Starting phenix.real_space_refine on Mon Feb 19 21:55:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jwy_22515/02_2024/7jwy_22515.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jwy_22515/02_2024/7jwy_22515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jwy_22515/02_2024/7jwy_22515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jwy_22515/02_2024/7jwy_22515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jwy_22515/02_2024/7jwy_22515.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jwy_22515/02_2024/7jwy_22515.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16366 2.51 5 N 4200 2.21 5 O 5183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 847": "NH1" <-> "NH2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 847": "NH1" <-> "NH2" Residue "B ASP 848": "OD1" <-> "OD2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 847": "NH1" <-> "NH2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C ASP 1139": "OD1" <-> "OD2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25860 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 7 bond proxies already assigned to first conformer: 8442 Chain: "B" Number of atoms: 8293 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8288 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 52, 'TRANS': 1008} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8288 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 52, 'TRANS': 1008} Chain breaks: 6 bond proxies already assigned to first conformer: 8471 Chain: "C" Number of atoms: 8285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8280 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1060, 8280 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 7 bond proxies already assigned to first conformer: 8462 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Time building chain proxies: 25.02, per 1000 atoms: 0.97 Number of scatterers: 25860 At special positions: 0 Unit cell: (139.68, 130.077, 178.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5183 8.00 N 4200 7.00 C 16366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.05 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=2.07 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1074 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 12.36 Conformation dependent library (CDL) restraints added in 12.0 seconds 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 47 sheets defined 24.8% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.159A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.547A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.553A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.661A pdb=" N LEU A 629 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 removed outlier: 3.555A pdb=" N SER A 637 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.811A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.942A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.180A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.125A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.009A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.840A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.541A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.502A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.647A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.624A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.773A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.957A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 removed outlier: 4.097A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.167A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.953A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.730A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.545A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.170A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.681A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.930A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.665A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.505A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.150A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.960A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.711A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.732A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.835A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.331A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.321A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.219A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.806A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.441A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.834A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.697A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.535A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.619A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.432A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.547A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.461A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.559A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.193A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.816A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.117A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.117A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.643A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.849A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.701A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.582A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.703A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.397A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.237A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 135 through 141 removed outlier: 7.380A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.294A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.134A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.134A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 538 through 539 removed outlier: 5.181A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.583A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.678A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.694A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 978 hydrogen bonds defined for protein. 2678 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: 13.23 Time building geometry restraints manager: 11.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8120 1.34 - 1.48: 7503 1.48 - 1.62: 10549 1.62 - 1.76: 16 1.76 - 1.91: 119 Bond restraints: 26307 Sorted by residual: bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.350 0.171 3.30e-02 9.18e+02 2.70e+01 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.337 1.393 -0.057 1.11e-02 8.12e+03 2.60e+01 bond pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 1.808 1.648 0.160 3.30e-02 9.18e+02 2.34e+01 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.394 0.127 3.30e-02 9.18e+02 1.49e+01 bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.397 0.124 3.30e-02 9.18e+02 1.42e+01 ... (remaining 26302 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.43: 733 106.43 - 113.65: 14254 113.65 - 120.86: 12062 120.86 - 128.07: 8595 128.07 - 135.28: 163 Bond angle restraints: 35807 Sorted by residual: angle pdb=" C ASP B 215 " pdb=" N LEU B 216 " pdb=" CA LEU B 216 " ideal model delta sigma weight residual 120.39 132.63 -12.24 1.39e+00 5.18e-01 7.75e+01 angle pdb=" CA CYS C 166 " pdb=" CB CYS C 166 " pdb=" SG CYS C 166 " ideal model delta sigma weight residual 114.40 132.82 -18.42 2.30e+00 1.89e-01 6.42e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 131.64 -17.24 2.30e+00 1.89e-01 5.62e+01 angle pdb=" C SER B 31 " pdb=" N PHE B 32 " pdb=" CA PHE B 32 " ideal model delta sigma weight residual 121.54 135.28 -13.74 1.91e+00 2.74e-01 5.18e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 130.43 -16.03 2.30e+00 1.89e-01 4.86e+01 ... (remaining 35802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 14954 17.57 - 35.14: 1259 35.14 - 52.70: 212 52.70 - 70.27: 59 70.27 - 87.84: 31 Dihedral angle restraints: 16515 sinusoidal: 7245 harmonic: 9270 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 23.36 69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.42 63.42 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.90 61.90 1 1.00e+01 1.00e-02 5.08e+01 ... (remaining 16512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3090 0.077 - 0.153: 1029 0.153 - 0.230: 117 0.230 - 0.307: 13 0.307 - 0.384: 12 Chirality restraints: 4261 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C2 NAG A1311 " pdb=" C1 NAG A1311 " pdb=" C3 NAG A1311 " pdb=" N2 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 4258 not shown) Planarity restraints: 4601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.030 2.00e-02 2.50e+03 2.63e-02 1.72e+01 pdb=" CG TRP A 886 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.027 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" CG TRP C 886 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " 0.030 2.00e-02 2.50e+03 2.51e-02 1.58e+01 pdb=" CG TRP B 886 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " 0.018 2.00e-02 2.50e+03 ... (remaining 4598 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4938 2.78 - 3.31: 20928 3.31 - 3.84: 41292 3.84 - 4.37: 48725 4.37 - 4.90: 84365 Nonbonded interactions: 200248 Sorted by model distance: nonbonded pdb=" OG SER A 469 " pdb=" O LYS B 113 " model vdw 2.248 2.440 nonbonded pdb=" OE2 GLU B1017 " pdb=" O HOH B1401 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR A 599 " pdb=" O PRO A 600 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR C 599 " pdb=" O PRO C 600 " model vdw 2.275 2.440 nonbonded pdb=" OD1 ASP C 294 " pdb=" OG SER C 297 " model vdw 2.284 2.440 ... (remaining 200243 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 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 954 or resid 956 through 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 828 or resid 834 throu \ gh 954 or resid 956 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 828 or resid 834 throu \ gh 954 or resid 956 through 1147 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 5.040 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: 0.040 Extract box with map and model: 16.870 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 99.040 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.011 0.171 26307 Z= 0.739 Angle : 1.199 18.422 35807 Z= 0.673 Chirality : 0.073 0.384 4261 Planarity : 0.008 0.072 4554 Dihedral : 13.664 87.839 10421 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.12), residues: 3135 helix: -1.38 (0.17), residues: 722 sheet: -0.50 (0.20), residues: 637 loop : -2.60 (0.11), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.006 TRP A 886 HIS 0.011 0.002 HIS A 66 PHE 0.038 0.004 PHE B 238 TYR 0.023 0.004 TYR C 369 ARG 0.010 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 276 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7181 (p0) cc_final: 0.6965 (p0) REVERT: B 985 ASP cc_start: 0.6743 (p0) cc_final: 0.6425 (p0) REVERT: C 904 TYR cc_start: 0.7329 (p90) cc_final: 0.6940 (p90) outliers start: 3 outliers final: 0 residues processed: 279 average time/residue: 1.3293 time to fit residues: 431.7490 Evaluate side-chains 204 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 218 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 450 ASN A 501 ASN A 779 GLN A 901 GLN A1002 GLN A1011 GLN A1113 GLN B 99 ASN B 519 HIS B 580 GLN B 901 GLN B1113 GLN B1142 GLN C 52 GLN C 81 ASN C 99 ASN C 121 ASN C 188 ASN C 218 GLN C 440 ASN C 501 ASN C 613 GLN C 779 GLN C 901 GLN C1005 GLN C1011 GLN C1113 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 26307 Z= 0.228 Angle : 0.676 9.955 35807 Z= 0.366 Chirality : 0.048 0.216 4261 Planarity : 0.005 0.062 4554 Dihedral : 7.592 59.627 4754 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.08 % Allowed : 7.70 % Favored : 91.22 % 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: -1.43 (0.14), residues: 3135 helix: 0.51 (0.20), residues: 718 sheet: 0.21 (0.20), residues: 654 loop : -2.15 (0.12), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 886 HIS 0.003 0.001 HIS C1064 PHE 0.030 0.002 PHE A 32 TYR 0.030 0.002 TYR C 904 ARG 0.008 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7285 (p0) cc_final: 0.7021 (p0) REVERT: A 776 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8241 (tmtm) REVERT: B 776 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8054 (tmtm) REVERT: B 834 ILE cc_start: 0.1659 (OUTLIER) cc_final: 0.1449 (pp) REVERT: C 776 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8202 (tmtm) REVERT: C 904 TYR cc_start: 0.7286 (p90) cc_final: 0.6850 (p90) outliers start: 30 outliers final: 12 residues processed: 247 average time/residue: 1.1470 time to fit residues: 336.8670 Evaluate side-chains 214 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 159 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 288 optimal weight: 0.5980 chunk 311 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 99 ASN B 580 GLN C 99 ASN C 218 GLN C 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26307 Z= 0.185 Angle : 0.602 13.961 35807 Z= 0.321 Chirality : 0.046 0.235 4261 Planarity : 0.004 0.057 4554 Dihedral : 7.211 90.269 4754 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.94 % Allowed : 8.60 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3135 helix: 1.19 (0.20), residues: 728 sheet: 0.63 (0.20), residues: 654 loop : -1.91 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 PHE 0.030 0.001 PHE A 32 TYR 0.030 0.001 TYR C 904 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7307 (p0) cc_final: 0.7071 (p0) REVERT: A 979 ASP cc_start: 0.7289 (t0) cc_final: 0.7015 (t0) REVERT: B 776 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7970 (tmtm) REVERT: C 239 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: C 904 TYR cc_start: 0.7124 (p90) cc_final: 0.6891 (p90) outliers start: 26 outliers final: 11 residues processed: 237 average time/residue: 1.2150 time to fit residues: 344.6583 Evaluate side-chains 215 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 284 optimal weight: 0.5980 chunk 216 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 193 optimal weight: 0.1980 chunk 289 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 274 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 99 ASN C 66 HIS C 99 ASN C 779 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26307 Z= 0.165 Angle : 0.560 9.876 35807 Z= 0.300 Chirality : 0.046 0.295 4261 Planarity : 0.004 0.052 4554 Dihedral : 6.100 58.927 4754 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.19 % Allowed : 9.18 % Favored : 89.63 % 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: -0.46 (0.15), residues: 3135 helix: 1.59 (0.21), residues: 726 sheet: 0.95 (0.20), residues: 661 loop : -1.75 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.002 0.001 HIS C1064 PHE 0.028 0.001 PHE A 32 TYR 0.030 0.001 TYR C 904 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7402 (p0) cc_final: 0.7174 (p0) REVERT: B 776 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7969 (tmtm) REVERT: C 239 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: C 613 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.6006 (mp10) outliers start: 33 outliers final: 14 residues processed: 245 average time/residue: 1.1296 time to fit residues: 330.4607 Evaluate side-chains 221 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 204 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 255 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 4 optimal weight: 0.0050 chunk 228 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 275 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 99 ASN B 121 ASN C 99 ASN C 121 ASN C 779 GLN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 26307 Z= 0.219 Angle : 0.601 10.016 35807 Z= 0.323 Chirality : 0.047 0.250 4261 Planarity : 0.004 0.047 4554 Dihedral : 5.990 58.496 4754 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.51 % Allowed : 9.54 % Favored : 88.95 % 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: -0.46 (0.14), residues: 3135 helix: 1.55 (0.20), residues: 725 sheet: 0.94 (0.20), residues: 638 loop : -1.69 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 886 HIS 0.014 0.001 HIS C 66 PHE 0.026 0.002 PHE B 318 TYR 0.025 0.001 TYR A 453 ARG 0.004 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 209 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7455 (p0) cc_final: 0.7211 (p0) REVERT: A 979 ASP cc_start: 0.7443 (t0) cc_final: 0.7064 (t0) REVERT: B 529 LYS cc_start: 0.7067 (ptmm) cc_final: 0.6857 (tptt) REVERT: B 776 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8088 (tmtm) REVERT: B 1017 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: C 239 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: C 271 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7219 (mt0) REVERT: C 564 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: C 613 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6055 (mp10) outliers start: 42 outliers final: 21 residues processed: 233 average time/residue: 1.1549 time to fit residues: 322.4289 Evaluate side-chains 228 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 103 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 75 optimal weight: 0.0670 chunk 306 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1135 ASN B 99 ASN B 121 ASN C 99 ASN C 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26307 Z= 0.195 Angle : 0.580 9.967 35807 Z= 0.311 Chirality : 0.046 0.236 4261 Planarity : 0.004 0.047 4554 Dihedral : 5.709 56.358 4754 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.30 % Allowed : 10.15 % Favored : 88.55 % 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: -0.36 (0.15), residues: 3135 helix: 1.62 (0.20), residues: 725 sheet: 0.92 (0.20), residues: 654 loop : -1.61 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 886 HIS 0.004 0.001 HIS C1064 PHE 0.029 0.001 PHE B 318 TYR 0.026 0.001 TYR A 453 ARG 0.004 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 207 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7457 (p0) cc_final: 0.7208 (p0) REVERT: A 850 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7244 (tp) REVERT: A 979 ASP cc_start: 0.7357 (t0) cc_final: 0.7013 (t0) REVERT: B 614 ASP cc_start: 0.7284 (p0) cc_final: 0.6940 (p0) REVERT: B 776 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8035 (tmtm) REVERT: B 1017 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6656 (tp30) REVERT: C 239 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: C 271 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: C 564 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: C 613 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.6040 (mp10) outliers start: 36 outliers final: 22 residues processed: 227 average time/residue: 1.1834 time to fit residues: 322.8727 Evaluate side-chains 227 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 295 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 0.0010 chunk 141 optimal weight: 5.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 99 ASN B 121 ASN C 99 ASN C 121 ASN C 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26307 Z= 0.199 Angle : 0.582 9.965 35807 Z= 0.312 Chirality : 0.046 0.227 4261 Planarity : 0.004 0.044 4554 Dihedral : 5.589 55.462 4754 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.44 % Allowed : 10.12 % Favored : 88.44 % 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: -0.33 (0.15), residues: 3135 helix: 1.58 (0.20), residues: 731 sheet: 0.84 (0.20), residues: 678 loop : -1.56 (0.13), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 886 HIS 0.004 0.001 HIS C1064 PHE 0.030 0.001 PHE B 318 TYR 0.026 0.001 TYR A 453 ARG 0.004 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 205 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7434 (p0) cc_final: 0.7191 (p0) REVERT: A 850 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7252 (tp) REVERT: A 979 ASP cc_start: 0.7367 (t0) cc_final: 0.6998 (t0) REVERT: B 614 ASP cc_start: 0.7314 (p0) cc_final: 0.6970 (p0) REVERT: B 776 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8060 (tmtm) REVERT: B 1017 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6696 (tp30) REVERT: C 239 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: C 271 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: C 564 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: C 613 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6085 (mp10) outliers start: 40 outliers final: 25 residues processed: 232 average time/residue: 1.1321 time to fit residues: 315.1182 Evaluate side-chains 231 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 121 ASN B1135 ASN C 99 ASN C 121 ASN C 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 26307 Z= 0.313 Angle : 0.677 10.181 35807 Z= 0.363 Chirality : 0.050 0.436 4261 Planarity : 0.004 0.045 4554 Dihedral : 5.927 56.627 4754 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.55 % Allowed : 10.22 % Favored : 88.23 % 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: -0.56 (0.14), residues: 3135 helix: 1.22 (0.20), residues: 731 sheet: 0.90 (0.20), residues: 620 loop : -1.62 (0.13), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 886 HIS 0.006 0.001 HIS C1064 PHE 0.035 0.002 PHE B 318 TYR 0.029 0.002 TYR C 904 ARG 0.003 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7520 (p0) cc_final: 0.7258 (p0) REVERT: A 850 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7312 (tp) REVERT: A 979 ASP cc_start: 0.7399 (t0) cc_final: 0.7042 (t0) REVERT: A 1005 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8152 (mm-40) REVERT: B 614 ASP cc_start: 0.7376 (p0) cc_final: 0.7047 (p0) REVERT: B 776 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8132 (tmtm) REVERT: B 1017 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6816 (tp30) REVERT: C 239 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: C 271 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7176 (mt0) REVERT: C 564 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: C 613 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.6187 (mp10) outliers start: 43 outliers final: 28 residues processed: 225 average time/residue: 1.2134 time to fit residues: 326.5124 Evaluate side-chains 231 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 277 optimal weight: 0.9990 chunk 292 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 284 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 87 optimal weight: 0.0870 chunk 257 optimal weight: 8.9990 chunk 269 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1101 HIS B 99 ASN B 121 ASN C 99 ASN C 121 ASN C 779 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26307 Z= 0.183 Angle : 0.571 9.916 35807 Z= 0.308 Chirality : 0.046 0.224 4261 Planarity : 0.004 0.044 4554 Dihedral : 5.483 54.885 4754 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.22 % Allowed : 10.58 % Favored : 88.19 % 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: -0.30 (0.15), residues: 3135 helix: 1.56 (0.20), residues: 731 sheet: 0.93 (0.20), residues: 660 loop : -1.52 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 PHE 0.032 0.001 PHE B 318 TYR 0.027 0.001 TYR B 453 ARG 0.004 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7505 (p0) cc_final: 0.7262 (p0) REVERT: A 850 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7208 (tp) REVERT: B 614 ASP cc_start: 0.7359 (p0) cc_final: 0.7025 (p0) REVERT: B 776 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8000 (tmtm) REVERT: B 1017 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6544 (tp30) REVERT: C 239 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: C 271 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7200 (mt0) REVERT: C 564 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.6461 (tm-30) REVERT: C 613 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.5989 (mp10) REVERT: C 776 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8128 (tttm) outliers start: 34 outliers final: 21 residues processed: 227 average time/residue: 1.1764 time to fit residues: 318.5144 Evaluate side-chains 229 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 200 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 186 optimal weight: 0.7980 chunk 301 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 251 optimal weight: 20.0000 chunk 26 optimal weight: 0.0970 chunk 194 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 99 ASN B 121 ASN C 99 ASN C 121 ASN C 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 26307 Z= 0.216 Angle : 0.594 9.980 35807 Z= 0.320 Chirality : 0.047 0.228 4261 Planarity : 0.004 0.044 4554 Dihedral : 5.407 55.504 4754 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.26 % Allowed : 10.94 % Favored : 87.80 % 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: -0.31 (0.15), residues: 3135 helix: 1.60 (0.20), residues: 725 sheet: 0.92 (0.20), residues: 638 loop : -1.50 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 886 HIS 0.004 0.001 HIS C1064 PHE 0.032 0.001 PHE B 318 TYR 0.026 0.001 TYR B 453 ARG 0.004 0.000 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7504 (p0) cc_final: 0.7265 (p0) REVERT: A 850 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7223 (tp) REVERT: A 979 ASP cc_start: 0.7496 (t0) cc_final: 0.7069 (t0) REVERT: B 614 ASP cc_start: 0.7383 (p0) cc_final: 0.7045 (p0) REVERT: B 776 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8064 (tmtm) REVERT: B 1017 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: C 239 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: C 271 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7199 (mt0) REVERT: C 564 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: C 613 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6054 (mp10) REVERT: C 776 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8180 (tttm) REVERT: C 933 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7906 (mmtm) outliers start: 35 outliers final: 23 residues processed: 227 average time/residue: 1.1198 time to fit residues: 303.8184 Evaluate side-chains 224 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 199 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 231 optimal weight: 0.0020 chunk 37 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 258 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 121 ASN C 99 ASN C 121 ASN C 779 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.200094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150434 restraints weight = 35447.992| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.11 r_work: 0.3152 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 26307 Z= 0.267 Angle : 0.639 10.075 35807 Z= 0.344 Chirality : 0.049 0.264 4261 Planarity : 0.004 0.044 4554 Dihedral : 5.588 56.007 4754 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.33 % Allowed : 10.87 % Favored : 87.80 % 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: -0.42 (0.14), residues: 3135 helix: 1.43 (0.20), residues: 725 sheet: 0.92 (0.20), residues: 625 loop : -1.54 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 886 HIS 0.005 0.001 HIS C1064 PHE 0.033 0.002 PHE B 318 TYR 0.027 0.002 TYR B 904 ARG 0.003 0.000 ARG B 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8028.20 seconds wall clock time: 144 minutes 7.70 seconds (8647.70 seconds total)