Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 18:13:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2023/7l6o_23124_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2023/7l6o_23124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2023/7l6o_23124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2023/7l6o_23124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2023/7l6o_23124_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6o_23124/04_2023/7l6o_23124_trim.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.065 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: 5 Type Number sf(0) Gaussians S 105 5.16 5 C 9717 2.51 5 N 2514 2.21 5 O 3336 1.98 5 H 13598 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 32": "OE1" <-> "OE2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 64": "OE1" <-> "OE2" Residue "a GLU 83": "OE1" <-> "OE2" Residue "a GLU 91": "OE1" <-> "OE2" Residue "a ASP 99": "OD1" <-> "OD2" Residue "a GLU 169": "OE1" <-> "OE2" Residue "a TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 211": "OE1" <-> "OE2" Residue "a GLU 269": "OE1" <-> "OE2" Residue "a GLU 293": "OE1" <-> "OE2" Residue "a TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 325": "OD1" <-> "OD2" Residue "a GLU 335": "OE1" <-> "OE2" Residue "a PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 612": "OD1" <-> "OD2" Residue "b GLU 622": "OE1" <-> "OE2" Residue "b GLU 636": "OE1" <-> "OE2" Residue "c PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c GLU 83": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 211": "OE1" <-> "OE2" Residue "c GLU 293": "OE1" <-> "OE2" Residue "c GLU 335": "OE1" <-> "OE2" Residue "c PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 464": "OE1" <-> "OE2" Residue "d PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ASP 612": "OD1" <-> "OD2" Residue "d GLU 636": "OE1" <-> "OE2" Residue "e GLU 32": "OE1" <-> "OE2" Residue "e PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "e ASP 99": "OD1" <-> "OD2" Residue "e GLU 169": "OE1" <-> "OE2" Residue "e TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 211": "OE1" <-> "OE2" Residue "e GLU 293": "OE1" <-> "OE2" Residue "e GLU 335": "OE1" <-> "OE2" Residue "e TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ASP 612": "OD1" <-> "OD2" Residue "f GLU 636": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29270 Number of models: 1 Model: "" Number of chains: 51 Chain: "a" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7192 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "b" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "c" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7192 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "d" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "e" Number of atoms: 7191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7191 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "f" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.15, per 1000 atoms: 0.42 Number of scatterers: 29270 At special positions: 0 Unit cell: (127.98, 139.711, 127.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 O 3336 8.00 N 2514 7.00 C 9717 6.00 H 13598 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS a 54 " - pdb=" SG CYS a 74 " distance=2.03 Simple disulfide: pdb=" SG CYS a 119 " - pdb=" SG CYS a 205 " distance=2.03 Simple disulfide: pdb=" SG CYS a 126 " - pdb=" SG CYS a 196 " distance=2.02 Simple disulfide: pdb=" SG CYS a 131 " - pdb=" SG CYS a 157 " distance=2.02 Simple disulfide: pdb=" SG CYS a 201 " - pdb=" SG CYS a 433 " distance=2.03 Simple disulfide: pdb=" SG CYS a 218 " - pdb=" SG CYS a 247 " distance=2.02 Simple disulfide: pdb=" SG CYS a 228 " - pdb=" SG CYS a 239 " distance=2.03 Simple disulfide: pdb=" SG CYS a 296 " - pdb=" SG CYS a 331 " distance=2.02 Simple disulfide: pdb=" SG CYS a 378 " - pdb=" SG CYS a 445 " distance=2.03 Simple disulfide: pdb=" SG CYS a 385 " - pdb=" SG CYS a 418 " distance=2.03 Simple disulfide: pdb=" SG CYS a 501 " - pdb=" SG CYS b 593 " distance=2.06 Simple disulfide: pdb=" SG CYS b 586 " - pdb=" SG CYS b 592 " distance=2.02 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.03 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 126 " - pdb=" SG CYS c 196 " distance=2.01 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.04 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.02 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.02 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.03 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.02 Simple disulfide: pdb=" SG CYS c 501 " - pdb=" SG CYS d 593 " distance=2.05 Simple disulfide: pdb=" SG CYS d 586 " - pdb=" SG CYS d 592 " distance=2.03 Simple disulfide: pdb=" SG CYS e 54 " - pdb=" SG CYS e 74 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 205 " distance=2.03 Simple disulfide: pdb=" SG CYS e 126 " - pdb=" SG CYS e 196 " distance=2.01 Simple disulfide: pdb=" SG CYS e 131 " - pdb=" SG CYS e 157 " distance=2.03 Simple disulfide: pdb=" SG CYS e 201 " - pdb=" SG CYS e 433 " distance=2.03 Simple disulfide: pdb=" SG CYS e 218 " - pdb=" SG CYS e 247 " distance=2.02 Simple disulfide: pdb=" SG CYS e 228 " - pdb=" SG CYS e 239 " distance=2.03 Simple disulfide: pdb=" SG CYS e 296 " - pdb=" SG CYS e 331 " distance=2.02 Simple disulfide: pdb=" SG CYS e 378 " - pdb=" SG CYS e 445 " distance=2.03 Simple disulfide: pdb=" SG CYS e 385 " - pdb=" SG CYS e 418 " distance=2.03 Simple disulfide: pdb=" SG CYS e 501 " - pdb=" SG CYS f 593 " distance=2.05 Simple disulfide: pdb=" SG CYS f 586 " - pdb=" SG CYS f 592 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA R 3 " - " MAN R 4 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA R 3 " - " MAN R 5 " " BMA k 3 " - " MAN k 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 1 " - " ASN a 362 " " NAG B 1 " - " ASN a 392 " " NAG C 1 " - " ASN a 234 " " NAG D 1 " - " ASN a 241 " " NAG E 1 " - " ASN a 262 " " NAG F 1 " - " ASN a 156 " " NAG H 1 " - " ASN a 301 " " NAG I 1 " - " ASN a 332 " " NAG J 1 " - " ASN a 339 " " NAG K 1 " - " ASN a 136 " " NAG L 1 " - " ASN a 160 " " NAG M 1 " - " ASN a 197 " " NAG N 1 " - " ASN c 362 " " NAG O 1 " - " ASN c 392 " " NAG P 1 " - " ASN c 234 " " NAG Q 1 " - " ASN c 241 " " NAG R 1 " - " ASN c 262 " " NAG S 1 " - " ASN c 156 " " NAG U 1 " - " ASN c 301 " " NAG V 1 " - " ASN c 332 " " NAG W 1 " - " ASN c 339 " " NAG X 1 " - " ASN c 136 " " NAG Y 1 " - " ASN c 160 " " NAG Z 1 " - " ASN c 197 " " NAG a 601 " - " ASN a 88 " " NAG a 602 " - " ASN a 276 " " NAG a 603 " - " ASN a 448 " " NAG a 604 " - " ASN a 442 " " NAG b 701 " - " ASN b 599 " " NAG b 702 " - " ASN b 625 " " NAG c 601 " - " ASN c 88 " " NAG c 602 " - " ASN c 276 " " NAG c 603 " - " ASN c 448 " " NAG c 604 " - " ASN c 442 " " NAG d 701 " - " ASN d 599 " " NAG d 702 " - " ASN d 625 " " NAG e 601 " - " ASN e 88 " " NAG e 602 " - " ASN e 276 " " NAG e 603 " - " ASN e 448 " " NAG e 604 " - " ASN e 442 " " NAG f 701 " - " ASN f 599 " " NAG f 702 " - " ASN f 625 " " NAG g 1 " - " ASN e 362 " " NAG h 1 " - " ASN e 392 " " NAG i 1 " - " ASN e 234 " " NAG j 1 " - " ASN e 241 " " NAG k 1 " - " ASN e 262 " " NAG l 1 " - " ASN e 156 " " NAG n 1 " - " ASN e 301 " " NAG o 1 " - " ASN e 332 " " NAG p 1 " - " ASN e 339 " " NAG q 1 " - " ASN e 136 " " NAG r 1 " - " ASN e 160 " " NAG s 1 " - " ASN e 197 " NAG-SER " NAG G 1 " - " SER a 388 " " NAG T 1 " - " SER c 388 " " NAG m 1 " - " SER e 388 " Time building additional restraints: 24.31 Conformation dependent library (CDL) restraints added in 2.2 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 27 sheets defined 25.6% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'a' and resid 59 through 63 removed outlier: 3.650A pdb=" N GLU a 62 " --> pdb=" O ARG a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 117 Processing helix chain 'a' and resid 122 through 126 removed outlier: 3.588A pdb=" N CYS a 126 " --> pdb=" O THR a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 198 Processing helix chain 'a' and resid 335 through 353 removed outlier: 3.787A pdb=" N HIS a 352 " --> pdb=" O GLU a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 368 through 373 Processing helix chain 'a' and resid 377 through 381 removed outlier: 3.860A pdb=" N GLY a 380 " --> pdb=" O ASN a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 397 through 401 Processing helix chain 'a' and resid 476 through 484 removed outlier: 4.754A pdb=" N GLU a 482 " --> pdb=" O ASN a 478 " (cutoff:3.500A) Processing helix chain 'b' and resid 517 through 522 Processing helix chain 'b' and resid 524 through 530 removed outlier: 3.571A pdb=" N GLN b 528 " --> pdb=" O THR b 524 " (cutoff:3.500A) Processing helix chain 'b' and resid 559 through 584 removed outlier: 3.629A pdb=" N GLN b 563 " --> pdb=" O TRP b 559 " (cutoff:3.500A) Processing helix chain 'b' and resid 606 through 612 Processing helix chain 'b' and resid 615 through 624 removed outlier: 3.679A pdb=" N LYS b 621 " --> pdb=" O LEU b 617 " (cutoff:3.500A) Processing helix chain 'b' and resid 625 through 627 No H-bonds generated for 'chain 'b' and resid 625 through 627' Processing helix chain 'b' and resid 628 through 636 removed outlier: 4.042A pdb=" N GLU b 636 " --> pdb=" O GLY b 632 " (cutoff:3.500A) Processing helix chain 'b' and resid 638 through 651 Processing helix chain 'c' and resid 59 through 63 removed outlier: 3.961A pdb=" N GLU c 62 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 99 through 117 Processing helix chain 'c' and resid 195 through 198 Processing helix chain 'c' and resid 335 through 351 removed outlier: 4.367A pdb=" N ASP c 340 " --> pdb=" O GLU c 336 " (cutoff:3.500A) Processing helix chain 'c' and resid 368 through 373 Processing helix chain 'c' and resid 377 through 381 removed outlier: 3.937A pdb=" N GLY c 380 " --> pdb=" O ASN c 377 " (cutoff:3.500A) Processing helix chain 'c' and resid 397 through 401 Processing helix chain 'c' and resid 476 through 484 removed outlier: 4.748A pdb=" N GLU c 482 " --> pdb=" O ASN c 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 517 through 522 Processing helix chain 'd' and resid 524 through 530 Processing helix chain 'd' and resid 559 through 585 removed outlier: 3.903A pdb=" N GLN d 563 " --> pdb=" O TRP d 559 " (cutoff:3.500A) Processing helix chain 'd' and resid 606 through 612 Processing helix chain 'd' and resid 615 through 624 removed outlier: 3.853A pdb=" N LYS d 621 " --> pdb=" O LEU d 617 " (cutoff:3.500A) Processing helix chain 'd' and resid 628 through 636 removed outlier: 3.858A pdb=" N GLU d 636 " --> pdb=" O GLY d 632 " (cutoff:3.500A) Processing helix chain 'd' and resid 638 through 651 Processing helix chain 'e' and resid 98 through 117 removed outlier: 4.262A pdb=" N ASP e 102 " --> pdb=" O ASN e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 195 through 198 Processing helix chain 'e' and resid 335 through 353 removed outlier: 3.751A pdb=" N HIS e 352 " --> pdb=" O GLU e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 368 through 373 Processing helix chain 'e' and resid 397 through 401 removed outlier: 3.532A pdb=" N SER e 401 " --> pdb=" O GLY e 398 " (cutoff:3.500A) Processing helix chain 'e' and resid 476 through 481 Processing helix chain 'e' and resid 482 through 484 No H-bonds generated for 'chain 'e' and resid 482 through 484' Processing helix chain 'f' and resid 517 through 522 Processing helix chain 'f' and resid 524 through 530 removed outlier: 3.528A pdb=" N GLN f 528 " --> pdb=" O THR f 524 " (cutoff:3.500A) Processing helix chain 'f' and resid 558 through 584 removed outlier: 3.579A pdb=" N LEU f 569 " --> pdb=" O GLN f 565 " (cutoff:3.500A) Processing helix chain 'f' and resid 607 through 612 Processing helix chain 'f' and resid 615 through 624 Processing helix chain 'f' and resid 628 through 636 removed outlier: 3.510A pdb=" N LEU f 633 " --> pdb=" O ILE f 629 " (cutoff:3.500A) Processing helix chain 'f' and resid 638 through 651 Processing sheet with id=AA1, first strand: chain 'a' and resid 494 through 499 removed outlier: 5.353A pdb=" N VAL b 596 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL a 38 " --> pdb=" O THR b 594 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR b 594 " --> pdb=" O VAL a 38 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR a 40 " --> pdb=" O CYS b 592 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N CYS b 592 " --> pdb=" O TYR a 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 45 through 47 removed outlier: 3.579A pdb=" N ILE a 225 " --> pdb=" O VAL a 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'a' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'a' and resid 169 through 177 removed outlier: 9.219A pdb=" N GLU a 150 " --> pdb=" O VAL a 139 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N VAL a 139 " --> pdb=" O GLU a 150 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET a 154 " --> pdb=" O ALA a 137 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA a 137 " --> pdb=" O MET a 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 202 through 203 removed outlier: 6.510A pdb=" N THR a 202 " --> pdb=" O TYR a 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 259 through 261 removed outlier: 4.472A pdb=" N GLY a 451 " --> pdb=" O LEU a 260 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N THR a 444 " --> pdb=" O ILE a 294 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N ILE a 294 " --> pdb=" O THR a 444 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG a 446 " --> pdb=" O VAL a 292 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N VAL a 292 " --> pdb=" O ARG a 446 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N ASN a 448 " --> pdb=" O THR a 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N THR a 290 " --> pdb=" O ASN a 448 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR a 450 " --> pdb=" O LEU a 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 284 through 297 current: chain 'a' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'a' and resid 271 through 273 removed outlier: 6.934A pdb=" N THR a 450 " --> pdb=" O LEU a 288 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N THR a 290 " --> pdb=" O ASN a 448 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N ASN a 448 " --> pdb=" O THR a 290 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N VAL a 292 " --> pdb=" O ARG a 446 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ARG a 446 " --> pdb=" O VAL a 292 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N ILE a 294 " --> pdb=" O THR a 444 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N THR a 444 " --> pdb=" O ILE a 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 444 through 456 current: chain 'a' and resid 413 through 420 Processing sheet with id=AA9, first strand: chain 'a' and resid 304 through 307 Processing sheet with id=AB1, first strand: chain 'c' and resid 494 through 499 removed outlier: 5.173A pdb=" N VAL d 596 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL c 38 " --> pdb=" O THR d 594 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR d 594 " --> pdb=" O VAL c 38 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR c 40 " --> pdb=" O CYS d 592 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N CYS d 592 " --> pdb=" O TYR c 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.504A pdb=" N ILE c 225 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'c' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'c' and resid 169 through 177 removed outlier: 9.150A pdb=" N GLU c 150 " --> pdb=" O VAL c 139 " (cutoff:3.500A) removed outlier: 11.519A pdb=" N VAL c 139 " --> pdb=" O GLU c 150 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET c 154 " --> pdb=" O ALA c 137 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA c 137 " --> pdb=" O MET c 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 202 through 203 removed outlier: 6.576A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 259 through 261 removed outlier: 3.769A pdb=" N GLY c 451 " --> pdb=" O LEU c 260 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N THR c 444 " --> pdb=" O ILE c 294 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE c 294 " --> pdb=" O THR c 444 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N ARG c 446 " --> pdb=" O VAL c 292 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N VAL c 292 " --> pdb=" O ARG c 446 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ASN c 448 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR c 290 " --> pdb=" O ASN c 448 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR c 450 " --> pdb=" O LEU c 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 284 through 297 current: chain 'c' and resid 358 through 361 Processing sheet with id=AB8, first strand: chain 'c' and resid 271 through 273 removed outlier: 6.846A pdb=" N THR c 450 " --> pdb=" O LEU c 288 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR c 290 " --> pdb=" O ASN c 448 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ASN c 448 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N VAL c 292 " --> pdb=" O ARG c 446 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N ARG c 446 " --> pdb=" O VAL c 292 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N ILE c 294 " --> pdb=" O THR c 444 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N THR c 444 " --> pdb=" O ILE c 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 444 through 456 current: chain 'c' and resid 413 through 420 Processing sheet with id=AB9, first strand: chain 'c' and resid 304 through 307 Processing sheet with id=AC1, first strand: chain 'e' and resid 494 through 499 removed outlier: 5.135A pdb=" N VAL f 596 " --> pdb=" O VAL e 36 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL e 38 " --> pdb=" O THR f 594 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR f 594 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N TYR e 40 " --> pdb=" O CYS f 592 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS f 592 " --> pdb=" O TYR e 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'e' and resid 53 through 56 Processing sheet with id=AC4, first strand: chain 'e' and resid 91 through 94 removed outlier: 3.521A pdb=" N GLU e 91 " --> pdb=" O CYS e 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 169 through 177 removed outlier: 9.687A pdb=" N GLU e 150 " --> pdb=" O VAL e 139 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N VAL e 139 " --> pdb=" O GLU e 150 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N MET e 154 " --> pdb=" O ALA e 137 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA e 137 " --> pdb=" O MET e 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 202 through 203 removed outlier: 6.513A pdb=" N THR e 202 " --> pdb=" O TYR e 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 259 through 261 removed outlier: 4.160A pdb=" N GLY e 451 " --> pdb=" O LEU e 260 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N THR e 444 " --> pdb=" O ILE e 294 " (cutoff:3.500A) removed outlier: 11.743A pdb=" N ILE e 294 " --> pdb=" O THR e 444 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ARG e 446 " --> pdb=" O VAL e 292 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N VAL e 292 " --> pdb=" O ARG e 446 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ASN e 448 " --> pdb=" O THR e 290 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR e 290 " --> pdb=" O ASN e 448 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR e 450 " --> pdb=" O LEU e 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 284 through 297 current: chain 'e' and resid 358 through 361 Processing sheet with id=AC8, first strand: chain 'e' and resid 271 through 273 removed outlier: 6.818A pdb=" N THR e 450 " --> pdb=" O LEU e 288 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR e 290 " --> pdb=" O ASN e 448 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ASN e 448 " --> pdb=" O THR e 290 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N VAL e 292 " --> pdb=" O ARG e 446 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ARG e 446 " --> pdb=" O VAL e 292 " (cutoff:3.500A) removed outlier: 11.743A pdb=" N ILE e 294 " --> pdb=" O THR e 444 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N THR e 444 " --> pdb=" O ILE e 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 444 through 456 current: chain 'e' and resid 413 through 421 removed outlier: 3.698A pdb=" N LYS e 421 " --> pdb=" O PHE e 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE e 382 " --> pdb=" O LYS e 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 301 through 306 removed outlier: 7.389A pdb=" N ASN e 301 " --> pdb=" O ILE e 323 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE e 323 " --> pdb=" O ASN e 301 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR e 303 " --> pdb=" O GLY e 321 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.24 Time building geometry restraints manager: 25.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.01: 2415 1.01 - 1.21: 11201 1.21 - 1.41: 6164 1.41 - 1.62: 9637 1.62 - 1.82: 138 Bond restraints: 29555 Sorted by residual: bond pdb=" N ALA c 436 " pdb=" H ALA c 436 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" N TRP e 427 " pdb=" H TRP e 427 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.59e+01 bond pdb=" NE2 HIS c 249 " pdb=" HE2 HIS c 249 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" N ASN d 639 " pdb=" H ASN d 639 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CE2 PHE c 468 " pdb=" HE2 PHE c 468 " ideal model delta sigma weight residual 0.930 1.079 -0.149 2.00e-02 2.50e+03 5.58e+01 ... (remaining 29550 not shown) Histogram of bond angle deviations from ideal: 97.10 - 105.09: 449 105.09 - 113.07: 33275 113.07 - 121.06: 13585 121.06 - 129.05: 5138 129.05 - 137.04: 135 Bond angle restraints: 52582 Sorted by residual: angle pdb=" C GLY a 312 " pdb=" N PRO a 313 " pdb=" CA PRO a 313 " ideal model delta sigma weight residual 119.84 133.28 -13.44 1.25e+00 6.40e-01 1.16e+02 angle pdb=" N GLY c 314 " pdb=" CA GLY c 314 " pdb=" C GLY c 314 " ideal model delta sigma weight residual 111.62 130.59 -18.97 1.77e+00 3.19e-01 1.15e+02 angle pdb=" N GLN e 315 " pdb=" CA GLN e 315 " pdb=" C GLN e 315 " ideal model delta sigma weight residual 108.76 125.45 -16.69 1.58e+00 4.01e-01 1.12e+02 angle pdb=" N GLY a 314 " pdb=" CA GLY a 314 " pdb=" C GLY a 314 " ideal model delta sigma weight residual 111.62 129.26 -17.64 1.77e+00 3.19e-01 9.93e+01 angle pdb=" C GLY c 312 " pdb=" N PRO c 313 " pdb=" CA PRO c 313 " ideal model delta sigma weight residual 119.84 131.93 -12.09 1.25e+00 6.40e-01 9.36e+01 ... (remaining 52577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10134 17.97 - 35.95: 739 35.95 - 53.92: 127 53.92 - 71.90: 191 71.90 - 89.87: 16 Dihedral angle restraints: 11207 sinusoidal: 5250 harmonic: 5957 Sorted by residual: dihedral pdb=" CB CYS a 378 " pdb=" SG CYS a 378 " pdb=" SG CYS a 445 " pdb=" CB CYS a 445 " ideal model delta sinusoidal sigma weight residual -86.00 -143.11 57.11 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS e 378 " pdb=" SG CYS e 378 " pdb=" SG CYS e 445 " pdb=" CB CYS e 445 " ideal model delta sinusoidal sigma weight residual -86.00 -139.42 53.42 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CA PRO c 313 " pdb=" C PRO c 313 " pdb=" N GLY c 314 " pdb=" CA GLY c 314 " ideal model delta harmonic sigma weight residual -180.00 -149.00 -31.00 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 11204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1698 0.107 - 0.214: 1003 0.214 - 0.321: 118 0.321 - 0.428: 27 0.428 - 0.535: 4 Chirality restraints: 2850 Sorted by residual: chirality pdb=" C1 BMA h 3 " pdb=" O4 NAG h 2 " pdb=" C2 BMA h 3 " pdb=" O5 BMA h 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.07e+02 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.05e+02 ... (remaining 2847 not shown) Planarity restraints: 4332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP d 598 " -0.372 2.00e-02 2.50e+03 1.29e-01 6.62e+02 pdb=" CG TRP d 598 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP d 598 " 0.091 2.00e-02 2.50e+03 pdb=" CD2 TRP d 598 " 0.084 2.00e-02 2.50e+03 pdb=" NE1 TRP d 598 " 0.127 2.00e-02 2.50e+03 pdb=" CE2 TRP d 598 " 0.040 2.00e-02 2.50e+03 pdb=" CE3 TRP d 598 " 0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 598 " -0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 598 " 0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP d 598 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP d 598 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TRP d 598 " 0.119 2.00e-02 2.50e+03 pdb=" HE3 TRP d 598 " 0.131 2.00e-02 2.50e+03 pdb=" HZ2 TRP d 598 " -0.141 2.00e-02 2.50e+03 pdb=" HZ3 TRP d 598 " 0.053 2.00e-02 2.50e+03 pdb=" HH2 TRP d 598 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 598 " 0.354 2.00e-02 2.50e+03 1.25e-01 6.27e+02 pdb=" CG TRP b 598 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP b 598 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP b 598 " -0.097 2.00e-02 2.50e+03 pdb=" NE1 TRP b 598 " -0.129 2.00e-02 2.50e+03 pdb=" CE2 TRP b 598 " -0.055 2.00e-02 2.50e+03 pdb=" CE3 TRP b 598 " -0.105 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 598 " 0.058 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 598 " -0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP b 598 " 0.074 2.00e-02 2.50e+03 pdb=" HD1 TRP b 598 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 TRP b 598 " -0.109 2.00e-02 2.50e+03 pdb=" HE3 TRP b 598 " -0.134 2.00e-02 2.50e+03 pdb=" HZ2 TRP b 598 " 0.116 2.00e-02 2.50e+03 pdb=" HZ3 TRP b 598 " -0.035 2.00e-02 2.50e+03 pdb=" HH2 TRP b 598 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP f 598 " 0.324 2.00e-02 2.50e+03 1.21e-01 5.85e+02 pdb=" CG TRP f 598 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP f 598 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TRP f 598 " -0.091 2.00e-02 2.50e+03 pdb=" NE1 TRP f 598 " -0.126 2.00e-02 2.50e+03 pdb=" CE2 TRP f 598 " -0.047 2.00e-02 2.50e+03 pdb=" CE3 TRP f 598 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 598 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 598 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP f 598 " 0.071 2.00e-02 2.50e+03 pdb=" HD1 TRP f 598 " 0.095 2.00e-02 2.50e+03 pdb=" HE1 TRP f 598 " -0.136 2.00e-02 2.50e+03 pdb=" HE3 TRP f 598 " -0.137 2.00e-02 2.50e+03 pdb=" HZ2 TRP f 598 " 0.112 2.00e-02 2.50e+03 pdb=" HZ3 TRP f 598 " -0.030 2.00e-02 2.50e+03 pdb=" HH2 TRP f 598 " 0.137 2.00e-02 2.50e+03 ... (remaining 4329 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2159 2.21 - 2.81: 50648 2.81 - 3.41: 76186 3.41 - 4.00: 100725 4.00 - 4.60: 147629 Nonbonded interactions: 377347 Sorted by model distance: nonbonded pdb=" H THR c 162 " pdb="HG23 ILE c 309 " model vdw 1.614 2.270 nonbonded pdb=" HG1 THR a 161 " pdb=" OE2 GLU a 172 " model vdw 1.626 1.850 nonbonded pdb=" H THR a 162 " pdb="HG23 ILE a 309 " model vdw 1.629 2.270 nonbonded pdb=" HG1 THR c 161 " pdb=" OE2 GLU c 172 " model vdw 1.644 1.850 nonbonded pdb=" HG1 THR e 161 " pdb=" OE2 GLU e 172 " model vdw 1.652 1.850 ... (remaining 377342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'K' selection = chain 'P' selection = chain 'U' selection = chain 'X' selection = chain 'i' selection = chain 'n' selection = chain 'q' } ncs_group { reference = chain 'E' selection = chain 'R' selection = chain 'k' } ncs_group { reference = (chain 'a' and (resid 31 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 250 through 506F or resid 601 through 604)) selection = (chain 'c' and (resid 31 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 250 through 506F or resid 601 through 604)) selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.420 Extract box with map and model: 6.390 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 84.950 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.016 0.087 15957 Z= 0.993 Angle : 1.999 18.975 21693 Z= 1.270 Chirality : 0.119 0.535 2850 Planarity : 0.019 0.182 2583 Dihedral : 14.168 89.870 5193 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.19 % Favored : 91.07 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.29 % 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: -1.91 (0.18), residues: 1758 helix: -1.58 (0.23), residues: 360 sheet: 0.05 (0.29), residues: 309 loop : -1.61 (0.17), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.6518 time to fit residues: 73.5983 Evaluate side-chains 59 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 2.467 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 6 average time/residue: 0.3486 time to fit residues: 6.6612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 66 HIS ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 531 ASN c 114 GLN f 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 15957 Z= 0.268 Angle : 0.820 9.572 21693 Z= 0.414 Chirality : 0.049 0.336 2850 Planarity : 0.005 0.045 2583 Dihedral : 8.787 86.761 1899 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -1.51 (0.19), residues: 1758 helix: -0.66 (0.26), residues: 372 sheet: 0.07 (0.27), residues: 357 loop : -1.58 (0.18), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.5774 time to fit residues: 60.2177 Evaluate side-chains 57 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 2.346 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.4120 time to fit residues: 9.5592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 114 GLN ** c 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15957 Z= 0.253 Angle : 0.683 7.086 21693 Z= 0.340 Chirality : 0.046 0.305 2850 Planarity : 0.004 0.029 2583 Dihedral : 7.662 87.365 1899 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.31 (0.19), residues: 1758 helix: -0.03 (0.28), residues: 372 sheet: 0.16 (0.27), residues: 357 loop : -1.63 (0.18), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 67 average time/residue: 0.5895 time to fit residues: 61.5952 Evaluate side-chains 57 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 2.359 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 9 average time/residue: 0.3882 time to fit residues: 8.6992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 15957 Z= 0.435 Angle : 0.720 7.479 21693 Z= 0.357 Chirality : 0.047 0.289 2850 Planarity : 0.004 0.041 2583 Dihedral : 7.298 89.857 1899 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.19), residues: 1758 helix: 0.02 (0.28), residues: 372 sheet: -0.04 (0.27), residues: 363 loop : -1.94 (0.18), residues: 1023 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.6438 time to fit residues: 55.0353 Evaluate side-chains 53 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 2.325 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.4136 time to fit residues: 7.8499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15957 Z= 0.160 Angle : 0.596 7.041 21693 Z= 0.291 Chirality : 0.044 0.272 2850 Planarity : 0.003 0.032 2583 Dihedral : 6.811 89.818 1899 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1758 helix: 0.44 (0.28), residues: 372 sheet: 0.12 (0.27), residues: 369 loop : -1.62 (0.19), residues: 1017 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 0.5628 time to fit residues: 49.5156 Evaluate side-chains 51 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 2.317 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.3336 time to fit residues: 5.2921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 15957 Z= 0.354 Angle : 0.657 7.329 21693 Z= 0.323 Chirality : 0.045 0.275 2850 Planarity : 0.004 0.034 2583 Dihedral : 6.724 86.880 1899 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 0.51 % 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: -1.38 (0.20), residues: 1758 helix: 0.38 (0.28), residues: 372 sheet: -0.12 (0.27), residues: 375 loop : -1.81 (0.18), residues: 1011 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.6204 time to fit residues: 53.0168 Evaluate side-chains 52 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 2.585 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 6 average time/residue: 0.3847 time to fit residues: 7.1131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 94 optimal weight: 40.0000 chunk 167 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 15957 Z= 0.317 Angle : 0.645 7.289 21693 Z= 0.318 Chirality : 0.045 0.254 2850 Planarity : 0.004 0.037 2583 Dihedral : 6.559 83.086 1899 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 0.77 % 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: -1.51 (0.19), residues: 1758 helix: 0.37 (0.28), residues: 378 sheet: -0.21 (0.27), residues: 375 loop : -1.94 (0.18), residues: 1005 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.6478 time to fit residues: 56.3350 Evaluate side-chains 53 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 2.378 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 9 average time/residue: 0.3488 time to fit residues: 8.9668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 160 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 15957 Z= 0.230 Angle : 0.592 7.254 21693 Z= 0.289 Chirality : 0.044 0.257 2850 Planarity : 0.003 0.031 2583 Dihedral : 6.273 81.813 1899 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1758 helix: 0.62 (0.28), residues: 378 sheet: -0.25 (0.27), residues: 378 loop : -1.83 (0.19), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.5754 time to fit residues: 46.8070 Evaluate side-chains 50 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 2.340 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 6 average time/residue: 0.3543 time to fit residues: 6.7865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 147 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 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 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 15957 Z= 0.123 Angle : 0.540 6.800 21693 Z= 0.260 Chirality : 0.043 0.266 2850 Planarity : 0.003 0.028 2583 Dihedral : 5.861 78.187 1899 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.20), residues: 1758 helix: 1.02 (0.28), residues: 378 sheet: -0.07 (0.27), residues: 381 loop : -1.52 (0.20), residues: 999 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 54 average time/residue: 0.5601 time to fit residues: 50.0118 Evaluate side-chains 51 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 2.248 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.3237 time to fit residues: 4.9839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 173 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15957 Z= 0.145 Angle : 0.531 6.915 21693 Z= 0.256 Chirality : 0.043 0.269 2850 Planarity : 0.003 0.028 2583 Dihedral : 5.667 75.871 1899 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1758 helix: 1.20 (0.28), residues: 372 sheet: -0.03 (0.27), residues: 381 loop : -1.50 (0.20), residues: 1005 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.5694 time to fit residues: 47.6209 Evaluate side-chains 50 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 2.492 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.3126 time to fit residues: 4.8564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.058953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.048177 restraints weight = 194003.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050076 restraints weight = 114705.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.051397 restraints weight = 80771.449| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15957 Z= 0.148 Angle : 0.523 6.825 21693 Z= 0.252 Chirality : 0.043 0.259 2850 Planarity : 0.003 0.027 2583 Dihedral : 5.449 71.520 1899 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1758 helix: 1.26 (0.28), residues: 378 sheet: 0.03 (0.27), residues: 381 loop : -1.46 (0.20), residues: 999 =============================================================================== Job complete usr+sys time: 3818.42 seconds wall clock time: 70 minutes 10.80 seconds (4210.80 seconds total)