Starting phenix.real_space_refine on Tue Feb 20 02:01:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybk_33724/02_2024/7ybk_33724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybk_33724/02_2024/7ybk_33724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybk_33724/02_2024/7ybk_33724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybk_33724/02_2024/7ybk_33724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybk_33724/02_2024/7ybk_33724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybk_33724/02_2024/7ybk_33724.pdb" } resolution = 3.9 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= 0.000 sd= 0.003 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 114 5.16 5 C 16823 2.51 5 N 4291 2.21 5 O 5263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26491 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8411 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1021} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8431 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8405 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1021} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: 14.31, per 1000 atoms: 0.54 Number of scatterers: 26491 At special positions: 0 Unit cell: (155.15, 153.01, 218.28, 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 114 16.00 O 5263 8.00 N 4291 7.00 C 16823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.04 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 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 282 " " NAG A1407 " - " ASN A 603 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG A1410 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 12.06 Conformation dependent library (CDL) restraints added in 5.1 seconds 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6040 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 50 sheets defined 26.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.898A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.959A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.022A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.522A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.684A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.527A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) 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: 3.699A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.501A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.604A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.985A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.867A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.648A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.909A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.632A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.510A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.010A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A1160 " --> pdb=" O PHE A1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.462A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.963A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.631A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.557A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.773A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.586A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.833A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.045A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.595A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.633A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) 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 982 removed outlier: 3.547A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 3.686A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.917A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.074A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.541A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.701A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.556A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.061A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.600A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.524A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.557A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.772A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C1001 " --> pdb=" O ILE C 997 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 4.101A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.234A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.035A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.756A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 removed outlier: 6.891A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.513A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 651 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.662A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.595A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 5.995A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.577A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.849A 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 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.351A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.718A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.763A pdb=" N ILE A 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.386A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.801A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.801A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.643A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.546A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 142 through 143 removed outlier: 5.893A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.272A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.826A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.726A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.868A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.755A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.919A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.568A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.568A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 6.018A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.659A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.626A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.713A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.604A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.476A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.451A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.661A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.750A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.516A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 642 through 645 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.624A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 5.289A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.537A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 897 hydrogen bonds defined for protein. 2448 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: 11.58 Time building geometry restraints manager: 12.73 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: 8292 1.34 - 1.46: 6792 1.46 - 1.59: 11842 1.59 - 1.71: 3 1.71 - 1.83: 144 Bond restraints: 27073 Sorted by residual: bond pdb=" C VAL A 991 " pdb=" N GLN A 992 " ideal model delta sigma weight residual 1.334 1.471 -0.136 1.27e-02 6.20e+03 1.15e+02 bond pdb=" CG PRO C 322 " pdb=" CD PRO C 322 " ideal model delta sigma weight residual 1.503 1.256 0.247 3.40e-02 8.65e+02 5.26e+01 bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.56e+01 bond pdb=" C LEU A 977 " pdb=" N ASN A 978 " ideal model delta sigma weight residual 1.334 1.432 -0.098 1.49e-02 4.50e+03 4.35e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.23e-02 6.61e+03 1.55e+01 ... (remaining 27068 not shown) Histogram of bond angle deviations from ideal: 88.83 - 98.09: 5 98.09 - 107.34: 902 107.34 - 116.60: 18585 116.60 - 125.86: 17029 125.86 - 135.11: 293 Bond angle restraints: 36814 Sorted by residual: angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 96.76 15.24 1.40e+00 5.10e-01 1.18e+02 angle pdb=" CA PRO C 322 " pdb=" N PRO C 322 " pdb=" CD PRO C 322 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.21e+01 angle pdb=" N PRO A 330 " pdb=" CD PRO A 330 " pdb=" CG PRO A 330 " ideal model delta sigma weight residual 103.20 88.83 14.37 1.50e+00 4.44e-01 9.18e+01 angle pdb=" N PRO C 322 " pdb=" CD PRO C 322 " pdb=" CG PRO C 322 " ideal model delta sigma weight residual 103.20 89.55 13.65 1.50e+00 4.44e-01 8.28e+01 angle pdb=" O LEU A 977 " pdb=" C LEU A 977 " pdb=" N ASN A 978 " ideal model delta sigma weight residual 122.39 111.73 10.66 1.30e+00 5.92e-01 6.72e+01 ... (remaining 36809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 16277 24.82 - 49.65: 814 49.65 - 74.47: 129 74.47 - 99.30: 59 99.30 - 124.12: 18 Dihedral angle restraints: 17297 sinusoidal: 7906 harmonic: 9391 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -174.61 88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 -178.40 -88.60 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 169.40 -76.40 1 1.00e+01 1.00e-02 7.34e+01 ... (remaining 17294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4298 0.112 - 0.224: 104 0.224 - 0.336: 10 0.336 - 0.448: 1 0.448 - 0.560: 3 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 4413 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 801 " -0.001 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" CG ASN B 801 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 801 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN B 801 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 321 " 0.080 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO C 322 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C1078 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO C1079 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C1079 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C1079 " 0.057 5.00e-02 4.00e+02 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 513 2.66 - 3.22: 25266 3.22 - 3.78: 38787 3.78 - 4.34: 51894 4.34 - 4.90: 83903 Nonbonded interactions: 200363 Sorted by model distance: nonbonded pdb=" O ASP C 290 " pdb=" OG SER C 297 " model vdw 2.106 2.440 nonbonded pdb=" OH TYR B 396 " pdb=" OH TYR C 200 " model vdw 2.113 2.440 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.181 2.440 nonbonded pdb=" O ASN A 99 " pdb=" NH1 ARG A 102 " model vdw 2.183 2.520 nonbonded pdb=" OG1 THR A 912 " pdb=" OD1 ASN A 914 " model vdw 2.184 2.440 ... (remaining 200358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 826 or resid 855 through 1162 or resid 1401 thr \ ough 1407)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1407)) selection = (chain 'C' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1407)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.640 Check model and map are aligned: 0.410 Set scattering table: 0.290 Process input model: 73.130 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.005 0.247 27073 Z= 0.309 Angle : 0.753 15.237 36814 Z= 0.414 Chirality : 0.050 0.560 4416 Planarity : 0.005 0.110 4640 Dihedral : 15.428 124.123 11131 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 0.32 % Allowed : 0.53 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.53 (0.14), residues: 3189 helix: -0.10 (0.20), residues: 661 sheet: -0.65 (0.21), residues: 559 loop : -1.49 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 436 HIS 0.011 0.001 HIS A 66 PHE 0.034 0.001 PHE B 135 TYR 0.017 0.001 TYR A 145 ARG 0.015 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 340 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.1291 (tpt) cc_final: -0.1712 (tpt) REVERT: A 461 LEU cc_start: 0.4209 (pp) cc_final: 0.3632 (mm) REVERT: A 508 TYR cc_start: 0.5571 (m-80) cc_final: 0.5242 (m-80) REVERT: B 258 TRP cc_start: -0.2661 (t60) cc_final: -0.3011 (t60) REVERT: B 663 ASP cc_start: 0.7290 (m-30) cc_final: 0.7032 (m-30) REVERT: C 99 ASN cc_start: 0.4809 (m-40) cc_final: 0.4150 (m110) REVERT: C 266 TYR cc_start: 0.5016 (m-80) cc_final: 0.4213 (m-80) REVERT: C 369 TYR cc_start: 0.5954 (t80) cc_final: 0.5683 (t80) REVERT: C 420 ASP cc_start: 0.5475 (t0) cc_final: 0.5085 (t70) REVERT: C 1115 ILE cc_start: 0.4105 (mm) cc_final: 0.3833 (mm) outliers start: 9 outliers final: 2 residues processed: 348 average time/residue: 0.3651 time to fit residues: 201.5535 Evaluate side-chains 193 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 251 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 152 optimal weight: 20.0000 chunk 187 optimal weight: 0.7980 chunk 291 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 965 GLN B 207 HIS B1135 ASN C 81 ASN C 448 ASN C 481 ASN C 542 ASN C 606 ASN C 658 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27073 Z= 0.232 Angle : 0.658 9.078 36814 Z= 0.334 Chirality : 0.049 0.713 4416 Planarity : 0.005 0.054 4640 Dihedral : 11.791 108.516 5347 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 8.27 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.25 (0.14), residues: 3189 helix: 0.41 (0.19), residues: 714 sheet: -0.32 (0.20), residues: 653 loop : -1.59 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.006 0.001 HIS A 655 PHE 0.023 0.002 PHE C 377 TYR 0.027 0.002 TYR B1067 ARG 0.006 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0946 (tpt) cc_final: -0.1379 (tpt) REVERT: A 237 ARG cc_start: 0.5914 (ptt90) cc_final: 0.5646 (ptt90) REVERT: A 461 LEU cc_start: 0.4444 (pp) cc_final: 0.3821 (mm) REVERT: A 1030 SER cc_start: 0.9185 (p) cc_final: 0.8827 (t) REVERT: B 258 TRP cc_start: -0.2598 (t60) cc_final: -0.2988 (t60) REVERT: B 663 ASP cc_start: 0.7340 (m-30) cc_final: 0.7131 (m-30) REVERT: C 177 MET cc_start: -0.3204 (ttt) cc_final: -0.3580 (ttt) REVERT: C 658 ASN cc_start: 0.6636 (OUTLIER) cc_final: 0.6375 (p0) REVERT: C 1105 THR cc_start: 0.8180 (p) cc_final: 0.7821 (p) outliers start: 35 outliers final: 11 residues processed: 257 average time/residue: 0.3858 time to fit residues: 163.3037 Evaluate side-chains 193 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 737 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 292 optimal weight: 0.9980 chunk 315 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 234 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 207 HIS A 965 GLN A1159 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 196 ASN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 606 ASN C 658 ASN C 804 GLN C 935 GLN C 955 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27073 Z= 0.179 Angle : 0.601 9.744 36814 Z= 0.300 Chirality : 0.046 0.487 4416 Planarity : 0.004 0.048 4640 Dihedral : 10.722 106.118 5345 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 1.24 % Allowed : 11.68 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.07 (0.14), residues: 3189 helix: 0.73 (0.20), residues: 724 sheet: -0.24 (0.20), residues: 640 loop : -1.54 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 353 HIS 0.007 0.001 HIS B 207 PHE 0.018 0.001 PHE C 541 TYR 0.021 0.001 TYR C 396 ARG 0.003 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.1032 (tpt) cc_final: -0.1443 (tpt) REVERT: A 237 ARG cc_start: 0.6161 (ptt90) cc_final: 0.5898 (ptt90) REVERT: A 461 LEU cc_start: 0.4344 (pp) cc_final: 0.3685 (mm) REVERT: B 258 TRP cc_start: -0.2553 (t60) cc_final: -0.2972 (t60) REVERT: B 753 LEU cc_start: 0.9182 (tp) cc_final: 0.8914 (tp) REVERT: C 658 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6508 (p0) REVERT: C 1105 THR cc_start: 0.8175 (p) cc_final: 0.7860 (p) outliers start: 35 outliers final: 15 residues processed: 226 average time/residue: 0.3545 time to fit residues: 133.2293 Evaluate side-chains 186 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 753 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 310 optimal weight: 0.4980 chunk 153 optimal weight: 6.9990 chunk 277 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 644 GLN A 965 GLN B 207 HIS ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 658 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27073 Z= 0.283 Angle : 0.667 12.183 36814 Z= 0.330 Chirality : 0.048 0.496 4416 Planarity : 0.004 0.051 4640 Dihedral : 9.997 100.655 5345 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.34 % Allowed : 13.28 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.19 (0.14), residues: 3189 helix: 0.67 (0.19), residues: 724 sheet: -0.20 (0.20), residues: 627 loop : -1.67 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 353 HIS 0.006 0.001 HIS A 655 PHE 0.026 0.002 PHE C 201 TYR 0.033 0.002 TYR C 204 ARG 0.005 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 192 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6944 (ptt90) cc_final: 0.6695 (ptt90) REVERT: B 228 ASP cc_start: 0.7259 (m-30) cc_final: 0.6844 (t70) REVERT: B 258 TRP cc_start: -0.2613 (t60) cc_final: -0.2982 (t60) REVERT: C 869 MET cc_start: 0.8288 (mtp) cc_final: 0.7954 (mtm) REVERT: C 1105 THR cc_start: 0.8273 (p) cc_final: 0.7954 (p) outliers start: 66 outliers final: 42 residues processed: 243 average time/residue: 0.3366 time to fit residues: 137.6519 Evaluate side-chains 206 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 264 optimal weight: 0.8980 chunk 214 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 158 optimal weight: 3.9990 chunk 278 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 901 GLN A 955 ASN A 965 GLN B 188 ASN B 949 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 27073 Z= 0.360 Angle : 0.716 12.042 36814 Z= 0.358 Chirality : 0.050 0.483 4416 Planarity : 0.005 0.056 4640 Dihedral : 9.476 100.420 5345 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 2.88 % Allowed : 14.91 % Favored : 82.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.36 (0.14), residues: 3189 helix: 0.52 (0.19), residues: 723 sheet: -0.34 (0.20), residues: 625 loop : -1.77 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 353 HIS 0.007 0.001 HIS B1083 PHE 0.023 0.002 PHE B 92 TYR 0.025 0.002 TYR B1067 ARG 0.007 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 173 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7357 (mptt) cc_final: 0.6963 (mmtm) REVERT: B 258 TRP cc_start: -0.2511 (t60) cc_final: -0.3068 (t60) REVERT: B 940 SER cc_start: 0.7468 (m) cc_final: 0.7224 (t) REVERT: B 990 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7469 (pp20) REVERT: C 452 LEU cc_start: 0.7666 (mm) cc_final: 0.7424 (mt) REVERT: C 1105 THR cc_start: 0.8468 (p) cc_final: 0.8198 (p) outliers start: 81 outliers final: 55 residues processed: 233 average time/residue: 0.3481 time to fit residues: 135.3801 Evaluate side-chains 214 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 158 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 658 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27073 Z= 0.243 Angle : 0.633 9.456 36814 Z= 0.314 Chirality : 0.047 0.463 4416 Planarity : 0.004 0.053 4640 Dihedral : 8.981 100.573 5345 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.89 % Rotamer: Outliers : 2.77 % Allowed : 15.97 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3189 helix: 0.80 (0.19), residues: 722 sheet: -0.19 (0.21), residues: 587 loop : -1.73 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.007 0.001 HIS B1083 PHE 0.022 0.002 PHE A 377 TYR 0.029 0.002 TYR B 380 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 173 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 ASN cc_start: 0.8367 (p0) cc_final: 0.8080 (m-40) REVERT: B 258 TRP cc_start: -0.2468 (t60) cc_final: -0.3099 (t60) REVERT: B 365 TYR cc_start: 0.7739 (m-80) cc_final: 0.6856 (m-80) REVERT: B 398 ASP cc_start: 0.7498 (t0) cc_final: 0.6911 (t0) REVERT: B 546 LEU cc_start: 0.8682 (tt) cc_final: 0.8415 (tt) REVERT: C 452 LEU cc_start: 0.7892 (mm) cc_final: 0.7363 (mt) REVERT: C 675 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6334 (tm-30) REVERT: C 1105 THR cc_start: 0.8446 (p) cc_final: 0.8176 (p) outliers start: 78 outliers final: 56 residues processed: 235 average time/residue: 0.3424 time to fit residues: 134.2080 Evaluate side-chains 208 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 151 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 175 optimal weight: 0.6980 chunk 261 optimal weight: 10.0000 chunk 173 optimal weight: 0.7980 chunk 309 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 965 GLN ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27073 Z= 0.194 Angle : 0.623 16.650 36814 Z= 0.305 Chirality : 0.047 0.452 4416 Planarity : 0.004 0.049 4640 Dihedral : 8.557 97.430 5343 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 2.34 % Allowed : 17.00 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.12 (0.14), residues: 3189 helix: 0.97 (0.20), residues: 724 sheet: -0.16 (0.21), residues: 589 loop : -1.72 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.006 0.001 HIS B1083 PHE 0.037 0.002 PHE A 392 TYR 0.028 0.001 TYR B 380 ARG 0.008 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 174 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 TRP cc_start: -0.2490 (t60) cc_final: -0.3098 (t60) REVERT: B 365 TYR cc_start: 0.7765 (m-80) cc_final: 0.6728 (m-80) REVERT: B 546 LEU cc_start: 0.8676 (tt) cc_final: 0.8404 (tt) REVERT: C 452 LEU cc_start: 0.8064 (mm) cc_final: 0.7822 (mt) REVERT: C 675 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6358 (tm-30) REVERT: C 1105 THR cc_start: 0.8493 (p) cc_final: 0.8222 (p) outliers start: 66 outliers final: 51 residues processed: 227 average time/residue: 0.3469 time to fit residues: 130.3828 Evaluate side-chains 210 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 158 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 243 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 658 ASN C 675 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27073 Z= 0.274 Angle : 0.664 9.526 36814 Z= 0.329 Chirality : 0.048 0.455 4416 Planarity : 0.005 0.096 4640 Dihedral : 8.209 94.389 5343 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 3.19 % Allowed : 16.51 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.24 (0.14), residues: 3189 helix: 0.83 (0.19), residues: 722 sheet: -0.21 (0.21), residues: 591 loop : -1.79 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 353 HIS 0.009 0.001 HIS B1083 PHE 0.022 0.002 PHE A 400 TYR 0.022 0.002 TYR B1067 ARG 0.006 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 172 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 TRP cc_start: -0.2353 (t60) cc_final: -0.3072 (t60) REVERT: B 353 TRP cc_start: 0.6366 (p-90) cc_final: 0.5998 (p-90) REVERT: B 546 LEU cc_start: 0.8750 (tt) cc_final: 0.8494 (tt) REVERT: B 819 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: C 658 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6535 (p0) outliers start: 90 outliers final: 71 residues processed: 240 average time/residue: 0.3542 time to fit residues: 141.3816 Evaluate side-chains 229 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 156 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 chunk 288 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 260 optimal weight: 0.0980 chunk 272 optimal weight: 0.6980 chunk 287 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 388 ASN C 658 ASN C 675 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27073 Z= 0.161 Angle : 0.608 10.193 36814 Z= 0.298 Chirality : 0.046 0.440 4416 Planarity : 0.004 0.078 4640 Dihedral : 7.607 91.105 5343 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 2.20 % Allowed : 17.82 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.96 (0.14), residues: 3189 helix: 1.25 (0.20), residues: 709 sheet: -0.09 (0.21), residues: 595 loop : -1.65 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 64 HIS 0.005 0.001 HIS B1048 PHE 0.018 0.001 PHE A 400 TYR 0.021 0.001 TYR A 369 ARG 0.005 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 175 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 TRP cc_start: -0.2459 (t60) cc_final: -0.3096 (t60) REVERT: B 353 TRP cc_start: 0.6293 (p-90) cc_final: 0.5977 (p-90) REVERT: B 697 MET cc_start: 0.8292 (ttp) cc_final: 0.7991 (ppp) REVERT: B 1115 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7148 (mt) REVERT: C 90 VAL cc_start: 0.8905 (t) cc_final: 0.8547 (m) REVERT: C 201 PHE cc_start: 0.7042 (t80) cc_final: 0.6783 (t80) REVERT: C 675 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6271 (tm-30) outliers start: 62 outliers final: 48 residues processed: 227 average time/residue: 0.3416 time to fit residues: 130.7437 Evaluate side-chains 210 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 160 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 211 optimal weight: 0.9990 chunk 319 optimal weight: 0.1980 chunk 294 optimal weight: 0.1980 chunk 254 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 196 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN B 949 GLN C 519 HIS ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27073 Z= 0.153 Angle : 0.601 9.326 36814 Z= 0.295 Chirality : 0.045 0.435 4416 Planarity : 0.004 0.067 4640 Dihedral : 7.098 84.288 5343 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Rotamer: Outliers : 1.70 % Allowed : 18.53 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.80 (0.14), residues: 3189 helix: 1.34 (0.20), residues: 714 sheet: 0.01 (0.21), residues: 607 loop : -1.55 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 64 HIS 0.010 0.001 HIS C 519 PHE 0.037 0.001 PHE A 400 TYR 0.022 0.001 TYR C 204 ARG 0.010 0.000 ARG B1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 174 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.7395 (tppt) cc_final: 0.6685 (tppt) REVERT: A 993 ILE cc_start: 0.8746 (mm) cc_final: 0.8464 (mt) REVERT: B 258 TRP cc_start: -0.2532 (t60) cc_final: -0.3127 (t60) REVERT: B 353 TRP cc_start: 0.6304 (p-90) cc_final: 0.5994 (p-90) REVERT: B 973 ILE cc_start: 0.8923 (mm) cc_final: 0.8500 (mt) REVERT: B 1107 ARG cc_start: 0.8321 (mmm160) cc_final: 0.8013 (mmm160) REVERT: C 90 VAL cc_start: 0.8881 (t) cc_final: 0.8506 (m) REVERT: C 314 GLN cc_start: 0.8467 (tp40) cc_final: 0.8031 (tp40) REVERT: C 552 LEU cc_start: 0.8354 (pt) cc_final: 0.8018 (pp) outliers start: 48 outliers final: 40 residues processed: 214 average time/residue: 0.3515 time to fit residues: 125.9303 Evaluate side-chains 201 residues out of total 2821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 161 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 0.0870 chunk 271 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 261 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 949 GLN B1135 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.154947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118566 restraints weight = 63595.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116483 restraints weight = 46556.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117267 restraints weight = 53452.453| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 27073 Z= 0.232 Angle : 0.630 8.959 36814 Z= 0.311 Chirality : 0.046 0.449 4416 Planarity : 0.004 0.062 4640 Dihedral : 7.019 73.295 5343 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 1.99 % Allowed : 18.46 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.90 (0.14), residues: 3189 helix: 1.20 (0.20), residues: 712 sheet: -0.07 (0.21), residues: 610 loop : -1.58 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 64 HIS 0.008 0.001 HIS B1083 PHE 0.026 0.002 PHE A 392 TYR 0.020 0.001 TYR C 204 ARG 0.010 0.001 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4354.94 seconds wall clock time: 81 minutes 52.05 seconds (4912.05 seconds total)