Starting phenix.real_space_refine (version: dev) on Sun Feb 26 01:34:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1w_24125/02_2023/7n1w_24125.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1w_24125/02_2023/7n1w_24125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1w_24125/02_2023/7n1w_24125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1w_24125/02_2023/7n1w_24125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1w_24125/02_2023/7n1w_24125.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1w_24125/02_2023/7n1w_24125.pdb" } resolution = 3.33 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= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "C PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26810 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8434 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 8522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8522 Classifications: {'peptide': 1088} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8554 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 53, 'TRANS': 1038} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.30, per 1000 atoms: 0.53 Number of scatterers: 26810 At special positions: 0 Unit cell: (151.812, 154.288, 216.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5321 8.00 N 4338 7.00 C 17037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 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 ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1406 " - " ASN A 282 " " NAG A1407 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 657 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 11.44 Conformation dependent library (CDL) restraints added in 4.2 seconds 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6102 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 48 sheets defined 27.8% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.695A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.846A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.312A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.898A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.593A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.826A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.984A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.105A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.586A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.595A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.625A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.614A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.529A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.973A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 987 through 1033 removed outlier: 3.554A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.254A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.163A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.357A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.612A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.652A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 624 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.885A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.566A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.031A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.617A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.544A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.538A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.632A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.770A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.220A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.965A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.526A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.961A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.496A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.607A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.746A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.581A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.096A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.604A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.383A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 3.702A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.024A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.980A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.938A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.163A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.138A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.930A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.868A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.050A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.115A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.969A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.003A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.536A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.405A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.992A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.741A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.053A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.134A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 142 through 144 removed outlier: 6.485A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.202A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.021A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.634A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.634A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.377A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.723A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.507A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.049A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.308A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.572A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.566A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.269A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.058A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.979A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.733A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.018A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.965A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.653A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.653A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.259A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.693A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1123 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.11 Time building geometry restraints manager: 12.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4335 1.30 - 1.43: 7309 1.43 - 1.56: 15615 1.56 - 1.69: 1 1.69 - 1.83: 144 Bond restraints: 27404 Sorted by residual: bond pdb=" C4 NAG T 2 " pdb=" O4 NAG T 2 " ideal model delta sigma weight residual 1.423 1.488 -0.065 1.00e-02 1.00e+04 4.20e+01 bond pdb=" C4 NAG f 2 " pdb=" O4 NAG f 2 " ideal model delta sigma weight residual 1.423 1.485 -0.062 1.00e-02 1.00e+04 3.88e+01 bond pdb=" C4 NAG Y 1 " pdb=" O4 NAG Y 1 " ideal model delta sigma weight residual 1.423 1.483 -0.060 1.00e-02 1.00e+04 3.61e+01 bond pdb=" C4 NAG U 2 " pdb=" O4 NAG U 2 " ideal model delta sigma weight residual 1.423 1.483 -0.060 1.00e-02 1.00e+04 3.60e+01 bond pdb=" C4 NAG K 2 " pdb=" O4 NAG K 2 " ideal model delta sigma weight residual 1.423 1.483 -0.060 1.00e-02 1.00e+04 3.56e+01 ... (remaining 27399 not shown) Histogram of bond angle deviations from ideal: 95.99 - 103.84: 290 103.84 - 111.69: 10629 111.69 - 119.53: 11878 119.53 - 127.38: 14323 127.38 - 135.22: 158 Bond angle restraints: 37278 Sorted by residual: angle pdb=" OD1 ASN B1074 " pdb=" CG ASN B1074 " pdb=" ND2 ASN B1074 " ideal model delta sigma weight residual 122.60 113.66 8.94 1.00e+00 1.00e+00 8.00e+01 angle pdb=" OD1 ASN B 331 " pdb=" CG ASN B 331 " pdb=" ND2 ASN B 331 " ideal model delta sigma weight residual 122.60 114.08 8.52 1.00e+00 1.00e+00 7.26e+01 angle pdb=" OD1 ASN A 149 " pdb=" CG ASN A 149 " pdb=" ND2 ASN A 149 " ideal model delta sigma weight residual 122.60 114.17 8.43 1.00e+00 1.00e+00 7.10e+01 angle pdb=" CB ASN B1074 " pdb=" CG ASN B1074 " pdb=" ND2 ASN B1074 " ideal model delta sigma weight residual 116.40 128.20 -11.80 1.50e+00 4.44e-01 6.19e+01 angle pdb=" OD1 ASN C 149 " pdb=" CG ASN C 149 " pdb=" ND2 ASN C 149 " ideal model delta sigma weight residual 122.60 114.79 7.81 1.00e+00 1.00e+00 6.11e+01 ... (remaining 37273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 15407 23.92 - 47.85: 625 47.85 - 71.77: 96 71.77 - 95.69: 36 95.69 - 119.61: 5 Dihedral angle restraints: 16169 sinusoidal: 6684 harmonic: 9485 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -152.40 66.40 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -151.22 65.22 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 145.08 -52.08 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 16166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.694: 4481 0.694 - 1.387: 4 1.387 - 2.081: 1 2.081 - 2.774: 0 2.774 - 3.468: 1 Chirality restraints: 4487 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 1.07 -3.47 2.00e-01 2.50e+01 3.01e+02 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.33 -2.07 2.00e-01 2.50e+01 1.07e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.41e+01 ... (remaining 4484 not shown) Planarity restraints: 4744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " -0.117 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN C 616 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " -0.172 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " 0.535 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " -0.315 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " 0.216 2.00e-02 2.50e+03 1.99e-01 4.95e+02 pdb=" CG ASN A 17 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " -0.293 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.068 2.00e-02 2.50e+03 1.95e-01 4.77e+02 pdb=" CG ASN A 603 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.196 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.306 2.00e-02 2.50e+03 pdb=" C1 NAG A1408 " 0.227 2.00e-02 2.50e+03 ... (remaining 4741 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 55 2.54 - 3.13: 19835 3.13 - 3.72: 40345 3.72 - 4.31: 58638 4.31 - 4.90: 94794 Nonbonded interactions: 213667 Sorted by model distance: nonbonded pdb=" ND2 ASN C 616 " pdb=" N2 NAG a 1 " model vdw 1.951 2.560 nonbonded pdb=" NH2 ARG A1107 " pdb=" CE1 TYR B 904 " model vdw 1.973 3.420 nonbonded pdb=" CD ARG A 815 " pdb=" OD1 ASP A 820 " model vdw 2.022 3.440 nonbonded pdb=" ND2 ASN A 234 " pdb=" C1 NAG A1405 " model vdw 2.071 3.550 nonbonded pdb=" O4 NAG F 1 " pdb=" O7 NAG F 2 " model vdw 2.076 2.440 ... (remaining 213662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 826 or resid 855 through 1162 or resid 1401 thr \ ough 1408)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1408)) selection = (chain 'C' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 17037 2.51 5 N 4338 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.910 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: 0.030 Extract box with map and model: 24.040 Check model and map are aligned: 0.430 Process input model: 69.790 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Set scattering table: 0.230 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.013 0.073 27404 Z= 0.846 Angle : 1.773 11.799 37278 Z= 1.194 Chirality : 0.121 3.468 4487 Planarity : 0.012 0.127 4690 Dihedral : 13.880 119.613 9941 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.96 % Favored : 93.52 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.56 % 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: -1.65 (0.13), residues: 3223 helix: -1.36 (0.16), residues: 734 sheet: 0.46 (0.20), residues: 573 loop : -1.52 (0.13), residues: 1916 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 779 time to evaluate : 2.870 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 outliers start: 23 outliers final: 9 residues processed: 795 average time/residue: 0.4136 time to fit residues: 503.1985 Evaluate side-chains 603 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 594 time to evaluate : 3.204 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4360 time to fit residues: 10.3136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 0.0770 chunk 294 optimal weight: 0.0770 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 234 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 658 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 30 ASN B 52 GLN B 388 ASN B 613 GLN B 751 ASN B1005 GLN B1118 HIS C 14 GLN C 188 ASN C 271 GLN C 343 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 762 GLN C 784 GLN C 901 GLN C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 27404 Z= 0.227 Angle : 0.705 11.841 37278 Z= 0.375 Chirality : 0.051 0.774 4487 Planarity : 0.004 0.058 4690 Dihedral : 8.759 113.599 4093 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3223 helix: 0.79 (0.19), residues: 734 sheet: 0.27 (0.20), residues: 630 loop : -1.07 (0.14), residues: 1859 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 645 time to evaluate : 3.261 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: 62 outliers final: 26 residues processed: 676 average time/residue: 0.4281 time to fit residues: 449.7271 Evaluate side-chains 586 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 560 time to evaluate : 3.475 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2652 time to fit residues: 17.5273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 chunk 262 optimal weight: 0.0060 chunk 292 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 872 GLN A 913 GLN A1005 GLN B 30 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1005 GLN C 271 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 580 GLN C 777 ASN C 784 GLN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 27404 Z= 0.234 Angle : 0.658 11.452 37278 Z= 0.343 Chirality : 0.049 0.738 4487 Planarity : 0.004 0.040 4690 Dihedral : 8.446 113.835 4093 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3223 helix: 1.30 (0.20), residues: 747 sheet: 0.16 (0.19), residues: 650 loop : -1.03 (0.14), residues: 1826 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 602 time to evaluate : 3.156 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: 58 outliers final: 26 residues processed: 633 average time/residue: 0.4251 time to fit residues: 416.2830 Evaluate side-chains 584 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 558 time to evaluate : 3.014 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2768 time to fit residues: 17.0840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 313 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 30 ASN B 115 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN C 271 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 580 GLN C 777 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 27404 Z= 0.286 Angle : 0.656 11.696 37278 Z= 0.341 Chirality : 0.049 0.641 4487 Planarity : 0.004 0.042 4690 Dihedral : 8.408 114.449 4093 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3223 helix: 1.46 (0.20), residues: 744 sheet: 0.06 (0.19), residues: 642 loop : -1.03 (0.14), residues: 1837 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 584 time to evaluate : 2.918 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 outliers start: 67 outliers final: 38 residues processed: 620 average time/residue: 0.4233 time to fit residues: 408.7833 Evaluate side-chains 586 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 548 time to evaluate : 2.901 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 38 outliers final: 1 residues processed: 38 average time/residue: 0.2847 time to fit residues: 24.4322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 281 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN B 960 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 580 GLN C 777 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.094 27404 Z= 0.363 Angle : 0.679 12.528 37278 Z= 0.355 Chirality : 0.049 0.582 4487 Planarity : 0.004 0.042 4690 Dihedral : 8.456 115.207 4093 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3223 helix: 1.32 (0.20), residues: 761 sheet: -0.11 (0.18), residues: 670 loop : -1.12 (0.14), residues: 1792 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 583 time to evaluate : 3.215 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: 66 outliers final: 37 residues processed: 619 average time/residue: 0.4089 time to fit residues: 395.0984 Evaluate side-chains 593 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 556 time to evaluate : 2.829 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2406 time to fit residues: 20.5653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 183 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 313 optimal weight: 0.0270 chunk 260 optimal weight: 4.9990 chunk 145 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 271 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 751 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 580 GLN C 777 ASN C 804 GLN C 907 ASN C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 27404 Z= 0.201 Angle : 0.633 12.527 37278 Z= 0.325 Chirality : 0.047 0.583 4487 Planarity : 0.004 0.043 4690 Dihedral : 8.241 113.554 4093 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3223 helix: 1.56 (0.20), residues: 752 sheet: 0.10 (0.18), residues: 690 loop : -1.12 (0.14), residues: 1781 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 584 time to evaluate : 3.253 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 outliers start: 35 outliers final: 16 residues processed: 601 average time/residue: 0.4264 time to fit residues: 397.4117 Evaluate side-chains 578 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 562 time to evaluate : 3.307 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2622 time to fit residues: 12.2165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 263 optimal weight: 0.0770 chunk 175 optimal weight: 0.5980 chunk 312 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 190 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 613 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 580 GLN C 777 ASN C 787 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 27404 Z= 0.216 Angle : 0.627 12.372 37278 Z= 0.322 Chirality : 0.047 0.579 4487 Planarity : 0.004 0.043 4690 Dihedral : 8.138 113.032 4093 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3223 helix: 1.65 (0.20), residues: 746 sheet: 0.10 (0.18), residues: 691 loop : -1.06 (0.14), residues: 1786 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 580 time to evaluate : 3.057 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: 29 outliers final: 14 residues processed: 592 average time/residue: 0.4500 time to fit residues: 411.3593 Evaluate side-chains 564 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 550 time to evaluate : 3.038 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2933 time to fit residues: 11.4382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.0270 chunk 124 optimal weight: 0.9980 chunk 186 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 914 ASN A1005 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 777 ASN C 787 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 27404 Z= 0.213 Angle : 0.630 13.073 37278 Z= 0.321 Chirality : 0.047 0.562 4487 Planarity : 0.004 0.043 4690 Dihedral : 8.089 112.857 4093 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.22 (0.14), residues: 3223 helix: 1.58 (0.20), residues: 753 sheet: 0.17 (0.19), residues: 663 loop : -1.05 (0.14), residues: 1807 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 572 time to evaluate : 3.149 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: 26 outliers final: 11 residues processed: 583 average time/residue: 0.4388 time to fit residues: 395.8323 Evaluate side-chains 565 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 554 time to evaluate : 3.363 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2682 time to fit residues: 9.7052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 1.9990 chunk 299 optimal weight: 0.2980 chunk 272 optimal weight: 2.9990 chunk 291 optimal weight: 0.0570 chunk 175 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 228 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 chunk 289 optimal weight: 4.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 777 ASN C 787 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 27404 Z= 0.200 Angle : 0.640 12.289 37278 Z= 0.325 Chirality : 0.047 0.549 4487 Planarity : 0.004 0.066 4690 Dihedral : 8.040 112.276 4093 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.17 (0.14), residues: 3223 helix: 1.64 (0.20), residues: 758 sheet: 0.18 (0.19), residues: 646 loop : -1.01 (0.14), residues: 1819 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 567 time to evaluate : 3.348 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: 25 outliers final: 9 residues processed: 580 average time/residue: 0.4259 time to fit residues: 385.6420 Evaluate side-chains 559 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 550 time to evaluate : 3.047 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2425 time to fit residues: 7.9816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.8980 chunk 307 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 213 optimal weight: 0.0040 chunk 322 optimal weight: 0.7980 chunk 297 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 872 GLN B 409 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 777 ASN C 787 GLN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 27404 Z= 0.223 Angle : 0.652 12.507 37278 Z= 0.331 Chirality : 0.047 0.538 4487 Planarity : 0.005 0.163 4690 Dihedral : 8.048 112.285 4093 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3223 helix: 1.78 (0.20), residues: 738 sheet: 0.20 (0.19), residues: 665 loop : -0.97 (0.14), residues: 1820 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 554 time to evaluate : 3.191 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: 12 outliers final: 6 residues processed: 558 average time/residue: 0.4684 time to fit residues: 412.0116 Evaluate side-chains 550 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 544 time to evaluate : 3.185 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4049 time to fit residues: 9.5269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 1.9990 chunk 273 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 264 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 914 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 777 ASN C 787 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.098897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080602 restraints weight = 71014.523| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.47 r_work: 0.3112 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 27404 Z= 0.248 Angle : 0.656 12.809 37278 Z= 0.335 Chirality : 0.047 0.531 4487 Planarity : 0.004 0.069 4690 Dihedral : 8.078 112.827 4093 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3223 helix: 1.68 (0.20), residues: 742 sheet: 0.24 (0.19), residues: 652 loop : -1.01 (0.14), residues: 1829 =============================================================================== Job complete usr+sys time: 7635.92 seconds wall clock time: 139 minutes 48.62 seconds (8388.62 seconds total)