Starting phenix.real_space_refine on Fri Aug 9 10:42:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7a_31764/08_2024/7v7a_31764.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7a_31764/08_2024/7v7a_31764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7a_31764/08_2024/7v7a_31764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7a_31764/08_2024/7v7a_31764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7a_31764/08_2024/7v7a_31764.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7a_31764/08_2024/7v7a_31764.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16279 2.51 5 N 4121 2.21 5 O 5068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25579 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "C" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8158 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 53, 'TRANS': 989} Chain breaks: 7 Chain: "B" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.62, per 1000 atoms: 0.61 Number of scatterers: 25579 At special positions: 0 Unit cell: (147.4, 154, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5068 8.00 N 4121 7.00 C 16279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 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 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=2.04 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 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 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 603 " " NAG A2005 " - " ASN A 657 " " NAG A2006 " - " ASN A 188 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 603 " " NAG B2005 " - " ASN B 657 " " NAG B2006 " - " ASN B 20 " " NAG B2007 " - " ASN B 188 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 331 " " NAG C2005 " - " ASN C 603 " " NAG C2006 " - " ASN C 657 " " NAG C2007 " - " ASN C 20 " " NAG C2008 " - " ASN C 188 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A 20 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 343 " " NAG S 1 " - " ASN C 616 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN B 234 " " NAG a 1 " - " ASN B 282 " " NAG b 1 " - " ASN B 331 " " NAG c 1 " - " ASN B 616 " " NAG d 1 " - " ASN B 709 " " NAG e 1 " - " ASN B 717 " " NAG f 1 " - " ASN B 801 " " NAG g 1 " - " ASN B1074 " " NAG h 1 " - " ASN B1098 " " NAG i 1 " - " ASN B1134 " Time building additional restraints: 12.00 Conformation dependent library (CDL) restraints added in 4.0 seconds 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5836 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 45 sheets defined 24.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.034A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.392A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.593A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.714A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.062A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.535A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 909 removed outlier: 4.054A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.550A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.636A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.908A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.567A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.879A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.734A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.143A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 633 through 638 removed outlier: 3.794A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.911A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.543A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.640A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.781A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.213A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.562A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.275A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.330A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.026A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.842A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.510A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 898 through 909 removed outlier: 3.768A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.613A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.763A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.465A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.674A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.904A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.527A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.166A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.662A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.250A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 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 573 through 576 removed outlier: 3.905A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.358A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.615A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.811A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.900A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.444A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.486A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.042A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.881A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.030A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 143 through 144 removed outlier: 5.783A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.810A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.866A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.776A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.680A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.929A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.993A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.071A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.747A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.213A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.210A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.114A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AE6, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.584A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.831A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 981 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.06 Time building geometry restraints manager: 12.70 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: 8008 1.34 - 1.47: 6749 1.47 - 1.59: 11251 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 26146 Sorted by residual: bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.77e+00 ... (remaining 26141 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 668 106.51 - 113.38: 14526 113.38 - 120.25: 8785 120.25 - 127.12: 11402 127.12 - 133.99: 206 Bond angle restraints: 35587 Sorted by residual: angle pdb=" N GLN B1002 " pdb=" CA GLN B1002 " pdb=" CB GLN B1002 " ideal model delta sigma weight residual 110.12 116.03 -5.91 1.47e+00 4.63e-01 1.62e+01 angle pdb=" N ILE C 805 " pdb=" CA ILE C 805 " pdb=" C ILE C 805 " ideal model delta sigma weight residual 113.53 110.01 3.52 9.80e-01 1.04e+00 1.29e+01 angle pdb=" CA GLN B1002 " pdb=" CB GLN B1002 " pdb=" CG GLN B1002 " ideal model delta sigma weight residual 114.10 120.76 -6.66 2.00e+00 2.50e-01 1.11e+01 angle pdb=" N GLY A 103 " pdb=" CA GLY A 103 " pdb=" C GLY A 103 " ideal model delta sigma weight residual 112.06 117.49 -5.43 1.66e+00 3.63e-01 1.07e+01 angle pdb=" N VAL A 729 " pdb=" CA VAL A 729 " pdb=" C VAL A 729 " ideal model delta sigma weight residual 113.71 110.68 3.03 9.50e-01 1.11e+00 1.02e+01 ... (remaining 35582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.63: 15488 22.63 - 45.26: 916 45.26 - 67.89: 166 67.89 - 90.52: 44 90.52 - 113.15: 28 Dihedral angle restraints: 16642 sinusoidal: 7561 harmonic: 9081 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -176.41 90.41 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -171.72 85.72 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -3.56 -82.44 1 1.00e+01 1.00e-02 8.34e+01 ... (remaining 16639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3669 0.067 - 0.135: 588 0.135 - 0.202: 18 0.202 - 0.269: 2 0.269 - 0.336: 8 Chirality restraints: 4285 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG C2002 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C2002 " pdb=" O5 NAG C2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 4282 not shown) Planarity restraints: 4534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO A 986 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 295 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.023 2.00e-02 2.50e+03 2.07e-02 5.37e+00 pdb=" CG ASN B 61 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.018 2.00e-02 2.50e+03 pdb=" C1 NAG B2001 " 0.021 2.00e-02 2.50e+03 ... (remaining 4531 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 629 2.69 - 3.24: 24297 3.24 - 3.79: 37674 3.79 - 4.35: 48125 4.35 - 4.90: 81809 Nonbonded interactions: 192534 Sorted by model distance: nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.137 3.040 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR A 716 " pdb=" O GLN A1071 " model vdw 2.177 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.189 3.040 nonbonded pdb=" NZ LYS C 378 " pdb=" OH TYR C 380 " model vdw 2.211 3.120 ... (remaining 192529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 1146 or resid 2001 through 2006)) selection = (chain 'C' and (resid 14 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2006)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 72.430 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.200 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:2.610 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26146 Z= 0.241 Angle : 0.609 10.027 35587 Z= 0.299 Chirality : 0.047 0.336 4285 Planarity : 0.004 0.060 4481 Dihedral : 14.861 113.148 10689 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.78 % Favored : 96.09 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3071 helix: 1.94 (0.21), residues: 655 sheet: 0.38 (0.19), residues: 697 loop : -1.10 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.002 0.000 HIS A1048 PHE 0.014 0.001 PHE B 759 TYR 0.014 0.001 TYR C1067 ARG 0.003 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 577 ARG cc_start: 0.7646 (ttm170) cc_final: 0.7302 (ttm-80) REVERT: A 969 ASN cc_start: 0.8878 (m110) cc_final: 0.8669 (m110) REVERT: C 31 SER cc_start: 0.9213 (t) cc_final: 0.8795 (p) REVERT: C 52 GLN cc_start: 0.8324 (pp30) cc_final: 0.7918 (pp30) REVERT: C 160 TYR cc_start: 0.8243 (p90) cc_final: 0.8039 (p90) REVERT: C 740 MET cc_start: 0.7754 (mtp) cc_final: 0.7517 (mtt) REVERT: C 776 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8663 (ptmm) REVERT: C 886 TRP cc_start: 0.8592 (p90) cc_final: 0.8021 (p90) REVERT: C 900 MET cc_start: 0.7182 (mtt) cc_final: 0.6955 (mtp) REVERT: C 950 ASP cc_start: 0.8612 (t70) cc_final: 0.8351 (t0) REVERT: B 329 PHE cc_start: 0.7689 (m-10) cc_final: 0.7186 (m-10) REVERT: B 740 MET cc_start: 0.7738 (mtp) cc_final: 0.7432 (mtm) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.3376 time to fit residues: 112.7118 Evaluate side-chains 125 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 30.0000 chunk 94 optimal weight: 0.6980 chunk 147 optimal weight: 0.0980 chunk 180 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 901 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN B 764 ASN B 777 ASN B 913 GLN B1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26146 Z= 0.184 Angle : 0.579 11.579 35587 Z= 0.286 Chirality : 0.046 0.331 4285 Planarity : 0.004 0.060 4481 Dihedral : 10.489 98.082 5152 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 0.51 % Allowed : 5.91 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3071 helix: 1.95 (0.21), residues: 639 sheet: 0.45 (0.20), residues: 690 loop : -1.05 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.003 0.001 HIS C1064 PHE 0.021 0.001 PHE C 429 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 52 GLN cc_start: 0.8225 (pp30) cc_final: 0.7865 (pp30) REVERT: C 495 TYR cc_start: 0.7552 (m-80) cc_final: 0.6980 (m-80) REVERT: C 697 MET cc_start: 0.7944 (ptp) cc_final: 0.7689 (ptm) REVERT: C 900 MET cc_start: 0.7474 (mtt) cc_final: 0.7204 (mtt) REVERT: C 950 ASP cc_start: 0.8600 (t70) cc_final: 0.8331 (t0) outliers start: 14 outliers final: 10 residues processed: 150 average time/residue: 0.3320 time to fit residues: 85.1758 Evaluate side-chains 136 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 234 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 0.7980 chunk 304 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 279 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 226 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN C 239 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN B 542 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26146 Z= 0.187 Angle : 0.545 9.130 35587 Z= 0.271 Chirality : 0.045 0.334 4285 Planarity : 0.004 0.058 4481 Dihedral : 9.169 93.933 5152 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 1.03 % Allowed : 8.70 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3071 helix: 1.96 (0.21), residues: 640 sheet: 0.33 (0.19), residues: 713 loop : -1.00 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C1064 PHE 0.022 0.001 PHE C 429 TYR 0.018 0.001 TYR C1067 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 856 ASN cc_start: 0.8350 (t0) cc_final: 0.7954 (t0) REVERT: C 52 GLN cc_start: 0.8214 (pp30) cc_final: 0.7839 (pp30) REVERT: C 153 MET cc_start: 0.6690 (ptm) cc_final: 0.6096 (pmm) REVERT: C 495 TYR cc_start: 0.7559 (m-80) cc_final: 0.7037 (m-80) REVERT: C 900 MET cc_start: 0.7555 (mtt) cc_final: 0.7285 (mtp) REVERT: B 1031 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7279 (mp0) outliers start: 28 outliers final: 17 residues processed: 162 average time/residue: 0.3095 time to fit residues: 86.4071 Evaluate side-chains 140 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.0050 chunk 212 optimal weight: 8.9990 chunk 146 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 134 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 268 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN A1106 GLN C 125 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN B1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26146 Z= 0.281 Angle : 0.588 9.218 35587 Z= 0.294 Chirality : 0.047 0.340 4285 Planarity : 0.004 0.053 4481 Dihedral : 8.515 88.259 5152 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 1.40 % Allowed : 10.61 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3071 helix: 1.80 (0.21), residues: 631 sheet: 0.24 (0.19), residues: 739 loop : -1.08 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.005 0.001 HIS B1088 PHE 0.025 0.002 PHE C1121 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 2.769 Fit side-chains revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8333 (tm-30) REVERT: C 52 GLN cc_start: 0.8232 (pp30) cc_final: 0.7841 (pp30) REVERT: C 441 LEU cc_start: 0.9301 (mm) cc_final: 0.9004 (mt) REVERT: C 900 MET cc_start: 0.7751 (mtt) cc_final: 0.7469 (mtt) REVERT: B 1031 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7222 (mp0) outliers start: 38 outliers final: 17 residues processed: 151 average time/residue: 0.3026 time to fit residues: 80.5921 Evaluate side-chains 134 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26146 Z= 0.216 Angle : 0.560 10.826 35587 Z= 0.278 Chirality : 0.046 0.343 4285 Planarity : 0.004 0.050 4481 Dihedral : 8.033 82.450 5152 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 1.58 % Allowed : 11.57 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3071 helix: 1.84 (0.21), residues: 632 sheet: 0.20 (0.19), residues: 734 loop : -1.09 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.003 0.001 HIS A1088 PHE 0.026 0.001 PHE C 429 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6324 (tt) REVERT: A 856 ASN cc_start: 0.8383 (t0) cc_final: 0.7911 (t0) REVERT: A 957 GLN cc_start: 0.8462 (pt0) cc_final: 0.8213 (pt0) REVERT: A 977 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7285 (tt) REVERT: C 52 GLN cc_start: 0.8241 (pp30) cc_final: 0.7824 (pp30) REVERT: C 242 LEU cc_start: 0.7335 (tp) cc_final: 0.7073 (tp) REVERT: C 441 LEU cc_start: 0.9237 (mm) cc_final: 0.8896 (mt) REVERT: C 495 TYR cc_start: 0.7515 (m-80) cc_final: 0.7129 (m-80) REVERT: C 661 GLU cc_start: 0.7517 (tp30) cc_final: 0.7199 (tm-30) REVERT: C 900 MET cc_start: 0.7640 (mtt) cc_final: 0.7354 (mtp) REVERT: B 902 MET cc_start: 0.8062 (tpp) cc_final: 0.7847 (tpt) REVERT: B 1031 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7222 (mp0) outliers start: 43 outliers final: 27 residues processed: 160 average time/residue: 0.2962 time to fit residues: 83.0407 Evaluate side-chains 144 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 73 optimal weight: 0.0870 chunk 299 optimal weight: 2.9990 chunk 248 optimal weight: 40.0000 chunk 138 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26146 Z= 0.175 Angle : 0.539 9.174 35587 Z= 0.266 Chirality : 0.045 0.340 4285 Planarity : 0.004 0.049 4481 Dihedral : 7.563 77.911 5152 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.28 % Rotamer: Outliers : 1.54 % Allowed : 12.41 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3071 helix: 2.03 (0.22), residues: 622 sheet: 0.23 (0.19), residues: 724 loop : -1.03 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 PHE 0.028 0.001 PHE C 429 TYR 0.018 0.001 TYR C1067 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6225 (tt) REVERT: A 560 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8572 (mp) REVERT: A 856 ASN cc_start: 0.8366 (t0) cc_final: 0.7888 (t0) REVERT: A 977 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7284 (tt) REVERT: C 52 GLN cc_start: 0.8233 (pp30) cc_final: 0.7805 (pp30) REVERT: C 242 LEU cc_start: 0.7337 (tp) cc_final: 0.7068 (tp) REVERT: C 495 TYR cc_start: 0.7566 (m-80) cc_final: 0.7096 (m-80) REVERT: C 661 GLU cc_start: 0.7487 (tp30) cc_final: 0.7105 (tm-30) REVERT: C 957 GLN cc_start: 0.9058 (tp40) cc_final: 0.8745 (tp-100) REVERT: C 1072 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: B 1031 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7274 (mp0) outliers start: 42 outliers final: 28 residues processed: 163 average time/residue: 0.3085 time to fit residues: 87.9750 Evaluate side-chains 152 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 182 optimal weight: 0.0670 chunk 137 optimal weight: 0.9980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26146 Z= 0.173 Angle : 0.534 9.163 35587 Z= 0.264 Chirality : 0.045 0.338 4285 Planarity : 0.004 0.049 4481 Dihedral : 7.316 75.791 5152 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.49 % Favored : 95.41 % Rotamer: Outliers : 1.54 % Allowed : 12.82 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3071 helix: 2.03 (0.21), residues: 627 sheet: 0.24 (0.19), residues: 734 loop : -1.04 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 104 HIS 0.003 0.001 HIS A1088 PHE 0.028 0.001 PHE C 429 TYR 0.018 0.001 TYR C1067 ARG 0.001 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6271 (tt) REVERT: A 856 ASN cc_start: 0.8366 (t0) cc_final: 0.7881 (t0) REVERT: C 52 GLN cc_start: 0.8247 (pp30) cc_final: 0.7814 (pp30) REVERT: C 242 LEU cc_start: 0.7372 (tp) cc_final: 0.7100 (tp) REVERT: C 495 TYR cc_start: 0.7579 (m-80) cc_final: 0.7060 (m-80) REVERT: C 581 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8473 (p) REVERT: C 900 MET cc_start: 0.7596 (mtt) cc_final: 0.7309 (mtt) REVERT: C 957 GLN cc_start: 0.9075 (tp40) cc_final: 0.8729 (tp-100) REVERT: C 1072 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: B 1031 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7262 (mp0) outliers start: 42 outliers final: 31 residues processed: 164 average time/residue: 0.2924 time to fit residues: 84.6371 Evaluate side-chains 154 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 178 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 203 optimal weight: 0.0570 chunk 147 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26146 Z= 0.162 Angle : 0.539 14.337 35587 Z= 0.266 Chirality : 0.045 0.337 4285 Planarity : 0.004 0.048 4481 Dihedral : 7.107 73.123 5152 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.49 % Favored : 95.41 % Rotamer: Outliers : 1.58 % Allowed : 13.26 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3071 helix: 2.03 (0.21), residues: 628 sheet: 0.28 (0.19), residues: 722 loop : -1.02 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 104 HIS 0.003 0.001 HIS C1064 PHE 0.029 0.001 PHE C 429 TYR 0.018 0.001 TYR C1067 ARG 0.001 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6250 (tt) REVERT: A 560 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8543 (mp) REVERT: A 856 ASN cc_start: 0.8353 (t0) cc_final: 0.7871 (t0) REVERT: A 977 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7259 (tt) REVERT: A 1132 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7698 (pp) REVERT: C 52 GLN cc_start: 0.8247 (pp30) cc_final: 0.7825 (pp30) REVERT: C 242 LEU cc_start: 0.7409 (tp) cc_final: 0.7133 (tp) REVERT: C 495 TYR cc_start: 0.7598 (m-80) cc_final: 0.7128 (m-80) REVERT: C 581 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8469 (p) REVERT: C 661 GLU cc_start: 0.7574 (tp30) cc_final: 0.7210 (tm-30) REVERT: C 900 MET cc_start: 0.7585 (mtt) cc_final: 0.7347 (mtt) REVERT: C 957 GLN cc_start: 0.9075 (tp40) cc_final: 0.8725 (tp-100) REVERT: C 1072 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: B 1031 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7257 (mp0) outliers start: 43 outliers final: 30 residues processed: 166 average time/residue: 0.3077 time to fit residues: 88.8808 Evaluate side-chains 156 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 0.1980 chunk 286 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 278 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 218 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 251 optimal weight: 50.0000 chunk 263 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26146 Z= 0.166 Angle : 0.538 9.153 35587 Z= 0.267 Chirality : 0.045 0.336 4285 Planarity : 0.004 0.048 4481 Dihedral : 6.971 70.493 5152 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 1.65 % Allowed : 13.29 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3071 helix: 2.09 (0.21), residues: 629 sheet: 0.30 (0.19), residues: 721 loop : -0.99 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.003 0.001 HIS C1064 PHE 0.031 0.001 PHE C 429 TYR 0.018 0.001 TYR C1067 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 125 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6108 (tt) REVERT: A 560 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8488 (mp) REVERT: A 856 ASN cc_start: 0.8354 (t0) cc_final: 0.7864 (t0) REVERT: A 957 GLN cc_start: 0.8382 (pt0) cc_final: 0.8147 (pt0) REVERT: A 977 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7264 (tt) REVERT: A 1132 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7742 (pp) REVERT: C 52 GLN cc_start: 0.8247 (pp30) cc_final: 0.7822 (pp30) REVERT: C 495 TYR cc_start: 0.7533 (m-80) cc_final: 0.6968 (m-80) REVERT: C 581 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8462 (p) REVERT: C 957 GLN cc_start: 0.9036 (tp40) cc_final: 0.8702 (tp-100) REVERT: C 1072 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: B 1031 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7249 (mp0) outliers start: 45 outliers final: 35 residues processed: 166 average time/residue: 0.3159 time to fit residues: 91.0572 Evaluate side-chains 162 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 120 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.1980 chunk 294 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 284 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26146 Z= 0.171 Angle : 0.541 9.149 35587 Z= 0.268 Chirality : 0.045 0.336 4285 Planarity : 0.004 0.049 4481 Dihedral : 6.915 69.053 5152 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 1.58 % Allowed : 13.51 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3071 helix: 2.09 (0.21), residues: 629 sheet: 0.31 (0.19), residues: 720 loop : -0.99 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.003 0.001 HIS C1064 PHE 0.031 0.001 PHE C 429 TYR 0.018 0.001 TYR C1067 ARG 0.001 0.000 ARG B 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 123 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6106 (tt) REVERT: A 560 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8481 (mp) REVERT: A 740 MET cc_start: 0.8557 (tpp) cc_final: 0.8337 (mtt) REVERT: A 856 ASN cc_start: 0.8355 (t0) cc_final: 0.7861 (t0) REVERT: A 957 GLN cc_start: 0.8418 (pt0) cc_final: 0.8179 (pt0) REVERT: A 977 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7266 (tt) REVERT: A 1132 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7807 (pp) REVERT: C 52 GLN cc_start: 0.8247 (pp30) cc_final: 0.7820 (pp30) REVERT: C 495 TYR cc_start: 0.7491 (m-80) cc_final: 0.6909 (m-80) REVERT: C 581 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8462 (p) REVERT: C 900 MET cc_start: 0.7592 (mtt) cc_final: 0.7356 (mtt) REVERT: C 957 GLN cc_start: 0.9019 (tp40) cc_final: 0.8667 (tp-100) REVERT: C 1072 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: B 902 MET cc_start: 0.7954 (tpp) cc_final: 0.7749 (tpp) REVERT: B 1031 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7247 (mp0) outliers start: 43 outliers final: 35 residues processed: 162 average time/residue: 0.3026 time to fit residues: 85.8429 Evaluate side-chains 163 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.642 > 50: distance: 15 - 61: 8.792 distance: 18 - 58: 17.607 distance: 48 - 50: 20.294 distance: 50 - 51: 7.824 distance: 51 - 52: 19.594 distance: 51 - 54: 11.973 distance: 52 - 53: 17.796 distance: 52 - 58: 21.030 distance: 54 - 55: 12.790 distance: 55 - 56: 10.996 distance: 55 - 57: 7.477 distance: 58 - 59: 5.037 distance: 59 - 60: 13.055 distance: 59 - 62: 11.983 distance: 60 - 61: 3.427 distance: 60 - 65: 8.396 distance: 62 - 63: 6.705 distance: 62 - 64: 11.236 distance: 65 - 66: 13.524 distance: 66 - 67: 23.800 distance: 66 - 69: 13.120 distance: 67 - 68: 5.687 distance: 67 - 72: 15.335 distance: 69 - 70: 10.150 distance: 69 - 71: 12.977 distance: 72 - 73: 6.401 distance: 73 - 74: 13.796 distance: 73 - 76: 23.571 distance: 74 - 75: 36.151 distance: 74 - 80: 22.905 distance: 76 - 77: 7.838 distance: 77 - 78: 23.949 distance: 77 - 79: 17.492 distance: 80 - 81: 23.821 distance: 80 - 86: 22.907 distance: 81 - 82: 17.496 distance: 81 - 84: 11.927 distance: 82 - 83: 31.584 distance: 82 - 87: 27.017 distance: 84 - 85: 10.679 distance: 85 - 86: 18.787 distance: 87 - 88: 25.817 distance: 87 - 93: 18.637 distance: 88 - 89: 22.553 distance: 88 - 91: 5.667 distance: 89 - 90: 13.115 distance: 89 - 94: 35.030 distance: 91 - 92: 18.973 distance: 92 - 93: 30.053 distance: 94 - 95: 17.965 distance: 95 - 96: 9.139 distance: 95 - 98: 16.329 distance: 96 - 97: 34.117 distance: 96 - 102: 12.539 distance: 98 - 99: 13.011 distance: 99 - 100: 14.397 distance: 99 - 101: 5.776 distance: 102 - 103: 16.525 distance: 103 - 106: 8.861 distance: 104 - 105: 14.736 distance: 106 - 107: 11.305 distance: 107 - 108: 14.149 distance: 107 - 109: 16.522 distance: 112 - 113: 22.114 distance: 112 - 117: 8.890 distance: 113 - 139: 25.076 distance: 114 - 115: 4.766 distance: 117 - 118: 4.631 distance: 118 - 119: 8.151 distance: 118 - 121: 7.646 distance: 119 - 120: 11.774 distance: 120 - 147: 14.145 distance: 121 - 122: 11.446 distance: 122 - 123: 4.782 distance: 122 - 124: 15.273