Starting phenix.real_space_refine (version: dev) on Thu Dec 15 17:06:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1y_24127/12_2022/7n1y_24127.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1y_24127/12_2022/7n1y_24127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1y_24127/12_2022/7n1y_24127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1y_24127/12_2022/7n1y_24127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1y_24127/12_2022/7n1y_24127.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1y_24127/12_2022/7n1y_24127.pdb" } resolution = 4.3 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= 0.005 sd= 0.052 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 26636 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8441 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8517 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 52, 'TRANS': 1034} Chain breaks: 5 Chain: "C" 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: "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: 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: "S" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: "a" 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: "b" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" 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 Time building chain proxies: 15.58, per 1000 atoms: 0.58 Number of scatterers: 26636 At special positions: 0 Unit cell: (153.462, 152.637, 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 5278 8.00 N 4314 7.00 C 16930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 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=2.00 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.01 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=1.99 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.00 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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=1.99 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 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=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.07 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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 S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG a 2 " - " MAN a 3 " " NAG b 2 " - " MAN b 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 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 3 " " NAG Z 1 " - " FUC Z 3 " NAG-ASN " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 234 " " 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 B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 331 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG B1410 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1403 " - " ASN C 149 " " NAG C1404 " - " ASN C 165 " " NAG C1406 " - " ASN C 282 " " NAG C1407 " - " ASN C 343 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 657 " " NAG C1410 " - " ASN C 709 " " NAG C1411 " - " 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 282 " " NAG O 1 " - " ASN B 616 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 17 " " NAG V 1 " - " ASN C 331 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " Time building additional restraints: 12.32 Conformation dependent library (CDL) restraints added in 4.1 seconds 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6074 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 47 sheets defined 25.2% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.502A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.742A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.052A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.762A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.603A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.685A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.781A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.895A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (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: 4.258A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.516A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.843A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.947A 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 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.548A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.483A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.601A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.214A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.712A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.846A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.584A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.572A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.727A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.555A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (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 978 through 983 Processing helix chain 'B' and resid 987 through 1033 removed outlier: 4.173A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1159 removed outlier: 3.911A pdb=" N GLU B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.557A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.123A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.615A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 623 removed outlier: 3.835A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.042A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.539A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.696A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 4.152A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.529A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.584A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.854A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) 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 966 removed outlier: 3.661A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 989 through 1032 removed outlier: 4.280A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 3.553A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.720A 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: 9.006A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.760A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N SER A 221 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.687A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.564A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.705A 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: 6.538A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.596A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.046A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.254A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.128A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.660A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.485A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.745A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.493A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.493A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.035A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.029A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.893A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.627A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 6.786A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.242A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.688A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.727A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.967A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.450A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.253A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (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 654 through 655 removed outlier: 6.170A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.527A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.745A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.745A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.252A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.504A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 9.733A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.722A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.360A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.523A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.503A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.843A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.007A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.576A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.892A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.216A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.155A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.609A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 2928 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: 12.43 Time building geometry restraints manager: 13.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4416 1.31 - 1.44: 7414 1.44 - 1.58: 15250 1.58 - 1.72: 0 1.72 - 1.85: 144 Bond restraints: 27224 Sorted by residual: bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.435 1.522 -0.087 1.10e-02 8.26e+03 6.20e+01 bond pdb=" CA ASP C 985 " pdb=" C ASP C 985 " ideal model delta sigma weight residual 1.517 1.565 -0.048 6.30e-03 2.52e+04 5.77e+01 bond pdb=" C5 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.435 1.514 -0.079 1.10e-02 8.26e+03 5.13e+01 bond pdb=" C5 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.435 1.511 -0.076 1.10e-02 8.26e+03 4.79e+01 bond pdb=" C4 NAG R 1 " pdb=" O4 NAG R 1 " ideal model delta sigma weight residual 1.423 1.489 -0.066 1.00e-02 1.00e+04 4.39e+01 ... (remaining 27219 not shown) Histogram of bond angle deviations from ideal: 94.46 - 102.94: 157 102.94 - 111.42: 9412 111.42 - 119.90: 15153 119.90 - 128.38: 12167 128.38 - 136.86: 138 Bond angle restraints: 37027 Sorted by residual: angle pdb=" N ARG C1091 " pdb=" CA ARG C1091 " pdb=" C ARG C1091 " ideal model delta sigma weight residual 111.03 97.92 13.11 1.11e+00 8.12e-01 1.39e+02 angle pdb=" N PHE B 374 " pdb=" CA PHE B 374 " pdb=" C PHE B 374 " ideal model delta sigma weight residual 109.96 123.84 -13.88 1.49e+00 4.50e-01 8.67e+01 angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 122.70 -8.90 1.00e+00 1.00e+00 7.92e+01 angle pdb=" N ARG A1091 " pdb=" CA ARG A1091 " pdb=" C ARG A1091 " ideal model delta sigma weight residual 111.14 101.70 9.44 1.08e+00 8.57e-01 7.63e+01 angle pdb=" OD1 ASN A 149 " pdb=" CG ASN A 149 " pdb=" ND2 ASN A 149 " ideal model delta sigma weight residual 122.60 114.25 8.35 1.00e+00 1.00e+00 6.97e+01 ... (remaining 37022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 15145 23.63 - 47.25: 770 47.25 - 70.88: 112 70.88 - 94.51: 45 94.51 - 118.13: 6 Dihedral angle restraints: 16078 sinusoidal: 6638 harmonic: 9440 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -174.36 88.36 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 159.74 -66.74 1 1.00e+01 1.00e-02 5.81e+01 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 93.00 156.88 -63.88 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 16075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.680: 4432 0.680 - 1.360: 5 1.360 - 2.039: 3 2.039 - 2.719: 1 2.719 - 3.399: 2 Chirality restraints: 4443 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 1.00 -3.40 2.00e-01 2.50e+01 2.89e+02 chirality pdb=" C1 NAG A1407 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 0.67 -3.07 2.00e-01 2.50e+01 2.35e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-02 2.50e+03 2.35e+02 ... (remaining 4440 not shown) Planarity restraints: 4714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " 0.202 2.00e-02 2.50e+03 2.22e-01 6.14e+02 pdb=" CG ASN C 165 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " -0.370 2.00e-02 2.50e+03 pdb=" C1 NAG C1404 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 17 " 0.164 2.00e-02 2.50e+03 1.78e-01 3.95e+02 pdb=" CG ASN C 17 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 17 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 17 " -0.284 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " 0.183 2.00e-02 2.50e+03 1.72e-01 3.70e+02 pdb=" CG ASN A1098 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " -0.270 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.190 2.00e-02 2.50e+03 ... (remaining 4711 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 9 1.86 - 2.62: 194 2.62 - 3.38: 34781 3.38 - 4.14: 65438 4.14 - 4.90: 111177 Nonbonded interactions: 211599 Sorted by model distance: nonbonded pdb=" CD ARG B1107 " pdb=" CE1 TYR C 904 " model vdw 1.099 3.740 nonbonded pdb=" NH1 ARG C 21 " pdb=" O PHE C 79 " model vdw 1.301 2.520 nonbonded pdb=" NE ARG B1107 " pdb=" CE1 TYR C 904 " model vdw 1.314 3.420 nonbonded pdb=" O PRO A 337 " pdb=" OE2 GLU A 340 " model vdw 1.382 3.040 nonbonded pdb=" CB TYR C 453 " pdb=" OH TYR C 495 " model vdw 1.452 3.440 ... (remaining 211594 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 854 through 1162 or resid 1401 thr \ ough 1410)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 854 throu \ gh 1162 or resid 1401 through 1410)) selection = (chain 'C' and (resid 14 through 826 or resid 854 through 1162 or resid 1401 thr \ ough 1410)) } 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 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' 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 16930 2.51 5 N 4314 2.21 5 O 5278 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 24.770 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.250 Process input model: 74.250 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 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 : 0.015 0.087 27224 Z= 1.006 Angle : 2.094 13.877 37027 Z= 1.405 Chirality : 0.153 3.399 4443 Planarity : 0.015 0.114 4664 Dihedral : 15.162 118.131 9878 Min Nonbonded Distance : 1.099 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.55 % Favored : 90.83 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.13), residues: 3206 helix: -2.14 (0.16), residues: 680 sheet: -0.56 (0.21), residues: 499 loop : -2.23 (0.12), residues: 2027 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 727 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 16 residues processed: 771 average time/residue: 0.3837 time to fit residues: 460.7566 Evaluate side-chains 533 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 517 time to evaluate : 3.076 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2603 time to fit residues: 11.5724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 5.9990 chunk 244 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 153 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 292 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 919 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN A1113 GLN B 321 GLN B 613 GLN B 856 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN B 957 GLN B1048 HIS C 115 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 655 HIS C 675 GLN C 926 GLN C 957 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 27224 Z= 0.257 Angle : 0.791 9.506 37027 Z= 0.432 Chirality : 0.065 1.652 4443 Planarity : 0.005 0.052 4664 Dihedral : 9.448 113.319 4051 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.35 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.87 (0.13), residues: 3206 helix: -0.50 (0.19), residues: 691 sheet: -0.44 (0.20), residues: 533 loop : -1.83 (0.13), residues: 1982 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 628 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 632 average time/residue: 0.3804 time to fit residues: 379.6688 Evaluate side-chains 497 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 496 time to evaluate : 3.424 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2384 time to fit residues: 4.8118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 0.0020 chunk 243 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 chunk 290 optimal weight: 0.2980 chunk 99 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 207 HIS A 394 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 953 ASN A1101 HIS B 134 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 872 GLN B1054 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 675 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1125 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 27224 Z= 0.222 Angle : 0.701 9.398 37027 Z= 0.375 Chirality : 0.058 1.246 4443 Planarity : 0.005 0.134 4664 Dihedral : 8.912 112.360 4051 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3206 helix: 0.12 (0.19), residues: 685 sheet: -0.51 (0.21), residues: 511 loop : -1.65 (0.13), residues: 2010 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 596 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 599 average time/residue: 0.3777 time to fit residues: 360.1178 Evaluate side-chains 468 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 466 time to evaluate : 3.045 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2271 time to fit residues: 5.0736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 311 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 278 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 613 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 27224 Z= 0.232 Angle : 0.683 9.566 37027 Z= 0.363 Chirality : 0.056 1.233 4443 Planarity : 0.004 0.055 4664 Dihedral : 8.755 111.945 4051 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3206 helix: 0.35 (0.20), residues: 683 sheet: -0.67 (0.20), residues: 577 loop : -1.63 (0.13), residues: 1946 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 577 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 577 average time/residue: 0.3759 time to fit residues: 345.4586 Evaluate side-chains 450 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 3.051 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 279 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 762 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1054 GLN B1108 ASN ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 27224 Z= 0.390 Angle : 0.830 9.861 37027 Z= 0.447 Chirality : 0.061 1.329 4443 Planarity : 0.006 0.062 4664 Dihedral : 9.216 115.104 4051 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.14), residues: 3206 helix: -0.43 (0.18), residues: 689 sheet: -0.96 (0.20), residues: 594 loop : -1.91 (0.13), residues: 1923 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 565 time to evaluate : 3.212 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: 2 outliers final: 1 residues processed: 567 average time/residue: 0.3833 time to fit residues: 348.3940 Evaluate side-chains 453 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 3.084 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2416 time to fit residues: 5.0227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 3.9990 chunk 280 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1108 ASN ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 27224 Z= 0.256 Angle : 0.708 9.285 37027 Z= 0.379 Chirality : 0.056 1.172 4443 Planarity : 0.005 0.078 4664 Dihedral : 8.879 114.874 4051 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3206 helix: -0.03 (0.19), residues: 700 sheet: -1.04 (0.21), residues: 538 loop : -1.85 (0.13), residues: 1968 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 554 time to evaluate : 3.189 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 outliers start: 3 outliers final: 2 residues processed: 557 average time/residue: 0.3918 time to fit residues: 346.9851 Evaluate side-chains 452 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 450 time to evaluate : 3.141 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2519 time to fit residues: 5.0719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 310 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 27224 Z= 0.225 Angle : 0.687 10.887 37027 Z= 0.364 Chirality : 0.056 1.137 4443 Planarity : 0.005 0.066 4664 Dihedral : 8.649 112.370 4051 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.71 (0.14), residues: 3206 helix: 0.25 (0.19), residues: 694 sheet: -0.91 (0.20), residues: 571 loop : -1.80 (0.13), residues: 1941 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.3832 time to fit residues: 335.0878 Evaluate side-chains 444 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 2.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 243 optimal weight: 0.0670 chunk 282 optimal weight: 4.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** B1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 27224 Z= 0.231 Angle : 0.684 9.872 37027 Z= 0.362 Chirality : 0.055 1.139 4443 Planarity : 0.005 0.067 4664 Dihedral : 8.552 112.254 4051 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.62 (0.14), residues: 3206 helix: 0.35 (0.20), residues: 699 sheet: -0.77 (0.20), residues: 583 loop : -1.79 (0.13), residues: 1924 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 548 time to evaluate : 3.346 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: 1 outliers final: 0 residues processed: 548 average time/residue: 0.3854 time to fit residues: 338.8643 Evaluate side-chains 444 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 3.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 227 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 273 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 189 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN B1113 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 27224 Z= 0.208 Angle : 0.681 11.190 37027 Z= 0.356 Chirality : 0.053 1.085 4443 Planarity : 0.005 0.064 4664 Dihedral : 8.422 111.442 4051 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.57 (0.14), residues: 3206 helix: 0.38 (0.20), residues: 702 sheet: -0.79 (0.21), residues: 591 loop : -1.74 (0.13), residues: 1913 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 552 time to evaluate : 3.299 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: 1 outliers final: 0 residues processed: 553 average time/residue: 0.3772 time to fit residues: 337.0777 Evaluate side-chains 444 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 3.185 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 0.5980 chunk 186 optimal weight: 0.6980 chunk 145 optimal weight: 0.0270 chunk 212 optimal weight: 0.9990 chunk 320 optimal weight: 0.0070 chunk 295 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 115 GLN C 196 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 564 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 901 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 27224 Z= 0.189 Angle : 0.656 9.148 37027 Z= 0.343 Chirality : 0.052 1.055 4443 Planarity : 0.004 0.057 4664 Dihedral : 8.260 110.347 4051 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.43 (0.14), residues: 3206 helix: 0.51 (0.20), residues: 707 sheet: -0.72 (0.21), residues: 599 loop : -1.66 (0.13), residues: 1900 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 569 time to evaluate : 3.216 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: 1 outliers final: 0 residues processed: 569 average time/residue: 0.3781 time to fit residues: 347.0821 Evaluate side-chains 449 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 3.247 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 262 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 762 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN C 207 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 540 ASN C 564 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 957 GLN C1005 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1118 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.075456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.063156 restraints weight = 143838.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065037 restraints weight = 87284.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066361 restraints weight = 58900.096| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.102 27224 Z= 0.455 Angle : 0.906 12.864 37027 Z= 0.483 Chirality : 0.061 1.247 4443 Planarity : 0.007 0.106 4664 Dihedral : 9.098 116.846 4051 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.14), residues: 3206 helix: -0.57 (0.18), residues: 714 sheet: -1.00 (0.21), residues: 538 loop : -2.11 (0.13), residues: 1954 =============================================================================== Job complete usr+sys time: 6698.96 seconds wall clock time: 122 minutes 22.90 seconds (7342.90 seconds total)