Starting phenix.real_space_refine (version: dev) on Sun Feb 26 02:18:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt9_12585/02_2023/7nt9_12585_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt9_12585/02_2023/7nt9_12585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt9_12585/02_2023/7nt9_12585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt9_12585/02_2023/7nt9_12585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt9_12585/02_2023/7nt9_12585_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nt9_12585/02_2023/7nt9_12585_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.009 sd= 0.153 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 Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26952 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8505 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1087, 8496 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1087, 8496 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 3 bond proxies already assigned to first conformer: 8684 Chain: "B" Number of atoms: 8505 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1087, 8496 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1087, 8496 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 3 bond proxies already assigned to first conformer: 8684 Chain: "C" Number of atoms: 8505 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1087, 8496 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1087, 8496 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 3 bond proxies already assigned to first conformer: 8684 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 chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 155 Unusual residues: {'BLA': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 155 Unusual residues: {'BLA': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 155 Unusual residues: {'BLA': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Time building chain proxies: 27.08, per 1000 atoms: 1.00 Number of scatterers: 26952 At special positions: 0 Unit cell: (168.95, 158.05, 178.76, 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 117 16.00 O 5433 8.00 N 4359 7.00 C 17043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 603 " " NAG B1302 " - " ASN B 149 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 603 " " NAG C1302 " - " ASN C 149 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 603 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 61 " " NAG N 1 " - " ASN B 17 " " NAG O 1 " - " ASN B 122 " " NAG P 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 616 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN A 61 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 61 " " NAG Y 1 " - " ASN C 17 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 12.36 Conformation dependent library (CDL) restraints added in 7.8 seconds 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 50 sheets defined 20.1% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.222A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.488A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.999A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 738 through 741 No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 748 through 755 removed outlier: 4.073A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.693A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.517A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 884 removed outlier: 3.684A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 898 through 906 removed outlier: 3.955A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 938 removed outlier: 3.512A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.169A pdb=" N ASP A 950 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 951 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 954 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 958 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 986 through 1031 removed outlier: 4.785A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 340 through 343 No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.440A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.513A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.818A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 409' Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 738 through 741 No H-bonds generated for 'chain 'B' and resid 738 through 741' Processing helix chain 'B' and resid 748 through 755 removed outlier: 4.169A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.643A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.935A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 884 removed outlier: 3.676A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 890 Processing helix chain 'B' and resid 898 through 904 removed outlier: 3.921A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 917 removed outlier: 3.548A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 917' Processing helix chain 'B' and resid 920 through 938 removed outlier: 4.013A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.179A pdb=" N ASP B 950 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 951 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 954 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 958 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 986 through 1031 removed outlier: 4.739A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1145 No H-bonds generated for 'chain 'B' and resid 1142 through 1145' Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.354A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.514A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 738 through 741 No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 748 through 755 removed outlier: 3.562A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 782 removed outlier: 3.947A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 824 Processing helix chain 'C' and resid 849 through 856 removed outlier: 4.191A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 884 removed outlier: 3.727A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 890 Processing helix chain 'C' and resid 898 through 906 removed outlier: 3.902A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 917 removed outlier: 3.518A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 917' Processing helix chain 'C' and resid 920 through 938 removed outlier: 3.649A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 966 removed outlier: 3.701A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 986 through 1031 removed outlier: 4.732A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1145 No H-bonds generated for 'chain 'C' and resid 1142 through 1145' Processing sheet with id= A, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.841A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.577A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 169 through 171 removed outlier: 3.510A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.607A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 354 through 358 Processing sheet with id= F, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.668A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 376 through 380 removed outlier: 4.220A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= I, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.599A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 551 through 554 Processing sheet with id= K, first strand: chain 'A' and resid 642 through 645 removed outlier: 3.679A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.529A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.197A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.781A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= P, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= Q, first strand: chain 'A' and resid 711 through 717 removed outlier: 6.293A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.040A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.515A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 169 through 171 removed outlier: 3.508A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.737A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.705A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.726A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 376 through 380 removed outlier: 4.025A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= Z, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.990A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 551 through 554 removed outlier: 3.621A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.942A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 670 through 675 Processing sheet with id= AD, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= AE, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.557A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AG, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= AH, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.945A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.551A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 168 through 171 removed outlier: 4.719A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 243 through 246 removed outlier: 6.385A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 354 through 358 Processing sheet with id= AM, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.824A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 376 through 380 removed outlier: 4.004A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AP, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.582A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 551 through 554 Processing sheet with id= AR, first strand: chain 'C' and resid 642 through 645 removed outlier: 3.654A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.529A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.604A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.770A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AW, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id= AX, first strand: chain 'C' and resid 711 through 717 removed outlier: 6.604A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2058 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: 10.42 Time building geometry restraints manager: 13.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8447 1.34 - 1.47: 7066 1.47 - 1.59: 11772 1.59 - 1.72: 0 1.72 - 1.85: 147 Bond restraints: 27432 Sorted by residual: bond pdb=" CGA BLA B1301 " pdb=" O2A BLA B1301 " ideal model delta sigma weight residual 1.246 1.308 -0.062 2.00e-02 2.50e+03 9.58e+00 bond pdb=" CGA BLA C1301 " pdb=" O2A BLA C1301 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 9.15e+00 bond pdb=" CGA BLA A1301 " pdb=" O2A BLA A1301 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 9.13e+00 bond pdb=" CGD BLA B1301 " pdb=" O2D BLA B1301 " ideal model delta sigma weight residual 1.248 1.307 -0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" CGD BLA A1301 " pdb=" O2D BLA A1301 " ideal model delta sigma weight residual 1.248 1.307 -0.059 2.00e-02 2.50e+03 8.58e+00 ... (remaining 27427 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.92: 842 106.92 - 113.68: 15319 113.68 - 120.44: 9875 120.44 - 127.20: 11045 127.20 - 133.96: 275 Bond angle restraints: 37356 Sorted by residual: angle pdb=" C2 NAG L 2 " pdb=" N2 NAG L 2 " pdb=" C7 NAG L 2 " ideal model delta sigma weight residual 123.12 129.03 -5.91 1.28e+00 6.08e-01 2.12e+01 angle pdb=" C2 NAG W 2 " pdb=" N2 NAG W 2 " pdb=" C7 NAG W 2 " ideal model delta sigma weight residual 123.12 129.02 -5.90 1.28e+00 6.08e-01 2.11e+01 angle pdb=" C2 NAG g 2 " pdb=" N2 NAG g 2 " pdb=" C7 NAG g 2 " ideal model delta sigma weight residual 123.12 129.01 -5.89 1.28e+00 6.08e-01 2.11e+01 angle pdb=" N ILE C 805 " pdb=" CA ILE C 805 " pdb=" C ILE C 805 " ideal model delta sigma weight residual 113.47 110.14 3.33 1.01e+00 9.80e-01 1.09e+01 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 113.47 110.17 3.30 1.01e+00 9.80e-01 1.07e+01 ... (remaining 37351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 14782 18.64 - 37.27: 1117 37.27 - 55.91: 162 55.91 - 74.55: 30 74.55 - 93.18: 31 Dihedral angle restraints: 16122 sinusoidal: 6609 harmonic: 9513 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 38.91 54.09 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 41.08 51.92 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 42.09 50.91 1 1.00e+01 1.00e-02 3.55e+01 ... (remaining 16119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4225 0.099 - 0.198: 203 0.198 - 0.297: 5 0.297 - 0.395: 4 0.395 - 0.494: 3 Chirality restraints: 4440 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 4437 not shown) Planarity restraints: 4776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA C1301 " -0.018 2.00e-02 2.50e+03 3.82e-02 3.65e+01 pdb=" C1A BLA C1301 " 0.085 2.00e-02 2.50e+03 pdb=" C1D BLA C1301 " -0.001 2.00e-02 2.50e+03 pdb=" C2D BLA C1301 " 0.010 2.00e-02 2.50e+03 pdb=" C3D BLA C1301 " -0.008 2.00e-02 2.50e+03 pdb=" C4D BLA C1301 " -0.028 2.00e-02 2.50e+03 pdb=" CAD BLA C1301 " -0.000 2.00e-02 2.50e+03 pdb=" CHA BLA C1301 " -0.067 2.00e-02 2.50e+03 pdb=" CHD BLA C1301 " -0.011 2.00e-02 2.50e+03 pdb=" CMD BLA C1301 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA A1301 " -0.018 2.00e-02 2.50e+03 3.81e-02 3.63e+01 pdb=" C1A BLA A1301 " 0.085 2.00e-02 2.50e+03 pdb=" C1D BLA A1301 " -0.001 2.00e-02 2.50e+03 pdb=" C2D BLA A1301 " 0.009 2.00e-02 2.50e+03 pdb=" C3D BLA A1301 " -0.008 2.00e-02 2.50e+03 pdb=" C4D BLA A1301 " -0.027 2.00e-02 2.50e+03 pdb=" CAD BLA A1301 " 0.001 2.00e-02 2.50e+03 pdb=" CHA BLA A1301 " -0.068 2.00e-02 2.50e+03 pdb=" CHD BLA A1301 " -0.010 2.00e-02 2.50e+03 pdb=" CMD BLA A1301 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1301 " -0.019 2.00e-02 2.50e+03 3.78e-02 3.57e+01 pdb=" C1A BLA B1301 " 0.084 2.00e-02 2.50e+03 pdb=" C1D BLA B1301 " -0.002 2.00e-02 2.50e+03 pdb=" C2D BLA B1301 " 0.009 2.00e-02 2.50e+03 pdb=" C3D BLA B1301 " -0.009 2.00e-02 2.50e+03 pdb=" C4D BLA B1301 " -0.027 2.00e-02 2.50e+03 pdb=" CAD BLA B1301 " -0.001 2.00e-02 2.50e+03 pdb=" CHA BLA B1301 " -0.065 2.00e-02 2.50e+03 pdb=" CHD BLA B1301 " -0.011 2.00e-02 2.50e+03 pdb=" CMD BLA B1301 " 0.040 2.00e-02 2.50e+03 ... (remaining 4773 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4024 2.76 - 3.30: 24868 3.30 - 3.83: 41351 3.83 - 4.37: 47730 4.37 - 4.90: 84730 Nonbonded interactions: 202703 Sorted by model distance: nonbonded pdb=" O ARG B 319 " pdb=" OH TYR B 636 " model vdw 2.229 2.440 nonbonded pdb=" O SER A 325 " pdb=" O HOH A1401 " model vdw 2.240 2.440 nonbonded pdb=" O ARG A 319 " pdb=" OH TYR A 636 " model vdw 2.243 2.440 nonbonded pdb=" O SER B 325 " pdb=" O HOH B1401 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE2 GLU B 191 " model vdw 2.248 2.440 ... (remaining 202698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 254 or resid 256 through 1044 or resid 1046 thr \ ough 1146 or resid 1301 through 1309)) selection = (chain 'B' and (resid 14 through 254 or resid 256 through 1044 or resid 1046 thr \ ough 1146 or resid 1301 through 1309)) selection = (chain 'C' and (resid 14 through 254 or resid 256 through 1044 or resid 1046 thr \ ough 1146 or resid 1301 through 1309)) } 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' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 17043 2.51 5 N 4359 2.21 5 O 5433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 1.630 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: 9.020 Check model and map are aligned: 0.420 Process input model: 88.830 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Set scattering table: 0.250 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.003 0.062 27432 Z= 0.224 Angle : 0.583 7.029 37356 Z= 0.327 Chirality : 0.047 0.494 4440 Planarity : 0.004 0.048 4722 Dihedral : 13.419 93.181 9888 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3243 helix: 0.42 (0.22), residues: 615 sheet: -0.06 (0.19), residues: 714 loop : -1.28 (0.14), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.3605 time to fit residues: 167.3914 Evaluate side-chains 191 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.153 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.0470 chunk 245 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 189 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 207 HIS A 271 GLN B 207 HIS B 271 GLN C 207 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 27432 Z= 0.196 Angle : 0.548 8.809 37356 Z= 0.297 Chirality : 0.047 0.376 4440 Planarity : 0.004 0.037 4722 Dihedral : 6.826 94.830 4053 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3243 helix: 0.42 (0.22), residues: 630 sheet: -0.00 (0.19), residues: 708 loop : -1.20 (0.14), residues: 1905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 207 time to evaluate : 3.004 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 215 average time/residue: 0.3436 time to fit residues: 125.6489 Evaluate side-chains 198 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 3.108 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2522 time to fit residues: 8.1294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 200 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 294 optimal weight: 5.9990 chunk 318 optimal weight: 3.9990 chunk 262 optimal weight: 0.0670 chunk 292 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 27432 Z= 0.157 Angle : 0.512 7.508 37356 Z= 0.276 Chirality : 0.046 0.381 4440 Planarity : 0.004 0.037 4722 Dihedral : 6.684 96.502 4053 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3243 helix: 0.58 (0.22), residues: 624 sheet: 0.00 (0.19), residues: 708 loop : -1.12 (0.14), residues: 1911 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 211 time to evaluate : 3.088 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 215 average time/residue: 0.3625 time to fit residues: 132.2378 Evaluate side-chains 193 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 3.187 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2773 time to fit residues: 7.1014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.7980 chunk 221 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 197 optimal weight: 0.3980 chunk 295 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A1010 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 27432 Z= 0.211 Angle : 0.520 6.625 37356 Z= 0.280 Chirality : 0.046 0.395 4440 Planarity : 0.004 0.037 4722 Dihedral : 6.665 96.535 4053 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3243 helix: 0.53 (0.22), residues: 627 sheet: 0.03 (0.19), residues: 720 loop : -1.16 (0.14), residues: 1896 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 204 time to evaluate : 4.064 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 208 average time/residue: 0.3560 time to fit residues: 125.6620 Evaluate side-chains 198 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 3.052 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2710 time to fit residues: 6.5595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 267 optimal weight: 8.9990 chunk 216 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 159 optimal weight: 8.9990 chunk 281 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.073 27432 Z= 0.604 Angle : 0.724 8.103 37356 Z= 0.389 Chirality : 0.053 0.359 4440 Planarity : 0.005 0.047 4722 Dihedral : 7.049 96.650 4053 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.63 % 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: -1.44 (0.14), residues: 3243 helix: -0.43 (0.21), residues: 624 sheet: -0.25 (0.18), residues: 756 loop : -1.47 (0.14), residues: 1863 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 209 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 222 average time/residue: 0.3582 time to fit residues: 132.6047 Evaluate side-chains 200 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 2.834 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2327 time to fit residues: 10.0561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 183 optimal weight: 0.0570 chunk 77 optimal weight: 2.9990 chunk 313 optimal weight: 0.7980 chunk 260 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 66 HIS B 992 GLN C 99 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C 992 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 27432 Z= 0.194 Angle : 0.546 8.677 37356 Z= 0.294 Chirality : 0.046 0.359 4440 Planarity : 0.004 0.116 4722 Dihedral : 6.766 97.561 4053 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.28 % 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: -1.10 (0.14), residues: 3243 helix: 0.26 (0.22), residues: 621 sheet: -0.15 (0.19), residues: 729 loop : -1.34 (0.14), residues: 1893 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 211 average time/residue: 0.3775 time to fit residues: 133.7088 Evaluate side-chains 199 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 193 time to evaluate : 3.267 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2340 time to fit residues: 7.0840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 263 optimal weight: 0.0010 chunk 175 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 27432 Z= 0.189 Angle : 0.526 9.673 37356 Z= 0.283 Chirality : 0.046 0.368 4440 Planarity : 0.004 0.086 4722 Dihedral : 6.657 98.611 4053 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3243 helix: 0.55 (0.22), residues: 621 sheet: -0.09 (0.19), residues: 729 loop : -1.25 (0.14), residues: 1893 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 201 time to evaluate : 3.494 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 204 average time/residue: 0.4144 time to fit residues: 141.8061 Evaluate side-chains 197 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 3.225 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2905 time to fit residues: 5.8475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 27432 Z= 0.311 Angle : 0.572 9.156 37356 Z= 0.308 Chirality : 0.056 2.059 4440 Planarity : 0.004 0.077 4722 Dihedral : 6.778 98.925 4053 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3243 helix: 0.36 (0.22), residues: 621 sheet: -0.14 (0.19), residues: 732 loop : -1.31 (0.14), residues: 1890 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 3.013 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.3889 time to fit residues: 123.6686 Evaluate side-chains 185 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 3.213 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 272 optimal weight: 3.9990 chunk 291 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 228 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 275 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 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 66 HIS A 99 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 27432 Z= 0.176 Angle : 0.526 9.419 37356 Z= 0.283 Chirality : 0.047 0.835 4440 Planarity : 0.004 0.071 4722 Dihedral : 6.675 99.548 4053 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3243 helix: 0.59 (0.22), residues: 621 sheet: -0.11 (0.19), residues: 732 loop : -1.27 (0.14), residues: 1890 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 198 average time/residue: 0.3822 time to fit residues: 127.6704 Evaluate side-chains 195 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 3.101 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2309 time to fit residues: 4.7238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.9990 chunk 307 optimal weight: 0.4980 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 322 optimal weight: 0.7980 chunk 297 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 198 optimal weight: 0.5980 chunk 157 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 27432 Z= 0.172 Angle : 0.513 8.530 37356 Z= 0.276 Chirality : 0.046 0.728 4440 Planarity : 0.004 0.050 4722 Dihedral : 6.605 100.268 4053 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3243 helix: 0.74 (0.23), residues: 618 sheet: -0.06 (0.19), residues: 744 loop : -1.23 (0.14), residues: 1881 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 205 average time/residue: 0.3779 time to fit residues: 130.8665 Evaluate side-chains 201 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 3.391 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2711 time to fit residues: 5.7553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 78 optimal weight: 2.9990 chunk 237 optimal weight: 0.0000 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 107 optimal weight: 0.0980 chunk 264 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124825 restraints weight = 54884.467| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.23 r_work: 0.3047 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 27432 Z= 0.239 Angle : 0.542 9.318 37356 Z= 0.291 Chirality : 0.047 0.670 4440 Planarity : 0.004 0.051 4722 Dihedral : 6.664 100.917 4053 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3243 helix: 0.57 (0.22), residues: 624 sheet: -0.06 (0.19), residues: 732 loop : -1.26 (0.14), residues: 1887 =============================================================================== Job complete usr+sys time: 4739.10 seconds wall clock time: 88 minutes 34.27 seconds (5314.27 seconds total)