Starting phenix.real_space_refine on Tue Feb 20 02:23:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df3_30660/02_2024/7df3_30660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df3_30660/02_2024/7df3_30660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df3_30660/02_2024/7df3_30660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df3_30660/02_2024/7df3_30660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df3_30660/02_2024/7df3_30660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df3_30660/02_2024/7df3_30660.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 16884 2.51 5 N 4341 2.21 5 O 5250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26595 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "B" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "C" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8501 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.00, per 1000 atoms: 0.49 Number of scatterers: 26595 At special positions: 0 Unit cell: (145.86, 147.9, 174.42, 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 120 16.00 O 5250 8.00 N 4341 7.00 C 16884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 61 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 61 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 149 " " NAG C1310 " - " ASN C 61 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 165 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 17 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 17 " " NAG T 1 " - " ASN C1134 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 165 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 17 " Time building additional restraints: 11.42 Conformation dependent library (CDL) restraints added in 4.8 seconds 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 51 sheets defined 23.3% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.641A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.570A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 836 through 843 removed outlier: 3.713A pdb=" N ASP A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.503A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.769A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.645A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.740A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.640A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.569A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.713A pdb=" N ASP B 843 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.502A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.769A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.644A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1031 removed outlier: 3.740A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.640A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.664A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.569A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 836 through 843 removed outlier: 3.714A pdb=" N ASP C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.502A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.769A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.645A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 3.740A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.679A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.503A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.271A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.654A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.260A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.662A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.831A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.169A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.189A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 807 through 808 removed outlier: 3.917A pdb=" N ARG A 815 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.679A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.502A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.271A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 157 removed outlier: 3.654A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.260A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.663A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.776A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.168A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 807 through 808 removed outlier: 3.917A pdb=" N ARG B 815 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.678A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.503A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.271A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.654A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.261A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.663A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.168A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 807 through 808 removed outlier: 3.917A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 959 hydrogen bonds defined for protein. 2616 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: 12.46 Time building geometry restraints manager: 12.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8428 1.34 - 1.46: 6524 1.46 - 1.58: 12075 1.58 - 1.70: 3 1.70 - 1.82: 150 Bond restraints: 27180 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" C2 NAG R 1 " ideal model delta sigma weight residual 1.532 1.630 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG Z 1 " pdb=" C2 NAG Z 1 " ideal model delta sigma weight residual 1.532 1.630 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG J 1 " pdb=" C2 NAG J 1 " ideal model delta sigma weight residual 1.532 1.630 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.236 0.098 2.34e-02 1.83e+03 1.75e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.236 0.098 2.34e-02 1.83e+03 1.75e+01 ... (remaining 27175 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 795 106.88 - 113.66: 15388 113.66 - 120.44: 9827 120.44 - 127.22: 10737 127.22 - 134.00: 228 Bond angle restraints: 36975 Sorted by residual: angle pdb=" N ASN C 234 " pdb=" CA ASN C 234 " pdb=" C ASN C 234 " ideal model delta sigma weight residual 109.59 102.06 7.53 1.61e+00 3.86e-01 2.19e+01 angle pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" C ASN A 234 " ideal model delta sigma weight residual 109.59 102.07 7.52 1.61e+00 3.86e-01 2.18e+01 angle pdb=" N ASN B 234 " pdb=" CA ASN B 234 " pdb=" C ASN B 234 " ideal model delta sigma weight residual 109.59 102.07 7.52 1.61e+00 3.86e-01 2.18e+01 angle pdb=" C6 NAG T 2 " pdb=" C5 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 108.73 120.40 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C6 NAG D 2 " pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 108.73 120.40 -11.67 3.00e+00 1.11e-01 1.51e+01 ... (remaining 36970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16710 17.99 - 35.97: 339 35.97 - 53.96: 120 53.96 - 71.94: 27 71.94 - 89.93: 12 Dihedral angle restraints: 17208 sinusoidal: 7710 harmonic: 9498 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 17205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 4352 0.208 - 0.415: 40 0.415 - 0.623: 6 0.623 - 0.830: 0 0.830 - 1.038: 6 Chirality restraints: 4404 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.59e+01 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.49e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.42e+01 ... (remaining 4401 not shown) Planarity restraints: 4749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG A1304 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.503 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG C1304 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " 0.337 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B1304 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.178 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " 0.072 2.00e-02 2.50e+03 ... (remaining 4746 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 393 2.63 - 3.20: 24649 3.20 - 3.77: 42776 3.77 - 4.33: 60723 4.33 - 4.90: 97866 Nonbonded interactions: 226407 Sorted by model distance: nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.067 2.440 nonbonded pdb=" O3 NAG M 2 " pdb=" O7 NAG M 2 " model vdw 2.067 2.440 nonbonded pdb=" O3 NAG U 2 " pdb=" O7 NAG U 2 " model vdw 2.067 2.440 nonbonded pdb=" O3 NAG B1301 " pdb=" O7 NAG B1301 " model vdw 2.094 2.440 nonbonded pdb=" O3 NAG C1301 " pdb=" O7 NAG C1301 " model vdw 2.094 2.440 ... (remaining 226402 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 8.160 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 72.830 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 27180 Z= 0.299 Angle : 0.697 11.672 36975 Z= 0.358 Chirality : 0.069 1.038 4404 Planarity : 0.016 0.287 4695 Dihedral : 8.697 89.926 10974 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.12), residues: 3234 helix: -2.80 (0.13), residues: 729 sheet: -0.73 (0.18), residues: 570 loop : -1.30 (0.12), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 64 HIS 0.011 0.001 HIS C1048 PHE 0.023 0.002 PHE B 275 TYR 0.025 0.002 TYR A 508 ARG 0.004 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 832 time to evaluate : 2.667 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: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 772 VAL cc_start: 0.8657 (t) cc_final: 0.8395 (p) REVERT: A 955 ASN cc_start: 0.7620 (m-40) cc_final: 0.7418 (m-40) REVERT: B 88 ASP cc_start: 0.6566 (m-30) cc_final: 0.6326 (m-30) REVERT: B 111 ASP cc_start: 0.5447 (t0) cc_final: 0.5177 (t0) REVERT: B 271 GLN cc_start: 0.8219 (mt0) cc_final: 0.7986 (mt0) REVERT: B 309 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6350 (mp0) REVERT: B 772 VAL cc_start: 0.8848 (t) cc_final: 0.8594 (p) REVERT: B 1141 LEU cc_start: 0.7917 (tp) cc_final: 0.7696 (mt) REVERT: C 309 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6792 (mp0) REVERT: C 1101 HIS cc_start: 0.7172 (m90) cc_final: 0.6941 (m170) REVERT: C 1141 LEU cc_start: 0.7828 (tp) cc_final: 0.7624 (mt) outliers start: 0 outliers final: 3 residues processed: 832 average time/residue: 1.2296 time to fit residues: 1202.9818 Evaluate side-chains 416 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 413 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 294 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 253 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 154 optimal weight: 0.0980 chunk 189 optimal weight: 0.5980 chunk 294 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 137 ASN A 185 ASN A 196 ASN A 317 ASN A 474 GLN A 487 ASN A 580 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 969 ASN A1010 GLN A1119 ASN A1135 ASN B 99 ASN B 115 GLN B 137 ASN B 487 ASN B 493 GLN B 641 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 784 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 969 ASN B1010 GLN B1119 ASN B1135 ASN C 99 ASN C 115 GLN C 137 ASN C 173 GLN C 185 ASN C 487 ASN C 675 GLN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1083 HIS C1119 ASN C1135 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27180 Z= 0.238 Angle : 0.665 8.398 36975 Z= 0.340 Chirality : 0.047 0.240 4404 Planarity : 0.005 0.050 4695 Dihedral : 7.238 59.627 5145 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.40 % Favored : 96.44 % Rotamer: Outliers : 3.73 % Allowed : 11.69 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 3234 helix: -0.69 (0.17), residues: 726 sheet: -0.50 (0.17), residues: 693 loop : -1.17 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 64 HIS 0.005 0.001 HIS A1048 PHE 0.023 0.002 PHE A 759 TYR 0.029 0.002 TYR B 200 ARG 0.009 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 422 time to evaluate : 2.860 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: symmetry clash REVERT: A 378 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7834 (tptp) REVERT: A 493 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 935 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6340 (mp10) REVERT: A 957 GLN cc_start: 0.8029 (tt0) cc_final: 0.7810 (tt0) REVERT: A 1086 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7693 (ptmt) REVERT: B 88 ASP cc_start: 0.6715 (m-30) cc_final: 0.6468 (m-30) REVERT: B 101 ILE cc_start: 0.7972 (mm) cc_final: 0.7723 (mp) REVERT: B 111 ASP cc_start: 0.5570 (t0) cc_final: 0.5336 (t0) REVERT: B 113 LYS cc_start: 0.7441 (mttt) cc_final: 0.6596 (mmpt) REVERT: B 309 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6972 (mp0) REVERT: B 326 ILE cc_start: 0.7640 (mm) cc_final: 0.7208 (pt) REVERT: B 378 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7934 (tptp) REVERT: B 487 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7450 (t0) REVERT: B 947 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7797 (mtmm) REVERT: B 954 GLN cc_start: 0.7861 (mt0) cc_final: 0.7431 (pt0) REVERT: B 1086 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7886 (ptmt) REVERT: C 309 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7115 (mm-30) REVERT: C 389 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: C 408 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.6332 (ptt90) REVERT: C 444 LYS cc_start: 0.6655 (pttt) cc_final: 0.6242 (ptpt) REVERT: C 505 TYR cc_start: 0.7318 (t80) cc_final: 0.7095 (m-80) REVERT: C 572 THR cc_start: 0.8513 (p) cc_final: 0.8112 (t) REVERT: C 646 ARG cc_start: 0.7534 (mtp180) cc_final: 0.7135 (ttp-170) REVERT: C 765 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8085 (ttp-110) REVERT: C 935 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6227 (mp10) REVERT: C 1086 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7915 (ptmt) outliers start: 106 outliers final: 23 residues processed: 496 average time/residue: 1.2771 time to fit residues: 747.7501 Evaluate side-chains 385 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 349 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 294 optimal weight: 0.0070 chunk 318 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 675 GLN A 762 GLN A 774 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 926 GLN A 955 ASN A1119 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 613 GLN C 675 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27180 Z= 0.256 Angle : 0.647 10.055 36975 Z= 0.334 Chirality : 0.049 0.618 4404 Planarity : 0.004 0.042 4695 Dihedral : 7.126 59.847 5139 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.99 % Favored : 95.83 % Rotamer: Outliers : 4.19 % Allowed : 12.32 % Favored : 83.49 % Cbeta Deviations : 0.03 % 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: -0.96 (0.13), residues: 3234 helix: 0.10 (0.18), residues: 714 sheet: -0.34 (0.18), residues: 651 loop : -1.03 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 64 HIS 0.006 0.002 HIS A1064 PHE 0.026 0.002 PHE B 643 TYR 0.029 0.002 TYR B 200 ARG 0.005 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 363 time to evaluate : 2.940 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: symmetry clash REVERT: A 113 LYS cc_start: 0.7737 (mttt) cc_final: 0.6960 (mmpt) REVERT: A 326 ILE cc_start: 0.7692 (mm) cc_final: 0.7369 (pt) REVERT: A 493 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: A 868 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: A 935 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6447 (mp10) REVERT: A 1086 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7808 (ptmt) REVERT: B 111 ASP cc_start: 0.5913 (t0) cc_final: 0.5664 (t0) REVERT: B 113 LYS cc_start: 0.7659 (mttt) cc_final: 0.6716 (mmpt) REVERT: B 309 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6957 (mp0) REVERT: B 378 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7784 (tptp) REVERT: B 487 ASN cc_start: 0.8161 (m-40) cc_final: 0.7613 (t0) REVERT: B 947 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7863 (mtmm) REVERT: B 1086 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7897 (ptmt) REVERT: C 113 LYS cc_start: 0.7672 (mttt) cc_final: 0.6901 (mmpt) REVERT: C 408 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.6236 (ptt90) REVERT: C 505 TYR cc_start: 0.7383 (t80) cc_final: 0.7156 (m-80) REVERT: C 569 ILE cc_start: 0.8124 (tp) cc_final: 0.7882 (pp) REVERT: C 572 THR cc_start: 0.8576 (p) cc_final: 0.8195 (t) REVERT: C 646 ARG cc_start: 0.7546 (mtp180) cc_final: 0.7201 (ttp-110) REVERT: C 935 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6548 (mp10) REVERT: C 1072 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7447 (pm20) REVERT: C 1086 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7930 (ptmt) outliers start: 119 outliers final: 44 residues processed: 448 average time/residue: 1.2577 time to fit residues: 666.9011 Evaluate side-chains 368 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 313 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 313 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 137 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 394 ASN A 613 GLN A 644 GLN A 675 GLN A 764 ASN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 955 ASN A1119 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 675 GLN B 784 GLN B 872 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B 957 GLN C 137 ASN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 784 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 27180 Z= 0.409 Angle : 0.722 9.575 36975 Z= 0.373 Chirality : 0.052 0.766 4404 Planarity : 0.005 0.043 4695 Dihedral : 7.368 59.312 5139 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.95 % Favored : 94.93 % Rotamer: Outliers : 4.36 % Allowed : 13.38 % Favored : 82.26 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.97 (0.13), residues: 3234 helix: 0.22 (0.19), residues: 720 sheet: -0.59 (0.17), residues: 699 loop : -0.99 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 64 HIS 0.008 0.002 HIS A1064 PHE 0.036 0.003 PHE C 906 TYR 0.033 0.002 TYR B 200 ARG 0.007 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 354 time to evaluate : 3.112 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 113 LYS cc_start: 0.7960 (mttt) cc_final: 0.7715 (mtmm) REVERT: A 370 ASN cc_start: 0.7093 (m-40) cc_final: 0.6802 (m-40) REVERT: A 554 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: A 935 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6494 (mp10) REVERT: A 1002 GLN cc_start: 0.7858 (pp30) cc_final: 0.7610 (pt0) REVERT: A 1086 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7875 (ptmt) REVERT: B 111 ASP cc_start: 0.6325 (t0) cc_final: 0.6092 (t70) REVERT: B 113 LYS cc_start: 0.7914 (mttt) cc_final: 0.6950 (mmpt) REVERT: B 408 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.6751 (ptt90) REVERT: B 487 ASN cc_start: 0.8202 (m-40) cc_final: 0.7697 (t0) REVERT: B 572 THR cc_start: 0.8590 (p) cc_final: 0.8235 (t) REVERT: B 814 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6616 (mttp) REVERT: B 1086 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7991 (ptmt) REVERT: C 408 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.6309 (ptt90) REVERT: C 444 LYS cc_start: 0.6774 (pttt) cc_final: 0.6425 (ptpt) REVERT: C 487 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7397 (t0) REVERT: C 572 THR cc_start: 0.8608 (p) cc_final: 0.8314 (t) REVERT: C 646 ARG cc_start: 0.7613 (mtp180) cc_final: 0.7259 (ttp-170) REVERT: C 1038 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8194 (mptt) REVERT: C 1072 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: C 1086 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8003 (ptmt) REVERT: C 1101 HIS cc_start: 0.7314 (m90) cc_final: 0.6994 (m170) outliers start: 124 outliers final: 51 residues processed: 439 average time/residue: 1.3781 time to fit residues: 704.1548 Evaluate side-chains 375 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 313 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 216 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 146 HIS A 196 ASN A 207 HIS A 487 ASN A 580 GLN A 675 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 675 GLN B 872 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 954 GLN B 957 GLN C 137 ASN C 164 ASN C 173 GLN C 245 HIS C 394 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27180 Z= 0.269 Angle : 0.629 9.506 36975 Z= 0.327 Chirality : 0.048 0.683 4404 Planarity : 0.004 0.044 4695 Dihedral : 7.022 53.631 5139 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.30 % Favored : 95.58 % Rotamer: Outliers : 4.29 % Allowed : 14.15 % Favored : 81.56 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.13), residues: 3234 helix: 0.42 (0.19), residues: 717 sheet: -0.70 (0.18), residues: 648 loop : -0.91 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 64 HIS 0.005 0.001 HIS C 66 PHE 0.029 0.002 PHE B 643 TYR 0.019 0.002 TYR B 28 ARG 0.006 0.001 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 342 time to evaluate : 3.238 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: symmetry clash REVERT: A 132 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: A 370 ASN cc_start: 0.7084 (m-40) cc_final: 0.6789 (m-40) REVERT: A 461 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7555 (pp) REVERT: A 487 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7573 (t0) REVERT: A 554 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: A 814 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6746 (mptp) REVERT: A 935 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6466 (mp10) REVERT: A 1002 GLN cc_start: 0.7708 (pp30) cc_final: 0.7454 (pt0) REVERT: A 1086 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7864 (ptmt) REVERT: B 113 LYS cc_start: 0.7871 (mttt) cc_final: 0.6987 (mmpt) REVERT: B 153 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.5336 (ppp) REVERT: B 202 LYS cc_start: 0.8197 (mttt) cc_final: 0.7796 (mtpt) REVERT: B 231 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7967 (pp) REVERT: B 408 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.6793 (ppt90) REVERT: B 487 ASN cc_start: 0.8180 (m-40) cc_final: 0.7667 (t0) REVERT: B 572 THR cc_start: 0.8576 (p) cc_final: 0.8222 (t) REVERT: B 814 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6614 (mttp) REVERT: B 1086 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7936 (ptmt) REVERT: B 1113 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: C 111 ASP cc_start: 0.6276 (t0) cc_final: 0.6036 (t0) REVERT: C 408 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.6248 (ptt90) REVERT: C 444 LYS cc_start: 0.6780 (pttt) cc_final: 0.6438 (ptpt) REVERT: C 572 THR cc_start: 0.8623 (p) cc_final: 0.8334 (t) REVERT: C 646 ARG cc_start: 0.7600 (mtp180) cc_final: 0.7262 (ttp-170) REVERT: C 1038 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8171 (mptt) REVERT: C 1101 HIS cc_start: 0.7207 (m90) cc_final: 0.6906 (m170) REVERT: C 1113 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7842 (mt0) outliers start: 122 outliers final: 48 residues processed: 423 average time/residue: 1.4198 time to fit residues: 700.6744 Evaluate side-chains 364 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 300 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.7980 chunk 282 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 260 optimal weight: 0.0970 chunk 145 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 675 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 580 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 954 GLN B 957 GLN C 137 ASN C 146 HIS C 440 ASN C 487 ASN C 644 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 957 GLN C1119 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27180 Z= 0.246 Angle : 0.609 8.934 36975 Z= 0.316 Chirality : 0.048 0.792 4404 Planarity : 0.004 0.046 4695 Dihedral : 6.821 51.955 5139 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.17 % Favored : 95.61 % Rotamer: Outliers : 4.29 % Allowed : 14.54 % Favored : 81.17 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3234 helix: 0.58 (0.19), residues: 717 sheet: -0.41 (0.18), residues: 591 loop : -0.96 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.006 0.001 HIS A1101 PHE 0.030 0.002 PHE B 643 TYR 0.018 0.002 TYR B 28 ARG 0.010 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 324 time to evaluate : 2.949 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: symmetry clash revert: symmetry clash REVERT: A 370 ASN cc_start: 0.7109 (m-40) cc_final: 0.6837 (m-40) REVERT: A 461 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7610 (pp) REVERT: A 487 ASN cc_start: 0.8065 (t0) cc_final: 0.7725 (t0) REVERT: A 516 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6370 (tm-30) REVERT: B 113 LYS cc_start: 0.7892 (mttt) cc_final: 0.7007 (mmpt) REVERT: B 231 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7914 (pp) REVERT: B 408 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.6795 (ppt90) REVERT: B 487 ASN cc_start: 0.8171 (m-40) cc_final: 0.7671 (t0) REVERT: B 572 THR cc_start: 0.8601 (p) cc_final: 0.8259 (t) REVERT: B 814 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6605 (mttp) REVERT: B 922 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8473 (tp) REVERT: B 947 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7975 (mtmm) REVERT: B 973 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8252 (tp) REVERT: B 1113 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: C 408 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.6246 (ptt90) REVERT: C 444 LYS cc_start: 0.6734 (pttt) cc_final: 0.6400 (ptpt) REVERT: C 516 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: C 569 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7788 (pp) REVERT: C 572 THR cc_start: 0.8601 (p) cc_final: 0.8328 (t) REVERT: C 646 ARG cc_start: 0.7574 (mtp180) cc_final: 0.7361 (mtm-85) REVERT: C 660 TYR cc_start: 0.8660 (m-10) cc_final: 0.8110 (m-10) REVERT: C 1038 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8208 (mptt) REVERT: C 1086 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7940 (ptmt) REVERT: C 1101 HIS cc_start: 0.7267 (m90) cc_final: 0.6961 (m170) REVERT: C 1113 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7799 (mt0) outliers start: 122 outliers final: 57 residues processed: 405 average time/residue: 1.3125 time to fit residues: 623.6211 Evaluate side-chains 368 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 296 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 675 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN B 137 ASN B 675 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B 957 GLN C 137 ASN C 487 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27180 Z= 0.273 Angle : 0.622 9.843 36975 Z= 0.322 Chirality : 0.048 0.747 4404 Planarity : 0.004 0.043 4695 Dihedral : 6.801 51.776 5139 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.27 % Favored : 95.49 % Rotamer: Outliers : 4.15 % Allowed : 14.99 % Favored : 80.85 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3234 helix: 0.59 (0.19), residues: 717 sheet: -0.56 (0.18), residues: 588 loop : -0.87 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.007 0.002 HIS A1101 PHE 0.032 0.002 PHE B 643 TYR 0.018 0.002 TYR B 28 ARG 0.009 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 322 time to evaluate : 3.263 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: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6163 (pmt) REVERT: A 370 ASN cc_start: 0.7119 (m-40) cc_final: 0.6882 (m-40) REVERT: A 461 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7716 (pp) REVERT: A 487 ASN cc_start: 0.8017 (t0) cc_final: 0.7611 (t0) REVERT: A 1086 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7772 (ptmt) REVERT: B 113 LYS cc_start: 0.8018 (mttt) cc_final: 0.7097 (mmpt) REVERT: B 231 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7912 (pp) REVERT: B 408 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.6778 (ppt90) REVERT: B 487 ASN cc_start: 0.8275 (m-40) cc_final: 0.7763 (t0) REVERT: B 572 THR cc_start: 0.8597 (p) cc_final: 0.8287 (t) REVERT: B 814 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6586 (mttp) REVERT: B 922 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8473 (tp) REVERT: B 947 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7976 (mtmm) REVERT: B 973 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8274 (tp) REVERT: B 1086 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7962 (ptmt) REVERT: B 1113 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: C 153 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.5162 (pmt) REVERT: C 408 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.6242 (ptt90) REVERT: C 444 LYS cc_start: 0.6778 (pttt) cc_final: 0.6432 (ptpt) REVERT: C 461 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7637 (pp) REVERT: C 516 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: C 569 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7823 (pp) REVERT: C 572 THR cc_start: 0.8624 (p) cc_final: 0.8351 (t) REVERT: C 646 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7362 (mtm-85) REVERT: C 979 ASP cc_start: 0.7628 (t0) cc_final: 0.7387 (m-30) REVERT: C 1038 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8245 (mptt) REVERT: C 1086 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7918 (ptmt) REVERT: C 1101 HIS cc_start: 0.7291 (m90) cc_final: 0.6974 (m170) REVERT: C 1113 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7793 (mt0) outliers start: 118 outliers final: 54 residues processed: 403 average time/residue: 1.3144 time to fit residues: 622.7495 Evaluate side-chains 366 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 293 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 198 optimal weight: 0.3980 chunk 212 optimal weight: 0.1980 chunk 154 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 245 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 675 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 137 ASN B 580 GLN B 675 GLN B 954 GLN B 957 GLN C 460 ASN C 487 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27180 Z= 0.208 Angle : 0.616 14.918 36975 Z= 0.317 Chirality : 0.048 0.931 4404 Planarity : 0.004 0.044 4695 Dihedral : 6.763 54.186 5139 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.14 % Favored : 95.61 % Rotamer: Outliers : 3.13 % Allowed : 16.44 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.66 (0.14), residues: 3234 helix: 0.74 (0.19), residues: 720 sheet: -0.39 (0.19), residues: 564 loop : -0.91 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.007 0.001 HIS A1101 PHE 0.033 0.001 PHE B 643 TYR 0.016 0.001 TYR C 660 ARG 0.010 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 311 time to evaluate : 3.172 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 153 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6091 (pmt) REVERT: A 370 ASN cc_start: 0.7053 (m-40) cc_final: 0.6795 (m-40) REVERT: A 461 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7666 (pp) REVERT: A 487 ASN cc_start: 0.8048 (t0) cc_final: 0.7650 (t0) REVERT: A 1086 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7778 (ptmt) REVERT: B 113 LYS cc_start: 0.8030 (mttt) cc_final: 0.7092 (mmpt) REVERT: B 231 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7800 (pp) REVERT: B 408 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.6734 (ppt90) REVERT: B 487 ASN cc_start: 0.8184 (m-40) cc_final: 0.7673 (t0) REVERT: B 572 THR cc_start: 0.8585 (p) cc_final: 0.8277 (t) REVERT: B 814 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6547 (mttp) REVERT: B 922 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8494 (tp) REVERT: B 947 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7931 (mtmm) REVERT: B 973 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 1086 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7962 (ptmt) REVERT: B 1113 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: C 153 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.5162 (pmt) REVERT: C 408 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.6202 (ptt90) REVERT: C 444 LYS cc_start: 0.6551 (pttt) cc_final: 0.6259 (ptpt) REVERT: C 461 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7559 (pp) REVERT: C 516 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: C 569 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7756 (pp) REVERT: C 572 THR cc_start: 0.8638 (p) cc_final: 0.8383 (t) REVERT: C 646 ARG cc_start: 0.7603 (mtp180) cc_final: 0.7356 (mtm-85) REVERT: C 979 ASP cc_start: 0.7651 (t0) cc_final: 0.7359 (m-30) REVERT: C 1019 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7639 (ttp-110) REVERT: C 1086 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7918 (ptmt) REVERT: C 1101 HIS cc_start: 0.7234 (m90) cc_final: 0.6921 (m170) REVERT: C 1113 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7765 (mt0) outliers start: 89 outliers final: 33 residues processed: 375 average time/residue: 1.3599 time to fit residues: 595.8200 Evaluate side-chains 338 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 287 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 1.9990 chunk 299 optimal weight: 0.9980 chunk 272 optimal weight: 0.1980 chunk 291 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 228 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 675 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN A1101 HIS B 580 GLN B 675 GLN B 690 GLN B 872 GLN B 957 GLN C 487 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27180 Z= 0.257 Angle : 0.632 15.647 36975 Z= 0.326 Chirality : 0.047 0.653 4404 Planarity : 0.004 0.044 4695 Dihedral : 6.793 58.302 5139 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.24 % Favored : 95.55 % Rotamer: Outliers : 2.99 % Allowed : 16.79 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.63 (0.14), residues: 3234 helix: 0.78 (0.19), residues: 723 sheet: -0.39 (0.19), residues: 558 loop : -0.89 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 64 HIS 0.008 0.001 HIS A1101 PHE 0.035 0.002 PHE B 643 TYR 0.015 0.002 TYR B 28 ARG 0.008 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 295 time to evaluate : 2.956 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: symmetry clash REVERT: A 153 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6119 (pmt) REVERT: A 370 ASN cc_start: 0.7040 (m-40) cc_final: 0.6822 (m-40) REVERT: A 461 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7778 (pp) REVERT: A 487 ASN cc_start: 0.8079 (m-40) cc_final: 0.7687 (t0) REVERT: A 1086 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7804 (ptmt) REVERT: B 113 LYS cc_start: 0.8048 (mttt) cc_final: 0.7110 (mmpt) REVERT: B 231 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7914 (pp) REVERT: B 408 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.6795 (ppt90) REVERT: B 487 ASN cc_start: 0.8173 (m-40) cc_final: 0.7666 (t0) REVERT: B 572 THR cc_start: 0.8513 (p) cc_final: 0.8230 (t) REVERT: B 814 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6513 (mttp) REVERT: B 834 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7206 (pp) REVERT: B 922 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8490 (tp) REVERT: B 947 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7960 (mtmm) REVERT: B 973 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8184 (tp) REVERT: B 1086 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7858 (ptmt) REVERT: B 1113 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: C 408 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.6207 (ptt90) REVERT: C 444 LYS cc_start: 0.6657 (pttt) cc_final: 0.6338 (ptpt) REVERT: C 461 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7572 (pp) REVERT: C 516 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: C 569 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7783 (pp) REVERT: C 572 THR cc_start: 0.8620 (p) cc_final: 0.8371 (t) REVERT: C 646 ARG cc_start: 0.7591 (mtp180) cc_final: 0.7350 (mtm-85) REVERT: C 979 ASP cc_start: 0.7650 (t0) cc_final: 0.7382 (m-30) REVERT: C 1019 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7871 (ttp-110) REVERT: C 1038 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8270 (mptt) REVERT: C 1086 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7982 (ptmt) REVERT: C 1101 HIS cc_start: 0.7259 (m90) cc_final: 0.6925 (m170) REVERT: C 1113 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7771 (mt0) outliers start: 85 outliers final: 41 residues processed: 355 average time/residue: 1.3097 time to fit residues: 546.1700 Evaluate side-chains 348 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 288 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.7980 chunk 307 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 322 optimal weight: 10.0000 chunk 297 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 196 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 675 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1101 HIS B 580 GLN B 644 GLN B 675 GLN B 872 GLN B 957 GLN C 487 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27180 Z= 0.260 Angle : 0.629 14.004 36975 Z= 0.324 Chirality : 0.046 0.535 4404 Planarity : 0.004 0.046 4695 Dihedral : 6.777 52.684 5139 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.42 % Favored : 95.36 % Rotamer: Outliers : 2.89 % Allowed : 17.11 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.66 (0.14), residues: 3234 helix: 0.75 (0.19), residues: 720 sheet: -0.40 (0.19), residues: 558 loop : -0.91 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 64 HIS 0.007 0.001 HIS A1101 PHE 0.035 0.002 PHE B 643 TYR 0.014 0.002 TYR B 28 ARG 0.009 0.001 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6468 Ramachandran restraints generated. 3234 Oldfield, 0 Emsley, 3234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 296 time to evaluate : 2.994 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 153 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.6083 (pmt) REVERT: A 461 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7783 (pp) REVERT: A 487 ASN cc_start: 0.8106 (m-40) cc_final: 0.7642 (t0) REVERT: A 1086 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7811 (ptmt) REVERT: B 231 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7862 (pp) REVERT: B 312 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7766 (mm) REVERT: B 408 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.6796 (ppt90) REVERT: B 487 ASN cc_start: 0.8201 (m-40) cc_final: 0.7679 (t0) REVERT: B 572 THR cc_start: 0.8546 (p) cc_final: 0.8261 (t) REVERT: B 814 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6506 (mttp) REVERT: B 834 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7205 (pp) REVERT: B 922 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8504 (tp) REVERT: B 973 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8207 (tp) REVERT: B 1086 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7876 (ptmt) REVERT: B 1113 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7652 (mt0) REVERT: C 408 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.6200 (ptt90) REVERT: C 444 LYS cc_start: 0.6658 (pttt) cc_final: 0.6337 (ptpt) REVERT: C 461 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7623 (pp) REVERT: C 516 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: C 569 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7797 (pp) REVERT: C 572 THR cc_start: 0.8605 (p) cc_final: 0.8355 (t) REVERT: C 646 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7363 (mtm-85) REVERT: C 979 ASP cc_start: 0.7667 (t0) cc_final: 0.7363 (m-30) REVERT: C 1019 ARG cc_start: 0.8094 (ttp-110) cc_final: 0.7872 (ttp-110) REVERT: C 1038 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8313 (mptt) REVERT: C 1086 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8000 (ptmt) REVERT: C 1101 HIS cc_start: 0.7259 (m90) cc_final: 0.6933 (m170) REVERT: C 1113 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7771 (mt0) outliers start: 82 outliers final: 43 residues processed: 352 average time/residue: 1.3695 time to fit residues: 564.5158 Evaluate side-chains 348 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 285 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 78 optimal weight: 0.0060 chunk 237 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 257 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 370 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 675 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1101 HIS B 580 GLN B 675 GLN B 872 GLN B 957 GLN C 487 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119753 restraints weight = 32722.895| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.09 r_work: 0.3285 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27180 Z= 0.230 Angle : 0.611 12.529 36975 Z= 0.315 Chirality : 0.046 0.438 4404 Planarity : 0.004 0.050 4695 Dihedral : 6.653 53.391 5139 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 3.10 % Allowed : 17.21 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.64 (0.14), residues: 3234 helix: 0.75 (0.19), residues: 729 sheet: -0.42 (0.19), residues: 558 loop : -0.89 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 152 HIS 0.007 0.001 HIS A1101 PHE 0.035 0.001 PHE B 643 TYR 0.014 0.001 TYR B 505 ARG 0.007 0.000 ARG C1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10722.17 seconds wall clock time: 192 minutes 19.20 seconds (11539.20 seconds total)