.6732 (pm20) REVERT: B 1114 ILE cc_start: 0.8677 (mt) cc_final: 0.8418 (tt) REVERT: C 32 PHE cc_start: 0.7376 (m-10) cc_final: 0.7065 (m-80) REVERT: C 168 PHE cc_start: 0.7677 (t80) cc_final: 0.7412 (t80) REVERT: C 347 PHE cc_start: 0.8016 (m-10) cc_final: 0.7642 (m-10) REVERT: C 465 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 551 VAL cc_start: 0.6815 (OUTLIER) cc_final: 0.6607 (m) REVERT: C 569 ILE cc_start: 0.4932 (OUTLIER) cc_final: 0.4674 (mp) REVERT: C 740 MET cc_start: 0.8199 (tpt) cc_final: 0.7681 (mtt) REVERT: C 918 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: C 950 ASP cc_start: 0.8022 (t70) cc_final: 0.7585 (m-30) outliers start: 76 outliers final: 48 residues processed: 224 average time/residue: 0.3295 time to fit residues: 125.6967 Evaluate side-chains 220 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 162 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 chunk 170 optimal weight: 0.3980 chunk 253 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 187 optimal weight: 0.0670 chunk 182 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26247 Z= 0.211 Angle : 0.561 10.317 35724 Z= 0.274 Chirality : 0.046 0.429 4304 Planarity : 0.004 0.051 4492 Dihedral : 8.015 74.233 5222 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.08 % Allowed : 14.11 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3077 helix: 1.62 (0.21), residues: 648 sheet: 0.28 (0.19), residues: 737 loop : -1.42 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C1088 PHE 0.020 0.001 PHE B1121 TYR 0.018 0.001 TYR C 453 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 163 time to evaluate : 3.240 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6655 (p90) cc_final: 0.5929 (p90) REVERT: A 153 MET cc_start: 0.4689 (pmm) cc_final: 0.3547 (tmm) REVERT: A 187 LYS cc_start: 0.7342 (mmmm) cc_final: 0.7119 (tptp) REVERT: A 210 ILE cc_start: 0.8608 (tp) cc_final: 0.8402 (tp) REVERT: A 212 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6772 (tt) REVERT: A 234 ASN cc_start: 0.5837 (t0) cc_final: 0.5581 (t0) REVERT: A 241 LEU cc_start: 0.6331 (mt) cc_final: 0.6038 (mt) REVERT: A 334 ASN cc_start: 0.9033 (t0) cc_final: 0.8403 (t0) REVERT: A 529 LYS cc_start: 0.8326 (mmpt) cc_final: 0.8038 (mmmt) REVERT: A 563 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.5564 (mp10) REVERT: A 754 LEU cc_start: 0.8237 (pp) cc_final: 0.7825 (mt) REVERT: A 878 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6835 (tt) REVERT: A 984 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7480 (pp) REVERT: A 1132 ILE cc_start: 0.8446 (pt) cc_final: 0.8155 (pt) REVERT: B 41 LYS cc_start: 0.7721 (mttt) cc_final: 0.7508 (mttm) REVERT: B 212 LEU cc_start: 0.5689 (OUTLIER) cc_final: 0.5428 (mp) REVERT: B 351 TYR cc_start: 0.7398 (p90) cc_final: 0.6839 (p90) REVERT: B 390 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7423 (mt) REVERT: B 461 LEU cc_start: 0.8262 (mt) cc_final: 0.8008 (mt) REVERT: B 1114 ILE cc_start: 0.8662 (mt) cc_final: 0.8402 (tt) REVERT: C 32 PHE cc_start: 0.7471 (m-10) cc_final: 0.7146 (m-80) REVERT: C 168 PHE cc_start: 0.7721 (t80) cc_final: 0.7439 (t80) REVERT: C 347 PHE cc_start: 0.7973 (m-10) cc_final: 0.7549 (m-10) REVERT: C 414 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7386 (mt0) REVERT: C 465 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7758 (tm-30) REVERT: C 551 VAL cc_start: 0.6779 (OUTLIER) cc_final: 0.6562 (m) REVERT: C 563 GLN cc_start: 0.6097 (OUTLIER) cc_final: 0.5759 (mp10) REVERT: C 569 ILE cc_start: 0.4907 (OUTLIER) cc_final: 0.4649 (mp) REVERT: C 740 MET cc_start: 0.8274 (tpt) cc_final: 0.7683 (mtt) REVERT: C 918 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: C 950 ASP cc_start: 0.8025 (t70) cc_final: 0.7608 (m-30) outliers start: 84 outliers final: 50 residues processed: 233 average time/residue: 0.3265 time to fit residues: 129.0830 Evaluate side-chains 217 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 157 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 204 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 235 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26247 Z= 0.189 Angle : 0.554 10.250 35724 Z= 0.270 Chirality : 0.046 0.428 4304 Planarity : 0.004 0.050 4492 Dihedral : 7.641 70.369 5222 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.71 % Allowed : 14.58 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.41 (0.15), residues: 3077 helix: 1.68 (0.21), residues: 648 sheet: 0.33 (0.19), residues: 736 loop : -1.39 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C1088 PHE 0.018 0.001 PHE B1121 TYR 0.017 0.001 TYR C 453 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 161 time to evaluate : 3.076 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6463 (p90) cc_final: 0.5887 (p90) REVERT: A 153 MET cc_start: 0.4714 (pmm) cc_final: 0.3567 (tmm) REVERT: A 187 LYS cc_start: 0.7323 (mmmm) cc_final: 0.7101 (tptp) REVERT: A 210 ILE cc_start: 0.8578 (tp) cc_final: 0.8373 (tp) REVERT: A 234 ASN cc_start: 0.5761 (t0) cc_final: 0.5528 (t0) REVERT: A 241 LEU cc_start: 0.6373 (mt) cc_final: 0.6073 (mt) REVERT: A 334 ASN cc_start: 0.9013 (t0) cc_final: 0.8384 (t0) REVERT: A 529 LYS cc_start: 0.8455 (mmpt) cc_final: 0.8223 (mmmt) REVERT: A 563 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.5627 (mp10) REVERT: A 754 LEU cc_start: 0.8201 (pp) cc_final: 0.7807 (mt) REVERT: A 878 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6887 (tt) REVERT: A 984 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7468 (pp) REVERT: A 1132 ILE cc_start: 0.8413 (pt) cc_final: 0.8156 (pt) REVERT: B 41 LYS cc_start: 0.7756 (mttt) cc_final: 0.7538 (mttm) REVERT: B 212 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5378 (mp) REVERT: B 351 TYR cc_start: 0.7459 (p90) cc_final: 0.6968 (p90) REVERT: B 390 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7405 (mt) REVERT: B 461 LEU cc_start: 0.8229 (mt) cc_final: 0.7988 (mt) REVERT: B 988 GLU cc_start: 0.7128 (pm20) cc_final: 0.6869 (pm20) REVERT: B 1114 ILE cc_start: 0.8646 (mt) cc_final: 0.8397 (tt) REVERT: C 32 PHE cc_start: 0.7461 (m-10) cc_final: 0.7138 (m-80) REVERT: C 168 PHE cc_start: 0.7684 (t80) cc_final: 0.7376 (t80) REVERT: C 347 PHE cc_start: 0.7957 (m-10) cc_final: 0.7547 (m-10) REVERT: C 414 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7390 (mt0) REVERT: C 465 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7792 (tm-30) REVERT: C 551 VAL cc_start: 0.6740 (OUTLIER) cc_final: 0.6537 (m) REVERT: C 563 GLN cc_start: 0.6096 (OUTLIER) cc_final: 0.5779 (mp10) REVERT: C 569 ILE cc_start: 0.4874 (OUTLIER) cc_final: 0.4630 (mp) REVERT: C 740 MET cc_start: 0.8274 (tpt) cc_final: 0.7668 (mtt) REVERT: C 918 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: C 950 ASP cc_start: 0.8005 (t70) cc_final: 0.7597 (m-30) outliers start: 74 outliers final: 47 residues processed: 222 average time/residue: 0.3152 time to fit residues: 119.1911 Evaluate side-chains 212 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 156 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 219 optimal weight: 20.0000 chunk 85 optimal weight: 0.5980 chunk 252 optimal weight: 8.9990 chunk 264 optimal weight: 0.9980 chunk 278 optimal weight: 0.3980 chunk 183 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26247 Z= 0.185 Angle : 0.555 10.330 35724 Z= 0.269 Chirality : 0.046 0.432 4304 Planarity : 0.004 0.050 4492 Dihedral : 7.364 66.275 5222 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.35 % Allowed : 15.17 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.15), residues: 3077 helix: 1.70 (0.21), residues: 649 sheet: 0.32 (0.19), residues: 738 loop : -1.36 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C1088 PHE 0.017 0.001 PHE B1121 TYR 0.017 0.001 TYR C 453 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 156 time to evaluate : 3.048 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6198 (p90) cc_final: 0.5626 (p90) REVERT: A 153 MET cc_start: 0.4700 (pmm) cc_final: 0.3554 (tmm) REVERT: A 187 LYS cc_start: 0.7323 (mmmm) cc_final: 0.7097 (tptp) REVERT: A 234 ASN cc_start: 0.5765 (t0) cc_final: 0.5519 (t0) REVERT: A 334 ASN cc_start: 0.9007 (t0) cc_final: 0.8381 (t0) REVERT: A 529 LYS cc_start: 0.8477 (mmpt) cc_final: 0.8233 (mmmt) REVERT: A 563 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.5643 (mp10) REVERT: A 754 LEU cc_start: 0.8182 (pp) cc_final: 0.7805 (mt) REVERT: A 878 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6902 (tt) REVERT: A 984 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7504 (pp) REVERT: A 1132 ILE cc_start: 0.8405 (pt) cc_final: 0.8150 (pt) REVERT: B 41 LYS cc_start: 0.7719 (mttt) cc_final: 0.7498 (mttm) REVERT: B 212 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5366 (mp) REVERT: B 351 TYR cc_start: 0.7467 (p90) cc_final: 0.6972 (p90) REVERT: B 461 LEU cc_start: 0.8225 (mt) cc_final: 0.7988 (mt) REVERT: B 1114 ILE cc_start: 0.8629 (mt) cc_final: 0.8387 (tt) REVERT: C 32 PHE cc_start: 0.7473 (m-10) cc_final: 0.7152 (m-80) REVERT: C 168 PHE cc_start: 0.7694 (t80) cc_final: 0.7380 (t80) REVERT: C 347 PHE cc_start: 0.7951 (m-10) cc_final: 0.7531 (m-10) REVERT: C 414 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7406 (mt0) REVERT: C 465 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7798 (tm-30) REVERT: C 563 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5795 (mp10) REVERT: C 569 ILE cc_start: 0.4947 (OUTLIER) cc_final: 0.4698 (mp) REVERT: C 740 MET cc_start: 0.8265 (tpt) cc_final: 0.7660 (mtt) REVERT: C 918 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: C 950 ASP cc_start: 0.7995 (t70) cc_final: 0.7593 (m-30) outliers start: 64 outliers final: 48 residues processed: 210 average time/residue: 0.3357 time to fit residues: 119.8552 Evaluate side-chains 208 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 153 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 309 optimal weight: 0.3980 chunk 285 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26247 Z= 0.315 Angle : 0.610 11.736 35724 Z= 0.300 Chirality : 0.048 0.470 4304 Planarity : 0.004 0.050 4492 Dihedral : 7.360 64.396 5222 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.49 % Allowed : 15.02 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.15), residues: 3077 helix: 1.38 (0.21), residues: 662 sheet: 0.22 (0.19), residues: 736 loop : -1.44 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.005 0.001 HIS C1064 PHE 0.026 0.002 PHE C1121 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG C1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 156 time to evaluate : 2.793 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6209 (p90) cc_final: 0.5554 (p90) REVERT: A 153 MET cc_start: 0.4733 (pmm) cc_final: 0.3582 (tmm) REVERT: A 187 LYS cc_start: 0.7256 (mmmm) cc_final: 0.7030 (tptp) REVERT: A 241 LEU cc_start: 0.6336 (mt) cc_final: 0.6041 (mt) REVERT: A 334 ASN cc_start: 0.8982 (t0) cc_final: 0.8335 (t0) REVERT: A 529 LYS cc_start: 0.8331 (mmpt) cc_final: 0.8095 (mmmt) REVERT: A 563 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.5262 (mp10) REVERT: A 754 LEU cc_start: 0.8220 (pp) cc_final: 0.7810 (mt) REVERT: A 817 PHE cc_start: 0.7785 (t80) cc_final: 0.7570 (t80) REVERT: A 878 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6731 (tt) REVERT: A 984 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7431 (pp) REVERT: A 1132 ILE cc_start: 0.8579 (pt) cc_final: 0.8314 (pt) REVERT: B 212 LEU cc_start: 0.5659 (OUTLIER) cc_final: 0.5394 (mp) REVERT: B 351 TYR cc_start: 0.7452 (p90) cc_final: 0.6939 (p90) REVERT: B 461 LEU cc_start: 0.8220 (mt) cc_final: 0.7988 (mt) REVERT: B 950 ASP cc_start: 0.7988 (m-30) cc_final: 0.7748 (m-30) REVERT: B 988 GLU cc_start: 0.7036 (pm20) cc_final: 0.6810 (pm20) REVERT: B 1114 ILE cc_start: 0.8660 (mt) cc_final: 0.8386 (tt) REVERT: C 32 PHE cc_start: 0.7512 (m-10) cc_final: 0.7199 (m-80) REVERT: C 52 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7283 (tm-30) REVERT: C 168 PHE cc_start: 0.7755 (t80) cc_final: 0.7519 (t80) REVERT: C 347 PHE cc_start: 0.7954 (m-10) cc_final: 0.7495 (m-10) REVERT: C 414 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7413 (mt0) REVERT: C 465 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 551 VAL cc_start: 0.6794 (OUTLIER) cc_final: 0.6593 (m) REVERT: C 563 GLN cc_start: 0.6049 (OUTLIER) cc_final: 0.5684 (mp10) REVERT: C 569 ILE cc_start: 0.4923 (OUTLIER) cc_final: 0.4691 (mp) REVERT: C 740 MET cc_start: 0.8312 (tpt) cc_final: 0.7727 (mtt) REVERT: C 918 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: C 950 ASP cc_start: 0.8049 (t70) cc_final: 0.7610 (m-30) outliers start: 68 outliers final: 53 residues processed: 215 average time/residue: 0.3134 time to fit residues: 114.6265 Evaluate side-chains 215 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 154 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 chunk 227 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.192568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.146001 restraints weight = 33122.399| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.87 r_work: 0.3541 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26247 Z= 0.225 Angle : 0.573 10.925 35724 Z= 0.281 Chirality : 0.047 0.457 4304 Planarity : 0.004 0.050 4492 Dihedral : 7.190 62.569 5222 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.49 % Allowed : 15.17 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3077 helix: 1.49 (0.21), residues: 661 sheet: 0.25 (0.19), residues: 736 loop : -1.42 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C1088 PHE 0.020 0.001 PHE B1121 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG B1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4833.66 seconds wall clock time: 90 minutes 28.60 seconds (5428.60 seconds total)