Starting phenix.real_space_refine on Wed Mar 20 09:08:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgi_11207/03_2024/6zgi_11207.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgi_11207/03_2024/6zgi_11207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgi_11207/03_2024/6zgi_11207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgi_11207/03_2024/6zgi_11207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgi_11207/03_2024/6zgi_11207.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgi_11207/03_2024/6zgi_11207.pdb" } resolution = 2.9 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= 0.003 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17097 2.51 5 N 4392 2.21 5 O 5292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26901 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "B" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "C" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 25.03, per 1000 atoms: 0.93 Number of scatterers: 26901 At special positions: 0 Unit cell: (154.154, 144.452, 178.948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5292 8.00 N 4392 7.00 C 17097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1305 " - " ASN A 149 " " NAG A1310 " - " ASN A 282 " " NAG A1311 " - " ASN A 331 " " NAG A1312 " - " ASN A 343 " " NAG A1315 " - " ASN A 657 " " NAG A1316 " - " ASN A 709 " " NAG A1321 " - " ASN A1074 " " NAG A1324 " - " ASN A1134 " " NAG B1305 " - " ASN B 149 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 343 " " NAG B1315 " - " ASN B 657 " " NAG B1316 " - " ASN B 709 " " NAG B1321 " - " ASN B1074 " " NAG B1324 " - " ASN B1134 " " NAG C1305 " - " ASN C 149 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 331 " " NAG C1312 " - " ASN C 343 " " NAG C1315 " - " ASN C 657 " " NAG C1316 " - " ASN C 709 " " NAG C1321 " - " ASN C1074 " " NAG C1324 " - " ASN C1134 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A 61 " " NAG M 1 " - " ASN B 17 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B 61 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C 61 " Time building additional restraints: 10.20 Conformation dependent library (CDL) restraints added in 8.7 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 23.8% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.645A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.676A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.048A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.713A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.762A 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 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.066A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.278A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.025A 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.645A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.676A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.048A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.713A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.065A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.278A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.645A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.676A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.048A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.713A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.762A 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 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.066A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.278A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.199A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.003A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.832A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 163 removed outlier: 6.721A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.361A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.122A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.137A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.581A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.079A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.540A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.200A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.004A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.832A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 151 through 163 removed outlier: 6.721A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.361A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.122A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.137A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.581A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.079A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.540A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.199A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.003A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.832A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 151 through 163 removed outlier: 6.720A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.361A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.122A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.137A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.581A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.080A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.540A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1044 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.82 Time building geometry restraints manager: 11.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8492 1.34 - 1.46: 6913 1.46 - 1.59: 11955 1.59 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 27510 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 27505 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.62: 512 105.62 - 112.75: 14543 112.75 - 119.88: 9036 119.88 - 127.01: 13098 127.01 - 134.14: 248 Bond angle restraints: 37437 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.06 -3.36 1.22e+00 6.72e-01 7.59e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.05 -3.35 1.22e+00 6.72e-01 7.53e+00 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.04 -3.34 1.22e+00 6.72e-01 7.51e+00 angle pdb=" C THR A 76 " pdb=" N LYS A 77 " pdb=" CA LYS A 77 " ideal model delta sigma weight residual 121.54 126.55 -5.01 1.91e+00 2.74e-01 6.88e+00 angle pdb=" C THR C 76 " pdb=" N LYS C 77 " pdb=" CA LYS C 77 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.81e+00 ... (remaining 37432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 16210 17.57 - 35.14: 887 35.14 - 52.71: 171 52.71 - 70.28: 105 70.28 - 87.84: 27 Dihedral angle restraints: 17400 sinusoidal: 7794 harmonic: 9606 Sorted by residual: dihedral pdb=" CA HIS B 66 " pdb=" C HIS B 66 " pdb=" N ALA B 67 " pdb=" CA ALA B 67 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA HIS A 66 " pdb=" C HIS A 66 " pdb=" N ALA A 67 " pdb=" CA ALA A 67 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA HIS C 66 " pdb=" C HIS C 66 " pdb=" N ALA C 67 " pdb=" CA ALA C 67 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 17397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2923 0.050 - 0.100: 1200 0.100 - 0.150: 310 0.150 - 0.199: 4 0.199 - 0.249: 6 Chirality restraints: 4443 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 4440 not shown) Planarity restraints: 4803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 60 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.76e+00 pdb=" C SER C 60 " 0.054 2.00e-02 2.50e+03 pdb=" O SER C 60 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN C 61 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 60 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C SER B 60 " -0.054 2.00e-02 2.50e+03 pdb=" O SER B 60 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN B 61 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 60 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.61e+00 pdb=" C SER A 60 " 0.054 2.00e-02 2.50e+03 pdb=" O SER A 60 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 61 " -0.018 2.00e-02 2.50e+03 ... (remaining 4800 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 8155 2.83 - 3.35: 22014 3.35 - 3.87: 42041 3.87 - 4.38: 49229 4.38 - 4.90: 86430 Nonbonded interactions: 207869 Sorted by model distance: nonbonded pdb=" OE2 GLU C 96 " pdb=" N ILE C 101 " model vdw 2.317 2.520 nonbonded pdb=" OE2 GLU A 96 " pdb=" N ILE A 101 " model vdw 2.317 2.520 nonbonded pdb=" OE2 GLU B 96 " pdb=" N ILE B 101 " model vdw 2.318 2.520 nonbonded pdb=" OE1 GLN A 787 " pdb=" ND2 ASN C 703 " model vdw 2.334 2.520 nonbonded pdb=" ND2 ASN B 703 " pdb=" OE1 GLN C 787 " model vdw 2.334 2.520 ... (remaining 207864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1146 or resid 1305 through 1324)) selection = (chain 'B' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1146 or resid 1305 through 1324)) selection = (chain 'C' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1146 or resid 1305 through 1324)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.150 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 87.280 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.470 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.007 0.044 27510 Z= 0.438 Angle : 0.801 8.140 37437 Z= 0.437 Chirality : 0.054 0.249 4443 Planarity : 0.005 0.035 4752 Dihedral : 12.752 87.844 11097 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 0.73 % Allowed : 3.17 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3270 helix: 1.01 (0.20), residues: 702 sheet: 0.46 (0.18), residues: 786 loop : -1.91 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 886 HIS 0.007 0.002 HIS C 66 PHE 0.028 0.003 PHE C 55 TYR 0.029 0.003 TYR B 756 ARG 0.011 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 390 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.7145 (m90) cc_final: 0.6798 (m-70) REVERT: A 428 ASP cc_start: 0.7204 (p0) cc_final: 0.6820 (p0) REVERT: A 878 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 1038 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8152 (mmtp) REVERT: B 146 HIS cc_start: 0.7081 (m90) cc_final: 0.6865 (m-70) REVERT: B 319 ARG cc_start: 0.7721 (mtt-85) cc_final: 0.7449 (mmt180) REVERT: B 321 GLN cc_start: 0.8206 (mm110) cc_final: 0.7835 (mm-40) REVERT: B 389 ASP cc_start: 0.7748 (m-30) cc_final: 0.7532 (m-30) REVERT: B 474 GLN cc_start: 0.8128 (tt0) cc_final: 0.7787 (tt0) REVERT: B 878 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 947 LYS cc_start: 0.8146 (mttm) cc_final: 0.7362 (mptt) REVERT: B 1038 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8191 (mmtp) REVERT: B 1101 HIS cc_start: 0.7509 (m90) cc_final: 0.7182 (m90) REVERT: C 319 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7357 (mmt180) REVERT: C 428 ASP cc_start: 0.7217 (p0) cc_final: 0.6918 (p0) REVERT: C 462 LYS cc_start: 0.8647 (mmtp) cc_final: 0.7810 (mtmt) REVERT: C 878 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8133 (mp) REVERT: C 1017 GLU cc_start: 0.7366 (tt0) cc_final: 0.7145 (tt0) REVERT: C 1038 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8199 (mmtp) outliers start: 21 outliers final: 3 residues processed: 408 average time/residue: 1.4223 time to fit residues: 668.7346 Evaluate side-chains 207 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 201 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 256 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 190 optimal weight: 0.6980 chunk 296 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 HIS A 218 GLN A 239 GLN A 245 HIS A 501 ASN A 540 ASN A 580 GLN A 607 GLN A 641 ASN A 658 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 804 GLN A 925 ASN A 954 GLN A1023 ASN A1036 GLN A1064 HIS B 99 ASN B 207 HIS B 239 GLN B 245 HIS B 440 ASN B 501 ASN B 540 ASN B 563 GLN B 580 GLN B 641 ASN B 658 ASN B 675 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 925 ASN B 954 GLN B1023 ASN B1036 GLN B1064 HIS C 66 HIS C 99 ASN C 146 HIS C 207 HIS C 239 GLN C 474 GLN C 540 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 606 ASN C 641 ASN C 658 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 751 ASN C 779 GLN C 925 ASN C 954 GLN C1010 GLN C1023 ASN C1036 GLN C1064 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27510 Z= 0.203 Angle : 0.585 8.131 37437 Z= 0.310 Chirality : 0.046 0.293 4443 Planarity : 0.004 0.037 4752 Dihedral : 8.001 58.861 5204 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 1.60 % Allowed : 8.94 % Favored : 89.46 % 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: -0.72 (0.14), residues: 3270 helix: 1.40 (0.20), residues: 708 sheet: 0.50 (0.18), residues: 792 loop : -1.84 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 152 HIS 0.012 0.001 HIS C 207 PHE 0.017 0.002 PHE A 55 TYR 0.018 0.001 TYR A 756 ARG 0.005 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 2.977 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7071 (ttt-90) REVERT: A 428 ASP cc_start: 0.7136 (p0) cc_final: 0.6774 (p0) REVERT: A 462 LYS cc_start: 0.8647 (mmtp) cc_final: 0.8353 (mmtm) REVERT: A 820 ASP cc_start: 0.7837 (m-30) cc_final: 0.7461 (m-30) REVERT: A 1029 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8536 (tpp) REVERT: A 1038 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8083 (mmtp) REVERT: B 319 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7502 (mmt180) REVERT: B 474 GLN cc_start: 0.8082 (tt0) cc_final: 0.7752 (tt0) REVERT: B 571 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7715 (t70) REVERT: B 947 LYS cc_start: 0.7968 (mttm) cc_final: 0.7320 (mptt) REVERT: B 1038 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8116 (mmtp) REVERT: B 1101 HIS cc_start: 0.7587 (m90) cc_final: 0.7249 (m90) REVERT: C 88 ASP cc_start: 0.7532 (t70) cc_final: 0.7235 (t70) REVERT: C 202 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8443 (mttp) REVERT: C 246 ARG cc_start: 0.8111 (mtp85) cc_final: 0.7908 (mtt-85) REVERT: C 389 ASP cc_start: 0.7579 (m-30) cc_final: 0.7288 (m-30) REVERT: C 428 ASP cc_start: 0.7187 (p0) cc_final: 0.6870 (p0) REVERT: C 462 LYS cc_start: 0.8598 (mmtp) cc_final: 0.7794 (mtmt) REVERT: C 525 CYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6168 (m) REVERT: C 1017 GLU cc_start: 0.7221 (tt0) cc_final: 0.7008 (tt0) REVERT: C 1038 LYS cc_start: 0.8377 (mtpp) cc_final: 0.8089 (mptt) REVERT: C 1113 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7282 (mm-40) outliers start: 46 outliers final: 20 residues processed: 239 average time/residue: 1.4377 time to fit residues: 397.5284 Evaluate side-chains 202 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 264 optimal weight: 0.0980 chunk 295 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 238 optimal weight: 0.0770 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 606 ASN B 607 GLN B 644 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 935 GLN C 188 ASN C 218 GLN C 501 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 607 GLN C 675 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27510 Z= 0.210 Angle : 0.561 8.309 37437 Z= 0.296 Chirality : 0.046 0.288 4443 Planarity : 0.004 0.041 4752 Dihedral : 7.375 59.888 5200 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.93 % Rotamer: Outliers : 1.84 % Allowed : 9.12 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3270 helix: 1.48 (0.20), residues: 708 sheet: 0.81 (0.19), residues: 774 loop : -1.81 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 152 HIS 0.009 0.001 HIS C 207 PHE 0.016 0.002 PHE A 55 TYR 0.017 0.002 TYR B 756 ARG 0.005 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 191 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7197 (p0) cc_final: 0.6832 (p0) REVERT: A 462 LYS cc_start: 0.8639 (mmtp) cc_final: 0.8339 (mmtm) REVERT: A 820 ASP cc_start: 0.7737 (m-30) cc_final: 0.7352 (m-30) REVERT: A 1029 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8543 (tpp) REVERT: A 1038 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8081 (mmtp) REVERT: B 214 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7460 (ptm-80) REVERT: B 319 ARG cc_start: 0.7801 (mtt-85) cc_final: 0.7535 (mmt180) REVERT: B 321 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7641 (mm-40) REVERT: B 740 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8211 (ttm) REVERT: B 1038 LYS cc_start: 0.8456 (mtpp) cc_final: 0.8107 (mmtp) REVERT: B 1101 HIS cc_start: 0.7651 (m90) cc_final: 0.7308 (m90) REVERT: C 309 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7243 (mp0) REVERT: C 428 ASP cc_start: 0.7148 (p0) cc_final: 0.6825 (p0) REVERT: C 525 CYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6610 (m) REVERT: C 567 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7765 (mtt90) REVERT: C 1038 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8096 (mptt) REVERT: C 1101 HIS cc_start: 0.7637 (m90) cc_final: 0.7233 (m90) outliers start: 53 outliers final: 27 residues processed: 231 average time/residue: 1.3745 time to fit residues: 370.8495 Evaluate side-chains 204 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 173 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 282 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 188 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 919 ASN B 164 ASN B 644 GLN B 658 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 99 ASN C 164 ASN C 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 907 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 27510 Z= 0.511 Angle : 0.752 9.703 37437 Z= 0.394 Chirality : 0.054 0.297 4443 Planarity : 0.006 0.068 4752 Dihedral : 7.549 59.554 5200 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 2.37 % Allowed : 9.74 % Favored : 87.89 % 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: -1.02 (0.14), residues: 3270 helix: 0.88 (0.20), residues: 702 sheet: 0.50 (0.18), residues: 813 loop : -2.02 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 152 HIS 0.007 0.002 HIS B1064 PHE 0.025 0.003 PHE B1121 TYR 0.030 0.003 TYR A 756 ARG 0.007 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 183 time to evaluate : 3.532 Fit side-chains REVERT: A 52 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: A 68 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6946 (pp) REVERT: A 138 ASP cc_start: 0.7225 (t0) cc_final: 0.6988 (t0) REVERT: A 153 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6891 (mtp) REVERT: A 428 ASP cc_start: 0.7219 (p0) cc_final: 0.6818 (p0) REVERT: A 820 ASP cc_start: 0.7828 (m-30) cc_final: 0.7400 (m-30) REVERT: A 1038 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8113 (mmtp) REVERT: A 1039 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7151 (ptm160) REVERT: B 214 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7606 (ptm-80) REVERT: B 321 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7836 (mm-40) REVERT: B 357 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7789 (ttt-90) REVERT: B 474 GLN cc_start: 0.8245 (tt0) cc_final: 0.7901 (tt0) REVERT: B 675 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7256 (mt0) REVERT: B 740 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8409 (ttm) REVERT: B 1038 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8084 (mmtp) REVERT: B 1101 HIS cc_start: 0.7732 (m90) cc_final: 0.7488 (m90) REVERT: C 52 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: C 153 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7149 (mtp) REVERT: C 182 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6540 (mptt) REVERT: C 213 VAL cc_start: 0.7989 (t) cc_final: 0.7675 (m) REVERT: C 428 ASP cc_start: 0.7200 (p0) cc_final: 0.6866 (p0) REVERT: C 474 GLN cc_start: 0.7992 (tt0) cc_final: 0.7761 (tt0) REVERT: C 567 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7822 (mtt90) REVERT: C 1038 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8155 (mptt) outliers start: 68 outliers final: 36 residues processed: 236 average time/residue: 1.3425 time to fit residues: 371.3924 Evaluate side-chains 216 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 235 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 607 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 164 ASN B 188 ASN B 394 ASN B 563 GLN B 658 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B1054 GLN C 164 ASN C 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 27510 Z= 0.204 Angle : 0.572 16.443 37437 Z= 0.301 Chirality : 0.046 0.449 4443 Planarity : 0.004 0.053 4752 Dihedral : 6.974 57.607 5199 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 1.98 % Allowed : 10.54 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3270 helix: 1.25 (0.20), residues: 708 sheet: 0.67 (0.19), residues: 783 loop : -1.90 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 152 HIS 0.006 0.001 HIS C 207 PHE 0.012 0.001 PHE B1121 TYR 0.021 0.001 TYR C 248 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 179 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6919 (pp) REVERT: A 138 ASP cc_start: 0.7167 (t0) cc_final: 0.6946 (t0) REVERT: A 153 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6901 (mtp) REVERT: A 428 ASP cc_start: 0.7209 (p0) cc_final: 0.6820 (p0) REVERT: A 820 ASP cc_start: 0.7710 (m-30) cc_final: 0.7332 (m-30) REVERT: A 964 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7335 (mttt) REVERT: A 1038 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8101 (mmtp) REVERT: B 474 GLN cc_start: 0.8107 (tt0) cc_final: 0.7767 (tt0) REVERT: B 567 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7760 (mtt-85) REVERT: B 740 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8343 (ttm) REVERT: B 1038 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8089 (mmtp) REVERT: B 1039 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8241 (ptm160) REVERT: B 1101 HIS cc_start: 0.7727 (m90) cc_final: 0.7453 (m90) REVERT: C 138 ASP cc_start: 0.7648 (t0) cc_final: 0.7234 (t0) REVERT: C 153 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6955 (mtp) REVERT: C 213 VAL cc_start: 0.7982 (t) cc_final: 0.7649 (m) REVERT: C 428 ASP cc_start: 0.7166 (p0) cc_final: 0.6856 (p0) REVERT: C 567 ARG cc_start: 0.8122 (mtt-85) cc_final: 0.7835 (mtt90) REVERT: C 1038 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8110 (mptt) outliers start: 57 outliers final: 32 residues processed: 222 average time/residue: 1.3851 time to fit residues: 359.9536 Evaluate side-chains 209 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 185 optimal weight: 0.0770 chunk 78 optimal weight: 0.6980 chunk 316 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 644 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 27510 Z= 0.194 Angle : 0.547 12.080 37437 Z= 0.288 Chirality : 0.046 0.395 4443 Planarity : 0.004 0.049 4752 Dihedral : 6.673 59.282 5199 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.50 % Allowed : 11.55 % Favored : 86.95 % 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: -0.64 (0.14), residues: 3270 helix: 1.41 (0.20), residues: 711 sheet: 0.72 (0.19), residues: 777 loop : -1.84 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.006 0.001 HIS C 207 PHE 0.015 0.001 PHE B 759 TYR 0.017 0.001 TYR B 756 ARG 0.007 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6863 (mtp) REVERT: A 428 ASP cc_start: 0.7226 (p0) cc_final: 0.6854 (p0) REVERT: A 820 ASP cc_start: 0.7683 (m-30) cc_final: 0.7295 (m-30) REVERT: A 1038 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8068 (mmtp) REVERT: A 1039 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7112 (ptm160) REVERT: B 214 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7685 (ptm-80) REVERT: B 321 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7716 (mm-40) REVERT: B 474 GLN cc_start: 0.8042 (tt0) cc_final: 0.7713 (tt0) REVERT: B 740 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8422 (ttm) REVERT: B 1038 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8095 (mmtp) REVERT: B 1039 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7978 (ptm160) REVERT: B 1101 HIS cc_start: 0.7722 (m90) cc_final: 0.7443 (m90) REVERT: C 138 ASP cc_start: 0.7642 (t0) cc_final: 0.7231 (t0) REVERT: C 213 VAL cc_start: 0.7982 (t) cc_final: 0.7629 (m) REVERT: C 567 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7822 (mtt90) REVERT: C 1038 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8081 (mmtp) outliers start: 43 outliers final: 29 residues processed: 204 average time/residue: 1.4190 time to fit residues: 337.0043 Evaluate side-chains 201 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 180 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 315 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 644 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27510 Z= 0.204 Angle : 0.549 9.591 37437 Z= 0.290 Chirality : 0.046 0.363 4443 Planarity : 0.004 0.047 4752 Dihedral : 6.499 58.574 5199 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.46 % Allowed : 12.11 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.61 (0.14), residues: 3270 helix: 1.49 (0.20), residues: 711 sheet: 0.64 (0.19), residues: 783 loop : -1.80 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 152 HIS 0.006 0.001 HIS C 207 PHE 0.013 0.001 PHE B1121 TYR 0.016 0.001 TYR B 756 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6835 (tt) REVERT: A 153 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6722 (mtp) REVERT: A 428 ASP cc_start: 0.7216 (p0) cc_final: 0.6853 (p0) REVERT: A 820 ASP cc_start: 0.7692 (m-30) cc_final: 0.7321 (m-30) REVERT: A 964 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7457 (mttt) REVERT: A 1038 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8067 (mmtp) REVERT: A 1039 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.6999 (ptm160) REVERT: B 214 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7708 (ptm-80) REVERT: B 321 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7777 (mm-40) REVERT: B 474 GLN cc_start: 0.8025 (tt0) cc_final: 0.7703 (tt0) REVERT: B 740 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8393 (ttm) REVERT: B 1038 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8091 (mmtp) REVERT: B 1039 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7969 (ptm160) REVERT: B 1101 HIS cc_start: 0.7708 (m90) cc_final: 0.7428 (m90) REVERT: C 213 VAL cc_start: 0.7992 (t) cc_final: 0.7637 (m) REVERT: C 567 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7750 (mtt90) REVERT: C 1038 LYS cc_start: 0.8337 (mtpp) cc_final: 0.7989 (mmtp) outliers start: 42 outliers final: 31 residues processed: 203 average time/residue: 1.4436 time to fit residues: 341.8924 Evaluate side-chains 201 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27510 Z= 0.313 Angle : 0.616 8.713 37437 Z= 0.323 Chirality : 0.048 0.379 4443 Planarity : 0.005 0.052 4752 Dihedral : 6.588 59.526 5199 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 1.64 % Allowed : 12.07 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.72 (0.14), residues: 3270 helix: 1.30 (0.20), residues: 711 sheet: 0.59 (0.19), residues: 783 loop : -1.84 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 152 HIS 0.006 0.001 HIS C 146 PHE 0.018 0.002 PHE B1121 TYR 0.023 0.002 TYR B 756 ARG 0.007 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 163 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6854 (mtp) REVERT: A 428 ASP cc_start: 0.7188 (p0) cc_final: 0.6796 (p0) REVERT: A 820 ASP cc_start: 0.7740 (m-30) cc_final: 0.7356 (m-30) REVERT: A 1038 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8070 (mmtp) REVERT: A 1039 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7058 (ptm160) REVERT: B 214 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7755 (ptm-80) REVERT: B 321 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7793 (mm-40) REVERT: B 474 GLN cc_start: 0.8082 (tt0) cc_final: 0.7756 (tt0) REVERT: B 740 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8482 (ttm) REVERT: B 1038 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8097 (mmtp) REVERT: B 1039 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7893 (ptm160) REVERT: B 1101 HIS cc_start: 0.7726 (m90) cc_final: 0.7449 (m90) REVERT: C 52 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: C 138 ASP cc_start: 0.7550 (t70) cc_final: 0.7259 (t0) REVERT: C 213 VAL cc_start: 0.8123 (t) cc_final: 0.7776 (m) REVERT: C 567 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7764 (mtt90) REVERT: C 1038 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8082 (mmtp) outliers start: 47 outliers final: 34 residues processed: 200 average time/residue: 1.3969 time to fit residues: 327.9820 Evaluate side-chains 200 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 chunk 293 optimal weight: 0.5980 chunk 176 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 292 optimal weight: 0.0570 chunk 192 optimal weight: 0.2980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 474 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 27510 Z= 0.154 Angle : 0.515 8.730 37437 Z= 0.272 Chirality : 0.044 0.343 4443 Planarity : 0.004 0.049 4752 Dihedral : 6.267 59.205 5199 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 1.22 % Allowed : 12.70 % Favored : 86.08 % 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: -0.49 (0.14), residues: 3270 helix: 1.66 (0.20), residues: 711 sheet: 0.68 (0.19), residues: 777 loop : -1.73 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.006 0.001 HIS C 207 PHE 0.010 0.001 PHE A 133 TYR 0.014 0.001 TYR A1067 ARG 0.008 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 3.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6537 (tt) REVERT: A 428 ASP cc_start: 0.7177 (p0) cc_final: 0.6812 (p0) REVERT: A 820 ASP cc_start: 0.7686 (m-30) cc_final: 0.7336 (m-30) REVERT: A 1038 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8049 (mmtp) REVERT: A 1039 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7031 (ptm160) REVERT: B 321 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7810 (mm-40) REVERT: B 474 GLN cc_start: 0.7977 (tt0) cc_final: 0.7682 (tt0) REVERT: B 740 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8362 (ttm) REVERT: B 820 ASP cc_start: 0.7544 (m-30) cc_final: 0.7098 (m-30) REVERT: B 1038 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8091 (mptt) REVERT: B 1039 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8003 (ptm160) REVERT: B 1101 HIS cc_start: 0.7696 (m90) cc_final: 0.7425 (m90) REVERT: C 138 ASP cc_start: 0.7389 (t70) cc_final: 0.7183 (t0) REVERT: C 213 VAL cc_start: 0.8000 (t) cc_final: 0.7621 (m) REVERT: C 567 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7771 (mtt90) REVERT: C 977 LEU cc_start: 0.8689 (mt) cc_final: 0.8248 (mp) REVERT: C 1038 LYS cc_start: 0.8364 (mtpp) cc_final: 0.7992 (mmtp) outliers start: 35 outliers final: 26 residues processed: 208 average time/residue: 1.3655 time to fit residues: 335.5101 Evaluate side-chains 194 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 1.9990 chunk 189 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 325 optimal weight: 0.9980 chunk 299 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 200 optimal weight: 0.0970 chunk 159 optimal weight: 0.5980 chunk 206 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 27510 Z= 0.184 Angle : 0.532 9.071 37437 Z= 0.281 Chirality : 0.045 0.347 4443 Planarity : 0.004 0.047 4752 Dihedral : 6.241 59.180 5199 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.71 % Rotamer: Outliers : 1.11 % Allowed : 12.91 % Favored : 85.98 % 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: -0.45 (0.14), residues: 3270 helix: 1.66 (0.20), residues: 711 sheet: 0.67 (0.18), residues: 822 loop : -1.72 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS C 207 PHE 0.012 0.001 PHE A 133 TYR 0.016 0.001 TYR C1067 ARG 0.007 0.000 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6499 (tt) REVERT: A 428 ASP cc_start: 0.7190 (p0) cc_final: 0.6830 (p0) REVERT: A 820 ASP cc_start: 0.7676 (m-30) cc_final: 0.7311 (m-30) REVERT: A 1038 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8050 (mmtp) REVERT: A 1039 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7123 (ptm160) REVERT: B 474 GLN cc_start: 0.7963 (tt0) cc_final: 0.7677 (tt0) REVERT: B 740 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8363 (ttm) REVERT: B 820 ASP cc_start: 0.7530 (m-30) cc_final: 0.7078 (m-30) REVERT: B 1038 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8091 (mptt) REVERT: B 1039 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.7954 (ptm160) REVERT: B 1101 HIS cc_start: 0.7747 (m90) cc_final: 0.7480 (m90) REVERT: C 213 VAL cc_start: 0.7991 (t) cc_final: 0.7607 (m) REVERT: C 567 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7770 (mtt90) REVERT: C 977 LEU cc_start: 0.8688 (mt) cc_final: 0.8241 (mp) REVERT: C 1038 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8008 (mmtp) outliers start: 32 outliers final: 29 residues processed: 194 average time/residue: 1.4547 time to fit residues: 330.0333 Evaluate side-chains 194 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 266 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 228 optimal weight: 0.3980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.099531 restraints weight = 58707.071| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.06 r_work: 0.2944 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27510 Z= 0.167 Angle : 0.521 8.818 37437 Z= 0.275 Chirality : 0.045 0.334 4443 Planarity : 0.004 0.047 4752 Dihedral : 6.178 59.158 5199 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 1.25 % Allowed : 12.98 % Favored : 85.77 % 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: -0.39 (0.14), residues: 3270 helix: 1.74 (0.21), residues: 711 sheet: 0.61 (0.19), residues: 834 loop : -1.66 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS C 207 PHE 0.011 0.001 PHE A 643 TYR 0.035 0.001 TYR A 248 ARG 0.007 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7673.06 seconds wall clock time: 137 minutes 35.32 seconds (8255.32 seconds total)