Starting phenix.real_space_refine on Fri Apr 12 21:31:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vv5_21391/04_2024/6vv5_21391_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vv5_21391/04_2024/6vv5_21391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vv5_21391/04_2024/6vv5_21391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vv5_21391/04_2024/6vv5_21391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vv5_21391/04_2024/6vv5_21391_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vv5_21391/04_2024/6vv5_21391_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 17100 2.51 5 N 4212 2.21 5 O 5415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26838 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8480 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 39, 'TRANS': 1057} Chain breaks: 18 Chain: "B" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8480 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 39, 'TRANS': 1057} Chain breaks: 18 Chain: "C" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8480 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 39, 'TRANS': 1057} Chain breaks: 18 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} 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: "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: 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: "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: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} 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: "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: 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: "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: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} 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: "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: 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: "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: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {'NAG': 5, 'PAM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {'NAG': 5, 'PAM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {'NAG': 5, 'PAM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 13.99, per 1000 atoms: 0.52 Number of scatterers: 26838 At special positions: 0 Unit cell: (141.45, 133.4, 171.35, 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 5415 8.00 N 4212 7.00 C 17100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.04 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.07 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.06 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.09 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.10 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.02 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.04 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.07 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.06 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.09 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.10 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.02 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.04 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.07 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.06 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.09 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.10 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.02 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN N 4 " - " MAN N 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA N 3 " - " MAN N 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " MAN D 6 " - " MAN D 8 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " BETA1-2 " MAN D 6 " - " NAG D 7 " " MAN N 6 " - " NAG N 7 " " MAN X 6 " - " NAG X 7 " 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 H 2 " - " BMA H 3 " " 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 N 2 " - " BMA N 3 " " 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 R 2 " - " BMA R 3 " " 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 X 2 " - " BMA X 3 " " 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 b 2 " - " BMA b 3 " " 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-ASN " NAG A1401 " - " ASN A 216 " " NAG A1402 " - " ASN A 300 " " NAG A1403 " - " ASN A 667 " " NAG A1404 " - " ASN A 781 " " NAG A1405 " - " ASN A1249 " " NAG B1401 " - " ASN B 216 " " NAG B1402 " - " ASN B 300 " " NAG B1403 " - " ASN B 667 " " NAG B1404 " - " ASN B 781 " " NAG B1405 " - " ASN B1249 " " NAG C1401 " - " ASN C 216 " " NAG C1402 " - " ASN C 300 " " NAG C1403 " - " ASN C 667 " " NAG C1404 " - " ASN C 781 " " NAG C1405 " - " ASN C1249 " " NAG D 1 " - " ASN A 264 " " NAG E 1 " - " ASN A 344 " " NAG F 1 " - " ASN A 514 " " NAG G 1 " - " ASN A 556 " " NAG H 1 " - " ASN A 688 " " NAG I 1 " - " ASN A 726 " " NAG J 1 " - " ASN A 743 " " NAG K 1 " - " ASN A 787 " " NAG L 1 " - " ASN A 873 " " NAG M 1 " - " ASN A1232 " " NAG N 1 " - " ASN B 264 " " NAG O 1 " - " ASN B 344 " " NAG P 1 " - " ASN B 514 " " NAG Q 1 " - " ASN B 556 " " NAG R 1 " - " ASN B 688 " " NAG S 1 " - " ASN B 726 " " NAG T 1 " - " ASN B 743 " " NAG U 1 " - " ASN B 787 " " NAG V 1 " - " ASN B 873 " " NAG W 1 " - " ASN B1232 " " NAG X 1 " - " ASN C 264 " " NAG Y 1 " - " ASN C 344 " " NAG Z 1 " - " ASN C 514 " " NAG a 1 " - " ASN C 556 " " NAG b 1 " - " ASN C 688 " " NAG c 1 " - " ASN C 726 " " NAG d 1 " - " ASN C 743 " " NAG e 1 " - " ASN C 787 " " NAG f 1 " - " ASN C 873 " " NAG g 1 " - " ASN C1232 " Time building additional restraints: 11.45 Conformation dependent library (CDL) restraints added in 4.8 seconds 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 51 sheets defined 21.1% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.525A pdb=" N LEU A 330 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 808 through 812 Processing helix chain 'A' and resid 817 through 851 removed outlier: 4.479A pdb=" N GLN A 825 " --> pdb=" O GLN A 821 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA A 828 " --> pdb=" O THR A 824 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 829 " --> pdb=" O GLN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 removed outlier: 3.985A pdb=" N LEU A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 905 Processing helix chain 'A' and resid 929 through 935 Processing helix chain 'A' and resid 947 through 962 removed outlier: 3.813A pdb=" N MET A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL A 962 " --> pdb=" O ILE A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 985 Processing helix chain 'A' and resid 994 through 1013 Processing helix chain 'A' and resid 1017 through 1020 Processing helix chain 'A' and resid 1031 through 1043 Processing helix chain 'A' and resid 1049 through 1057 removed outlier: 3.895A pdb=" N LEU A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1071 Processing helix chain 'A' and resid 1076 through 1122 Processing helix chain 'A' and resid 1217 through 1219 No H-bonds generated for 'chain 'A' and resid 1217 through 1219' Processing helix chain 'A' and resid 1235 through 1240 Proline residue: A1239 - end of helix No H-bonds generated for 'chain 'A' and resid 1235 through 1240' Processing helix chain 'A' and resid 1248 through 1253 Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.525A pdb=" N LEU B 330 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'B' and resid 808 through 812 Processing helix chain 'B' and resid 817 through 851 removed outlier: 4.479A pdb=" N GLN B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA B 828 " --> pdb=" O THR B 824 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 829 " --> pdb=" O GLN B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 861 removed outlier: 3.985A pdb=" N LEU B 861 " --> pdb=" O GLU B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 905 Processing helix chain 'B' and resid 929 through 935 Processing helix chain 'B' and resid 947 through 962 removed outlier: 3.813A pdb=" N MET B 961 " --> pdb=" O LEU B 957 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 962 " --> pdb=" O ILE B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 985 Processing helix chain 'B' and resid 994 through 1013 Processing helix chain 'B' and resid 1017 through 1020 Processing helix chain 'B' and resid 1031 through 1043 Processing helix chain 'B' and resid 1049 through 1057 removed outlier: 3.895A pdb=" N LEU B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B1057 " --> pdb=" O THR B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1071 Processing helix chain 'B' and resid 1076 through 1122 Processing helix chain 'B' and resid 1217 through 1219 No H-bonds generated for 'chain 'B' and resid 1217 through 1219' Processing helix chain 'B' and resid 1235 through 1240 Proline residue: B1239 - end of helix No H-bonds generated for 'chain 'B' and resid 1235 through 1240' Processing helix chain 'B' and resid 1248 through 1253 Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 234 through 240 Processing helix chain 'C' and resid 326 through 330 removed outlier: 3.526A pdb=" N LEU C 330 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 474 Processing helix chain 'C' and resid 578 through 580 No H-bonds generated for 'chain 'C' and resid 578 through 580' Processing helix chain 'C' and resid 808 through 812 Processing helix chain 'C' and resid 817 through 851 removed outlier: 4.479A pdb=" N GLN C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA C 828 " --> pdb=" O THR C 824 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA C 829 " --> pdb=" O GLN C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 861 removed outlier: 3.986A pdb=" N LEU C 861 " --> pdb=" O GLU C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 905 Processing helix chain 'C' and resid 929 through 935 Processing helix chain 'C' and resid 947 through 962 removed outlier: 3.813A pdb=" N MET C 961 " --> pdb=" O LEU C 957 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 962 " --> pdb=" O ILE C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 985 Processing helix chain 'C' and resid 994 through 1013 Processing helix chain 'C' and resid 1017 through 1020 Processing helix chain 'C' and resid 1031 through 1043 Processing helix chain 'C' and resid 1049 through 1057 removed outlier: 3.895A pdb=" N LEU C1056 " --> pdb=" O LEU C1052 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN C1057 " --> pdb=" O THR C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1071 Processing helix chain 'C' and resid 1076 through 1122 Processing helix chain 'C' and resid 1217 through 1219 No H-bonds generated for 'chain 'C' and resid 1217 through 1219' Processing helix chain 'C' and resid 1235 through 1240 Proline residue: C1239 - end of helix No H-bonds generated for 'chain 'C' and resid 1235 through 1240' Processing helix chain 'C' and resid 1248 through 1253 Processing sheet with id= A, first strand: chain 'A' and resid 45 through 51 Processing sheet with id= B, first strand: chain 'A' and resid 203 through 207 Processing sheet with id= C, first strand: chain 'A' and resid 191 through 193 removed outlier: 3.524A pdb=" N ARG A 191 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 270 through 277 Processing sheet with id= E, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.989A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU A 375 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE A 387 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 377 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR A 385 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR A 379 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 406 through 408 removed outlier: 6.643A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.549A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 498 through 502 removed outlier: 5.284A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR A 676 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 548 through 558 Processing sheet with id= J, first strand: chain 'A' and resid 541 through 543 removed outlier: 6.987A pdb=" N LEU A 603 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER A 617 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 601 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR A 619 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS A 599 " --> pdb=" O TYR A 619 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 762 through 764 Processing sheet with id= L, first strand: chain 'A' and resid 780 through 786 Processing sheet with id= M, first strand: chain 'A' and resid 789 through 798 removed outlier: 6.171A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 804 through 806 Processing sheet with id= O, first strand: chain 'A' and resid 1230 through 1233 removed outlier: 7.274A pdb=" N GLY A1171 " --> pdb=" O VAL A1231 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU A1233 " --> pdb=" O GLY A1171 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N CYS A1173 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 1187 through 1190 Processing sheet with id= Q, first strand: chain 'A' and resid 583 through 585 removed outlier: 3.751A pdb=" N LEU A 583 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 45 through 51 Processing sheet with id= S, first strand: chain 'B' and resid 203 through 207 Processing sheet with id= T, first strand: chain 'B' and resid 191 through 193 removed outlier: 3.524A pdb=" N ARG B 191 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 270 through 277 Processing sheet with id= V, first strand: chain 'B' and resid 296 through 298 removed outlier: 6.990A pdb=" N HIS B 338 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 422 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 336 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU B 375 " --> pdb=" O PHE B 387 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE B 387 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 377 " --> pdb=" O TYR B 385 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR B 385 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR B 379 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 406 through 408 removed outlier: 6.643A pdb=" N ASN B 445 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL B 281 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 483 through 488 removed outlier: 3.549A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 498 through 502 removed outlier: 5.284A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR B 676 " --> pdb=" O LEU B 684 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 548 through 558 Processing sheet with id= AA, first strand: chain 'B' and resid 541 through 543 removed outlier: 6.986A pdb=" N LEU B 603 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER B 617 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B 601 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 619 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS B 599 " --> pdb=" O TYR B 619 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 762 through 764 Processing sheet with id= AC, first strand: chain 'B' and resid 780 through 786 Processing sheet with id= AD, first strand: chain 'B' and resid 789 through 798 removed outlier: 6.172A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 804 through 806 Processing sheet with id= AF, first strand: chain 'B' and resid 1230 through 1233 removed outlier: 7.273A pdb=" N GLY B1171 " --> pdb=" O VAL B1231 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU B1233 " --> pdb=" O GLY B1171 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N CYS B1173 " --> pdb=" O LEU B1233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B1179 " --> pdb=" O ILE B1223 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id= AH, first strand: chain 'B' and resid 583 through 585 removed outlier: 3.752A pdb=" N LEU B 583 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 45 through 51 Processing sheet with id= AJ, first strand: chain 'C' and resid 203 through 207 Processing sheet with id= AK, first strand: chain 'C' and resid 191 through 193 removed outlier: 3.524A pdb=" N ARG C 191 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 270 through 277 Processing sheet with id= AM, first strand: chain 'C' and resid 296 through 298 removed outlier: 6.989A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU C 375 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE C 387 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 377 " --> pdb=" O TYR C 385 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR C 385 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR C 379 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 406 through 408 removed outlier: 6.643A pdb=" N ASN C 445 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL C 281 " --> pdb=" O ASN C 445 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 483 through 488 removed outlier: 3.549A pdb=" N GLY C 715 " --> pdb=" O ALA C 707 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 709 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE C 713 " --> pdb=" O VAL C 709 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 498 through 502 removed outlier: 5.283A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR C 676 " --> pdb=" O LEU C 684 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 548 through 558 Processing sheet with id= AR, first strand: chain 'C' and resid 541 through 543 removed outlier: 6.987A pdb=" N LEU C 603 " --> pdb=" O PHE C 615 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER C 617 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE C 601 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR C 619 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS C 599 " --> pdb=" O TYR C 619 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 762 through 764 Processing sheet with id= AT, first strand: chain 'C' and resid 780 through 786 Processing sheet with id= AU, first strand: chain 'C' and resid 789 through 798 removed outlier: 6.171A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 804 through 806 Processing sheet with id= AW, first strand: chain 'C' and resid 1230 through 1233 removed outlier: 7.273A pdb=" N GLY C1171 " --> pdb=" O VAL C1231 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU C1233 " --> pdb=" O GLY C1171 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N CYS C1173 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'C' and resid 1187 through 1190 Processing sheet with id= AY, first strand: chain 'C' and resid 583 through 585 removed outlier: 3.751A pdb=" N LEU C 583 " --> pdb=" O GLY C 630 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 2916 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: 14.16 Time building geometry restraints manager: 12.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5483 1.32 - 1.45: 8317 1.45 - 1.58: 13386 1.58 - 1.71: 12 1.71 - 1.84: 138 Bond restraints: 27336 Sorted by residual: bond pdb=" C10 PAM B1406 " pdb=" C9 PAM B1406 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.37e+01 bond pdb=" C10 PAM C1406 " pdb=" C9 PAM C1406 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.34e+01 bond pdb=" C10 PAM C1407 " pdb=" C9 PAM C1407 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" C10 PAM A1406 " pdb=" C9 PAM A1406 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.29e+01 bond pdb=" C10 PAM A1407 " pdb=" C9 PAM A1407 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.29e+01 ... (remaining 27331 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.80: 632 105.80 - 112.92: 14334 112.92 - 120.04: 10882 120.04 - 127.16: 11161 127.16 - 134.29: 107 Bond angle restraints: 37116 Sorted by residual: angle pdb=" C CYS C 572 " pdb=" N PRO C 573 " pdb=" CA PRO C 573 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 angle pdb=" C CYS A 572 " pdb=" N PRO A 573 " pdb=" CA PRO A 573 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 angle pdb=" C CYS B 572 " pdb=" N PRO B 573 " pdb=" CA PRO B 573 " ideal model delta sigma weight residual 119.82 127.71 -7.89 9.80e-01 1.04e+00 6.48e+01 angle pdb=" C TYR A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta sigma weight residual 119.56 127.35 -7.79 1.01e+00 9.80e-01 5.94e+01 angle pdb=" C TYR C 606 " pdb=" N PRO C 607 " pdb=" CA PRO C 607 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.01e+00 9.80e-01 5.91e+01 ... (remaining 37111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 16773 21.77 - 43.54: 396 43.54 - 65.32: 162 65.32 - 87.09: 66 87.09 - 108.86: 27 Dihedral angle restraints: 17424 sinusoidal: 7848 harmonic: 9576 Sorted by residual: dihedral pdb=" CB CYS B1173 " pdb=" SG CYS B1173 " pdb=" SG CYS B1226 " pdb=" CB CYS B1226 " ideal model delta sinusoidal sigma weight residual -86.00 -135.35 49.35 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS C1173 " pdb=" SG CYS C1173 " pdb=" SG CYS C1226 " pdb=" CB CYS C1226 " ideal model delta sinusoidal sigma weight residual -86.00 -135.34 49.34 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS A1173 " pdb=" SG CYS A1173 " pdb=" SG CYS A1226 " pdb=" CB CYS A1226 " ideal model delta sinusoidal sigma weight residual -86.00 -135.33 49.33 1 1.00e+01 1.00e-02 3.34e+01 ... (remaining 17421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3180 0.088 - 0.176: 1185 0.176 - 0.263: 231 0.263 - 0.351: 21 0.351 - 0.439: 3 Chirality restraints: 4620 Sorted by residual: chirality pdb=" C1 NAG D 7 " pdb=" O2 MAN D 6 " pdb=" C2 NAG D 7 " pdb=" O5 NAG D 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG N 7 " pdb=" O2 MAN N 6 " pdb=" C2 NAG N 7 " pdb=" O5 NAG N 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 chirality pdb=" C1 NAG X 7 " pdb=" O2 MAN X 6 " pdb=" C2 NAG X 7 " pdb=" O5 NAG X 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 ... (remaining 4617 not shown) Planarity restraints: 4629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG N 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG D 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG X 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " -0.120 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.149 2.00e-02 2.50e+03 ... (remaining 4626 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6537 2.79 - 3.32: 24534 3.32 - 3.84: 44929 3.84 - 4.37: 53149 4.37 - 4.90: 88777 Nonbonded interactions: 217926 Sorted by model distance: nonbonded pdb=" O3 NAG b 1 " pdb=" O7 NAG b 1 " model vdw 2.262 2.440 nonbonded pdb=" O3 NAG R 1 " pdb=" O7 NAG R 1 " model vdw 2.263 2.440 nonbonded pdb=" O3 NAG H 1 " pdb=" O7 NAG H 1 " model vdw 2.263 2.440 nonbonded pdb=" O4 BMA X 3 " pdb=" O2 MAN X 8 " model vdw 2.296 2.440 nonbonded pdb=" O4 BMA D 3 " pdb=" O2 MAN D 8 " model vdw 2.297 2.440 ... (remaining 217921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'R' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.020 Extract box with map and model: 6.460 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 76.330 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.017 0.194 27336 Z= 1.120 Angle : 1.676 14.477 37116 Z= 1.107 Chirality : 0.089 0.439 4620 Planarity : 0.026 0.301 4584 Dihedral : 12.915 108.859 11112 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.61 % Favored : 98.30 % Rotamer: Outliers : 1.26 % Allowed : 1.26 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3177 helix: 0.72 (0.17), residues: 678 sheet: 1.53 (0.18), residues: 705 loop : 0.22 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.005 TRP C 439 HIS 0.007 0.002 HIS B1058 PHE 0.036 0.005 PHE A 185 TYR 0.083 0.008 TYR A 676 ARG 0.008 0.001 ARG C1112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 598 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.6123 (m-80) cc_final: 0.5643 (m-10) REVERT: A 263 SER cc_start: 0.9264 (t) cc_final: 0.9038 (p) REVERT: A 303 ILE cc_start: 0.9195 (pt) cc_final: 0.8951 (pt) REVERT: A 850 SER cc_start: 0.8970 (t) cc_final: 0.8703 (m) REVERT: A 899 ASP cc_start: 0.8453 (t70) cc_final: 0.8071 (t0) REVERT: A 1059 ASN cc_start: 0.8051 (t0) cc_final: 0.7839 (p0) REVERT: A 1104 LYS cc_start: 0.8805 (tptt) cc_final: 0.8574 (mtpt) REVERT: B 397 GLU cc_start: 0.8234 (tt0) cc_final: 0.7767 (tt0) REVERT: B 850 SER cc_start: 0.8968 (t) cc_final: 0.8689 (m) REVERT: B 899 ASP cc_start: 0.8526 (t70) cc_final: 0.8051 (t0) REVERT: B 1059 ASN cc_start: 0.8252 (t0) cc_final: 0.8044 (p0) REVERT: B 1104 LYS cc_start: 0.8626 (tptt) cc_final: 0.8301 (mtpt) REVERT: C 38 LYS cc_start: 0.8017 (mttm) cc_final: 0.7774 (mtpt) REVERT: C 303 ILE cc_start: 0.9223 (pt) cc_final: 0.8924 (pt) REVERT: C 758 LYS cc_start: 0.8244 (pttt) cc_final: 0.8033 (tptt) REVERT: C 850 SER cc_start: 0.8983 (t) cc_final: 0.8585 (m) REVERT: C 899 ASP cc_start: 0.8394 (t70) cc_final: 0.8087 (t0) REVERT: C 1059 ASN cc_start: 0.8085 (t0) cc_final: 0.7797 (p0) REVERT: C 1104 LYS cc_start: 0.8797 (tptt) cc_final: 0.8539 (mtpt) outliers start: 36 outliers final: 14 residues processed: 620 average time/residue: 0.4185 time to fit residues: 403.4701 Evaluate side-chains 277 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 263 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 714 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 190 optimal weight: 0.0670 chunk 296 optimal weight: 0.9980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN B 110 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 GLN B1051 GLN B1061 GLN B1139 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 ASN C 988 GLN C1045 GLN C1051 GLN C1058 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27336 Z= 0.210 Angle : 0.671 11.641 37116 Z= 0.337 Chirality : 0.051 0.675 4620 Planarity : 0.004 0.035 4584 Dihedral : 10.619 94.333 5563 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.54 % Allowed : 7.50 % Favored : 90.96 % 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: 0.76 (0.14), residues: 3177 helix: 1.62 (0.19), residues: 711 sheet: 1.09 (0.19), residues: 705 loop : -0.16 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 168 HIS 0.007 0.001 HIS B 110 PHE 0.024 0.002 PHE A 39 TYR 0.018 0.001 TYR B 227 ARG 0.005 0.001 ARG B 924 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 320 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: A 263 SER cc_start: 0.9155 (t) cc_final: 0.8941 (p) REVERT: A 704 GLU cc_start: 0.7965 (pt0) cc_final: 0.7688 (pt0) REVERT: A 850 SER cc_start: 0.9078 (t) cc_final: 0.8781 (m) REVERT: A 899 ASP cc_start: 0.8360 (t70) cc_final: 0.7845 (t0) REVERT: A 1057 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 397 GLU cc_start: 0.8426 (tt0) cc_final: 0.7911 (tt0) REVERT: B 850 SER cc_start: 0.9202 (t) cc_final: 0.8863 (m) REVERT: B 899 ASP cc_start: 0.8403 (t70) cc_final: 0.7930 (t70) REVERT: B 1051 GLN cc_start: 0.8374 (mm110) cc_final: 0.7786 (mt0) REVERT: B 1104 LYS cc_start: 0.8521 (tptt) cc_final: 0.8250 (mtpt) REVERT: C 303 ILE cc_start: 0.9116 (pt) cc_final: 0.8893 (pt) REVERT: C 372 TYR cc_start: 0.7992 (m-10) cc_final: 0.7755 (m-80) REVERT: C 850 SER cc_start: 0.9116 (t) cc_final: 0.8745 (m) REVERT: C 899 ASP cc_start: 0.8270 (t70) cc_final: 0.7820 (t0) REVERT: C 1104 LYS cc_start: 0.8710 (tptt) cc_final: 0.8454 (mtpt) outliers start: 44 outliers final: 30 residues processed: 352 average time/residue: 0.3605 time to fit residues: 208.7693 Evaluate side-chains 254 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 223 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1229 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1191 THR Chi-restraints excluded: chain C residue 1229 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 297 optimal weight: 4.9990 chunk 321 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS A 356 HIS A 571 ASN A 821 GLN A 979 GLN A 996 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN A1059 ASN A1139 HIS ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN C 110 HIS C 147 ASN C 247 ASN C 270 HIS ** C 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1061 GLN C1139 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 27336 Z= 0.554 Angle : 0.757 9.361 37116 Z= 0.386 Chirality : 0.051 0.323 4620 Planarity : 0.004 0.041 4584 Dihedral : 8.846 66.992 5548 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.83 % Allowed : 8.66 % Favored : 88.52 % 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: 0.02 (0.14), residues: 3177 helix: 1.00 (0.19), residues: 714 sheet: 0.58 (0.18), residues: 765 loop : -0.66 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 259 HIS 0.013 0.002 HIS C1155 PHE 0.025 0.002 PHE A 39 TYR 0.029 0.002 TYR A 652 ARG 0.010 0.001 ARG B1090 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 246 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: A 214 MET cc_start: 0.7714 (tmm) cc_final: 0.6970 (tmm) REVERT: A 899 ASP cc_start: 0.8539 (t70) cc_final: 0.7997 (t0) REVERT: A 1057 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 39 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: B 157 HIS cc_start: 0.3705 (t-90) cc_final: 0.3483 (t70) REVERT: B 850 SER cc_start: 0.9313 (t) cc_final: 0.9044 (m) REVERT: B 899 ASP cc_start: 0.8593 (t70) cc_final: 0.8058 (t0) REVERT: B 984 TYR cc_start: 0.7912 (m-80) cc_final: 0.7422 (t80) REVERT: B 1104 LYS cc_start: 0.8576 (tptt) cc_final: 0.8348 (mtpt) REVERT: C 303 ILE cc_start: 0.9193 (pt) cc_final: 0.8959 (pt) REVERT: C 899 ASP cc_start: 0.8470 (t70) cc_final: 0.8218 (t70) REVERT: C 1051 GLN cc_start: 0.8342 (mm110) cc_final: 0.8117 (mt0) REVERT: C 1061 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8176 (mm-40) REVERT: C 1082 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: C 1104 LYS cc_start: 0.8803 (tptt) cc_final: 0.8518 (mtpt) outliers start: 81 outliers final: 63 residues processed: 315 average time/residue: 0.3661 time to fit residues: 187.4932 Evaluate side-chains 264 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 198 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1229 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Chi-restraints excluded: chain C residue 1229 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 0.7980 chunk 223 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 chunk 316 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 282 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN A 979 GLN A 996 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B 979 GLN B 996 GLN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 ASN C 979 GLN C 996 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27336 Z= 0.156 Angle : 0.533 8.561 37116 Z= 0.273 Chirality : 0.045 0.391 4620 Planarity : 0.003 0.043 4584 Dihedral : 7.038 59.961 5548 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.71 % Allowed : 10.92 % Favored : 87.36 % 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: 0.28 (0.14), residues: 3177 helix: 1.67 (0.19), residues: 723 sheet: 0.59 (0.18), residues: 738 loop : -0.64 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 168 HIS 0.002 0.001 HIS A 338 PHE 0.017 0.001 PHE C1141 TYR 0.013 0.001 TYR C 708 ARG 0.003 0.000 ARG B1085 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 237 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7891 (tmm) cc_final: 0.6942 (tmm) REVERT: A 704 GLU cc_start: 0.7938 (pt0) cc_final: 0.7689 (pt0) REVERT: A 899 ASP cc_start: 0.8316 (t70) cc_final: 0.7845 (t0) REVERT: A 1051 GLN cc_start: 0.8035 (mm110) cc_final: 0.7681 (mt0) REVERT: A 1057 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7817 (tm-30) REVERT: B 111 LYS cc_start: 0.6368 (pttp) cc_final: 0.5881 (tptt) REVERT: B 157 HIS cc_start: 0.3621 (t-90) cc_final: 0.3324 (t70) REVERT: B 214 MET cc_start: 0.7356 (ttp) cc_final: 0.7032 (ttp) REVERT: B 640 ASP cc_start: 0.7317 (p0) cc_final: 0.7094 (p0) REVERT: B 850 SER cc_start: 0.9301 (t) cc_final: 0.9034 (m) REVERT: B 899 ASP cc_start: 0.8322 (t70) cc_final: 0.7777 (t0) REVERT: B 984 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7305 (t80) REVERT: B 1051 GLN cc_start: 0.8208 (mm110) cc_final: 0.7818 (mt0) REVERT: C 303 ILE cc_start: 0.9115 (pt) cc_final: 0.8863 (pt) REVERT: C 397 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: C 899 ASP cc_start: 0.8174 (t70) cc_final: 0.7695 (t0) REVERT: C 1104 LYS cc_start: 0.8716 (tptt) cc_final: 0.8498 (mtpt) outliers start: 49 outliers final: 34 residues processed: 277 average time/residue: 0.3759 time to fit residues: 170.6673 Evaluate side-chains 244 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 208 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1010 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 235 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 283 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 257 ASN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 ASN B 187 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN C 270 HIS C 571 ASN C 860 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 27336 Z= 0.486 Angle : 0.672 8.441 37116 Z= 0.343 Chirality : 0.049 0.319 4620 Planarity : 0.004 0.044 4584 Dihedral : 7.197 59.879 5544 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.79 % Allowed : 10.61 % Favored : 86.60 % 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: -0.22 (0.14), residues: 3177 helix: 1.15 (0.19), residues: 708 sheet: 0.34 (0.19), residues: 714 loop : -0.90 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 259 HIS 0.010 0.001 HIS C1155 PHE 0.022 0.002 PHE C 39 TYR 0.023 0.002 TYR A 652 ARG 0.008 0.001 ARG C1090 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 216 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8066 (tmm) cc_final: 0.6969 (tmm) REVERT: A 899 ASP cc_start: 0.8566 (t70) cc_final: 0.7993 (t0) REVERT: A 1057 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 38 LYS cc_start: 0.8111 (mttm) cc_final: 0.7493 (mttm) REVERT: B 111 LYS cc_start: 0.6165 (pttp) cc_final: 0.5759 (pttm) REVERT: B 214 MET cc_start: 0.7423 (ttp) cc_final: 0.7026 (ttp) REVERT: B 899 ASP cc_start: 0.8496 (t70) cc_final: 0.7955 (t0) REVERT: B 984 TYR cc_start: 0.7864 (m-80) cc_final: 0.7380 (t80) REVERT: C 111 LYS cc_start: 0.6311 (pttp) cc_final: 0.6028 (pttm) REVERT: C 303 ILE cc_start: 0.9131 (pt) cc_final: 0.8870 (pt) REVERT: C 1082 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: C 1104 LYS cc_start: 0.8768 (tptt) cc_final: 0.8530 (mtpt) outliers start: 80 outliers final: 65 residues processed: 280 average time/residue: 0.3842 time to fit residues: 174.4616 Evaluate side-chains 269 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 203 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1229 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Chi-restraints excluded: chain C residue 1229 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 1.9990 chunk 284 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 262 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 GLN A 996 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27336 Z= 0.165 Angle : 0.511 9.506 37116 Z= 0.262 Chirality : 0.044 0.307 4620 Planarity : 0.003 0.047 4584 Dihedral : 6.536 59.292 5544 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.02 % Allowed : 11.45 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3177 helix: 1.68 (0.19), residues: 726 sheet: 0.47 (0.19), residues: 708 loop : -0.87 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.003 0.001 HIS A 338 PHE 0.018 0.001 PHE A1141 TYR 0.011 0.001 TYR C 407 ARG 0.002 0.000 ARG B 894 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 228 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7938 (tmm) cc_final: 0.6894 (tmm) REVERT: A 704 GLU cc_start: 0.7910 (pt0) cc_final: 0.7671 (pt0) REVERT: A 899 ASP cc_start: 0.8307 (t70) cc_final: 0.7917 (t0) REVERT: A 1057 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 38 LYS cc_start: 0.8031 (mttm) cc_final: 0.7451 (mttm) REVERT: B 111 LYS cc_start: 0.5905 (pttp) cc_final: 0.5528 (pttm) REVERT: B 214 MET cc_start: 0.7356 (ttp) cc_final: 0.7024 (ttp) REVERT: B 443 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8466 (p) REVERT: B 899 ASP cc_start: 0.8212 (t70) cc_final: 0.7820 (t0) REVERT: B 984 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7301 (t80) REVERT: B 1051 GLN cc_start: 0.8085 (mm110) cc_final: 0.7737 (mt0) REVERT: B 1124 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9145 (mtpp) REVERT: C 111 LYS cc_start: 0.6115 (pttp) cc_final: 0.5873 (pttm) REVERT: C 303 ILE cc_start: 0.9054 (pt) cc_final: 0.8802 (pt) REVERT: C 1104 LYS cc_start: 0.8701 (tptt) cc_final: 0.8489 (mtpt) outliers start: 58 outliers final: 48 residues processed: 274 average time/residue: 0.3771 time to fit residues: 167.4637 Evaluate side-chains 264 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 213 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 315 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 257 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 27336 Z= 0.339 Angle : 0.588 9.659 37116 Z= 0.300 Chirality : 0.046 0.300 4620 Planarity : 0.004 0.042 4584 Dihedral : 6.672 59.997 5544 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.41 % Allowed : 11.80 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3177 helix: 1.39 (0.19), residues: 726 sheet: 0.37 (0.19), residues: 720 loop : -0.96 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 168 HIS 0.007 0.001 HIS C1155 PHE 0.020 0.002 PHE B1141 TYR 0.017 0.002 TYR A 652 ARG 0.005 0.000 ARG B1090 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 217 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8058 (tmm) cc_final: 0.6910 (tmm) REVERT: A 443 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8434 (p) REVERT: A 899 ASP cc_start: 0.8519 (t70) cc_final: 0.7929 (t0) REVERT: A 1057 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8143 (tm-30) REVERT: B 38 LYS cc_start: 0.8035 (mttm) cc_final: 0.7478 (mttm) REVERT: B 111 LYS cc_start: 0.5663 (pttp) cc_final: 0.5463 (pttm) REVERT: B 214 MET cc_start: 0.7451 (ttp) cc_final: 0.7078 (ttp) REVERT: B 443 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8543 (p) REVERT: B 899 ASP cc_start: 0.8461 (t70) cc_final: 0.7965 (t0) REVERT: B 984 TYR cc_start: 0.7792 (m-80) cc_final: 0.7346 (t80) REVERT: B 1051 GLN cc_start: 0.8196 (mm110) cc_final: 0.7852 (mt0) REVERT: B 1124 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9149 (mtpp) REVERT: C 111 LYS cc_start: 0.6119 (pttp) cc_final: 0.5856 (pttm) REVERT: C 303 ILE cc_start: 0.9049 (pt) cc_final: 0.8766 (pt) REVERT: C 443 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8639 (t) REVERT: C 1104 LYS cc_start: 0.8745 (tptt) cc_final: 0.8533 (mtpt) outliers start: 69 outliers final: 56 residues processed: 271 average time/residue: 0.3725 time to fit residues: 164.7742 Evaluate side-chains 266 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 206 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 214 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27336 Z= 0.151 Angle : 0.494 9.156 37116 Z= 0.253 Chirality : 0.043 0.303 4620 Planarity : 0.003 0.046 4584 Dihedral : 6.195 58.705 5544 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.88 % Allowed : 12.32 % Favored : 85.79 % 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: 0.11 (0.15), residues: 3177 helix: 1.82 (0.20), residues: 726 sheet: 0.45 (0.19), residues: 717 loop : -0.87 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 168 HIS 0.003 0.000 HIS C 157 PHE 0.017 0.001 PHE B1141 TYR 0.009 0.001 TYR C 227 ARG 0.004 0.000 ARG B 793 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 233 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8066 (tmm) cc_final: 0.7140 (tmm) REVERT: A 443 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8326 (p) REVERT: A 899 ASP cc_start: 0.8156 (t70) cc_final: 0.7932 (t0) REVERT: A 1057 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 38 LYS cc_start: 0.8062 (mttm) cc_final: 0.7512 (mttm) REVERT: B 443 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 581 ASP cc_start: 0.8318 (t0) cc_final: 0.7865 (t0) REVERT: B 899 ASP cc_start: 0.8193 (t70) cc_final: 0.7857 (t0) REVERT: B 984 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7273 (t80) REVERT: B 1051 GLN cc_start: 0.8065 (mm110) cc_final: 0.7808 (mt0) REVERT: C 111 LYS cc_start: 0.5786 (pttp) cc_final: 0.5552 (pttm) REVERT: C 214 MET cc_start: 0.7722 (tmm) cc_final: 0.7311 (tmm) REVERT: C 303 ILE cc_start: 0.9014 (pt) cc_final: 0.8789 (pt) REVERT: C 397 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: C 1071 TYR cc_start: 0.8919 (m-80) cc_final: 0.8393 (m-80) outliers start: 54 outliers final: 43 residues processed: 277 average time/residue: 0.3840 time to fit residues: 172.7406 Evaluate side-chains 270 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 223 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 10.0000 chunk 275 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 176 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 277 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 27336 Z= 0.287 Angle : 0.556 12.101 37116 Z= 0.284 Chirality : 0.045 0.349 4620 Planarity : 0.003 0.038 4584 Dihedral : 6.337 57.703 5544 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.16 % Allowed : 12.39 % Favored : 85.45 % 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: 3177 helix: 1.58 (0.20), residues: 729 sheet: 0.44 (0.19), residues: 735 loop : -0.94 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 168 HIS 0.006 0.001 HIS C1155 PHE 0.024 0.001 PHE C 176 TYR 0.014 0.001 TYR A 652 ARG 0.004 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 222 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8070 (tmm) cc_final: 0.7139 (tmm) REVERT: A 443 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8390 (p) REVERT: A 899 ASP cc_start: 0.8461 (t70) cc_final: 0.7925 (t0) REVERT: A 1057 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 38 LYS cc_start: 0.8031 (mttm) cc_final: 0.7467 (mttm) REVERT: B 443 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8507 (p) REVERT: B 790 MET cc_start: 0.8486 (mtt) cc_final: 0.8264 (mtt) REVERT: B 899 ASP cc_start: 0.8466 (t70) cc_final: 0.8111 (t0) REVERT: B 984 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7329 (t80) REVERT: B 1051 GLN cc_start: 0.8112 (mm110) cc_final: 0.7818 (mt0) REVERT: C 111 LYS cc_start: 0.6044 (pttp) cc_final: 0.5802 (pttm) REVERT: C 303 ILE cc_start: 0.9049 (pt) cc_final: 0.8779 (pt) REVERT: C 443 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8591 (t) REVERT: C 899 ASP cc_start: 0.8149 (t0) cc_final: 0.7904 (t0) outliers start: 62 outliers final: 53 residues processed: 268 average time/residue: 0.3900 time to fit residues: 170.9231 Evaluate side-chains 272 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 215 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 325 optimal weight: 0.0470 chunk 299 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 27336 Z= 0.276 Angle : 0.546 11.144 37116 Z= 0.279 Chirality : 0.045 0.354 4620 Planarity : 0.003 0.045 4584 Dihedral : 6.436 59.882 5544 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.88 % Allowed : 12.64 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3177 helix: 1.53 (0.19), residues: 729 sheet: 0.41 (0.19), residues: 735 loop : -0.95 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 168 HIS 0.005 0.001 HIS C1155 PHE 0.017 0.001 PHE A 176 TYR 0.013 0.001 TYR B 407 ARG 0.004 0.000 ARG B1090 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 219 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8091 (tmm) cc_final: 0.7144 (tmm) REVERT: A 443 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8408 (p) REVERT: B 38 LYS cc_start: 0.8025 (mttm) cc_final: 0.7473 (mttm) REVERT: B 443 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8513 (p) REVERT: B 790 MET cc_start: 0.8474 (mtt) cc_final: 0.8247 (mtt) REVERT: B 899 ASP cc_start: 0.8420 (t70) cc_final: 0.7913 (t0) REVERT: B 984 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.7313 (t80) REVERT: B 1051 GLN cc_start: 0.8056 (mm110) cc_final: 0.7806 (mt0) REVERT: C 111 LYS cc_start: 0.5969 (pttp) cc_final: 0.5721 (pttm) REVERT: C 303 ILE cc_start: 0.8996 (pt) cc_final: 0.8716 (pt) REVERT: C 443 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8567 (t) outliers start: 54 outliers final: 49 residues processed: 261 average time/residue: 0.3833 time to fit residues: 162.7927 Evaluate side-chains 268 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 215 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 259 optimal weight: 7.9990 chunk 108 optimal weight: 0.0470 chunk 266 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101914 restraints weight = 36725.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.104105 restraints weight = 24806.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.105516 restraints weight = 19355.888| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 27336 Z= 0.158 Angle : 0.498 11.205 37116 Z= 0.255 Chirality : 0.043 0.340 4620 Planarity : 0.003 0.043 4584 Dihedral : 6.081 57.539 5544 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.71 % Allowed : 13.02 % Favored : 85.27 % 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: 0.15 (0.15), residues: 3177 helix: 1.82 (0.20), residues: 729 sheet: 0.51 (0.19), residues: 735 loop : -0.86 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 168 HIS 0.002 0.001 HIS A 338 PHE 0.018 0.001 PHE B 35 TYR 0.010 0.001 TYR A 403 ARG 0.002 0.000 ARG B1090 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4845.55 seconds wall clock time: 90 minutes 38.13 seconds (5438.13 seconds total)